Association for Molecular Pathology v. United States Patent & Trademark Office

United States Court of Appeals
for the Federal Circuit
__________________________

THE ASSOCIATION FOR MOLECULAR
PATHOLOGY, THE AMERICAN COLLEGE OF
MEDICAL GENETICS, THE AMERICAN SOCIETY
FOR CLINICAL PATHOLOGY, THE COLLEGE OF
AMERICAN PATHOLOGISTS, HAIG KAZAZIAN,
MD, ARUPA GANGULY, PHD, WENDY CHUNG, MD,
PHD, HARRY OSTRER, MD, DAVID LEDBETTER,
PHD, STEPHEN WARREN, PHD, ELLEN
MATLOFF, M.S., ELSA REICH, M.S., BREAST
CANCER ACTION, BOSTON WOMEN’S HEALTH
BOOK COLLECTIVE, LISBETH CERIANI, RUNI
LIMARY, GENAE GIRARD, PATRICE FORTUNE,
VICKY THOMASON, AND KATHLEEN RAKER,
Plaintiffs-Appellees,
v.
UNITED STATES PATENT AND TRADEMARK
OFFICE,
Defendant,
and
MYRIAD GENETICS, INC.,
Defendant-Appellant,
and
LORRIS BETZ, ROGER BOYER, JACK BRITTAIN,
ARNOLD B. COMBE, RAYMOND GESTELAND,
JAMES U. JENSEN, JOHN KENDALL MORRIS,
THOMAS PARKS, DAVID W. PERSHING, AND
MICHAEL K. YOUNG,
ASSOCIATION FOR MOLECULAR v. PTO 2

IN THEIR OFFICIAL CAPACITY AS DIRECTORS OF THE
UNIVERSITY OF UTAH RESEARCH FOUNDATION,
Defendants-Appellants.
__________________________

2010-1406
__________________________

Appeal from the United States District Court for the
Southern District of New York in Case No. 09-CV-4515,
Senior Judge Robert W. Sweet.
____________________________

Decided: August 16, 2012
____________________________

CHRISTOPHER A. HANSEN, American Civil Liberties
Union Foundation, of New York, New York, argued for
plaintiffs-appellees. With him on the brief were SANDRA
S. PARK, ADEN FINE, and LENORA M. LAPIDUS. Of counsel
on the brief were DANIEL B. RAVICHER and SABRINA Y.
HASSAN, Public Patent Foundation, Benjamin N. Cardozo,
School of Law, of New York, New York.

GREGORY A. CASTANIAS, Jones Day, of Washington,
DC, argued for all defendant-appellants. With him on the
brief were JENNIFER L. SWIZE, of Washington, DC, ISRAEL
SASHA MAYERGOYZ and DENNIS MURASHKO, of Chicago,
Illinois, BRIAN M. POISSANT, LAURA A. CORUZZI and
EILEEN FALVEY, of New York, New York. Of counsel were
BENJAMIN JACKSON, and JAY Z. ZHANG, Myriad Genetics,
of Salt Lake City, Utah.

MELISSA N. PATTERSON, Attorney, Civil Division, Ap-
pellate Staff, United States Department of Justice, of
3 ASSOCIATION FOR MOLECULAR v. PTO

Washington, DC, argued for amicus curiae, United States.
With her on the brief were STUART F. DELERY, Acting
Assistant Attorney General, BETH S. BRINKMANN, Deputy
Assistant Attorney General and SCOTT R. MCINTOSH,
Attorney. Of counsel was MARK R. FREEMAN.

THOMAS J. KOWALSKI, Vedder Price PC, of New York,
New York, for amicus curiae Protein Sciences Corpora-
tion. With him on the brief were DEBORAH L. LU; and
ROBERT S. RIGG, of Chicago, Illinois.

ROBERT A. ARMITAGE, Eli Lilly and Company, Indian-
apolis, Indiana, for amicus curiae, Eli Lilly and Company.
With him on the brief was JAMES J. KELLEY.

CHRISTOPHER M. HOLMAN, University of Missouri-
Kansas City School of Law, of Kansas City, Missouri, for
amicus curiae Law Professor Christopher M. Holman.

CHARLES R. MACEDO, Amster Rothstein & Ebenstein,
LLP, of New York, New York, for amicus curiae, New
York Intellectual Property Law Association. Of counsel
on the brief were RONALD M. DAIGNAULT and MATTHEW B.
MCFARLANE, Robins, Kaplan, Miller & Ciresi, L.L.P. of
New York, New York.

LORI B. ANDREWS, IIT Chicago-Kent College of Law, of
Chicago, Illinois, for amicus curiae, The American College
of Embryology, et al. Of counsel was JOSHUA D. SARNOFF,
DePaul University College of Law, of Chicago, Illinois.

DEBRA L. GREENFIELD, UCLA Institute for Society and
Genetics, of Los Angeles, California, for amici curiae, The
National Women’s Health Network, et al.
ASSOCIATION FOR MOLECULAR v. PTO 4

KRISTA L. COX, Knowledge Ecology International, of
Washington, DC, for amicus curiae, Knowledge Ecology
International, et al.

RICHARD F. PHILLIPS, Intellectual Property Owners
Association, of Washington, DC, for amicus curiae, Intel-
lectual Property Owners Association. With him on the
brief was KEVIN H. RHODES. Of counsel on the brief were
PAUL H. BERGHOFF, KEVIN E. NOONAN and JEFFREY P.
ARMSTRONG, McDonnell Boehnen Hulbert & Berghoff,
LLP, of Chicago, Illinois. Of counsel were HERBERT C.
WAMSLEY, Intellectual Property Owners, of Washington,
DC, and DOUGLAS KENT NORMAN, Eli Lilly & Company, of
Indianapolis, Indiana.

BARBARA R. RUDOLPH, Finnegan, Henderson,
Farabow, Garrett & Dunner, LLP, of Washington, DC, for
amicus curiae, American Intellectual Property Law Asso-
ciation. With her on the brief were ROBERT D. LITOWITZ,
ERIKA HARMON ARNER and DAVID S. FORMAN. Of counsel
on the brief was WILLIAM G. BARBER, American Intellec-
tual Property Law Association, of Arlington, Virginia. Of
counsel were DAVID WARREN HILL, American Intellectual
Property, of Arlington, Virginia, and ROBERT C. STANLEY,
Finnegan, Henderson, Farabow, Garrett & Dunner, LLP,
of Atlanta, Georgia.

WILLIAM T. ROBINSON, III, American Bar Association,
of Chicago, Illinois, for amicus curiae, American Bar
Association. Of counsel on the brief were JOHN P.
ELWOOD, Vinson & Elkins, LLP, of Washington, DC; and
MICHAEL A. VALEK, STEPHEN C. STOUT, of Austin, Texas.

MARK J. GATSCHET, Mark John Gatschet, P.L.L.C., of
Houston, Texas, for amicus curiae, Mark J. Gatschet and
5 ASSOCIATION FOR MOLECULAR v. PTO

Richard W. Knight. Of counsel on the brief was RICHARD
W. KNIGHT, R.W. Knight P.C. of San Antonio, Texas.

CLAIRE LAPORTE, Foley Hoag, LLP, of Boston, Massa-
chusetts, for amicus curiae Federal Circuit Bar Associa-
tion. With her on the brief was JAMES M. FLAHERTY, JR.

JOHN L. HENDRICKS, Hitchcock Evert, LLP, of Dallas,
Texas, for amicus curiae, AARP, et al. With him on the
brief were MEGAN M. O’LAUGHLIN and JOHN T. TOWER. Of
counsel was MICHAEL R. SCHUSTER.

J. TIMOTHY KEANE, Harness, Dickey & Pierce, PLC, of
St. Louis, Missouri, for amicus curiae, BioGenerator, et al

SUSAN E. MCBEE, Baker, Donelson, Bearman, Cald-
well, and Berkowitz, P.C., of Washington, DC, for amicus
curiae, Immatics Biotechnologie, GmbH. With her on the
brief was BRYAN W. JONES.

SETH P. WAXMAN, Wilmer Cutler Pickering Hale and
Dorr, LLP, of Washington, DC, for amicus curiae, Bio-
technology Industry Organization, et al. With him on the
brief was THOMAS G. SAUNDERS. Of counsel on the brief
was MARK C. FLEMING, of Boston, Massachusetts, and
HANSJORG SAUER, Biotechnology Industry Organization,
of Washington, DC. Of counsel was ALLEN C. NUNNALLY,
Wilmer Cutler Pickering Hale and Dorr, LLP, of Boston,
Massachusetts.

Jennifer Gordon, Baker Botts, L.L.P. of New York,
New York, for amicus curiae, Croplife International.
With her on the brief were STEVEN LENDARIS and
JENNIFER C. TEMPESTA.
ASSOCIATION FOR MOLECULAR v. PTO 6

MATTHEW J. DOWD, Wiley Rein LLP, of Washington,
DC, for amicus curiae, JAMES D. WATSON. With him on
the brief was JAMES H. WALLACE, JR.

KURT G. CALIA, Covington & Burling, LLP, of Red-
wood Shores, California, for amicus curiae, Pharmaceuti-
cal Research and Manufacturers of America. With him on
the brief were ROBERT A. LONG, JR. and ALLISON E.
KERNDT, of Washington, DC, and ALEXA R. HANSEN, of
San Francisco, California.

EILEEN M. KANE, Penn State Dickinson School of Law,
of University Park, Pennsylvania, for amicus curiae,
Professor Eileen M. Kane.

GENEVIEVE E. SCOTT, Yale School of Law, of Brooklyn,
New York, for amicus curiae, Information Society Project
at Yale Law School Scholars. With her on the brief was
PRISCILLA J. SMITH.

ROBERT SACHS, Fenwick & West, LLP, of San Fran-
cisco, California, for amicus curiae, Advanced Biological
Laboratories, SA.
__________________________

Before LOURIE, BRYSON, and MOORE, Circuit Judges.
Opinion for the court filed by Circuit Judge LOURIE.
Opinion concurring in part filed by Circuit Judge MOORE.
Opinion concurring in part and dissenting in part filed by
Circuit Judge BRYSON.
LOURIE, Circuit Judge.
Myriad Genetics, Inc. and the Directors of the Univer-
sity of Utah Research Foundation (collectively, “Myriad”)
appeal from the decision of the United States District
7 ASSOCIATION FOR MOLECULAR v. PTO

Court for the Southern District of New York holding that
an assortment of medical organizations, researchers,
genetic counselors, and patients (collectively, “Plaintiffs”)
have standing under the Declaratory Judgment Act to
challenge Myriad’s patents. Ass’n for Molecular Pathol-
ogy v. U.S. Patent & Trademark Office, 669 F. Supp. 2d
365 (S.D.N.Y. 2009) (“DJ Op.”). Myriad also appeals from
the district court’s decision granting summary judgment
that all of the challenged claims are drawn to non-
patentable subject matter under 35 U.S.C. § 101. Ass’n
for Molecular Pathology v. U.S. Patent & Trademark
Office, 702 F. Supp. 2d 181 (S.D.N.Y. 2010) (“SJ Op.”).
We affirm in part and reverse in part.
This appeal has returned to us as, a petition for cer-
tiorari having been filed from our decision of July 29,
2011, the Supreme Court of the United States granted the
petition, vacated our decision, and remanded the case to
us for further consideration in light of its decision in Mayo
Collaborative Services v. Prometheus, Inc., 566 U.S. ___,
132 S. Ct. 1289 (2012). Ass’n for Molecular Pathology v.
Myriad Genetics, Inc., 132 S. Ct. 1794 (2012). We invited
and received briefing by the parties and interested amici
and held oral argument on July 20, 2012. Our decision on
remand follows. It both decides the issues that were
before us in the original appeal and evaluates the effect of
Mayo on those issues.
On the threshold issue of jurisdiction, we affirm the
district court’s decision to exercise declaratory judgment
jurisdiction because we conclude that at least one plain-
tiff, Dr. Harry Ostrer, has standing to challenge the
validity of Myriad’s patents. On the merits, we reverse
the district court’s decision that Myriad’s composition
claims to “isolated” DNA molecules cover patent-ineligible
products of nature under § 101 because each of the
claimed molecules represents a nonnaturally occurring
ASSOCIATION FOR MOLECULAR v. PTO 8

composition of matter. We also reverse the district court’s
decision that Myriad’s method claim to screening poten-
tial cancer therapeutics via changes in cell growth rates of
transformed cells is directed to a patent-ineligible scien-
tific principle. We affirm the court’s decision, however,
that Myriad’s method claims directed to “comparing” or
“analyzing” DNA sequences are patent ineligible; such
claims include no transformative steps and cover only
patent-ineligible abstract, mental steps.
BACKGROUND
Plaintiffs brought suit against Myriad, challenging
the patentability of certain composition and method
claims relating to human genetics. See DJ Op., 669 F.
Supp. 2d at 369-76. Specifically, Plaintiffs sought a
declaration that fifteen claims from seven patents as-
signed to Myriad are drawn to patent-ineligible subject
matter under 35 U.S.C. § 101: claims 1, 2, 5, 6, 7, and 20
of U.S. Patent 5,747,282 (“the ’282 patent”); claims 1, 6,
and 7 of U.S. Patent 5,837,492 (“the ’492 patent”); claim 1
of U.S. Patent 5,693,473 (“the ’473 patent”); claim 1 of
U.S. Patent 5,709,999 (“the ’999 patent”); claim 1 of U.S.
Patent 5,710,001 (“the ’001 patent”); claim 1 of U.S.
Patent 5,753,441 (“the ’441 patent”); and claims 1 and 2 of
U.S. Patent 6,033,857 (“the ’857 patent”).
The challenged composition claims cover two “iso-
lated” human genes, BRCA1 and BRCA2 (collectively,
“BRCA1/2” or “BRCA”), and certain alterations, or muta-
tions, in these genes associated with a predisposition to
breast and ovarian cancers. Representative composition
claims include claims 1, 2, and 5 of the ’282 patent:
1. An isolated DNA coding for a BRCA1 polypep-
tide, said polypeptide having the amino acid se-
quence set forth in SEQ ID NO:2.
9 ASSOCIATION FOR MOLECULAR v. PTO

2. The isolated DNA of claim 1, wherein said
DNA has the nucleotide sequence set forth in SEQ
ID NO:1.
5. An isolated DNA having at least 15 nucleotides
of the DNA of claim 1.
’282 patent col.153 l.55 – col.154 l.56. 1 SEQ ID NO:2
depicts the amino acid sequence of the BRCA1 protein,
and SEQ ID NO:1 depicts the nucleotide sequence of the
BRCA1 DNA coding region; the latter sequence is collo-
quially referred to as cDNA. Id. col.19 ll.48-50.
All but one of the challenged method claims cover
methods of “analyzing” or “comparing” a patient’s BRCA
sequence with the normal, or wild-type, sequence to
identify the presence of cancer-predisposing mutations.
Representative method claims include claims 1 of the ’999
and ’001 patents:
1. A method for detecting a germline alteration in
a BRCA1 gene, said alteration selected from the
group consisting of the alterations set forth in Ta-
bles 12A, 14, 18 or 19 in a human which comprises
analyzing a sequence of a BRCA1 gene or BRCA1
RNA from a human sample or analyzing a se-
quence of BRCA1 cDNA made from mRNA from
said human sample with the proviso that said
germline alteration is not a deletion of 4 nucleo-
tides corresponding to base numbers 4184-4187 of
SEQ ID NO:1.
’999 patent col.161 ll.17-25 (emphases added).

1 In addition to representative claims 1, 2, and 5 of
the ’282 patent, other claims to isolated DNA molecules at
issue in this appeal include: claims 6 and 7 of the ’282
patent; claims 1, 6, and 7 of the ’492 patent; and claim 1
of the ’473 patent.
ASSOCIATION FOR MOLECULAR v. PTO 10

1. A method for screening a tumor sample from a
human subject for a somatic alteration in a
BRCA1 gene in said tumor which comprises []
comparing a first sequence selected from the
group consisting of a BRCA1 gene from said tu-
mor sample, BRCA1 RNA from said tumor sample
and BRCA1 cDNA made from mRNA from said
tumor sample with a second sequence selected
from the group consisting of BRCA1 gene from a
nontumor sample of said subject, BRCA1 RNA
from said nontumor sample and BRCA1 cDNA
made from mRNA from said nontumor sample,
wherein a difference in the sequence of the
BRCA1 gene, BRCA1 RNA or BRCA1 cDNA from
said tumor sample from the sequence of the
BRCA1 gene, BRCA1 RNA or BRCA1 cDNA from
said nontumor sample indicates a somatic altera-
tion in the BRCA1 gene in said tumor sample.
’001 patent col.155 ll.2-17 (emphasis added). 2
The final method claim challenged by Plaintiffs is di-
rected to a method of screening potential cancer therapeu-
tics. Specifically, claim 20 of the ’282 patent reads as
follows:
20. A method for screening potential cancer
therapeutics which comprises: growing a trans-
formed eukaryotic host cell containing an altered
BRCA1 gene causing cancer in the presence of a
compound suspected of being a cancer therapeu-
tic, growing said transformed eukaryotic host cell
in the absence of said compound, determining the

2 The claims currently before us that recite methods
of “analyzing” or “comparing” BRCA sequences are: claims
1 of the ’999, ’001, and ’441 patents and claims 1 and 2 of
the ’857 patent.
11 ASSOCIATION FOR MOLECULAR v. PTO

rate of growth of said host cell in the presence of
said compound and the rate of growth of said host
cell in the absence of said compound and compar-
ing the growth rate of said host cells, wherein a
slower rate of growth of said host cell in the pres-
ence of said compound is indicative of a cancer
therapeutic.
’282 patent col.156 ll.13–24 (emphases added).
The challenged claims thus relate to isolated gene se-
quences and diagnostic methods of identifying mutations
in these sequences. To place this suit in context, we take
a step back to provide background on the science involved,
including the identification of the BRCA genes, and the
Plaintiffs’ connections to the invention and to Myriad.
I.
Human genetics is the study of heredity in human be-
ings. 3 The human genome, the entirety of human genetic
information, contains approximately 22,000 genes, which
form the basis of human inheritance. The majority of
genes act by guiding the production of polypeptide chains
that form proteins. Proteins in turn make up living
matter and catalyze a variety of cellular processes.
Chemically, the human genome is composed of deoxy-
ribonucleic acid (“DNA”). Each DNA molecule is made up
of repeating units of four nucleotide bases—adenine (“A”),
thymine (“T”), cytosine (“C”), and guanine (“G”)—which
are covalently linked, or bonded, 4 together via a sugar-

3 The district court’s opinion, SJ Op., 702 F. Supp.
2d at 192-203, contains a detailed and comprehensive
discussion of the science involved in this case. We repeat
only the basics here.
4 Covalent bonds are chemical bonds characterized
by the sharing of electrons between atoms in a molecule.
ASSOCIATION FOR MOLECULAR v. PTO 12

phosphate, or phosphodiester, backbone. DNA generally
exists as two DNA strands intertwined as a double helix
in which each base on a strand pairs, or hybridizes, with a
complementary base on the other strand: A pairs with T,
and C with G. Figure 1 below depicts the structure of a
DNA double helix and the complementary pairing of the
four nucleotide bases, represented by A, T, C, and G.

Figure 1
The linear order of nucleotide bases in a DNA mole-
cule is referred to as its “sequence.” The sequence of a
gene is thus denoted by a linear sequence of As, Ts, Gs,
and Cs. “DNA sequencing” or “gene sequencing” refers to
the process by which the precise linear order of nucleo-
tides in a DNA segment or gene is determined. A gene’s
nucleotide sequence in turn encodes for a linear sequence
of amino acids that comprise the protein encoded by the
gene, e.g., the BRCA1 gene encodes for the BRCA1 pro-
tein. Most genes have both “exon” and “intron” se-
quences. Exons are DNA segments that are necessary for
the creation of a protein, i.e., that code for a protein.
Introns are segments of DNA interspersed between the
exons that, unlike exons, do not code for a protein.
The creation of a protein from a gene comprises two
steps: transcription and translation. First, the gene
sequence is “transcribed” into a different nucleic acid
13 ASSOCIATION FOR MOLECULAR v. PTO

called ribonucleic acid (“RNA”). RNA has a chemically
different sugar-phosphate backbone than DNA, and it
utilizes the nucleotide base uracil (“U”) in place of
thymine (“T”). During transcription, the DNA double
helix is unwound and each nucleotide on the non-coding,
or template, DNA strand is used to make a complemen-
tary, single-stranded RNA molecule that mirrors the
coding DNA strand, i.e., adenine on the template DNA
strand results in uracil in the RNA molecule, thymine
results in adenine, guanine in cytosine, and cytosine in
guanine. The resulting “pre-RNA,” like the DNA from
which it was generated, contains both exon and intron
sequences. Next, the introns are physically excised from
the pre-RNA molecule, followed by “splicing” the exons to
produce a messenger RNA (“mRNA”). Figure 2 below
shows the steps of transcribing a gene that contains three
exons (exon 1-3) and two introns (intron 1 and 2) into a
pre-RNA, followed by RNA excising the introns and
splicing of the exons to produce an mRNA containing only
exon sequences.

Figure 2
ASSOCIATION FOR MOLECULAR v. PTO 14

Following transcription and splicing, the resulting
mRNA is “translated” into the encoded protein. Genes,
and their corresponding mRNAs, encode proteins via
three-nucleotide combinations called codons. Each codon
triplet corresponds to one of the twenty amino acids that
make up all proteins or a “stop” signal that terminates
protein translation. For example, the codon adenine-
thymine-guanine (ATG, or AUG in the corresponding
mRNA), encodes the amino acid methionine. The rela-
tionship between the sixty-four possible codon sequences
and their corresponding amino acids is known as the
genetic code. Figure 3 below represents an mRNA mole-
cule that translates into a protein of six amino acids
(Codon 1, AUG, methionine; Codon 2, ACG, threonine;
Codon 3, GAG, glutamic acid; Codon 4, CUU, leucine;
Codon 5, CGG, arginine; Codon 6, AGC, serine), and ends
with one of the three stop codons, UAG.

Figure 3
Changes, or mutations, in the sequence of a human
gene can alter the production, structure, and/or function
of the resulting protein. Small-scale changes include
point mutations in which a change to a single nucleotide
15 ASSOCIATION FOR MOLECULAR v. PTO

alters a single amino acid in the encoded protein. For
example, a base change in the codon GCU to CCU
changes an alanine in the encoded protein to a proline.
Larger scale variations include the deletion, rearrange-
ment, or duplication of larger DNA segments—ranging
from several hundreds to over a million nucleotides—and
can result in the elimination, misplacement, or duplica-
tion of an entire gene or genes. While some mutations
have little or no effect on the body’s processes, others
result in disease or an increased risk of developing a
particular disease. DNA sequencing is used in clinical
diagnostic testing to determine whether a gene contains
mutations associated with a particular disease or disease
risk.
Nearly every cell in the human body contains an indi-
vidual’s entire genome. DNA in the cell, called “native” or
“genomic” DNA, is packaged into twenty-three pairs of
chromosomes. Chromosomes are complex structures
comprising a single extended DNA molecule wrapped
around proteins called histones, as shown in Figure 4
below.
ASSOCIATION FOR MOLECULAR v. PTO 16

Figure 4
Each chromosome contiguously spans millions of bases
and encompasses many discrete genes. Humans have
twenty-two pairs of autosomal chromosomes, numbered
one to twenty-two according to size from largest to small-
est, and one pair of sex chromosomes, two X chromosomes
in females and one X and one Y chromosome in males.
Genomic DNA can be extracted from its cellular envi-
ronment using a number of well-established laboratory
techniques. A particular segment of DNA, such as a gene,
can then be excised or amplified from the DNA to obtain
the isolated DNA segment of interest. DNA molecules
can also be synthesized in the laboratory. One type of
synthetic DNA molecule is complementary DNA
(“cDNA”). cDNA is synthesized from mRNA using com-
plementary base pairing in a manner analogous to RNA
17 ASSOCIATION FOR MOLECULAR v. PTO

transcription. The process results in a double-stranded
DNA molecule with a sequence corresponding to the
sequence of an mRNA produced by the body. Because it is
synthesized from mRNA, cDNA contains only the exon
sequences, and thus none of the intron sequences, from a
chromosomal gene sequence.
II.
Certain mutations in the BRCA genes correlate with
an increased risk of breast and ovarian cancer. The
average woman in the United States has around a twelve
to thirteen percent risk of developing breast cancer in her
lifetime. Women with BRCA mutations, in contrast, face
a cumulative risk of between fifty to eighty percent of
developing breast cancer and a cumulative risk of ovarian
cancer of between twenty to fifty percent. Diagnostic
genetic testing for the existence of BRCA mutations is
therefore an important consideration in the provision of
clinical care for breast or ovarian cancer. This testing
provides a patient with information on her risk for heredi-
tary breast and ovarian cancers, and thus aids in the
difficult decision regarding whether to undertake preven-
tive options, including prophylactic surgery. Diagnostic
results can also be an important factor in structuring an
appropriate course of cancer treatment, since certain
forms of therapy are more effective in treating cancers
related to BRCA mutations.
The inventors of the patents in suit identified the ge-
netic basis of BRCA1- and BRCA2-related cancers using
an analysis called positional cloning. Relying on a large
set of DNA samples from families with inherited breast
and ovarian cancers, the inventors correlated the occur-
rence of cancer in individual family members with the
inheritance of certain marker DNA sequences. This
allowed the inventors to identify, or “map,” the physical
ASSOCIATION FOR MOLECULAR v. PTO 18

location of the BRCA genes within the human genome
and to isolate the BRCA genes and determine their exact
nucleotide sequences. This in turn allowed Myriad to
provide BRCA diagnostic testing services to women. 5
III.
Myriad, however, was not the only entity to imple-
ment clinical BRCA testing services. Starting in 1996,
the University of Pennsylvania’s Genetic Diagnostic
Laboratory (“GDL”), co-directed by plaintiffs Haig H.
Kazazian, Jr., M.D. and Arupa Ganguly, Ph.D., provided
BRCA1/2 diagnostic services to women. By 1999, how-
ever, accusations by Myriad that GDL’s BRCA testing
services infringed its patents forced the lab to stop provid-
ing such services.
The first sign of a dispute came in early 1998. At that
time, Dr. Kazazian recalls a dinner with Dr. Mark Skol-
nick, inventor and Chief Science Officer at Myriad. At the
dinner, Skolnick informed Kazazian that Myriad was
planning to stop GDL from providing clinical BRCA
testing in light of Myriad’s patents. A month or two later,
in May 1998, Kazazian received a letter from William A.
Hockett, Director of Corporate Communications at Myr-
iad. The letter stated that Myriad knew that Kazazian
was currently providing BRCA1 diagnostic testing ser-
vices, and that Myriad, as patent holder of five U.S.
patents covering the isolated BRCA1 gene and diagnostic

5 Myriad filed the first patent application leading to
the patents in suit covering isolated BRCA1 DNA and
associated diagnostic methods in August 1994. The first
resulting patent, the ’473 patent, issued on December 2,
1997. Myriad filed the first application leading to the
patents in suit covering isolated BRCA2 DNA and associ-
ated diagnostic methods in December 1995, and the first
such patent, the ’492 patent, issued on November 17,
1998.
19 ASSOCIATION FOR MOLECULAR v. PTO

testing, was making available to select institutions a
collaborative license. Attached to the letter was a copy of
Myriad’s collaborative agreement, which proposed se-
verely limiting GDL’s testing services to certain tests for
patients of Ashkenazi Jewish descent. Plaintiff Harry
Ostrer, M.D, a researcher at New York University
(“NYU”) School of Medicine, received the same letter and
collaborative agreement in May 1998, although his labo-
ratory did not, at the time, provide such testing services.
Rather, Ostrer sent patient samples to GDL for BRCA
genetic testing.
Months later, in August 1998, Dr. Kazazian received a
second letter, this time from George A. Riley of the law
firm O’Melveny & Myers LLP. The letter identified by
number five Myriad patents “covering, among other
things, the BRCA1 gene sequence . . . and methods for
detecting alterations in the BRCA1 sequence.” J.A. 1145.
The letter also indicated that it “has come to Myriad’s
attention that you are engaged in commercial testing
activities that infringe Myriad’s patents,” and that
“[u]nless and until a licensing arrangement is completed
. . . you should cease all infringing testing activity.” Id.
The letter noted, however, that the cease-and-desist
notification did not apply to research testing “for the
purpose of furthering non-commercial research programs,
the results of which are not provided to the patient and
for which no money is received from the patient or the
patient’s insurance.” Id.
In June 1999, Robert Terrell, the General Counsel for
the University of Pennsylvania, received a similar cease-
and-desist letter from Christopher Wight, Myriad’s Gen-
eral Counsel. The letter stated, “It has come to our atten-
tion that Dr. Haig H. Kazazian, Jr. of the University of
Pennsylvania is continuing to willfully engage in commer-
cial BRCA1 and BRCA2 genetic testing activities, in
ASSOCIATION FOR MOLECULAR v. PTO 20

violation of the University of Pennsylvania’s previous
assurances that such commercial testing activities would
be discontinued.” J.A. 2890. Terrell responded to Wight
by letter on September 10, 1999, stating that “the Univer-
sity agrees that it will not accept samples for BRCA1
research testing from third parties.” J.A. 2891. Kazazian
thus informed Dr. Ostrer that GDL would no longer be
accepting patient samples for BRCA testing from him or
anyone else as a result of the patent infringement asser-
tions made by Myriad. As a result, Ostrer started send-
ing patient samples for BRCA genetic testing to Myriad,
which became (and remains today) the only provider of
such services in the United States.
During this period, Myriad also initiated several pat-
ent infringement suits against entities providing clinical
BRCA testing. Myriad filed suit against Oncormed Inc. in
1997 and again in 1998, Myriad Genetics v. Oncormed,
Nos. 2:97-cv-922, 2:98-cv-35 (D. Utah), and the University
of Pennsylvania in 1998, Myriad Genetics v. Univ. of Pa.,
No. 2:98-cv-829 (D. Utah). Both lawsuits were later
dismissed without prejudice after each defendant agreed
to discontinue all allegedly infringing activity.
None of the plaintiffs besides Drs. Kazazian, Ganguly,
and Ostrer, allege that Myriad directed any letters or
other communications regarding its patents at them.
Rather, the other researchers and medical organization
members state simply that knowledge of Myriad’s vigor-
ous enforcement of its patent rights against others
stopped them from engaging in clinical BRCA genetic
testing, although they have the personnel, expertise, and
facilities as well as the desire to provide such testing. The
patient plaintiffs state that they have been unable to
obtain any BRCA genetic testing or their desired BRCA
testing, either covered by their insurance or at a price
21 ASSOCIATION FOR MOLECULAR v. PTO

that they can afford, because of Myriad’s patent protec-
tion.
Like the other researchers, Dr. Kazazian states that if
Myriad’s patents were held invalid, he and Dr. Ganguly
would be able to resume BRCA testing within a matter of
a few weeks. He notes, however, that this is only if they
“decided to resume BRCA testing.” J.A. 2852. Ganguly
concurs, stating that if the patents were invalidated, “I
would immediately consider resuming BRCA testing in
my laboratory.” J.A. 2892. Dr. Ostrer 6 also indicates that
his lab has all the personnel, facilities, and expertise
necessary to undertake clinical BRCA testing and em-
phatically states that his lab “would immediately begin to
perform BRCA1/2-related genetic testing upon invalida-
tion of the Myriad patents.” J.A. 2936-38.
IV.
After Plaintiffs filed suit, Myriad moved to have the
case dismissed, alleging that the Plaintiffs lacked stand-
ing to bring a declaratory judgment suit challenging the
validity of its patents. The district court disagreed,

6 On July 27, 2011, two days before we issued our
initial, now-vacated decision in this case, Myriad notified
the court that Dr. Ostrer was leaving NYU to assume a
position at the Albert Einstein College of Medicine and
Montefiore Medical Center, effective August 29, 2011. In
response, Plaintiffs submitted a supplemental declaration
from Dr. Ostrer stating that, in his new position, he still
seeks to undertake BRCA diagnostic testing, still has the
resources and expertise to conduct such testing, and
would immediately do so if Myriad’s patents were invali-
dated. Following remand from the Supreme Court, we
have also received from Myriad a related “suggestion of
mootness” and motion to remand or dismiss. We declined
the suggestion and denied the motion. We now review
this case on the facts and arguments briefed and pre-
sented to us.
ASSOCIATION FOR MOLECULAR v. PTO 22

however, holding that the Plaintiffs had established
Article III standing under the “all the circumstances” test
articulated by the Supreme Court in MedImmune, Inc. v.
Genentech, Inc., 549 U.S. 118, 127 (2007). DJ Op., 669 F.
Supp. 2d at 385-92. The court first found that Myriad had
engaged in sufficient “affirmative acts” based on the
company’s assertion of its “right to preclude others from
engaging in BRCA1/2 genetic testing through personal
communications, cease-and-desist letters, licensing offers,
and litigation,” the result of which was “the widespread
understanding that one may engage in BRCA1/2 testing
at the risk of being sued for infringement liability by
Myriad.” Id. at 390. Myriad’s actions, the court con-
cluded, had placed “the Plaintiffs in precisely the situa-
tion that the Declaratory Judgment Act was designed to
address: the Plaintiffs have the ability and desire to
engage in BRCA1/2 testing as well as the belief that such
testing is within their rights, but cannot do so without
risking infringement liability.” Id.
In so holding, the court rejected Myriad’s argument
that there must be some act directed toward the Plain-
tiffs, noting that Myriad had, in fact, taken affirmative
acts toward plaintiffs Dr. Kazazian and Dr. Ganguly. Id.
at 387-88. The court also rejected Myriad’s arguments
that the cease-and-desist letter sent to plaintiff Kazazian
was too old to support declaratory judgment jurisdiction
and that the legal actions brought against third parties
could not be considered in the jurisdictional analysis. Id.
at 388-89. The court concluded that rigid adherence to
either of these requirements would be inconsistent with
MedImmune’s mandate that the court assess the facts
alleged under all the circumstances. Id.
The district court also found that the Plaintiffs had al-
leged sufficient meaningful preparations for infringement
to establish declaratory judgment jurisdiction. Id. at 390-
23 ASSOCIATION FOR MOLECULAR v. PTO

92. With respect to the researchers, the court held it was
sufficient that they were all “ready, willing, and able” to
begin BRCA1/2 testing within the normal course of their
laboratories’ research, rejecting Myriad’s argument that
they needed to allege specific preparatory activities. Id.
at 390-91. The court also rejected Myriad’s argument
that plaintiffs Kazazian and Ganguly testified only that
they would “consider” engaging in allegedly infringing
activities, concluding that the proper focus of the inquiry
is whether they are meaningfully prepared, not whether
they have made a final, conclusive decision to engage in
such activities. Id. at 391 n.18.
The parties then moved for summary judgment on the
merits of Plaintiffs’ § 101 challenge to Myriad’s patent
claims. The district court held for Plaintiffs, concluding
that the fifteen challenged claims were drawn to non-
patentable subject matter and thus invalid under § 101.
SJ Op., 702 F. Supp. 2d at 220-37. Regarding the compo-
sition claims, the court held that isolated DNA molecules
fall within the judicially created “products of nature”
exception to § 101 because such isolated DNAs are not
“markedly different” from native DNAs. Id. at 222, 232
(quoting Diamond v. Chakrabarty, 447 U.S. 303 (1980)).
The court relied on the fact that, unlike other biological
molecules, DNAs are the “physical embodiment of infor-
mation,” and that this information is not only preserved
in the claimed isolated DNA molecules, but also essential
to their utility as molecular tools. Id. at 228-32.
Turning to the method claims, the court held them
patent ineligible under this court’s then-definitive ma-
chine-or-transformation test. Id. at 233 (citing In re
Bilski, 545 F.3d 943 (Fed. Cir. 2008) (en banc), aff’d on
other grounds, Bilski v. Kappos, 130 S. Ct. 3218, 3225
(2010)). The court held that the claims covered “analyz-
ing” or “comparing” DNA sequences by any method, and
ASSOCIATION FOR MOLECULAR v. PTO 24

thus covered mental processes independent of any physi-
cal transformations. Id. at 233-35. In so holding, the
court distinguished Myriad’s claims from those at issue in
Mayo based on the “determining” step in the latter being
construed to include the extraction and measurement of
metabolite levels from a patient sample. SJ Op., 702 F.
Supp. 2d at 234-35 (citing Prometheus Labs., Inc. v. Mayo
Collaborative Servs., 628 F.3d 1347, 1350 (Fed. Cir. 2010),
rev’d, 132 S. Ct. 1289 (2012)). Alternatively, the court
continued, even if the claims could be read to include the
transformations associated with isolating and sequencing
human DNA, these transformations would constitute no
more than preparatory data-gathering steps. Id. at 236
(citing In re Grams, 888 F.2d 835, 840 (Fed. Cir. 1989)).
Finally, the court held that the one method claim to
“comparing” the growth rate of cells claimed a basic
scientific principle and that the transformative steps
amounted to only preparatory data gathering. Id. at 237.
Myriad appealed. We have jurisdiction pursuant to
28 U.S.C. § 1295(a)(1).
DISCUSSION
I. Declaratory Judgment Jurisdiction
A.
The first question we must address is whether the
district court correctly exercised declaratory judgment
jurisdiction over this suit. The Declaratory Judgment Act
provides that, “In a case of actual controversy within its
jurisdiction . . . any court of the United States . . . may
declare the rights and other legal relations of any inter-
ested party seeking such declaration, whether or not
further relief is or could be sought.” 28 U.S.C. § 2201(a).
The phrase “a case of actual controversy” in the Act refers
to the types of “cases” and “controversies” that are justici-
25 ASSOCIATION FOR MOLECULAR v. PTO

able under Article III of the U.S. Constitution. Aetna Life
Ins. v. Haworth, 300 U.S. 227, 239-40 (1937).
Although no bright-line rule exists for determining
whether a declaratory judgment action satisfies Article
III’s case-or-controversy requirement, the Supreme Court
has held that the dispute must be “definite and concrete,
touching the legal relations of parties having adverse
legal interests,” “real and substantial,” and “admi[t] of
specific relief through a decree of a conclusive character,
as distinguished from an opinion advising what the law
would be upon a hypothetical state of facts.” MedIm-
mune, 549 U.S. at 127 (quoting Aetna Life, 300 U.S. at
240-41). “Basically, the question in each case is whether
the facts alleged, under all the circumstances, show that
there is a substantial controversy, between parties having
adverse legal interests, of sufficient immediacy and
reality to warrant the issuance of a declaratory judg-
ment.” Id. (quoting Md. Cas. Co. v. Pac. Coal & Oil Co.,
312 U.S. 270, 273 (1941)).
In applying MedImmune’s all-the-circumstances test
to a declaratory judgment action, we are guided by the
Supreme Court’s three-part framework for determining
whether an action presents a justiciable Article III con-
troversy: standing, ripeness, and mootness. See Caraco
Pharm. Labs., Ltd. v. Forest Labs., Inc., 527 F.3d 1278,
1291 (Fed. Cir. 2008). In this case, the parties have
framed the jurisdictional issue as one of standing. See
MedImmune, 549 U.S. at 128 n.8. (“The justiciability
problem that arises, when the party seeking declaratory
relief is himself preventing the complained-of injury from
occurring, can be described in terms of standing . . . or . . .
ripeness.” (internal citations omitted)).
“[T]he irreducible constitutional minimum of standing
contains three elements.” Lujan v. Defenders of Wildlife,
ASSOCIATION FOR MOLECULAR v. PTO 26

504 U.S. 555, 560 (1992). “First, the plaintiff must have
suffered an injury in fact—an invasion of a legally pro-
tected interest which is (a) concrete and particularized,
and (b) actual or imminent, not conjectural or hypotheti-
cal.” Id. (internal citations and quotations omitted).
“Second, there must be a causal connection between the
injury and the conduct complained of–the injury has to be
‘fairly . . . trace[able] to the challenged action of the
defendant . . . .’” Id. (quoting Simon v. E. Ky. Welfare
Rights Org., 426 U.S. 26, 41-42 (1976)). “Third, it must be
‘likely,’ as opposed to merely ‘speculative,’ that the injury
will be ‘redressed by a favorable decision.’” Id. at 561
(quoting Simon, 426 U.S. at 38, 43).
“Whether an actual case or controversy exists so that
a district court may entertain an action for a declaratory
judgment of non-infringement and/or invalidity is gov-
erned by Federal Circuit law.” MedImmune, Inc. v. Cen-
tocor, Inc., 409 F.3d 1376, 1378 (Fed. Cir. 2005), overruled
on other grounds, MedImmune, 549 U.S. at 130-31.
Following MedImmune, this court has held that, to estab-
lish an injury in fact traceable to the patentee, a declara-
tory judgment plaintiff must allege both (1) an affirmative
act by the patentee related to the enforcement of his
patent rights, SanDisk Corp. v. STMicroelecs., Inc., 480
F.3d 1372, 1380-81 (Fed. Cir. 2007), and (2) meaningful
preparation to conduct potentially infringing activity, Cat
Tech LLC v. TubeMaster, Inc., 528 F.3d 871, 880 (Fed.
Cir. 2008). We review the exercise of declaratory judg-
ment jurisdiction in light of a particular set of facts de
novo. SanDisk Corp., 480 F.3d at 1377.
B.
Myriad challenges the district court’s jurisdictional
decision on the grounds that Myriad and the Plaintiffs do
not have adverse legal interests and that Plaintiffs have
27 ASSOCIATION FOR MOLECULAR v. PTO

failed to allege a controversy of sufficient immediacy and
reality to warrant the issuance of a declaratory judgment.
Specifically, Myriad argues that Plaintiffs have failed to
allege any “affirmative acts” by Myriad within the past
ten years relating to the patents in suit or directed at any
Plaintiff. According to Myriad, the district court erred by
relying on “stale communications” directed at Drs. Ka-
zazian, Ganguly, and Ostrer over a decade ago, as well as
ten-year-old licensing and litigation activities directed at
third parties, and thus exercised jurisdiction based solely
on Plaintiffs’ subjective fear of suit, arising from rumor
and innuendo in the research community.
Plaintiffs respond that they have standing under
MedImmune’s all-the-circumstances test because, not only
are they undisputedly prepared to immediately undertake
potentially infringing activities, but also Myriad took
sufficient affirmative acts with respect to the patents in
suit. Regarding the latter, Plaintiffs assert that Myriad
sued, threatened to sue, or demanded license agreements
from every known institution offering BRCA clinical
testing, including university labs directed by plaintiffs
Kazazian, Ganguly, and Ostrer, forcing each to cease such
testing. And, according to Plaintiffs, the awareness of
Myriad’s vigorous assertion of its patent rights still con-
tinues to suppress their ability to perform clinical BRCA
testing, placing Plaintiffs in the very dilemma the De-
claratory Judgment Act was intended to address: they
must either proceed with BRCA-related activities and risk
liability for patent infringement, or refrain from such
activities despite believing Myriad’s patents are invalid.
Under the facts alleged in this case, we conclude that
one Plaintiff, Dr. Ostrer, has established standing to
maintain this declaratory judgment suit. All Plaintiffs
claim standing under the Declaratory Judgment Act
based on the same alleged injury: that they cannot un-
ASSOCIATION FOR MOLECULAR v. PTO 28

dertake the BRCA-related activities that they desire
because of Myriad’s enforcement of its patent rights
covering BRCA1/2. 7 Only three plaintiffs, however,
allege an injury traceable to Myriad; only Drs. Kazazian,
Ganguly, and Ostrer allege affirmative patent enforce-
ment actions directed at them by Myriad. Of these three,
Dr. Ostrer clearly alleges a sufficiently real and imminent
injury because he alleges an intention to actually and
immediately engage in allegedly infringing BRCA-related
activities. We address each in turn.
Although MedImmune relaxed this court’s more re-
strictive “reasonable apprehension of suit” test for de-
claratory judgment jurisdiction, SanDisk, 480 F.3d at
1380, it did not alter “the bedrock rule that a case or
controversy must be based on a real and immediate injury
or threat of future injury that is caused by the defen-
dants,” Prasco, LLC v. Medicis Pharm. Corp., 537 F.3d
1329, 1339 (Fed. Cir. 2008). Accordingly, following
MedImmune, this court has continued to hold that de-
claratory judgment jurisdiction will not arise merely on
the basis that a party learns of the existence of an ad-
versely held patent, or even perceives that such a patent
poses a risk of infringement, in the absence of some
affirmative act by the patentee. SanDisk, 480 F.3d at
1380-81. Thus, without defining the outer boundaries of
declaratory judgment jurisdiction, we have held that

7 Certain patients also allege an injury based on
their inability to gain access to affordable BRCA genetic
testing because of Myriad’s patent dominance of such
services. While denial of health services can, in certain
circumstances, state a judicially cognizable injury, see
Simon, 426 U.S. at 40-41, Plaintiffs have not pressed this
as an independent ground for standing. Moreover, we fail
to see how the inability to afford a patented invention
could establish an invasion of a legally protected interest
for purposes of standing.
29 ASSOCIATION FOR MOLECULAR v. PTO

“where a patentee asserts rights under a patent based on
certain identified ongoing or planned activity of another
party, and where that party contends that it has the right
to engage in the accused activity without license, an
Article III case or controversy will arise . . . .” Id. at 1381;
see also Prasco, 537 F.3d at 1338 (“A patentee can cause
. . . an injury [sufficient to create an actual controversy] in
a variety of ways, for example, by creating a reasonable
apprehension of an infringement suit, [or] demanding the
right to royalty payments.” (internal citations omitted)).
In this case, Myriad demanded a royalty under its
patents from Dr. Ostrer based on his clinical BRCA-
related activities. In May 1998, Myriad’s Director of
Corporate Communications sent Ostrer a letter proposing
a collaborative license. The letter stated that Myriad was
aware that Ostrer was either currently providing, or was
interested in initiating, BRCA1 diagnostic testing services
and that Myriad, as holder of U.S. patents covering the
BRCA1 gene and diagnostic testing of BRCA1, was mak-
ing available to his institution, NYU Medical Center, a
limited collaborative license. The collaborative license
required NYU to make a payment to Myriad for each non-
research BRCA test performed.
At the same time, as Ostrer was aware, Myriad was
asserting its patent rights against other similarly situated
parties, a fact to be considered in assessing the existence
of an actual controversy under the totality of circum-
stances. See Micron Tech., Inc. v. Mosaid Techs., Inc., 518
F.3d 897, 901 (Fed. Cir. 2008). Soon after Ostrer received
Myriad’s letter, Dr. Kazazian informed him that, because
of Myriad’s assertion of its patent rights against him,
GDL would no longer be accepting patient samples for
BRCA genetic testing. Myriad’s assertion of its patent
rights against Kazazian escalated into a patent infringe-
ment suit by Myriad against the University of Pennsyl-
ASSOCIATION FOR MOLECULAR v. PTO 30

vania, which was later dismissed without prejudice after
the University agreed to cease all accused BRCA testing
services. Myriad also sued Oncormed for patent in-
fringement based on its BRCA genetic testing services.
As a result of Myriad’s patent enforcement actions, Dr.
Ostrer was forced to send all patient samples to Myriad,
now the sole provider of BRCA diagnostic testing services.
Dr. Ostrer, on the other hand, maintains that he could
have proceeded with his BRCA-related clinical activities
without taking a license from Myriad. This assertion is
based on his belief that the patents Myriad claims cover
such activities are invalid because genes are patent-
ineligible products of nature. Acting on his belief, Ostrer
seeks in this lawsuit a declaration of his right to under-
take BRCA-related clinical activities without a license.
Accordingly, Myriad and Dr. Ostrer have taken adverse
legal positions regarding whether or not Ostrer can en-
gage in BRCA genetic testing without infringing any valid
claim to “isolated” BRCA DNAs or methods of “analyzing”
or “comparing” BRCA sequences, as recited in Myriad’s
patents. See Aetna Life, 300 U.S. at 242 (holding declara-
tory judgment jurisdiction existed when “the parties had
taken adverse positions with respect to their existing
obligations” on an insurance contract).
Dr. Ostrer has also alleged a controversy of sufficient
reality and immediacy, MedImmune, 549 U.S. at 127; he
has alleged a concrete and actual injury traceable to
Myriad’s assertion of its patent rights, see Lujan, 504 U.S.
at 560. First, Ostrer seeks to undertake specific BRCA-
related activities—BRCA diagnostic testing—for which
Myriad has demanded a license under specific patents—
those that cover the isolated BRCA genes and BRCA
diagnostic testing. Thus, Ostrer does not request “an
opinion advising what the law would be upon a hypotheti-
cal state of facts,” Aetna Life, 300 U.S. at 241, but rather
31 ASSOCIATION FOR MOLECULAR v. PTO

whether his proposed BRCA testing services are covered
by valid patent claims to “isolated” BRCA genes and
methods of “comparing” the genes’ sequences. Second,
Ostrer not only has the resources and expertise to imme-
diately undertake clinical BRCA testing, but also states
unequivocally that he will immediately begin such test-
ing. In contrast to Ostrer, who alleges an actual and
imminent injury for purposes of standing, Drs. Kazazian
and Ganguly allege only that they will “consider” resum-
ing BRCA testing. These “‘some day’ intentions” are
insufficient to support an “actual or imminent” injury for
standing “without . . . any specification of when the some
day will be.” Lujan, 504 U.S. at 564. As a result, Drs.
Kazazian and Ganguly do not have standing.
Myriad seeks to avoid this result based on the timing
of its enforcement actions. Specifically, Myriad argues
that time has extinguished the immediacy and reality of
any controversy, relying on language that hearkens back
to our pre-MedImmune reasonable apprehension of suit
test. See, e.g., Appellants’ Br., 2010 WL 4600106, at 26
(“[A] patentee’s ten-year silence presumptively extin-
guishes any reasonable objective fear of suit.”). We dis-
agree. In many cases a controversy made manifest by a
patentee’s affirmative assertion of its patent rights will
dissipate as market players and products change. In this
case, however, the relevant circumstances surrounding
Myriad’s assertion of its patent rights have not changed
despite the passage of time. 8

8 Myriad’s analogy to laches is also unconvincing.
Laches bars the recovery of pre-filing damages; it does not
preclude a patent action for prospective relief, the type of
relief sought here. See A.C. Aukerman Co. v. R.L. Chaides
Const. Co., 960 F.2d 1020, 1041 (Fed. Cir. 1992) (en banc)
(“[L]aches bars relief on a patentee’s claim only with
respect to damages accrued prior to suit.”).
ASSOCIATION FOR MOLECULAR v. PTO 32

Myriad’s active enforcement of its patent rights forced
Dr. Ostrer, as well as every other similarly situated
researcher and institution, to cease performing the chal-
lenged BRCA testing services, leaving Myriad as the sole
provider of BRCA clinical testing to patients in the United
States. Since that time, neither the accused activities nor
the parties’ positions have changed. First, Myriad does
not allege that genetic testing technology has changed in
any way that renders its past assertions of its patent
rights irrelevant to Ostrer’s currently proposed BRCA
testing. Rather, the patents cover, as Myriad asserted in
the late 1990s, the basic components of any such test: the
isolated BRCA genes and the diagnostic step of comparing
the genes’ sequences.
Second, ever since Myriad’s enforcement efforts elimi-
nated all competition, Myriad and Ostrer have not altered
their respective positions. Ostrer, still laboring under
Myriad’s threat of infringement liability, has not at-
tempted to provide BRCA testing; yet, as a researcher, he
remains in the same position with respect to his ability
and his desire to provide BRCA testing as in the late
1990s. Furthermore, nothing in the record suggests that
any researcher or institution has successfully attempted
to compete with Myriad, or that Myriad has in any way
changed its position with regard to its patent rights. Just
as active enforcement of one’s patent rights against others
can maintain a real and immediate controversy despite
the passage of time, see Micron, 518 F.3d at 901, so too
can the successful assertion of such rights when the
relevant circumstances remain unchanged. Thus, consis-
tent with the purpose of the Declaratory Judgment Act,
Ostrer need not risk liability and treble damages for
patent infringement before seeking a declaration of his
contested legal rights. See MedImmune, 549 U.S. at 134.
33 ASSOCIATION FOR MOLECULAR v. PTO

Myriad also argues that the record refutes Ostrer’s
claim that he has been restrained from engaging in
BRCA-related gene sequencing. Specifically, Myriad
argues that since Myriad published its discoveries of the
BRCA1 and BRCA2 genes in October 1994 and March
1996, respectively, over 18,000 scientists have conducted
research on the BRCA genes and over 8,600 research
papers have been published. Furthermore, according to
Myriad, plaintiff Wendy Chung concedes that her lab
currently conducts sequencing of BRCA genes. Yet, both
Drs. Chung and Ostrer state that, although they conduct
gene sequencing, they are forbidden from informing their
research subjects of the results of their BRCA tests with-
out first sending the samples to Myriad. Accordingly,
Ostrer is restrained from the BRCA-related activity that
he desires to undertake: clinical diagnostic testing.
Myriad’s communications with Dr. Ostrer confirm this
understanding. The licensing letter Myriad sent to Ostrer
proposed a collaborative agreement giving NYU the right
to perform “Research Tests” without payment to Myriad.
J.A. 2967. “Research Tests” are defined as tests that
further “non-commercial research programs, the results of
which are not provided to the patient and for which no
money is received.” J.A. 2965 (emphasis added). In
contrast, the agreement requires payment to Myriad for
each “Testing Service” performed, with “Testing Services”
defined as “medical laboratory testing . . . for the presence
or absence of BRCA1 mutations for the purpose of deter-
mining or predicting predisposition to, or assessing the
risk of breast or ovarian cancer in humans.” J.A. 2966-67.
Thus, Myriad’s patent enforcement actions never targeted
the non-clinical BRCA research now cited by Myriad, and
Ostrer’s ability to perform such research does not address
the injury asserted here.
ASSOCIATION FOR MOLECULAR v. PTO 34

Finally, Myriad argued in its reply brief and at oral
argument that Plaintiffs’ declaratory action will not afford
them the relief they want, a requirement for standing.
Lujan, 504 U.S. at 560-61; see also MedImmune, 549 U.S.
at 127 n.7 (“[A] litigant may not use a declaratory-
judgment action to obtain piecemeal adjudication of
defenses that would not finally and conclusively resolve
the underlying controversy.”). Specifically, Myriad as-
serts that because Plaintiffs have challenged just fifteen
composition and method claims, while admitting that
other unchallenged claims to BRCA probes and primers
will still prevent them from engaging in BRCA sequenc-
ing, a favorable decision will not redress the Plaintiffs’
alleged injury. Again, we disagree.
The Supreme Court has required only that it is
“likely,” rather than “merely ‘speculative,’” that the al-
leged injury will be “redressed by a favorable decision.”
Lujan, 504 U.S. at 561. The Court has not required
certainty. For example, in Village of Arlington Heights v.
Metropolitan Housing Development Corp., the Court held
that the plaintiffs had standing to challenge a suburb’s
exclusionary zoning ordinance, as the ordinance stood as
“an absolute barrier” to the housing development Metro-
politan Housing Development Corp. (“MHDC”) had con-
tracted to provide in the village. 429 U.S. 252, 261 (1977).
The Court noted that injunctive relief, while removing the
“barrier” of the ordinance, would not “guarantee” that the
housing would be built since MHDC still had to secure
financing, qualify for federal subsidies, and carry through
with construction. Id. The Court nevertheless recognized
that “all housing developments are subject to some extent
to similar uncertainties,” and concluded that it was suffi-
cient that there was a “substantial probability” that the
housing development would be built. Id. at 261, 264.
35 ASSOCIATION FOR MOLECULAR v. PTO

In this case, Myriad’s challenged composition and
method claims undisputedly provide “an absolute barrier”
to Dr. Ostrer’s ability to undertake BRCA diagnostic
testing activities, and a declaration of those claims’ inva-
lidity would remove that barrier. See id. at 261. More-
over, while there may be other patent claims directed to
BRCA probes and primers that prevent Ostrer from
performing BRCA diagnostic testing free of infringement
liability, Myriad has failed to direct us to any specific
unchallenged claim that will have that effect. And Plain-
tiffs’ counsel stated at the first oral argument in this case
that his clients can sequence the BRCA genes without
using BRCA probes and primers. Oral Arg. at 34:07-25,
34:53-35:29 available at http://www.cafc.uscourts.gov/
oral-argument-recordings/2010-1406/all. Accordingly, we
decline to construe the asserted claims and decline to hold
on this record that Dr. Ostrer’s proposed BRCA-related
activities would infringe unchallenged claims to primers
and probes. We thus conclude that it is likely, not merely
speculative, that Dr. Ostrer’s injury will be redressed by a
favorable decision.
Although we affirm the district court’s decision to ex-
ercise declaratory judgment jurisdiction over this case, we
do so on narrower grounds. The district court failed to
limit its jurisdictional holding to affirmative acts by the
patentee directed at specific Plaintiffs, see SanDisk, 480
F.3d at 1380-81, erroneously holding all the Plaintiffs had
standing based on “the widespread understanding that
one may engage in BRCA1/2 testing at the risk of being
sued for infringement liability by Myriad,” DJ Op., 669 F.
Supp. 2d at 390. We disagree, and thus we reverse the
district court’s holding that the various plaintiffs other
than Dr. Ostrer have standing to maintain this declara-
tory judgment action. Simply disagreeing with the exis-
tence of a patent on isolated DNA sequences or even
ASSOCIATION FOR MOLECULAR v. PTO 36

suffering an attenuated, non-proximate, effect from the
existence of a patent does not meet the Supreme Court’s
requirement for an adverse legal controversy of sufficient
immediacy and reality to warrant the issuance of a de-
claratory judgment. See MedImmune, 549 U.S. at 127.
The various organizational plaintiffs in this suit in par-
ticular were not the target of any enforcement action or
offered license agreements by Myriad and had made no
preparation to undertake potentially infringing activities.
They accordingly suffered no injury and thus lack stand-
ing to bring this action. See Prasco, 537 F.3d at 1338-42;
Cat Tech, 528 F.3d at 880-81.
Having found one plaintiff with standing to maintain
this declaratory judgment action, see Horne v. Flores, 129
S. Ct. 2579, 2592-93 (2009), we may turn now to the
merits of Myriad’s appeal of the district court’s summary
judgment decision, which held all fifteen challenged
composition and method claims invalid under § 101.
II. Subject Matter Eligibility
Under the Patent Act, “Whoever invents or discovers
any new and useful process, machine, manufacture, or
composition of matter, or any new and useful improve-
ment thereof, may obtain a patent therefor, subject to the
conditions and requirements of this title.” 35 U.S.C.
§ 101. The Supreme Court has consistently construed
§ 101 broadly, explaining that “[i]n choosing such expan-
sive terms . . . modified by the comprehensive ‘any,’ Con-
gress plainly contemplated that the patent laws would be
given wide scope.” Bilski v. Kappos, 130 S. Ct. 3218, 3225
(2010) (quoting Chakrabarty, 447 U.S. at 308).
The Supreme Court, however, has also consistently
held that § 101, although broad, is not unlimited. Id. The
Court’s precedents provide three judicially created excep-
tions to § 101’s broad patent-eligibility principles: “‘Laws
37 ASSOCIATION FOR MOLECULAR v. PTO

of nature, natural phenomena, and abstract ideas’ are not
patentable.” Mayo, 132 S. Ct. at 1293 (quoting Diamond
v. Diehr, 450 U.S. 175, 185 (1981)). The Court has also
referred to those exceptions as precluding the patenting of
mental processes, Gottschalk v. Benson, 409 U.S. 63, 67
(1972), and products of nature, Chakrabarty, 447 U.S. at
313 (“[T]he relevant distinction for purposes of § 101 is . . .
between products of nature . . . and human-made inven-
tions.”). The Court has explained that, although not
required by the statutory text, “[t]he concepts covered by
these exceptions are ‘part of the storehouse of knowledge
of all men . . . free to all men and reserved exclusively to
none.’” Bilski, 130 S. Ct. at 3225 (quoting Funk Bros.
Seed Co. v. Kalo Inoculant Co., 333 U.S. 127, 130 (1948)).
Plaintiffs challenge under § 101 Myriad’s composition
claims directed to “isolated” DNA molecules, its method
claims directed to “analyzing” or “comparing” DNA se-
quences, and its claim to a method for screening potential
cancer therapeutics. We address each in turn. Before
reviewing the applicability of the Supreme Court’s Mayo
holding to the claims of the Myriad patents, however, it is
important to state what this appeal is not about. It is not
about whether individuals suspected of having an in-
creased risk of developing breast cancer are entitled to a
second opinion. Nor is it about whether the University of
Utah, the owner of the instant patents, or Myriad, the
exclusive licensee, has acted improperly in its licensing or
enforcement policies with respect to the patents. The
question is also not whether is it desirable for one com-
pany to hold a patent or license covering a test that may
save people’s lives, or for other companies to be excluded
from the market encompassed by such a patent—that is
the basic right provided by a patent, i.e., to exclude others
from practicing the patented subject matter. It is also not
whether the claims at issue are novel or nonobvious or too
ASSOCIATION FOR MOLECULAR v. PTO 38

broad. Those questions are not before us. It is solely
whether the claims to isolated BRCA DNA, to methods for
comparing DNA sequences, and to a process for screening
potential cancer therapeutics meet the threshold test for
patent-eligible subject matter under 35 U.S.C. § 101 in
light of various Supreme Court holdings, particularly
including Mayo. The issue is patent eligibility, not pat-
entability.
We would further note, in the context of discussing
what this case is not about, that patents on life-saving
material and processes, involving large amounts of risky
investment, would seem to be precisely the types of sub-
ject matter that should be subject to the incentives of
exclusive rights. But disapproving of patents on medical
methods and novel biological molecules are policy ques-
tions best left to Congress, and other general questions
relating to patentability and use of patents are issues not
before us. As will be seen, on the limited questions before
us, we conclude that the composition claims and the
screening claim involving growing a transformed host cell
meet the standards for patent eligibility, while the
claimed methods for “analyzing” or “comparing” do not.
A. Composition Claims: Isolated DNA Molecules
i.
The principal claims of the patents before us on re-
mand relate to isolated DNA molecules. Mayo does not
control the question of patent-eligibility of such claims.
They are claims to compositions of matter, expressly
authorized as suitable patent-eligible subject matter in
§ 101. As to those claims, the issue of patent-eligibility
remains, as it was on the first appeal to this court,
whether they claim patent-ineligible products of nature.
We hold that they do not. The isolated DNA molecules
before us are not found in nature. They are obtained in
39 ASSOCIATION FOR MOLECULAR v. PTO

the laboratory and are man-made, the product of human
ingenuity. While they are prepared from products of
nature, so is every other composition of matter. All new
chemical or biological molecules, whether made by syn-
thesis or decomposition, are made from natural materials.
For example, virtually every medicine utilized by today’s
medical practitioners, and every manufactured plastic
product, is either synthesized from natural materials
(most often petroleum fractions) or derived from natural
plant materials. But, as such, they are different from
natural materials, even if they are ultimately derived
from them. The same is true of isolated DNA molecules.
ii.
Myriad argues that its challenged composition claims
to “isolated” DNAs cover patent-eligible compositions of
matter within the meaning of § 101. According to Myriad,
the district court came to a contrary conclusion by (1)
misreading Supreme Court precedent as excluding from
patent eligibility all “products of nature” unless “mark-
edly different” from naturally occurring ones; and (2)
incorrectly focusing not on the differences between iso-
lated and native DNAs, but on one similarity: their infor-
mational content. Rather, Myriad argues, an isolated
DNA molecule is patent eligible because it is, as claimed,
“a nonnaturally occurring manufacture or composition of
matter” with “a distinctive name, character, and use.”
Appellants’ Br., 2010 WL 4600106, at 41-42 (quoting
Chakrabarty, 447 U.S. at 309-10). Myriad contends that
isolated DNA does not exist in nature and that isolated
DNAs, unlike native DNAs, can be used as primers and
probes for diagnosing cancer. Moreover, Myriad asserts
that an ultimately-derived-from “products of nature”
exception not only would be unworkable, as every compo-
sition of matter is, at some level, composed of natural
materials, but also would be contrary to this court’s
ASSOCIATION FOR MOLECULAR v. PTO 40

precedents, the PTO’s 2001 Utility Examination Guide-
lines, and Congress’s role in enacting the patent laws.
Regarding Mayo, Myriad argues that the Supreme Court’s
decision did not address or alter the established patent-
eligibility test for composition claims, such that the stan-
dards announced in Chakrabarty still govern this appeal.
To the extent that the general principles discussed in
Mayo bear on the DNA claims, Myriad maintains that
isolated DNA represents a nonnatural, man-made inven-
tion distinct from the lack of human ingenuity underlying
the method claims there at issue.
Plaintiffs respond that claims to isolated DNA mole-
cules fail to satisfy § 101 because such claims cover natu-
ral phenomena and products of nature. According to
Plaintiffs, Supreme Court precedent establishes that a
product of nature is not patent eligible even if, as claimed,
it has undergone some highly useful change from its
natural form. Rather, Plaintiffs assert, to be patent
eligible a composition of matter must also have a distinc-
tive name, character, and use, making it “markedly
different” from the natural product. In this case, Plain-
tiffs conclude that because isolated DNAs retain part of
the same nucleotide sequence as native DNAs, they do not
have any “markedly different” characteristics. Further-
more, according to Plaintiffs, the isolated DNA claims
preempt products and laws of nature, excluding anyone
from working with the BRCA genes and the genetic
information they convey. Under Mayo, Plaintiffs assert
that any structural differences relative to the chromoso-
mal BRCA genes do not add “enough” to the underlying
natural genetic sequences to render Myriad’s isolated
DNA molecules patentable under § 101.
The government as amicus curiae does not defend the
longstanding position of the PTO, a government agency,
that isolated DNA molecules are patent eligible, arguing
41 ASSOCIATION FOR MOLECULAR v. PTO

instead for a middle ground. Specifically, the government
argues that DNA molecules engineered by man, including
cDNAs, 9 are patent-eligible compositions of matter be-
cause, with rare exceptions, they do not occur in nature,
either in isolation or as contiguous sequences within a
chromosome. In contrast, the government asserts, iso-
lated and unmodified genomic DNAs are not patent
eligible, but rather patent-ineligible products of nature,
since their nucleotide sequences exist because of evolu-
tion, not man.
At the first oral argument, the government illustrated
its position by way of a so-called “magic microscope” test
(an invention in and of itself, although probably not
patent-eligible). Oral Arg. at 46:50-47:50. According to
the government’s test then, if an imaginary microscope
could focus in on the claimed DNA molecule as it exists in
the human body, the claim covers ineligible subject mat-
ter. The government thus argued that because such a
microscope could focus in on the claimed isolated BRCA1
or BRCA2 sequences as they exist in the human body, the
claims covering those sequences are not patent eligible.
In contrast, the government contended, because an
imaginary microscope could not focus in vivo on a cDNA
sequence, which is engineered by man to splice together
non-contiguous coding sequences (i.e., exons), claims
covering cDNAs are patent eligible.
In sum, although the parties and the government ap-
pear to agree that isolated DNAs are compositions of
matter, they disagree on whether and to what degree such
molecules fall within the exception for products of nature.

9 According to the government, several of the com-
position claims at issue in this suit, including claim 2 of
the ’282 patent, are limited to cDNA and thus patent
eligible. We agree.
ASSOCIATION FOR MOLECULAR v. PTO 42

As set forth below, we conclude that the challenged claims
to isolated DNAs, whether limited to cDNAs or not, are
directed to patent-eligible subject matter under § 101.
iii.
While Mayo and earlier decisions concerning method
claim patentability provide valuable insights and illumi-
nate broad, foundational principles, the Supreme Court’s
decisions in Chakrabarty and Funk Brothers set out the
primary framework for deciding the patent eligibility of
compositions of matter, including isolated DNA mole-
cules. 10
In Chakrabarty, the Court addressed the question
whether a man-made, living microorganism is a patent-

10 Other Supreme Court decisions cited by the par-
ties and amici relating to patented manufactures and
compositions of matter were decided based on lack of
novelty, not patent-eligible subject matter. In American
Wood-Paper Co. v. Fibre Disintegrating Co., the Court
held the challenged patent “void for want of novelty in the
manufacture patented,” because the “[p]aper-pulp ob-
tained from various vegetable substances was in common
use before the original patent was granted . . . , and
whatever may be said of their process for obtaining it, the
product was in no sense new.” 90 U.S. 566, 596 (1874).
Similarly, in Cochrane v. Badische Anilin & Soda Fabrik,
the Court held that a claim to artificial alizarine covered
an old and well-known substance, the alizarine of madder,
which could not be patented although made artificially for
the first time. 111 U.S. 293, 311 (1884); see also id. at
308-09 (“It is very plain that the specification of the
original patent, No. 95,465, states the invention to be a
process for preparing alizarine, not as a new substance
prepared for the first time, but as the substance already
known as alizarine, to be prepared, however, by the new
process, which process is to be the subject of the patent,
and is the process of preparing the known product aliza-
rine from anthracine.” (emphases added)).
43 ASSOCIATION FOR MOLECULAR v. PTO

eligible manufacture or composition of matter within the
meaning of § 101. 447 U.S. at 305, 307. The microorgan-
isms were bacteria genetically engineered with four
naturally occurring DNA plasmids, each of which enabled
the breakdown of a different component of crude oil. Id.
at 305, 305 n.1. The bacteria, as a result, could break
down multiple components of crude oil, a trait possessed
by no single naturally occurring bacterium and of signifi-
cant use in more efficiently treating oil spills. Id. at 305,
305 n.2. The Court held that the bacteria qualified as
patent-eligible subject matter because the “claim is not to
a hitherto unknown natural phenomenon, but to a non-
naturally occurring manufacture or composition of mat-
ter—a product of human ingenuity ‘having a distinctive
name, character [and] use.’” Id. at 309-10 (quoting Har-
tranft v. Wiegmann, 121 U.S. 609, 615 (1887)).
To underscore the point, the Court compared Chakra-
barty’s engineered bacteria with the mixed bacterial
cultures found unpatentable in Funk Brothers, again
casting this case, more relating to obviousness, in terms of
§ 101. See Parker v. Flook, 437 U.S. 584, 591 (1978);
Benson, 409 U.S. at 67. In Funk Brothers, the patentee
discovered that certain strains of nitrogen-fixing bacteria
associated with leguminous plants do not mutually inhibit
each other. 333 U.S. at 129-30. Based on that discovery,
the patentee produced (and claimed) mixed cultures of
nitrogen-fixing species capable of inoculating a broader
range of leguminous plants than single-species cultures.
Id. The Court held that the bacteria’s cooperative quali-
ties were, “like the heat of the sun, electricity, or the
qualities of metals,” the “work of nature,” and thus not
patentable. Id. at 130. The Court also held that applying
the newly discovered bacterial compatibility to create a
mixed culture was not a patentable advance because no
species acquired a different property or use. Id. at 131.
ASSOCIATION FOR MOLECULAR v. PTO 44

The Chakrabarty Court thus concluded that what distin-
guished Chakrabarty’s oil-degrading bacteria from the
mixed cultures claimed in Funk Brothers, and made the
former patent-eligible, was that Chakrabarty’s bacteria
had “markedly different characteristics from any [bacte-
rium] found in nature” based on the efforts of the pat-
entee. Chakrabarty, 447 U.S. at 310.
One distinction, therefore, between products of nature
and human-made invention for purposes of § 101 turns on
a change in the claimed composition’s identity compared
with what exists in nature. Specifically, the Supreme
Court has drawn a line between compositions that, even if
arrayed in useful combinations or harnessed to exploit
newly discovered properties, have similar characteristics
as in nature, and compositions that human intervention
has given “markedly different,” or “distinctive,” character-
istics. Id. (citing Hartranft, 121 U.S. at 615); see also Am.
Fruit Growers v. Brogdex Co., 283 U.S. 1, 11 (1931).
Applying this test to the isolated DNAs in this case, the
challenged claims are drawn to patent-eligible subject
matter because the claims cover molecules that are mark-
edly different—have a distinctive chemical structure and
identity—from those found in nature.
It is undisputed that Myriad’s claimed isolated DNAs
exist in a distinctive chemical form—as distinctive chemi-
cal molecules—from DNAs in the human body, i.e., native
DNA. Natural DNA exists in the body as one of forty-six
large, contiguous DNA molecules. Each of those DNA
molecules is condensed and intertwined with various
proteins, including histones, to form a complex tertiary
structure known as chromatin that makes up a larger
structural complex, a chromosome. See supra, Figure 3.
Inside living cells, the chromosomes are further encapsu-
lated within a series of membranes and suspended in a
complex intracellular milieu.
45 ASSOCIATION FOR MOLECULAR v. PTO

Isolated DNA, in contrast, is a free-standing portion of
a larger, natural DNA molecule. Isolated DNA has been
cleaved (i.e., had covalent bonds in its backbone chemi-
cally severed) or synthesized to consist of just a fraction of
a naturally occurring DNA molecule. For example, the
BRCA1 gene in its native state resides on chromosome 17,
a DNA molecule of around eighty million nucleotides.
Similarly, BRCA2 in its native state is located on chromo-
some 13, a DNA of approximately 114 million nucleotides.
In contrast, isolated BRCA1 and BRCA2, with introns,
each consists of just 80,000 or so nucleotides. And with-
out introns, BRCA2 shrinks to approximately 10,200
nucleotides and BRCA1 to just around 5,500 nucleotides.
Furthermore, claims 5 and 6 of the ’282 patent cover
isolated DNAs, e.g., primers or probes, having as few as
fifteen nucleotides of a BRCA sequence. Accordingly,
BRCA1 and BRCA2 in their isolated states are different
molecules from DNA that exists in the body; isolated DNA
results from human intervention to cleave or synthesize a
discrete portion of a native chromosomal DNA, imparting
on that isolated DNA a distinctive chemical identity as
compared to native DNA.
As the above description indicates, isolated DNA is
not just purified DNA. Purification makes pure what was
the same material, but was combined, or contaminated,
with other materials. Although isolated DNA is removed
from its native cellular and chromosomal environment, it
has also been manipulated chemically so as to produce a
molecule that is markedly different from that which exists
in the body. Accordingly, this is not a situation, as in
Parke-Davis & Co. v. H.K. Mulford Co., in which purifica-
tion of adrenaline resulted in the identical molecule,
albeit being “for every practical purpose a new thing
commercially and therapeutically.” 189 F. 95, 103
(C.C.S.D.N.Y. 1911). Judge Learned Hand’s opinion for
ASSOCIATION FOR MOLECULAR v. PTO 46

the district court in that oft-cited case held the purified
“Adrenalin” to be patent-eligible subject matter. Id. The
In re Marden cases are similarly inapposite, directed as
they are to the patent ineligibility of purified natural
elements—ductile uranium, 47 F.2d 957 (CCPA 1931),
and vanadium, 47 F.2d 958 (CCPA 1931)—that are inher-
ently ductile in purified form. While purified natural
products thus may or may not qualify for patent under
§ 101, the isolated DNAs of the present patents constitute
an a fortiori situation, where they are not only purified;
they are different from the natural products in “name,
character, and use.” Chakrabarty, 447 U.S. at 309-10. 11
Parke-Davis and Marden address a situation in which
claimed compound A is purified from a physical mixture
that contains compound A. In this case, the claimed

11 In re Bergy, relating to a purified microorganism,
596 F.2d 952, 967-68 (CCPA 1979), was once a companion
case to Chakrabarty but was vacated by the Supreme
Court and remanded for dismissal as moot when the
inventors withdrew their claim from the pending applica-
tion. Diamond v. Chakrabarty, 444 U.S. 1028 (1980).
Other CCPA cases cited by the parties and amici were not
decided based on patent eligibility. In In re Bergstrom,
the court held that pure prostaglandin compounds,
PGE(2) and PGE(3), were improperly rejected as lacking
novelty. 427 F.2d 1394, 1394 (CCPA 1970); see Bergy, 596
F.2d at 961 (recognizing Bergstrom as a case decided
under § 102). Similarly in In re Kratz, the court held
nonobvious claims to synthetically produced, substan-
tially pure 2-methyl-2-pentenoic acid, a chemical that
gives strawberries their flavor. 592 F.2d 1169, 1170
(CCPA 1979); see also In re King, 107 F.2d 618, 619
(CCPA 1939) (holding claims to vitamin C invalid for lack
of novelty, as “[a]ppellants were not the first to discover or
produce [vitamin C] in its pure form”); In re Merz, 97 F.2d
599, 601 (CCPA 1938) (holding claims to artificial ultra-
marine that contains non-floatable impurities invalid as
not “inventive,” and thus obvious).
47 ASSOCIATION FOR MOLECULAR v. PTO

isolated DNA molecules do not exist in nature within a
physical mixture to be purified. They have to be chemi-
cally cleaved from their native chemical combination with
other genetic materials. In other words, in nature, the
claimed isolated DNAs are covalently bonded to such
other materials. Thus, when cleaved, an isolated DNA
molecule is not a purified form of a natural material, but
a distinct chemical entity that is obtained by human
intervention. See Chakrabarty, 447 U.S. at 313 (“the
relevant distinction [is] between products of nature . . .
and human-made inventions”). In fact, some forms of
isolated DNA may require no purification at all, because
DNAs can be chemically synthesized directly as isolated
molecules.
The above analysis holding the isolated DNA mole-
cules to be patent-eligible subject matter applies to all of
the asserted composition claims on appeal in this case.
However, as the government has pointed out, claim 2 of
the ’282 patent is narrower than claim 1 and reads only
on cDNAs, which lack the non-coding introns present in
the genomic BRCA1 gene. 12 While, as we have held, all of
the claimed isolated DNAs are eligible for patent as
compositions of matter distinct from natural DNA, the
claimed cDNAs are especially distinctive, lacking the non-
coding introns present in naturally occurring chromoso-
mal DNA. They are even more the result of human
intervention into nature and are hence patent-eligible
subject matter. The government, as noted earlier, has
agreed with that conclusion. Br. United States, 2010 WL
4853320, at 14-17.
The dissent disparages the significance of a “chemical
bond,” presumably meaning a covalent bond, in distin-

12 Claims 2 and 7 of the ’282 patent and claim 7 of
the ’492 patent recite isolated cDNA molecules.
ASSOCIATION FOR MOLECULAR v. PTO 48

guishing structurally between one molecular species and
another. But a covalent bond is the defining boundary
between one molecule and another, and the dissent’s
citation of Linus Pauling’s comment that covalent bonds
“make it convenient for the chemist to consider [the
aggregate] as an independent molecular species” under-
lines the point. The covalent bonds in this case connect
different chemical moieties to one another.
Plaintiffs argue that because the claimed isolated
DNAs retain the same nucleotide sequence as native
DNAs, they do not have any “markedly different” charac-
teristics. This approach, however, looks not at whether
isolated DNAs are markedly different—have a distinctive
characteristic—from naturally occurring DNAs, as the
Supreme Court has directed, but at one similarity, albeit
a key one: the information content contained in isolated
and native DNAs’ nucleotide sequences. Adopting this
approach, the district court disparaged the patent eligibil-
ity of isolated DNA molecules because their genetic func-
tion is to transmit information. We disagree, as it is the
distinctive nature of DNA molecules as isolated composi-
tions of matter that determines their patent eligibility
rather than their physiological use or benefit. Uses of
chemical substances may be relevant to the nonobvious-
ness of these substances or to method claims embodying
those uses, but the patent eligibility of an isolated DNA is
not negated because it has similar informational proper-
ties to a different, more complex natural material. The
claimed isolated DNA molecules are distinct from their
natural existence as portions of larger entities, and their
informational content is irrelevant to that fact. We rec-
ognize that biologists may think of molecules in terms of
their uses, but genes are in fact materials having a
chemical nature and, as such, are best described in pat-
ents by their structures rather than by their functions. In
49 ASSOCIATION FOR MOLECULAR v. PTO

fact, many different materials may have the same func-
tion (e.g., aspirin, ibuprofen, and naproxen).
The district court in effect created a categorical rule
excluding isolated genes from patent eligibility. See SJ
Op., 702 F. Supp. 2d at 228-29. But the Supreme Court
has “more than once cautioned that courts ‘should not
read into the patent laws limitations and conditions
which the legislature has not expressed,’” Bilski, 130 S.
Ct. at 3226 (quoting Diehr, 450 U.S. at 182), and has
repeatedly rejected new categorical exclusions from
§ 101’s scope, see id. at 3227-28 (rejecting the argument
that business method patents should be categorically
excluded from § 101); Chakrabarty, 447 U.S. at 314-17
(same for living organisms). Contrary to the conclusions
of the district court and the suggestions of Plaintiffs and
some amici, § 101 applies equally to all putative inven-
tions, and isolated DNA is not and should not be consid-
ered a special case for purposes of patent eligibility under
existing law. See, e.g., SJ Op., 702 F. Supp. 2d at 185
(“DNA represents the physical embodiment of biological
information, distinct in its essential characteristics from
any other chemical found in nature.”); Appellees’ Suppl.
Br. at 4-5 (“Unlike other chemicals, the information
encoded by DNA reflects its primary biological function . .
. .”).
Under the statutory rubric of § 101, isolated DNA is a
tangible, man-made composition of matter defined and
distinguished by its objectively discernible chemical
structure. Whether its unusual status as a chemical
entity that conveys genetic information warrants singular
treatment under the patent laws as the district court did
is a policy question that we are not entitled to address.
Cf. Nat’l Fed’n of Indep. Bus. v. Sebelius, 132 S. Ct. 2566,
slip op. at 6 (2012) (“[W]e possess neither the expertise
nor the prerogative to make policy judgments. Those
ASSOCIATION FOR MOLECULAR v. PTO 50

decisions are entrusted to our Nation’s elected leaders,
who can be thrown out of office if the people disagree with
them.”). Congress is presumed to have been aware of the
issue, having enacted a comprehensive patent reform act
during the pendency of this case, and it is ultimately for
Congress if it wishes to overturn case law and the long
practice of the PTO to determine that isolated DNA must
be treated differently from other compositions of matter to
account for its perceived special function. We therefore
reject the district court’s unwarranted categorical exclu-
sion of isolated DNA molecules.
Because isolated DNAs, not just cDNAs, have a mark-
edly different chemical structure compared to native
DNAs, we reject the government’s earlier proposed “magic
microscope” test, as it misunderstands the difference
between science and invention and fails to take into
account the existence of molecules as separate chemical
entities. The ability to visualize a DNA molecule through
a microscope, or by any other means, when it is bonded to
other genetic material, is worlds apart from possessing an
isolated DNA molecule that is in hand and usable. It is
the difference between knowledge of nature and reducing
a portion of nature to concrete form, the latter activity
being what the patent laws seek to encourage and protect.
The government’s microscope could focus in on a claimed
portion of any complex molecule, rendering that claimed
portion patent ineligible, even though that portion never
exists as a separate molecule in the body or anywhere else
in nature, and may have an entirely different utility.
That would discourage innovation. One cannot visualize
a portion of a complex molecule, including a DNA contain-
ing a particular gene, and will it into isolation as a unique
entity. Visualization does not cleave and isolate the
particular DNA; that is the act of human invention.
51 ASSOCIATION FOR MOLECULAR v. PTO

The Supreme Court in Mayo focused on its concern
that permitting patents on particular subject matter
would prevent use by others of, in Mayo, the correlation
recited in the method claims. Plaintiffs argue here that
they are preempted from using the patented DNA mole-
cules. The answer to that concern is that permitting
patents on isolated genes does not preempt a law of
nature. A composition of matter is not a law of nature.
Moreover, as indicated earlier, a limited preemption is
inherent in every patent: the right to exclude for a limited
period of time. 35 U.S.C. § 154(a)(1) (“Every patent shall
contain . . . a grant to the patentee, his heirs or assigns, of
the right to exclude others from making, using, offering
for sale, or selling the invention throughout the United
States . . . .”). When the patent expires, the public is
entitled to practice the invention of the patent. That is
true of all inventions; during the term of the patent,
unauthorized parties are “preempted” from practicing the
patent, but only for its limited term. The seven patents
being challenged here all expire by December 18, 2015. 13
Any preemption thus is limited, very limited in the case of
the present patents. Moreover, patents are rarely en-
forced against scientific research, even during their terms.
The remand of this case for reconsideration in light of
Mayo might suggest, as Plaintiffs and certain amici state,
that the composition claims are mere reflections of a law
of nature. Respectfully, they are not, any more than any
product of man reflects and is consistent with a law of
nature. Everything and everyone comes from nature,
following its laws. But the compositions here are not

13 Specifically, the ’441 patent will expire on August
12, 2014; the ’473 patent will expire on December 2, 2014;
the ’999 and ’001 patents will expire on January 20, 2015;
the ’282 patent will expire on May 5, 2015; and the ’492
and ’857 patents will expire on December 18, 2015.
ASSOCIATION FOR MOLECULAR v. PTO 52

natural products. They are the products of man, albeit
following, as all materials do, laws of nature.
The dissent indicates that “elemental lithium (like
other elements) would not be patentable subject matter,
even if it could only be extracted from nature through an
isolation process.” But the isolation here is not a simple
separation from extraneous materials, but conversion to a
different molecular entity. And again, these facts are not
before us, so we do not attempt to evaluate the patentabil-
ity of one form of lithium over another. Courts decide
cases; they do not draft comprehensive legal treatises.
Suffice it to say, however, that if lithium is found in the
earth as other than elemental lithium because it reacts
with air and water to form, for example, lithium oxide or
lithium hydroxide, it is a different material. A lithium
compound is not elemental lithium.
It is also important to dispute the dissent’s analogy to
snapping a leaf from a tree. With respect, no one could
contemplate that snapping a leaf from a tree would be
worthy of a patent, whereas isolating genes to provide
useful diagnostic tools and medicines is surely what the
patent laws are intended to encourage and protect.
Snapping a leaf from a tree is a physical separation,
easily done by anyone. Creating a new chemical entity is
the work of human transformation, requiring skill,
knowledge, and effort. See Mayo, 132 S. Ct. at 1294
(“While a scientific truth . . . is not a patentable invention,
a novel and useful structure created with the aid of
knowledge of scientific truth may be.”) (quoting Mackay
Radio & Tel. Co. v. Radio Corp. of Am., 306 U.S. 86, 94
(1939)).
The dissent also mentions several times in its opinion
the “breathtaking[]” breadth of certain claims as grounds
for objecting to their patentability. However, we do not
53 ASSOCIATION FOR MOLECULAR v. PTO

have here any rejection or invalidation on the various
grounds relating to breadth, such as in 35 U.S.C. § 112.
The issue before us is patent eligibility under § 101, not
the adequacy of the patents’ disclosure to support particu-
lar claims. Nor is it lack of patentability for obviousness,
as the dissent intimates, that is before us.
The dissent finally attempts to analogize the creation
of the isolated DNAs in this case to the removal of a
kidney from the human body, indicating that the latter
does not create patent-eligible subject matter, hence the
claimed isolated DNAs also do not. Such an analogy is
misplaced. Extracting a kidney from a body does not
result in a patent-eligible composition, as an isolated gene
has been and should be. A kidney is an organ, not a well
defined composition of matter or an article of manufacture
specified by § 101. No one could confuse extensive re-
search needed to locate, identify, and isolate a gene with
the extraction of an organ from a body. One is what
patents are intended to stimulate research on and hence
are properly patent eligible, and the other, while obvi-
ously essential to human wellbeing, is not what patents
are understood to cover under the patent statute. An
isolated DNA is properly characterized as a composition of
matter under § 101; no one would so characterize an
isolated body organ.
Finally, our decision that isolated DNA molecules are
patent eligible comports with the longstanding practice of
the PTO and the courts. The Supreme Court has repeat-
edly stated that changes to longstanding practice should
come from Congress, not the courts. In J.E.M. Ag Supply,
Inc. v. Pioneer Hi-Bred International, Inc., the Court
rejected the argument that plants did not fall within the
scope of § 101, relying in part on the fact that “the PTO
has assigned utility patents for plants for at least 16
years and there has been no indication from either Con-
ASSOCIATION FOR MOLECULAR v. PTO 54

gress or agencies with expertise that such coverage is
inconsistent with [federal law].” 534 U.S. 124, 144-45
(2001); see also Festo Corp. v. Shoketsu Kinzoku Kogyo
Kabushiki Co., 535 U.S. 722, 739 (2002) (“[C]ourts must
be cautious before adopting changes that disrupt the
settled expectations of the inventing community.” (citing
Warner-Jenkinson Co. v. Hilton Davis Chem. Co., 520
U.S. 17, 28 (1997))); Ariad Pharms., Inc. v. Eli Lilly & Co.,
598 F.3d 1336, 1347 (Fed. Cir. 2010) (en banc) (upholding
a written description requirement separate from enable-
ment based in part on stare decisis).
In this case, the PTO has issued patents relating to
DNA molecules for almost thirty years. In the early
1980s, the Office granted the first human gene patents.
See Eric J. Rogers, Can You Patent Genes? Yes and No,
93 J. Pat. & Trademark Off. Soc’y 19 (2010). It is esti-
mated that the PTO has issued 2,645 patents claiming
“isolated DNA” over the past twenty-nine years, J.A.
3710, and that by 2005, had granted 40,000 DNA-related
patents relating to, in non-native form, genes in the
human genome, Rogers, supra at 40. In 2001, the PTO
issued Utility Examination Guidelines, which reaffirmed
the agency’s position that isolated DNA molecules are
patent eligible, 66 Fed. Reg. 1092-94 (Jan. 5, 2001), and
Congress has not indicated that the PTO’s position is
inconsistent with § 101. If the law is to be changed, and
DNA inventions excluded from the broad scope of § 101,
contrary to the settled expectation of the inventing and
investing communities, the decision must come, not from
the courts, but from Congress. The dissent mentions
possible “adverse effects” that may occur if isolated DNAs
are held to be patent eligible. But, respectfully, it is the
adverse effects on innovation that a holding of ineligibility
might cause. Patents encourage innovation and even
55 ASSOCIATION FOR MOLECULAR v. PTO

encourage inventing around; we must be careful not to
rope off far-reaching areas of patent eligibility.
Accordingly, we once again conclude that claims 1, 2,
5, 6, and 7 of the ’282 patent; claims 1, 6, and 7 of the ’492
patent; and claim 1 of the ’473 patent directed to isolated
DNA molecules recite patent-eligible subject matter under
§ 101. Mayo does not change that result. In so doing, we
reiterate that the issue before us is patent eligibility, not
patentability, about which we express no opinion.
II. Method Claims
We turn next to Myriad’s challenged method claims.
This court in its now-vacated decision of July 29, 2011,
had held method claims 1 of the ’999, ’001, and ’441
patents, as well as method claims 1 and 2 of the ’857
patent—all of which consist of analyzing and comparing
certain DNA sequences—not to be patent-eligible subject
matter on the ground that they claim only abstract men-
tal processes. In light of the Supreme Court’s decision in
Mayo, we reaffirm that prior holding. The Court made
clear that such diagnostic methods in that case essentially
claim natural laws that are not eligible for patent. With-
out expressly analyzing the instant method claims in the
context of the Court’s reasoning, but in light of the Court’s
holding, and in view of our own prior reasoning, set forth
herein below, those method claims cannot stand.
In our prior decision, however, we reversed the dis-
trict court’s holding that claim 20 of the ’282 patent was
not eligible for patent. We did so on the ground, inter
alia, that, in addition to the step of comparing the cells’
growth rates, the claim also recites the steps of growing
transformed cells and determining those growth rates.
We relied on the fact that those steps were transforma-
tive. Although the Court has now held that certain trans-
formative steps are not necessarily sufficient under § 101
ASSOCIATION FOR MOLECULAR v. PTO 56

if the recited steps only rely on natural laws, we once
again, even in light of Mayo, arrive at the same conclusion
of patent-eligibility because at the heart of claim 20 is a
transformed cell, which is made by man, in contrast to a
natural material.
A. Methods of “Comparing” or “Analyzing” Sequences
Myriad argued that its claims to methods of “compar-
ing” or “analyzing” BRCA sequences satisfy the machine-
or-transformation test because each requires a transfor-
mation—extracting and sequencing DNA molecules from
a human sample—before the sequences can be compared
or analyzed. According to Myriad, the district court failed
to recognize the transformative nature of the claims by (1)
misconstruing the claim term “sequence” as merely in-
formation, rather than a physical molecule; and (2) erro-
neously concluding, in the alternative, that Myriad’s
proposed transformations were mere data-gathering
steps, rather than central to the purpose of the claims.
Plaintiffs responded that these method claims are
drawn to the abstract idea of comparing one sequence to a
reference sequence and preempt a phenomenon of na-
ture—the correlation of genetic mutations with a predis-
position to cancer. And, according to the Plaintiffs,
limiting the claims’ application to a specific technological
field, i.e., BRCA gene sequences, is insufficient to render
the claims patent eligible. Plaintiffs also assert that the
claims do not meet the machine-or-transformation test
because the claims’ plain language includes just the one
step of “comparing” or “analyzing” two gene sequences.
We renew our conclusion that Myriad’s claims to
“comparing” or “analyzing” two gene sequences fall out-
side the scope of § 101 because they claim only abstract
mental processes. See Benson, 409 U.S. at 67 (“Phenom-
ena of nature, . . . mental processes, and abstract intellec-
57 ASSOCIATION FOR MOLECULAR v. PTO

tual concepts are not patentable, as they are the basic
tools of scientific and technological work.”). The claims
recite, for example, a “method for screening a tumor
sample,” by “comparing” a first BRCA1 sequence from a
tumor sample and a second BRCA1 sequence from a non-
tumor sample, wherein a difference in sequence indicates
an alteration in the tumor sample. ’001 patent claim 1.
This claim thus recites nothing more than the abstract
mental steps necessary to compare two different nucleo-
tide sequences: one looks at the first position in a first
sequence; determines the nucleotide sequence at that first
position; looks at the first position in a second sequence;
determines the nucleotide sequence at that first position;
determines if the nucleotide at the first position in the
first sequence and the first position in the second se-
quence are the same or different, wherein the latter
indicates an alteration; and repeats the process for the
next position.
Limiting the comparison to just the BRCA genes or,
as in the case of claim 1 of the ’999 patent, to just the
identification of particular alterations, fails to render the
claimed process patent-eligible. As the Supreme Court
has held, “the prohibition against patenting abstract ideas
‘cannot be circumvented by attempting to limit the use of
the formula to a particular technological environment.’”
Bilski, 130 S. Ct. at 3230 (quoting Diehr, 450 U.S. at 191-
92); see also id. at 3231 (“Flook established that limiting
an abstract idea to one field of use . . . did not make the
concept patentable.”). Although the application of a
formula or abstract idea in a process may describe patent-
eligible subject matter, id. at 3230, Myriad’s claims do not
apply the step of comparing two nucleotide sequences in a
process. Rather, the step of comparing two DNA se-
quences is the entire process that is claimed.
ASSOCIATION FOR MOLECULAR v. PTO 58

To avoid this result, Myriad attempts to read into its
method claims additional, allegedly transformative steps.
As described above, Myriad reads into its claims the steps
of (1) extracting DNA from a human sample, and (2)
sequencing the BRCA DNA molecule, arguing that both
steps necessarily precede the step of comparing nucleotide
sequences. The claims themselves, however, do not
include either of these steps. The claims do not specify
any action prior to the step of “comparing” or “analyzing”
two sequences; the claims recite just the one step of
“comparing” or “analyzing.” Moreover, those terms’ plain
meaning does not include Myriad’s proposed sample-
processing steps; neither comparing nor analyzing means
or implies “extracting” or “sequencing” DNA or otherwise
“processing” a human sample.
Myriad claims that “comparing” and “analyzing” take
on such meaning when read in light of the patent specifi-
cations. Specifically, Myriad argues that the specifica-
tions show that the claim term “sequence” refers not to
information, but rather to a physical DNA molecule,
whose sequence must be determined before it can be
compared. That may be true, but the claims only recite
mental steps, not the structure of physical DNA mole-
cules.
Accordingly, Myriad’s challenged method claims are
indistinguishable from the claims the Supreme Court
found invalid under § 101 in Mayo. In Mayo, the patents
claimed methods for optimizing the dosage of thiopurine
drugs administered to patients with gastrointestinal
disorders. 132 S. Ct. at 1295. As written, the claimed
methods included the steps of (a) “administering” a thio-
purine drug to a subject, and/or (b) “determining” the
drug’s metabolite levels in the subject, wherein the meas-
ured metabolite levels are compared with predetermined
levels to optimize drug dosage. Id. In holding that the
59 ASSOCIATION FOR MOLECULAR v. PTO

claims satisfied § 101, this court concluded that, in addi-
tion to the “administering” step being transformative, the
“determining” step was both transformative and central
to the purpose of the claims. Prometheus, 628 F.3d at
1357. However, the Supreme Court held that the steps of
administering and determining, combined with a correla-
tive “wherein” clause, were not sufficiently transformative
of what was otherwise a claim to a natural law. That
holding governs Myriad’s claims to methods of “compar-
ing” and “analyzing” DNA sequences.
Myriad’s other claims do not even include a Mayo-like
step of “determining” the sequence of BRCA genes by, e.g.,
isolating the genes from a blood sample and sequencing
them, or any other putatively transformative step.
Rather, the comparison between the two sequences can be
accomplished by mere inspection alone. Accordingly,
Myriad’s claimed methods of comparing or analyzing
nucleotide sequences are only directed to the abstract
mental process of comparing two nucleotide sequences.
As such, we hold claims 1 of the ’999 patent, ’001 patent,
and ’441 patent and claims 1 and 2 of the ’857 patent
invalid under § 101 for claiming patent-ineligible proc-
esses.
B. Method of Screening Potential Cancer Therapeutics
Lastly, we turn to claim 20 of the ’282 patent, directed
to a method for screening potential cancer therapeutics
via changes in cell growth rates of transformed cells. The
parties agree that those transformed cells arose from
human effort; i.e., they are not natural products. Plain-
tiffs nonetheless challenge claim 20 as directed to the
abstract idea of comparing the growth rates of two cell
populations and as preempting a basic scientific princi-
ple—that a slower growth rate in the presence of a poten-
tial therapeutic compound suggests that the compound is
ASSOCIATION FOR MOLECULAR v. PTO 60

a cancer therapeutic. Plaintiffs therefore contend that
claim 20 is indistinguishable from the claims held ineligi-
ble in Mayo. We disagree.
Claim 20 recites a method that comprises the steps of
(1) growing host cells transformed with an altered BRCA1
gene in the presence or absence of a potential cancer
therapeutic, (2) determining the growth rate of the host
cells with or without the potential therapeutic, and (3)
comparing the growth rate of the host cells. Claim 20
thus recites a screening method premised on the use of
“transformed” host cells. Those cells, like the patent-
eligible cells in Chakrabarty, are not naturally occurring.
Rather, they are derived by altering a cell to include a
foreign gene, resulting in a man-made, transformed cell
with enhanced function and utility. See ’282 patent col.27
ll.28-33. The claim thus includes more than the abstract
mental step of looking at two numbers and “comparing”
two host cells’ growth rates.
In Mayo, the Supreme Court invalidated claims di-
rected to the relationship between concentrations of
certain metabolites in the blood and the likelihood that a
particular dosage of a thiopurine drug will be optimum,
stating that steps of “administering” and “determining,”
coupled with a correlative “wherein” clause, were insuffi-
cient to differentiate the claimed method from the natural
laws encompassed by the claims. In short, “to transform
an unpatentable law of nature into a patent-eligible
application of such a law, one must do more than simply
state the law of nature while adding the words ‘apply it’.”
132 S. Ct. at 1294.
Here, claim 20 does do more; it does not simply apply
a law of nature. Of course, all activity, whether chemical,
biological, or physical, relies on natural laws. But, more
to the point here is that claim 20 applies certain steps to
61 ASSOCIATION FOR MOLECULAR v. PTO

transformed cells that, as has been pointed out above, are
a product of man, not of nature. The Court, in its evalua-
tion of the Mayo method claims, found that the additional
steps of those claims were not sufficient to “transform” the
nature of the claims from mere expression of natural laws
to patent-eligible subject matter. By definition, however,
performing operations, even known types of steps, on, or
to create, novel, i.e., transformed subject matter is the
stuff of which most process or method invention consists.
All chemical processes, for example, consist of hydrolyz-
ing, hydrogenating, reacting, etc. In situations where the
objects or results of such steps are novel and nonobvious,
they should be patent-eligible. It is rare that a new
reaction or method is invented; much process activity is to
make new compounds or products using established
processes. Thus, once one has determined that a claimed
composition of matter is patent-eligible subject matter,
applying various known types of procedures to it is not
merely applying conventional steps to a law of nature.
The transformed, man-made nature of the underlying
subject matter in claim 20 makes the claim patent-
eligible. The fact that the claim also includes the steps of
determining the cells’ growth rates and comparing growth
rates does not change the fact that the claim is based on a
man-made, non-naturally occurring transformed cell—
patent-eligible subject matter.
Furthermore, the claim does not cover all cells, all
compounds, or all methods of determining the therapeutic
effect of a compound. Rather, it is tied to specific host
cells transformed with specific genes and grown in the
presence or absence of a specific type of therapeutic.
Accordingly, we hold that claim 20 of the ’282 patent
recites patent-eligible subject matter under § 101.
Whether such processes, including claim 20, meet other
ASSOCIATION FOR MOLECULAR v. PTO 62

tests for patentability, such as novelty or nonobviousness,
is not before us.
CONCLUSION
For the foregoing reasons, we affirm the district
court’s decision to exercise declaratory judgment jurisdic-
tion over this case, we reverse the district court’s grant of
summary judgment with regard to Myriad’s composition
claims to isolated DNAs, including cDNAs, we affirm the
district court’s grant of summary judgment with regard to
Myriad’s method claims directed to comparing or analyz-
ing gene sequences, and we reverse the district court’s
grant of summary judgment with regard to Myriad’s
method claim to screening potential cancer therapeutics
via changes in cell growth rates of novel, man-made
transformed cells.
AFFIRMED IN PART and REVERSED IN PART
COSTS
Costs to Myriad.
 United States Court of Appeals
for the Federal Circuit
__________________________

THE ASSOCIATION FOR MOLECULAR
PATHOLOGY, THE AMERICAN COLLEGE OF
MEDICAL GENETICS, THE AMERICAN SOCIETY
FOR CLINICAL PATHOLOGY, THE COLLEGE OF
AMERICAN PATHOLOGISTS, HAIG KAZAZIAN,
MD, ARUPA GANGULY, PHD, WENDY CHUNG, MD,
PHD, HARRY OSTRER, MD, DAVID LEDBETTER,
PHD, STEPHEN WARREN, PHD, ELLEN
MATLOFF, M.S., ELSA REICH, M.S., BREAST
CANCER ACTION, BOSTON WOMEN’S HEALTH
BOOK COLLECTIVE, LISBETH CERIANI, RUNI
LIMARY, GENAE GIRARD, PATRICE FORTUNE,
VICKY THOMASON, AND KATHLEEN RAKER,
Plaintiffs-Appellees,
v.
UNITED STATES PATENT AND TRADEMARK
OFFICE,
Defendant,
and
MYRIAD GENETICS, INC.,
Defendant-Appellant,
and
LORRIS BETZ, ROGER BOYER, JACK BRITTAIN,
ARNOLD B. COMBE, RAYMOND GESTELAND,
JAMES U. JENSEN, JOHN KENDALL MORRIS,
THOMAS PARKS, DAVID W. PERSHING, AND
MICHAEL K. YOUNG,
ASSOCIATION FOR MOLECULAR v. PTO 2

IN THEIR OFFICIAL CAPACITY AS DIRECTORS OF THE
UNIVERSITY OF UTAH RESEARCH FOUNDATION,
Defendants-Appellants.
__________________________

2010-1406
__________________________

Appeal from the United States District Court for the
Southern District of New York in case No. 09-CV-4515,
Senior Judge Robert W. Sweet.
__________________________

MOORE, Circuit Judge, concurring in part.
I join the majority opinion with respect to standing
and the patentability of the method claims at issue. I join
the majority with respect to claims to isolated cDNA
sequences, and concur in the judgment with respect to
isolated DNA sequences. I write separately to explain my
reasoning.
I.
The Patent Act, 35 U.S.C. § 101, allows “[w]hoever in-
vents or discovers any new and useful process, machine,
manufacture, or composition of matter, or any new and
useful improvement thereof” to obtain a patent. The plain
language of this statute only requires that an invention be
“new and useful,” and fall into one of four categories: a
“process, machine, manufacture, or composition of mat-
ter.” “Congress intended statutory subject matter to
‘include anything under the sun that is made by man.’”
Diamond v. Chakrabarty, 447 U.S. 303, 309 (1980) (quot-
ing the statutory history).
While the plain language used by Congress did not
limit the scope of patentable subject matter in the statute,
3 ASSOCIATION FOR MOLECULAR v. PTO

the “Court’s precedents provide three specific exceptions
to § 101’s broad patent-eligibility principles: ‘laws of
nature, physical phenomena, and abstract ideas.’” Bilski
v. Kappos, 130 S. Ct. 3218, 3226 (2010) (quoting Chakra-
barty, 447 U.S. at 309). These exceptions “rest[], not on
the notion that natural phenomena are not processes [or
other articulated statutory categories], but rather on the
more fundamental understanding that they are not the
kind of ‘discoveries’ that the statute was enacted to pro-
tect.” Parker v. Flook, 437 U.S. 584, 593 (1978).
Applying the judicially created exception to the oth-
erwise broad demarcation of statutory subject matter in
section 101 can be difficult. See Funk Bros. Seed Co. v.
Kalo Inoculant Co., 333 U.S. 127, 134-45 (1948) (Frank-
furter, J., concurring) (“[S]uch terms as ‘the work of
nature’ and the ‘laws of nature’ . . . are vague and malle-
able . . . . Arguments drawn from such terms for ascer-
taining patentability could fairly be employed to challenge
almost every patent.”). The analysis is relatively simple if
the invention previously existed in nature exactly as
claimed. For example, naturally existing minerals, a
plant found in the wild, and physical laws such as gravity
or E=mc2 are not patentable subject matter, even if they
were “discovered” by an enterprising inventor. Chakra-
barty, 447 U.S. at 309.
Even when an invention does not exist in nature in
the claimed state, it may still be directed to subject mat-
ter that is not patentable. For example, in Funk Brothers,
the Supreme Court held a patent to a combination of
multiple naturally occurring bacterial strains was not
patentable. Although there was “an advantage in the
combination,” which was apparently “new and useful,”
none of the bacterial strains “acquire[ed] a different use”
in combination. Funk Bros., 333 U.S. at 131-32. The
aggregation of the bacterial strains into a single product
ASSOCIATION FOR MOLECULAR v. PTO 4

produced “no new bacteria, no change in the six species of
bacteria, and no enlargement of the range of their utility.
Each species has the same effect it always had. The
bacteria perform in their natural way. . . . They serve the
ends nature originally provided and act quite independ-
ently of any effort of the patentee.” Id.
In contrast, the Supreme Court held bacteria that in-
cluded extra genetic material introduced by the inventor
were “a nonnaturally occurring manufacture or composi-
tion of matter—a product of human ingenuity ‘having a
distinctive name, character [and] use’” and therefore
patentable. Chakrabarty, 447 U.S. at 309-310 (quoting
Hartranft v. Wiegmann, 121 U.S. 609, 615 (1887)). Chak-
rabarty explained that there is no distinction between
inventions based on living and inanimate objects for the
purpose of the patent statute; instead, the “relevant
distinction” for the section 101 analysis is “between
products of nature . . . and human-made inventions.” Id.
at 312-13. Even if the invention was based on nature, and
resulted in a living organism, it may fall within the scope
of section 101. For example, “the work of the plant
breeder ‘in aid of nature’ was patentable invention” be-
cause “‘a plant discovery resulting from cultivation is
unique, isolated, and is not repeated by nature, nor can it
be reproduced by nature unaided by man.’” Id. (quoting
S. Rep. No. 315, 71st Cong., 2d Sess., 6-8 (1930)). In
Chakrabarty, the intervention of man resulted in bacteria
with “markedly different characteristics” from nature and
“the potential for significant utility,” resulting in pat-
entable subject matter. Id. at 310.
Funk Brothers and Chakrabarty do not stake out the
exact bounds of patentable subject matter. Instead, each
applies a flexible test to the specific question presented in
order to determine whether the claimed invention falls
within one of the judicial exceptions to patentability.
5 ASSOCIATION FOR MOLECULAR v. PTO

Funk Brothers indicates that an invention which “serve[s]
the ends nature originally provided” is likely unpat-
entable subject matter, but an invention that is an
“enlargement of the range of . . . utility” as compared to
nature may be patentable. 333 U.S. at 131. Likewise,
Chakrabarty illustrates that an invention with a distinc-
tive name, character, and use, e.g., markedly different
characteristics with the potential for significant utility, is
patentable subject matter. 447 U.S. at 309-10. Although
the two cases result in different outcomes, the inquiry
itself is similar.
Courts applied an analogous patentability inquiry
long before Funk Brothers or Chakrabarty. In one notable
case, Judge Learned Hand held that purified adrenaline,
a natural product, was patentable subject matter. Judge
Hand explained that even if the claimed purified adrena-
line were “merely an extracted product without change,
there is no rule that such products are not patentable.”
Parke-Davis & Co. v. H.K. Mulford Co., 189 F. 95, 103
(S.D.N.Y. 1911). This is because “while it is of course
possible logically to call this a purification of the princi-
ple” the resulting purified adrenaline was “for every
practical purpose a new thing commercially and thera-
peutically.” Id. Similarly, in a case applying the Patent
Act of 1952, 1 purified vitamin B-12, another natural
product, was also held patentable subject matter within
the meaning of section 101. Merck & Co. v. Olin Mathi-
eson Chem. Corp., 253 F.2d 156 (4th Cir. 1958). The
Fourth Circuit explained that purified vitamin B-12 was
“far from the premise of the [naturally occurring] princi-

1 The Patent Act of 1952 was the first time pat-
entable subject matter (the current section 101) was
separated out from novelty (the current section 102).
Previously, these two concepts were combined into a
single section.
ASSOCIATION FOR MOLECULAR v. PTO 6

ple. . . . The new product, not just the method, had such
advantageous characteristics as to replace the [naturally
occurring] liver products. What was produced was, in no
sense, an old product.” Id. at 162-63. These purified
pharmaceutical cases are both consistent with Supreme
Court precedent: the purified substance was “a new thing
. . . therapeutically,” Parke-Davis, 189 F. at 103, and had
such “advantageous characteristics” that what was pro-
duced by purification “was, in no sense, an old product.”
Merck, 253 F.2d at 162-63. In other words, the purified
natural products were held to have “markedly different
characteristics,” as compared to the impure products,
which resulted in “the potential for significant utility.”
Chakrabarty, 447 U.S. at 310.
In contrast, mere purification of a naturally occurring
element is typically insufficient to make it patentable
subject matter. For example, our predecessor court held
that claims to purified vanadium and purified uranium
were not patentable subject matter since these were
naturally occurring elements with inherent physical
properties unchanged upon purification. See In re
Marden, 47 F.2d 958, 959 (CCPA 1931) (“[P]ure vanadium
is not new in the inventive sense, and, it being a product
of nature, no one is entitled to a monopoly of the same.”);
In re Marden, 47 F.2d 957 (CCPA 1931) (“ductile ura-
nium” not patentable because uranium is inherently
ductile). Likewise, claims to purified ductile tungsten
were not patentable subject matter since pure tungsten
existed in nature and was inherently ductile. General
Electric Co. v. De Forest Radio Co., 28 F.2d 641, 643 (3d
Cir. 1928). In each of these cases, purification did not
result in an element with new properties. Instead, the
court held the naturally occurring element inherently had
the same characteristics and utility (e.g. ductility) as the
claimed invention. Consistent with Funk Brothers and
7 ASSOCIATION FOR MOLECULAR v. PTO

Chakrabarty, the claims all fell within the laws of nature
exception.
As illustrated by these examples, courts have long ap-
plied the principles articulated in Funk Brothers and
Chakrabarty to different factual scenarios in order to
determine whether an invention, as claimed, falls into the
laws of nature exception. I see no reason to deviate from
this longstanding flexible approach in this case.
II.
We reconsider whether the claims at issue in this case
are directed to patentable subject matter following the
remand from the Supreme Court in light of its opinion in
Mayo Collaborative Services v. Prometheus Laboratories,
Inc., 132 S. Ct. 1289 (2012) (Prometheus). While the
Prometheus decision does not control the outcome in this
case, it is nonetheless instructive regarding the scope of
the law of nature exception. As an initial matter, the
Prometheus discussion of laws of nature (process claims)
clearly ought to apply equally to manifestations of nature
(composition claims). Myriad’s argument that Prome-
theus is constrained to methods is an untenable position.
As the Prometheus court explained: “If a law of nature
is not patentable, then neither is a process reciting a law
of nature, unless that process has additional features that
provide practical assurance that the process is more than
a drafting effort designed to monopolize the law of nature
itself.” Id. at 1297. Prometheus did not, however, over-
turn Funk Brothers or Chakrabarty; cases clearly more
analogous to the one before us. Using the framework of
Funk Brothers and Chakrabarty in conjunction with the
direction of Prometheus, the applicable principles are: (1)
laws of nature/manifestations of nature are not pat-
entable; (2) a composition of matter with “markedly
different characteristics” from that found in nature with
ASSOCIATION FOR MOLECULAR v. PTO 8

the potential for significant utility is directed to pat-
entable subject matter.
Does the isolation process change the DNA from an
unpatentable manifestation of nature into a patentable
composition of matter? Id. at 1299. Does the claimed
isolated DNA have markedly different characteristics
with the potential for significant utility, e.g., an
“enlargement of the range of . . . utility” as compared to
nature? Chakrabarty, 447 U.S. at 309-310; Funk Bros.,
333 U.S. at 131.
The isolated DNA claims of the patents in suit fall
into two categories. The first category of claims is di-
rected to isolated sequences that are identical to naturally
occurring gene sequences. These include claims encom-
passing both the isolated full length gene sequence (e.g.
claim 1 of ’282 patent), which are thousands of nucleo-
tides, and claims to shorter isolated DNA strands, with as
few as fifteen nucleotides, whose nucleotide sequence is
found on the chromosome (e.g. claim 5 of ’282 patent).
The second category of claims is directed to isolated DNA
sequences that are different from the naturally occurring
gene sequences. These include claims to isolated cDNA
molecules (e.g. claim 2 of the ’282 patent), which differ
from the natural gene sequence in that the introns are
removed, and are the opposite (complementary) sequence
of the naturally occurring RNA.
The cDNA claims present the easiest analysis. Al-
though the plaintiffs (now plaintiff) in the suit argue, and
the district court held, that cDNA falls within the “laws of
nature” exception to section 101 patentability, the claimed
cDNA sequences do not exist in nature. Moreover, since
cDNA has all of the introns removed, and only contains
the coding nucleotides, it can be used to express a protein
in a cell which does not normally produce it. Of course,
9 ASSOCIATION FOR MOLECULAR v. PTO

the claimed isolated cDNA is inspired by nature—after all
naturally occurring RNA is the template upon which
cDNA is constructed. Because it is used as a template,
however, cDNA has a complementary sequence of nucleo-
tides, and therefore has a completely different nucleotide
sequence than the RNA. Moreover, DNA has a different
chemical structure than RNA, including a different base
(T instead of U, respectively) and sugar units (deoxyribose
instead of ribose, respectively). This results in, among
other things, greater stability for the DNA sequence as
compared to the RNA sequence.
cDNA sequences thus have a distinctive character and
use, with markedly different chemical characteristics
from either the naturally occurring RNA or any continu-
ous DNA sequence found on the chromosome. The
claimed isolated cDNA sequences are the creation of man,
made using biological tools and the naturally occurring
mRNA as a template. cDNA is therefore not one of the
“‘manifestations of . . . nature, free to all men and re-
served exclusively to none’” that falls outside of the patent
system. Chakrabarty, 447 U.S. at 309 (quoting Funk
Bros., 333 U.S. at 130). I decline to extend the laws of
nature exception to reach entirely manmade sequences of
isolated cDNA, even if those sequences are inspired by a
natural template. I therefore join the majority opinion
with respect to the claims to cDNA sequences. 2
DNA sequences that have the same pattern of DNA
bases as a natural gene, in whole or in part, present a
more difficult issue. Unlike the isolated cDNA molecules,
whose sequence is not present in nature, the isolated

2 To the extent the claims to shorter portions of
cDNA include only naturally occurring sequences found in
the chromosome, for example claim 6 of the ’282 patent,
my reasoning is the same as for the isolated sequences of
claim 5, discussed below.
ASSOCIATION FOR MOLECULAR v. PTO 10

DNA claims include nucleotide sequences which are found
in the human body, albeit as part of a much larger mole-
cule, the chromosome. To the extent the majority rests its
conclusion on the chemical differences between genomic
and isolated DNA (breaking the covalent bonds), I cannot
agree that this is sufficient to hold that the claims to
human genes are directed to patentable subject matter. I
agree that isolated genes are a different molecule and are
therefore not squarely analogous to unpatentable miner-
als, created by nature without the assistance of man. The
claimed isolated DNA molecules, which are truncations
(with different ends) of the naturally occurring DNA
found as part of the chromosome in nature, are not natu-
rally produced without the intervention of man.
I begin with the short isolated sequences such as
those covered by claim 5 which is directed to “an isolated
DNA having at least 15 nucleotides of the DNA of claim
1.” This claim covers a sequence as short as 15 nucleo-
tides and arguably as long as the entire gene. For this
claim to be patent eligible, all of the sequences ranging
from the 15 nucleotide sequence to the full gene must be
patentable subject matter. The shorter isolated DNA
sequences have a variety of applications and uses in
isolation that are new and distinct as compared to the
sequence as it occurs in nature. For example, these
sequences can be used as primers in a diagnostic screen-
ing process to detect gene mutations. These smaller
isolated DNA sequences—including isolated radiolabeled
sequences mirroring those on the chromosome—can also
be used as the basis for probes. Naturally occurring DNA
cannot do this. Unlike the isolated DNA, naturally occur-
ring DNA simply does not have the requisite chemical and
physical properties needed to perform these functions.
The ability to use isolated DNA molecules as the basis
for diagnostic genetic testing is clearly an “enlargement of
11 ASSOCIATION FOR MOLECULAR v. PTO

the range of . . . utility” as compared to nature. Funk
Bros., 333 U.S. at 131. In Prometheus, the Supreme
Court held that the claims at issue were not directed to
patentable subject matter because they merely “set forth
laws of nature—namely, relationships between concentra-
tions of certain metabolites in the blood and the likelihood
that a dosage of a thiopurine drug will prove ineffective or
cause harm.” 132 S. Ct. at 1296-97. The claimed rela-
tionship was “a consequence of the ways in which thio-
purine compounds are metabolized by the body—entirely
natural processes.” Id. at 1297.
There is no suggestion that the human body naturally
uses 15-mers as primers to synthesize DNA, or that the
attendant process of “probing” a patient’s DNA to detect a
mutation is somehow a natural law. The ability to use a
short strand of DNA as a primer or probe to determine
whether a patient has a mutation is a new and important
utility substantially different from the role of that DNA as
it occurs in nature. Indeed, many of the plaintiffs in this
case submitted declarations indicating that they wanted
to either offer such testing or receive such testing. Unlike
Prometheus, the claims to short isolated strands of DNA
are not directed to the relationship between the mutation
and cancer, but rather to a new tool that can be used to
determine if that relationship exists. The short isolated
DNA sequences have markedly different properties which
are directly responsible for their new and significant
utility. Chakrabarty, 447 U.S. at 309-10. It is not the
chemical change alone, but that change combined with
the different and beneficial utility that leads me to con-
clude that small isolated DNA fragments are patentable
subject matter. Id. at 310.
In fact, much of the dissent’s analysis with regard to
the full gene would seem to support my conclusion that
small isolated DNA molecules are directed to patent-
ASSOCIATION FOR MOLECULAR v. PTO 12

eligible subject matter. The dissent explains why the
baseball bat is directed to patent eligible subject matter:
“man has defined the parts that are to be retained and the
parts that are to be discarded, and he has molded the
retained portion into a product that bears little resem-
blance to that which occurs naturally.” Dissent at 11-12.
The exact same thing is true with regard to primer and
probe claims. Man has whittled the chromosomal DNA
molecule down to a 15 nucleotide sequence – defining the
parts to be retained and discarded. 3 And the result is a
product with a function (primer or probe) that is entirely
different from the full gene from which it was obtained. 4
I conclude that the small, isolated DNA molecules are an
alteration of the natural product “with markedly different
characteristics from any found in nature and one having
the potential for significant utility.” 447 U.S. at 310.
Turning now to the longer strands of isolated DNA,
isolated strands which include most or all of the gene
present a more difficult case. Some of the claims at issue,
for example ’282 patent claim 5, are genus claims, drafted

3 If adding functionality to a naturally occurring
molecule, for example adding a lipid chain, is a creation of
man then removing functionality, for example truncating
a natural DNA sequence or protein to yield smaller mole-
cules with new properties should also be. In either case,
it is the intervention of man that created a new molecule.
After all, the hand of man is just as apparent in the
David, created by removing stone from a block of marble,
as the ceiling of the Sistine Chapel, created by adding
layers of paint to an existing structure.
4 The dissent analogizes the full BRCA gene to a
slab of marble found in the earth as distinct from the
sculpture carved into it – which the dissent indicates
would be worthy of intellectual property protection. If the
multi-thousand nucleotide BRCA gene is the slab, isn’t
the 15 nucleotide primer the sculpture?
13 ASSOCIATION FOR MOLECULAR v. PTO

broadly enough to include both short fragments as well as
the entire isolated gene sequence. While I ultimately
conclude that these longer isolated sequences, including
the isolated gene sequence as a whole, are also patentable
subject matter, I do so for a reason different than for the
shorter sequences.
All of the same structural arguments apply to any
length of isolated DNA so, like the shorter strands, an
isolated DNA coding for a gene does have a literal chemi-
cal difference from the gene as it appears on the chromo-
some. Unlike the shorter strands of isolated DNA, the
chemical and structural differences in the isolated gene do
not clearly lead to an “enlargement of the range of . . .
utility” as compared to nature. Funk Bros., 333 U.S. at
131. For example, the full length gene is too large to be
used as a probe. See J.A. 4322 (a probe is a DNA molecule
usually 100-1,000 bases long). Likewise, an entire iso-
lated gene appears unsuitable for use as a primer in
genetic screening for mutations in that same gene. See
J.A. 4323 (Primers “are complementary to an exact loca-
tion of a much larger target DNA molecule.”). The iso-
lated full length gene does not clearly have a new utility
and appears to simply serve the same ends devised by
nature, namely to act as a gene encoding a protein se-
quence.
If I were deciding this case on a blank canvas, I might
conclude that an isolated DNA sequence that includes
most or all of a gene is not patentable subject matter. The
scope of the law of nature/manifestation of nature excep-
tion was certainly enlarged in Prometheus. But we do not
decide this case on a blank canvas. Congress has, for
centuries, authorized an expansive scope of patentable
subject matter. Likewise, the United States Patent Office
has allowed patents on isolated DNA sequences for dec-
ades, and, more generally, has allowed patents on purified
ASSOCIATION FOR MOLECULAR v. PTO 14

natural products for centuries. There are now thousands
of patents with claims to isolated DNA, and some un-
known (but certainly large) number of patents to purified
natural products or fragments thereof. 5 As I explain
below, I believe we must be particularly wary of expand-
ing the judicial exception to patentable subject matter
where both settled expectations and extensive property
rights are involved. 6
III.
For more than a decade the Patent Office’s policy has
been that “[a]n isolated and purified DNA molecule that
has the same sequence as a naturally occurring gene is
eligible for a patent because . . . that DNA molecule does

5 See, e.g., U.S. Patent 3,067,099 (claiming vanco-
mycin, an antibiotic produced by bacteria found in soil)
and U.S. Patent 4,552,701 (claiming a vancomycin frag-
ment produced by removing a sugar unit). A natural
product fragment, for example a naturally occurring
antibiotic with a sugar moiety removed, is highly analo-
gous to isolated DNA. In each case, the claimed molecule
is a smaller fragment of a naturally occurring molecule,
with some naturally occurring functionality removed. See
U.S. Patent 4,552,701, col.3-4 (compare entry 2 with
entries 10 and 13).
6 My analysis of the claims at issue assumes that
they do not include an isolated, full length chromosome. I
do not believe that a claim to an entire chromosome, for
example chromosome 17, is patentable subject matter.
First, there is no indication that the chromosome in
isolation has markedly different characteristics compared
to the chromosome in nature. Second, unlike claims to
isolated genes, there is no indication of either settled
expectations or extensive property rights for claims to
isolated chromosomes. This is undoubtedly due to the
small number of chromosomes as compared to the number
of genes.
15 ASSOCIATION FOR MOLECULAR v. PTO

not occur in that isolated form in nature . . . .” 66 Fed.
Reg. 1092, 1093 (Jan. 5, 2001). I do not agree with the
dissent’s characterization of the PTO position as perfunc-
tory. The PTO concluded that isolated DNA is patentable
because it is different from what is found in nature – the
process of synthesizing it or isolating it changes it. While
the PTO lacks substantive rule making authority, it is not
without expertise in this area. The explicit statement of
the Patent Office’s position on isolated DNA, however, is
simply a continuation of a longstanding and consistent
policy of allowing patents for isolated natural products.
See id. (noting U.S. Patent 141,072, claiming “[y]east, free
from organic germs of disease,” issued to Louis Pasteur in
1873); cf. In re Bergstrom, 427 F.2d 1394 (CCPA 1970)
(isolated prostaglandins patentable). According to the
Patent Office, isolated DNA is no different from the
isolated natural products of Parke-Davis. See 66 Fed.
Reg. at 1093 (quoting Parke-Davis).
Even before the current guidelines formalized the
Patent Office’s position, it granted patents to human
genes in the early 1980s, and subsequently issued thou-
sands of patents on “isolated DNA.” Majority at 54. In
fact, claims similar to the ones at issue in this case have
been the focal point of important litigation. For example,
Amgen, Inc. v. Chugai Pharmaceutical Co., 927 F.2d 1200
(Fed. Cir. 1991) involved a claim to “‘[a] purified and
isolated DNA sequence consisting essentially of a DNA
sequence encoding human erythropoietin.’” Id. at 1203-04
(quoting U.S. Patent No. 4,703,008, claim 2). We affirmed
that this claim was valid and infringed. Id. at 1219.
Erythropoietin, also known as EPO, went on to become
the biggest-selling biotechnology drug developed to that
point, resulted in billions of dollars in sales, and ac-
counted for over 50% of Amgen’s revenue in 1997. Amgen,
Inc. v. Hoechst Marion Roussel, Inc., 126 F.Supp.2d 69, 77
ASSOCIATION FOR MOLECULAR v. PTO 16

(D. Mass. 2001). Isolated DNA claims, at least in the case
of Amgen, represent crucial and exceedingly valuable
property rights.
The settled expectations of the biotechnology industry
– not to mention the thousands of issued patents – cannot
be taken lightly and deserve deference. This outpouring
of scientific creativity, spurred by the patent system,
reflects a substantial investment of time and money by
the biotechnology industry to obtain property rights
related to DNA sequences. The type of fundamental
alteration in the scope of patentable subject matter ar-
gued in this case “risk[s] destroying the legitimate expec-
tations of inventors in their property.” Festo Corp. v.
Shoketsu Kinzoku Kogyo Kabushiki Co., 535 U.S. 722, 739
(2002). I believe leaving intact the settled expectations of
property owners is particularly important in light of the
large number of property rights involved, both to isolated
DNA and to purified natural products generally.
The Supreme Court has warned that “courts must be
cautious before adopting changes that disrupt the settled
expectations of the inventing community.” Id. at 739.
The settled expectations of the inventing community with
respect to isolated DNA claims are built upon the broad
language of the statute, judicial precedent, such as Parke-
Davis and Merck, and the Patent Office’s longstanding
policy and practice. Neither Funk Brothers nor Chakra-
barty purported to overrule either the early cases or the
Patent Office’s practice; indeed, as discussed supra, these
cases weigh the same considerations as Parke-Davis and
Merck. “‘To change so substantially the rules of the game
now,’” after more than a century of practice, “‘could very
well subvert the various balances the PTO sought to
strike when issuing the numerous patents which have not
yet expired and which would be affected by our decision.’”
17 ASSOCIATION FOR MOLECULAR v. PTO

Festo, 535 U.S. at 739 (quoting Warner-Jenkinson Co. v.
Hilton Davis Chem. Co., 520 U.S. 17, 32 n.6 (1997)).
Although the Patent Office has consistently followed
the same policy for a decade (and arguably a century or
more), the United States, as an amicus, now argues that
the Patent Office’s published guidelines are incorrect and
a misstatement of the law. In place of these guidelines,
the government suggested that a “magic microscope”
would provide a useful metaphor for guiding our section
101 analysis. The magic microscope, however, would not
see the claimed DNA molecules at issue in this case. An
isolated DNA molecule has different chemical bonds as
compared to the “unisolated” sequence in the chromosome
(the ends are different). In short, the claimed molecules
cannot be seen in nature through the magic microscope.
While you may be able to see the order of DNA nucleo-
tides in the chromosome, the isolated fragment of DNA is
a different molecule. Creating the claimed isolated DNA
sequences therefore results in a distinctly unnatural
molecule. 7 Even the dissent agrees that the isolated DNA
molecules at issue require cleaving chemical bonds,
though it disputes the importance of the resulting distinct

7 This also illustrates why the government’s analo-
gies to situations dealing with elements, for example
lithium, are inapposite. Even assuming the government’s
contention that lithium does not currently exist in iso-
lated form in nature, it is nevertheless clear that elemen-
tal lithium, a basic building block provided by nature, at
some point must have reacted with, e.g., water to form the
naturally occurring lithium salts. In contrast, an isolated
DNA sequence did not necessarily exist before reacting
further to produce the corresponding naturally occurring
chromosomal DNA. Unlike a lithium salt, the chromo-
some does not imply that an isolated DNA molecule of 15
nucleotides – or even a gene – necessarily previously
existed as an isolated molecule in nature.
ASSOCIATION FOR MOLECULAR v. PTO 18

“‘molecular species.’” Dissent at 7 (quoting Linus Pauling,
The Nature of the Chemical Bond 6 (3d ed. 1960)).
The dissent claims that the Patent Office’s past views
are “substantially undermined by the position the gov-
ernment has taken in this case.” Dissent at 20. The
Patent Office’s prior practice, however, is particularly
important since it resulted in a large number of property
rights over the past decades. If the government decided
to change course in the Patent Office, and decline to issue
new patents to isolated genes, it would not impact these
existing property rights. This, however, is not what the
government argues in this case. Instead the government
argues for an entirely different interpretation of the law
that would destroy existing property rights. Although the
dissent points out that Chakrabarty overturned the
Patent Office’s practice of denying patents to microorgan-
isms, there is a clear difference between allowing addi-
tional patent protection where none previously existed,
and denying patent protection decades (or centuries) after
the fact, thereby eliminating a large number of property
rights. Chakrabarty, consistent with the broad language
of the statute, allowed additional patents where none
previously existed. In contrast, the government proposes
to destroy existing property rights based on a judge made
exception to that same broad language. This is a dra-
matic step that I believe is best left to the Congress.
Nevertheless, the government claims that “this is a
pure question of law” and that we can therefore feel free
to ignore the years of Patent Office practice and the
accompanying expectations that practice created within
the industry. The government argues that we should not
defer to the broad language (all but unchanged since
1793) provided by Congress in the patent statute, or allow
Congress to decide whether it is necessary to correct the
Patent Office’s practice through legislation. It is tempting
19 ASSOCIATION FOR MOLECULAR v. PTO

to use our judicial power in this fashion, especially when
the patents in question raise substantial moral and
ethical issues related to awarding a property right to
isolated portions of human DNA – the very thing that
makes us humans, and not chimpanzees.
The invitation is tempting, but I decline the opportu-
nity to act where Congress has chosen not to. Congress at
least implicitly approved of the Patent Office’s policy of
awarding patents on genes and DNA sequences. For
example, Congress included, as part of the Patent Office’s
appropriations, language affirming the Patent Office’s
interpretation of section 101 to prohibit patents on human
organisms. Consolidated Appropriations Act, 2004, Pub.
L. No. 108-199, § 634, 118 Stat. 3, 101. Although Con-
gress was aware “that there are many institutions . . .
that have extensive patents on human genes,” 149 Cong.
Rec. H7248, H7274, it explicitly declined to implement
legislation to “affect any of those current existing pat-
ents.” 149 Cong. Rec. E2417-01. To the contrary, it made
clear that the language related to “human organisms” was
not intended to change the Patent Office’s policy with
respect to claims to genes, stem cells, or other similar
inventions. 8 Far from oblivious to the patenting of genes,
Congress introduced and declined to pass several bills

8 “What I want to point out is that the U.S. Patent
Office has already issued patents on genes, stem cells,
animals with human genes, and a host of non-biologic
products used by humans, but it has not issued patents on
claims directed to human organisms, including human
embryos and fetuses. My amendment would not affect the
former, but would simply affirm the latter.” 149 Cong.
Rec. E2417-01 (emphasis added); see also 157 Cong. Rec.
E1177-04 (resubmitting this testimony in the context of
the current patent reform legislation).
ASSOCIATION FOR MOLECULAR v. PTO 20

which would put a moratorium on gene patents, 9 author-
ize funding for the study of whether genes ought to be
patentable, 10 and exempt from patent infringement
anyone who uses patented genes for non-commercial
research purposes or medical practitioners who use ge-
netic diagnostic tests. 11 Congress is obviously aware of
the issues presented in this case and I believe “[a]ny re-
calibration of the standard of [patentability] remains in
its hands.” Microsoft Corp. v. i4i Ltd., 131 S. Ct. 2238,
2252 (2011).
The judiciary cannot engage in an ad hoc innovation-
based analysis, which is why the exceptions to patentabil-
ity apply only to the clearest cases: a new mineral discov-
ered in the earth, or a new plant found in the wild, or
E=mc2, or the law of gravity. It is Congress, with “the
constitutional authority and the institutional ability to
accommodate fully the varied permutations of competing
interests that are inevitably implicated by such new
technology,” Sony Corp. of America v. Universal City
Studios, Inc., 464 U.S. 417, 431 (1984), who must decide
whether it is necessary to change the scope of section 101
9 At least one bill was introduced in Congress to put
a moratorium on patents to human genes or gene se-
quences. See, e.g., The Animal and Gene Patent Morato-
rium Bill (S.387 1993).
10 The Genomic Science and Technology Innovation
Act of 2002 (H.R. 3966).
11 The Genomic Research and Diagnostic Accessibil-
ity Act of 2002 (H.R. 3967). As the bill’s sponsor ex-
plained: “It is important to note that this section would
not overturn the commercial rights of patent holders. If a
research [organization] utilizing the exemption makes a
commercially viable finding, he or she would still have to
negotiate any rights to market the new discovery with the
patent holder.” 148 Cong. Rec. E353-03.
21 ASSOCIATION FOR MOLECULAR v. PTO

to exclude the kind of isolated DNA claims at issue here.
It is not clear to me that Chakrabarty, Funk Brothers, or
Prometheus leads inexorably to the conclusion that iso-
lated DNA molecules are not patentable subject matter. I
decline the invitation to broaden the law of nature excep-
tion.
Given the complicated technology and conflicting in-
centives at issue here, any change must come from Con-
gress. See Gottschalk v. Benson, 409 U.S. 63, 72-73 (1972)
(A section 101 analysis raises “considerable problems . . .
which only committees of Congress can manage, for broad
powers of investigation are needed, including hearings
which canvass the wide variety of views which those
operating in this field entertain. The technological prob-
lems tendered [by the parties] . . . indicate to us that
considered action by the Congress is needed.”).
IV.
“The rule that the discovery of a law of nature cannot
be patented rests . . . on the . . . fundamental understand-
ing that they are not the kind of ‘discoveries’ that the
statute was enacted to protect.” Flook, 437 U.S. at 593.
Is an isolated kidney patentable? Probably not, but as far
as I can tell nobody ever thought isolating organs from
someone’s body was the kind of discovery “that the statute
was enacted to protect.” In contrast, purifying or isolating
natural products has historically been exactly the kind of
discovery protected by the patent statutes. There is a
century-long history of affirming patent protection for
isolated and purified biological products ranging from
hormones to vitamins to proteins to antibiotics. These
inventions must have seemed miraculous at the time,
providing previously unknown therapeutic options to
treat sickness. The fact that these molecules might have
existed in nature did not foreclose patent protection in
ASSOCIATION FOR MOLECULAR v. PTO 22

view of the extraordinary benefits accessible to man after
isolation.
The Patent Office has, for more than a decade, af-
firmatively stated its belief that isolated DNA is pat-
entable for the same reasons as isolated vitamins or
hormones. There is no indication from Congress that this
view is wrong; to the contrary, it appears Congress also
believes DNA is patentable. This long-term policy of
protecting isolated DNA molecules has resulted in an
explosion of innovation in the biotechnology industry, an
industry which, unlike the financial services industry or
even the software industry, depends on patents to sur-
vive. Holding isolated DNA not patentable would destroy
long settled industry expectations for no reason other
than a gut feeling that DNA is too close to nature to be
patentable, an arbitrary decision based on a judge-made
exception. I believe that isolated DNA fragments, which
have both chemical changes from the naturally occurring
genomic DNA as well as new utility, are “the kind of
‘discoveries’ that the statute was enacted to protect.” I
therefore decline to extend the “laws of nature” exception
to include isolated DNA sequences.
This case typifies an observation by the late Chief
Judge Markey, our first Chief Judge, that “[o]nly God
works from nothing. Men must work with old elements.”
Fromson v. Advance Offset Plate, Inc., 755 F.2d 1549,
1556 n.3 (Fed. Cir. 1985) (quotation, citations omitted).
Human DNA is, for better or worse, one of the old ele-
ments bequeathed to men to use in their work. The
patents in this case revealed a new molecular understand-
ing about ourselves; “the inventions most benefiting
mankind are those that ‘push back the frontiers of chem-
istry, physics, and the like.’” Chakrabarty, 447 U.S. at
316 (quoting Great A.&P. Tea Co. v. Supermarket Corp.,
340 U.S. 147, 154 (1950)). We cannot, after decades of
23 ASSOCIATION FOR MOLECULAR v. PTO

patents and judicial precedent, now call human DNA fruit
from the poisonous tree, and punish those inquisitive
enough to investigate, isolate, and patent it. “Our task
. . . is the narrow one of determining what Congress
meant by the words it used in the statute; once that is
done our powers are exhausted.” Id. at 318. This inquiry
does not have moral, ethical, or theological components.
Cf. id. at 316-17 (“[W]e are without competence to enter-
tain” arguments about “the grave risks” generated by
genetic research.). “The choice we are urged to make is a
matter of high policy for resolution within the legislative
process after the kind of investigation, examination, and
study that legislative bodies can provide and courts
cannot.” Id. at 317. The patents in this case might well
deserve to be excluded from the patent system, but that is
a debate for Congress to resolve. I will not strip an entire
industry of the property rights it has invested in, earned,
and owned for decades unchallenged under the facts of
this case.
 United States Court of Appeals
for the Federal Circuit
__________________________

THE ASSOCIATION FOR MOLECULAR
PATHOLOGY, THE AMERICAN COLLEGE OF
MEDICAL GENETICS, THE AMERICAN SOCIETY
FOR CLINICAL PATHOLOGY, THE COLLEGE OF
AMERICAN PATHOLOGISTS, HAIG KAZAZIAN,
MD, ARUPA GANGULY, PHD, WENDY CHUNG, MD,
PHD, HARRY OSTRER, MD, DAVID LEDBETTER,
PHD, STEPHEN WARREN, PHD, ELLEN
MATLOFF, M.S., ELSA REICH, M.S., BREAST
CANCER ACTION, BOSTON WOMEN’S HEALTH
BOOK COLLECTIVE, LISBETH CERIANI, RUNI
LIMARY, GENAE GIRARD, PATRICE FORTUNE,
VICKY THOMASON, AND KATHLEEN RAKER,
Plaintiffs-Appellees,

v.
UNITED STATES PATENT AND TRADEMARK
OFFICE,
Defendant,
and
MYRIAD GENETICS, INC.,
Defendant-Appellant,
and
LORRIS BETZ, ROGER BOYER, JACK BRITTAIN,
ARNOLD B. COMBE, RAYMOND GESTELAND,
JAMES U. JENSEN, JOHN KENDALL MORRIS,
THOMAS PARKS, DAVID W. PERSHING, AND
MICHAEL K. YOUNG,
ASSOCIATION FOR MOLECULAR v. PTO 2

IN THEIR OFFICIAL CAPACITY AS DIRECTORS OF THE
UNIVERSITY OF UTAH RESEARCH FOUNDATION,
Defendants-Appellants.
__________________________

2010-1406
__________________________

Appeal from the United States District Court for the
Southern District of New York in case No. 09-CV-4515,
Senior Judge Robert W. Sweet.
__________________________

BRYSON, Circuit Judge, concurring in part and dissenting
in part:

I concur with the portions of this court’s judgment
that are directed to standing, the patentability of the
cDNA claims, and the patentability of the method claims.
I respectfully dissent from the court’s holding that Myr-
iad’s BRCA gene claims and its claims to gene fragments
are patent-eligible. In my view, those claims are not
directed to patentable subject matter, and the court’s
decision, if sustained, will likely have broad consequences,
such as preempting methods for whole-genome sequenc-
ing, even though Myriad’s contribution to the field is not
remotely consonant with such effects.

In its simplest form, the question in this case is
whether an individual can obtain patent rights to a hu-
man gene. From a common-sense point of view, most
observers would answer, “Of course not. Patents are for
inventions. A human gene is not an invention.” The
essence of Myriad’s argument in this case is to say that it
has not patented a human gene, but something quite
different—an isolated human gene, which differs from a
3 ASSOCIATION FOR MOLECULAR v. PTO

native gene because the process of extracting it results in
changes in its molecular structure (although not in its
genetic code). We are therefore required to decide
whether the process of isolating genetic material from a
human DNA molecule makes the isolated genetic mate-
rial a patentable invention. The court concludes that it
does; I conclude that it does not.

At the outset, it is important to identify the inventive
contribution underlying Myriad’s patents. Myriad was
not the first to map a BRCA gene to its chromosomal
location. That discovery was made by a team of research-
ers led by Dr. Mary-Claire King. See Jeff M. Hall et al.,
Linkage of Early-Onset Familial Breast Cancer to Chro-
mosome 17q21, 250 Science 1684 (1990). And Myriad did
not invent a new method of nucleotide sequencing. In-
stead, it applied known sequencing techniques to identify
the nucleotide order of the BRCA genes. 1 Myriad’s dis-
covery of those sequences entailed difficult work, and the
identified sequences have had important applications in
the fight against breast cancer. But the discovery of the
sequences is an unprotectable fact, just like Dr. King’s
discovery of the chromosomal location of the BRCA1 gene.

Of course, Myriad is free to patent applications of its
discovery. As the first party with knowledge of the se-
quences, Myriad was in an excellent position to claim
applications of that knowledge. Many of its unchallenged
claims are limited to such applications. See, e.g., ’441
patent, claim 21; ’492 patent, claim 22; ’282 patent, claim

1 There is some dispute over whether other inven-
tors helped Myriad discover the BRCA sequences or
discovered the BRCA2 sequence before Myriad. Because
those disputes are irrelevant to the question of patentable
subject matter, I refer to the discovery of the BRCA
sequences as Myriad’s work.
ASSOCIATION FOR MOLECULAR v. PTO 4

9. Yet some of Myriad’s challenged composition claims
effectively preempt any attempt to sequence the BRCA
genes, including whole-genome sequencing. In my view,
those claims encompass unpatentable subject matter, and
a contrary ruling is likely to have substantial adverse
effects on research and treatment in this important field.

I

As the majority and concurring opinions explain, the
DNA claims at issue in this case fall into three categories:
claims that cover the isolated BRCA genes (claim 1 of the
’282 patent, claim 1 of the ’473 patent, and claims 1 and 6
of the ’492 patent); claims that cover only the BRCA
cDNA (claims 2 and 7 of the ’282 patent and claim 7 of the
’492 patent); and claims that cover portions of the BRCA
genes and cDNA as small as 15 nucleotides long (claims 5
and 6 of the ’282 patent). I first address the claims to the
BRCA genes.

A

In the seminal case of Diamond v. Chakrabarty, 447
U.S. 303 (1980), the Supreme Court held that an artificial
life form could be patented. In the course of its opinion,
and critically for purposes of its reasoning, the Court
stated that not all living things or other items found in
nature were subject to patenting. The Court explained
that although the language of section 101 of the Patent
Act is broad, it is not the case that it “has no limits or that
it embraces every discovery.” Id. at 309. The Court then
set forth the general proposition that “laws of nature,
physical phenomena, and abstract ideas have been held
not patentable.” Id. As examples, the Court noted that “a
new mineral discovered in the earth or a new plant found
in the wild is not patentable subject matter.” Thus, even
5 ASSOCIATION FOR MOLECULAR v. PTO

though a mineral or a plant is a “composition of matter,”
and could be viewed as falling within a broad construction
of section 101, the Court explained that those “manifesta-
tions of . . . nature” are not patentable subject matter, but
are “free to all men and reserved exclusively to none.” Id.,
quoting Funk Bros. Seed Co. v. Kalo Inoculant Co., 333
U.S. 127, 130 (1948); see also Bilski v. Kappos, 130 S. Ct.
3218, 3225 (2010).

The Court in Chakrabarty held the artificial life form
at issue in that case to be patentable because the claim
was “not to a hitherto unknown natural phenomenon, but
to a nonnaturally occurring manufacture or composition
of matter—a product of human ingenuity ‘having a dis-
tinctive name, character [and] use.’” 447 U.S. at 309-10,
quoting Hartranft v. Wiegmann, 121 U.S. 609, 615 (1887).
In distinguishing between naturally occurring substances
and nonnaturally occurring manufactures, the Court
relied heavily on its earlier decision in Funk Brothers, in
which the inventor discovered that certain useful bacte-
rial strains did not exert an inhibitive effect on one an-
other. Based on that discovery, the inventor obtained a
patent on a mixed culture of those non-inhibitive strains.
The Supreme Court held the product unpatentable,
however, because the bacteria remained structurally and
functionally the same as in their natural state. Funk
Bros., 333 U.S. at 131. By contrast, because Chakrabarty
had produced “a new bacterium with markedly different
characteristics from any found in nature and one having
the potential for significant utility,” the Court held Chak-
rabarty’s invention to be patentable. Chakrabarty, 447
U.S. at 310.
ASSOCIATION FOR MOLECULAR v. PTO 6

B

Myriad’s claims to the isolated BRCA genes seem to
me to fall clearly on the “unpatentable” side of the line the
Court drew in Chakrabarty. Myriad is claiming the genes
themselves, which appear in nature on the chromosomes
of living human beings. The only material change made
to those genes from their natural state is the change that
is necessarily incidental to the extraction of the genes
from the environment in which they are found in nature.
While the process of extraction is no doubt difficult, and
may itself be patentable, the isolated genes are not mate-
rially different from the native genes. In this respect, the
genes are analogous to the “new mineral discovered in the
earth,” or the “new plant found in the wild” that the
Supreme Court referred to in Chakrabarty. It may be
very difficult to extract the newly found mineral or to
find, extract, and propagate the newly discovered plant.
But that does not make those naturally occurring items
the products of invention.

The same is true for human genes. Like some miner-
als, they are hard to extract from their natural setting.
Also like minerals, they can be used for purposes that
would be infeasible if they remained in their natural
setting. And the process of extracting minerals, or taking
cuttings from wild plants, like the process of isolating
genetic material, can result in some physical or chemical
changes to the natural substance. But such changes do
not make extracted minerals or plant cuttings patentable,
and they should not have that effect for isolated genes. In
each case, merely isolating the products of nature by
extracting them from their natural location and making
those alterations that are attendant to their extraction
does not give the extractor the right to patent the prod-
ucts themselves.
7 ASSOCIATION FOR MOLECULAR v. PTO

The majority characterizes the isolated genes as new
molecules and considers them different substances from
the corresponding native DNA. 2 Because the native
BRCA genes are chemically bonded to other genes and
histone proteins, the majority concludes that cleaving
those bonds to isolate the BRCA genes turns the isolated
genes into “different materials.” Yet there is no magic to
a chemical bond that requires us to recognize a new
product when a chemical bond is created or broken, but
not when other atomic or molecular forces are altered. 3 A
chemical bond is merely a force between two atoms or
groups of atoms strong enough “to make it convenient for
the chemist to consider [the aggregate] as an independent
molecular species.” Linus Pauling, The Nature of the
Chemical Bond 6 (3d ed. 1960). Weaker interatomic
forces will be broken when, for example, a dirty diamond
is cleaned with water or another solvent, but that does
not make the clean diamond a human-made invention.
See Am. Fruit Growers, Inc. v. Brogdex Co., 283 U.S. 1, 12

2 Although I recognize that Judge Lourie and Judge
Moore, while reaching the same ultimate conclusions,
have taken analytical paths that differ in some respects,
for convenience I will refer to Judge Lourie’s opinion as
the majority opinion and Judge Moore’s opinion as the
concurring opinion.
3 The majority characterizes the question in this
case as turning on the breaking of covalent bonds linking
the BRCA genes to the rest of the DNA in chromosomes
13 and 17, but its analysis appears to place patentable
weight on the breaking of other chemical bonds, such as
the hydrogen bonds that are broken when separating
DNA from histones or—in an example unrelated to this
case—the ionic bonds that are broken when lithium is
derived from a salt. It is difficult to see why differences
between types of chemical bonds should matter for pat-
entability purposes, and I see little support for such a
distinction in the governing precedents.
ASSOCIATION FOR MOLECULAR v. PTO 8

(1931) (cleaning a shell by acid and then grinding off a
layer with an emery wheel did not convert it into a differ-
ent product). Nor should it make a difference for pur-
poses of patentability if the portion of a wild plant that is
collected for purposes of later regeneration is separated
from the original plant by chemical means or by scissors.

If the changes in the DNA molecule that occur as part
of the process of isolation render the gene claims pat-
entable, the same analysis would seem to apply to chemi-
cal elements that do not appear in their atomic form in
nature. For example, isolated lithium does not occur
naturally because it reacts with air and water and thus is
found in nature only as part of a chemical compound,
ionically bound to other elements. Robert E. Krebs, The
History and Use of Our Earth’s Chemical Elements 48 (2d
ed. 2006). Once isolated, lithium has many industrial
applications, and in order to isolate lithium, it is neces-
sary to break ionic bonds in the lithium compounds that
are found in nature. But it seems plain that elemental
lithium (like other elements) would not be patentable
subject matter, even if it could only be extracted from
nature through an isolation process.

The principles underlying that analysis apply to ge-
netic material as well. In order to isolate the BRCA gene,
it is necessary to break chemical bonds that hold the gene
in its place in the body, but the genetic coding sequence
that is the subject of each of the BRCA gene claims re-
mains the same whether the gene is in the body or iso-
lated. If we are to apply the conventional nomenclature of
any field to determine whether Myriad’s isolated DNA
claims are “new,” it would seem to make more sense to
look to genetics, which provides the language of the
claims, than to chemistry. Aside from Myriad’s cDNA
claims, its composition claims are not defined by any
9 ASSOCIATION FOR MOLECULAR v. PTO

particular chemical formula. For example, claim 1 of the
’282 patent covers all isolated DNAs coding for the
BRCA1 protein, with the protein being defined by the
amino acid sequence encoded by the naturally occurring
BRCA1 gene. From a molecular perspective, that claim
covers a truly immense range of substances from the
cDNA that is 5,914 nucleotides long to the isolated gene
that contains more than 120,000 nucleotides. And the
patent does not define the upper end of that range be-
cause the patent does not identify a unique nucleotide
sequence for the 120,000-nucleotide-long isolated BRCA1
gene. Instead, the patent contains a sequence that is just
24,000 nucleotides long with numerous gaps denoted
“vvvvvvvvvvvvv.” ’282 patent, fig. 10. An almost incalcu-
lably large number of new molecules could be created by
filling in those gaps with almost any nucleotide sequence,
and all of those molecules would fall within the scope of
claim 1. Included in that set are many important molecu-
lar variations to the BRCA1 gene that Myriad had not yet
discovered and could not have chemically described. Yet
those molecules would share only one unifying character-
istic: each would code for the same protein as the natu-
rally occurring BRCA1 gene.

From a genetic perspective, that claim covers one
“composition of matter”—the BRCA1 gene. The isolated
BRCA genes are identical to the BRCA genes found on
chromosomes 13 and 17. They have the same sequence,
they code for the same proteins, and they represent the
same units of heredity. It is true that the claimed mole-
cules have been cleaved and that they possess terminal
groups that differ from those found on naturally occurring
genes. The majority attaches significance to those facts.
But the function of the isolated DNA molecules is attrib-
utable not to the nature of the isolation process or to the
identity of the terminal groups on the molecules; the
ASSOCIATION FOR MOLECULAR v. PTO 10

function of the claimed molecules is dictated by the nu-
cleotide sequence of the gene—a sequence that is deter-
mined by nature and that appears in nature exactly as it
appears in the claimed isolated DNA. During the tran-
scription phase of protein synthesis, the BRCA genes are
separated from chromosomal proteins. The transcription
process then proceeds from a starting point called the
promoter to a stopping point often called the terminator.
James D. Watson et al., Molecular Biology of the Gene
382, 394-96 (6th ed. 2008). The only difference between
the naturally occurring BRCA genes during transcription
and the claimed isolated DNA is that the claimed genes
have been isolated according to nature’s predefined
boundaries, i.e., at points that preserve the ability of the
gene to express the protein for which it is coded.

In that respect, extracting a gene is akin to snapping
a leaf from a tree. Like a gene, a leaf has a natural start-
ing and stopping point. It buds during spring from the
same place that it breaks off and falls during autumn.
Yet prematurely plucking the leaf would not turn it into a
human-made invention. See Intervet Inc. v. Merial Ltd.,
617 F.3d 1282, 1295 (Fed. Cir. 2010) (Dyk, J., concurring
in part and dissenting in part). That would remain true if
there were minor differences between the plucked leaf
and the fallen autumn leaf, unless those differences
imparted “markedly different characteristics” to the
plucked leaf. Chakrabarty, 447 U.S. at 310.

Another example underscores the problem with char-
acterizing the isolated gene as a patentable invention. A
human kidney is a product of nature; it does not become a
patentable invention when it is removed from the body,
even if the patentee has developed an improved procedure
for extracting the kidney, and even if the improved proce-
dure results in some physical or chemical changes to the
11 ASSOCIATION FOR MOLECULAR v. PTO

kidney at the points where the kidney was attached to the
host body. But if that is so, then why should an isolated
gene be treated differently for purposes of section 101?
While the isolation of a gene involves the alteration of a
single molecule, it is difficult to accept that it should
make a difference, for purposes of patentability, whether
the isolated substance is part of a single molecule, as in
the case of the BRCA genes, or part of a very large aggre-
gation of molecules, as in the case of a kidney.

Both the majority and the concurring opinions attach
significant weight to the fact that the claimed coding
portions of the native BRCA genes are part of a much
larger molecule and that the isolated BRCA genes, being
smaller molecules extracted from the larger one, are
therefore man-made inventions. But to argue that the
isolated BRCA gene is patentable because in its native
environment it is part of a much larger structure is no
more persuasive than arguing that although an atom may
not be patentable, a subatomic particle is patentable
because it was previously part of a larger structure, or
that while a tree is not patentable, a limb of the tree
becomes a patentable invention when it is removed from
the tree.

Of course, it is an oversimplification to say that some-
thing that can be characterized as “isolated” or “ex-
tracted” from its natural setting always remains a natural
product and is not patentable. One could say, for exam-
ple, that a baseball bat is “extracted” or “isolated” from an
ash tree, but in that case the process of “extracting” the
baseball bat necessarily changes the nature, form, and
use of the ash tree and thus results in a manmade manu-
facture, not a naturally occurring product. In that set-
ting, man has defined the parts that are to be retained
and the parts that are to be discarded, and he has molded
ASSOCIATION FOR MOLECULAR v. PTO 12

the retained portion into a product that bears little re-
semblance to that which occurs naturally. The result of
the process of selection is a product with a function that is
entirely different from that of the raw material from
which it was obtained. In the case of the BRCA genes, by
contrast, nature has defined the genes as independent
entities by virtue of their capacity for protein synthesis
and, ultimately, trait inheritance. Biochemists extract
the target genes along lines defined by nature so as to
preserve the structure and function that the gene pos-
sessed in its natural environment. In such a case, the
extraction of a product in a manner that retains the
character and function of the product as found in nature
does not result in the creation of a human invention. 4
That principle was captured by the Supreme Court’s
statement in Chakrabarty that the invention in that case
was not to “a hitherto unknown natural phenomenon, but
to a nonnaturally occurring manufacture or composition
of matter ‘having a distinctive name, character [and]
use.’” 447 U.S. at 309-10.

Cases involving the “purification” of a natural sub-
stance employ similar analysis. Our predecessor court
recognized that merely purifying a naturally occurring
substance does not render the substance patentable
unless it results in a marked change in functionality. In
re Merz, 97 F.2d 599, 601 (CCPA 1938) (holding that there
was no right to a patent on a purer version of ultrama-
rine, but recognizing that if a claimed article is “of such

4 By analogy, extracting a slab of marble from the
earth does not give rise to protectable intellectual prop-
erty rights, but “extracting” a piece of sculpture from that
slab of marble does. In the case of the BRCA gene claims,
what Myriad has claimed is more akin to the slab of
marble found in the earth than to the sculpture carved
from it after its extraction.
13 ASSOCIATION FOR MOLECULAR v. PTO

purity that it differs not only in degree but in kind it may
be patentable”); see also In re King, 107 F.2d 618, 620
(CCPA 1939) (same, for purified vitamin C); In re Marden,
47 F.2d 958, 959 (CCPA 1931) (same, for purified vana-
dium); Gen. Elec. Co. v. DeForest Radio Co., 28 F.2d 641,
643 (3d Cir. 1928) (same, for purified tungsten). On the
other hand, the purified natural substance is patentable if
the “purification” results in a product with such distinct
characteristics that it becomes “for every practical pur-
pose a new thing commercially and therapeutically.”
Parke-Davis & Co. v. H.K. Mulford Co., 189 F. 95, 103
(C.C.S.D.N.Y. 1911); see also Merck & Co. v. Olin Mathi-
eson Chem. Corp., 253 F.2d 156, 161-64 (4th Cir. 1958)
(holding that a purified composition of vitamin B-12 was
patentable because the purification process resulted in a
product that was therapeutically effective, whereas the
natural form was not).

In sum, the test employed by the Supreme Court in
Chakrabarty requires us to focus on two things: (1) the
similarity in structure between what is claimed and what
is found in nature and (2) the similarity in utility between
what is claimed and what is found in nature. What is
claimed in the BRCA genes is the genetic coding material;
that material is the same, structurally and functionally,
in both the native gene and the isolated form of the gene.

The structural differences between the claimed “iso-
lated” genes and the corresponding portion of the native
genes are irrelevant to the claim limitations, to the func-
tioning of the genes, and to their utility in their isolated
form. The use to which the genetic material can be put,
i.e., determining its sequence in a clinical setting, is not a
new use; it is only a consequence of possession. In order
to sequence an isolated gene, each gene must function in
the same manner in the laboratory as it does in the
ASSOCIATION FOR MOLECULAR v. PTO 14

human body. Indeed, that identity of function in the
isolated gene is the key to its value. The naturally occur-
ring genetic material thus has not been altered in a way
that would matter under the standard set forth in Chak-
rabarty. For that reason, the isolation of the naturally
occurring genetic material does not make the claims to
the isolated BRCA genes patent-eligible.

The Supreme Court’s recent decision in Mayo Col-
laborative Services v. Prometheus Laboratories, Inc., 132
S. Ct. 1289, 1293 (2012), does not decide this case, but the
Court’s analysis is nonetheless instructive. In Mayo,
which involved method claims, the representative claim
involved the steps of administering a drug to a subject,
determining a metabolite concentration in the subject’s
blood, and inferring the need for a change in dosage based
on that metabolite concentration. Id. at 1295. The Court
found that the method was not directed to patent-eligible
subject matter because it contributed nothing “inventive”
to the law of nature that lay at the heart of the claimed
invention, i.e., “the relationships between the concentra-
tion in the blood of certain thiopurine metabolites and the
likelihood that the drug dosage will be ineffective or
induce harmful side-effects.” Id. at 1294. The Court
examined “whether the claims do significantly more than
simply describe these natural relations” and whether the
“claims add enough to their statements of the correlations
to allow the processes they described to qualify as patent-
eligible processes that apply natural laws.” Id. at 1297
(emphasis in original). In concluding that the claims did
not add “enough” to the natural laws, the Court was
particularly persuaded by the fact that “the steps of the
claimed processes . . . involve well-understood, routine,
conventional activity previously engaged in by research-
ers in the field.” Id. at 1294.
15 ASSOCIATION FOR MOLECULAR v. PTO

Just as a patent involving a law of nature must have
an “inventive concept” that does “significantly more than
simply describe . . . natural relations,” Mayo, 132 S. Ct. at
1294, 1297, a patent involving a product of nature should
have an inventive concept that involves more than merely
incidental changes to the naturally occurring product. In
cases such as this one, in which the applicant claims a
composition of matter that is nearly identical to a product
of nature, it is appropriate to ask whether the applicant
has done “enough” to distinguish his alleged invention
from the similar product of nature. Has the applicant
made an “inventive” contribution to the product of na-
ture? Does the claimed composition involve more than
“well-understood, routine, conventional” elements? Here,
the answer to those questions is no.

Neither isolation of the naturally occurring material
nor the resulting breaking of covalent bonds makes the
claimed molecules patentable. We have previously stated
that “isolation of interesting compounds is a mainstay of
the chemist’s art,” and that “[i]f it is known how to per-
form such an isolation doing so ‘is likely the product not of
innovation but of ordinary skill and common sense.’”
Aventis Pharma Deutschland GmbH v. Lupin, Ltd., 499
F.3d 1293, 1302 (Fed. Cir. 2007), quoting KSR Int’l Co. v.
Teleflex, Inc., 550 U.S. 398, 421 (2007). Similarly, the
structural changes ancillary to the isolation of the gene do
not render these claims patentable. The cleaving of
covalent bonds incident to isolation is itself not inventive,
and the fact that the cleaved molecules have terminal
groups that differ from the naturally occurring nucleotide
sequences does nothing to add any inventive character to
the claimed molecules. The functional portion of the
composition—the nucleotide sequence—remains identical
to that of the naturally occurring gene.
ASSOCIATION FOR MOLECULAR v. PTO 16

The majority suggests that I have “focus[ed] not on
the differences between isolated and native DNAs, but on
one similarity: their informational content.” In light of
Mayo, that approach seems appropriate. The informa-
tional content of the nucleotide sequences is the critical
aspect of these molecules; the terminal groups added to
the molecules when the covalent bonds are broken—to
which the majority and concurring opinions attribute
such significance—are not even mentioned in the claims.
The nucleotide sequences of the claimed molecules are the
same as the nucleotide sequences found in naturally
occurring human genes. In my view, that structural
similarity dwarfs the significance of the structural differ-
ences between isolated DNA and naturally occurring
DNA, especially where the structural differences are
merely ancillary to the breaking of covalent bonds, a
process that is itself not inventive.

II

As noted, in addition to the BRCA gene claims dis-
cussed above, the claims at issue in this appeal include
four claims to BRCA cDNA and two claims to portions of
the BRCA genes and cDNA as small as 15 nucleotides
long.

I agree with the court that the claims to BRCA cDNA
are eligible for patenting. The cDNA cannot be isolated
from nature, but instead must be created in the labora-
tory. 5 The end product is a human-made invention with

5 The appellees argue that the BRCA1 cDNA can be
isolated from nature, and they refer to a BRCA1 pseu-
dogene called BRCA1P1 that is found in the human
genome. However, the appellees have failed to demon-
strate that the pseudogene consists of the same sequence
as the BRCA1 cDNA.
17 ASSOCIATION FOR MOLECULAR v. PTO

distinct structure because the introns that are found in
the native gene are removed from the cDNA segment.
Additionally, the cDNA has a utility not present in the
naturally occurring BRCA DNA and mRNA because
cDNA can be attached to a promoter and inserted into a
non-human cell to drive protein expression.

However, I disagree with the court as to the two
claims to short segments of DNA having at least 15
nucleotides. Claim 6 of the ’282 patent covers any se-
quence of the BRCA1 cDNA that is at least 15 nucleotides
long. That claim encompasses each BRCA1 exon, even
though each exon is naturally defined by transcription.
Moreover, because small sequences of DNA are repeated
throughout the three billion nucleotides of the human
genome, the claim covers portions of the cDNA of more
than 4% of human genes. It also covers portions of the
DNA of nearly all human genes. Accordingly, efforts to
sequence almost any gene could infringe claim 6 even
though Myriad’s specification has contributed nothing to
human understanding of other genes. Myriad is not
entitled to such broad protection. See Mayo, 132 S. Ct. at
1301, 1303 (examining “how much future innovation is
foreclosed relative to the contribution of the inventor” and
warning of the “danger” that overly broad patent claims
might “foreclose[] more future invention than the underly-
ing discovery could reasonably justify").

Myriad could easily have claimed more narrowly to
achieve the utility it attaches to segments of cDNA. It
contends that those segments can be used as probes and
primers. DNA probes must be chemically altered or
“tagged” before they can be so used, and Myriad could
have claimed the tagged segments to achieve probe func-
tionality. A claim to tagged segments would not encom-
pass the BRCA1 exons. As to primer functionality, many
ASSOCIATION FOR MOLECULAR v. PTO 18

of the cDNA segments will not work. Some will be too
long. Some will be too short. Some will be palindromic
and fold in on themselves. Myriad could have identified a
subset of the segments that work as primers, and such a
claim could be patentable if it were limited to species with
“markedly different characteristics from any found in
nature and . . . having the potential for significant util-
ity.” Chakrabarty, 447 U.S. at 310. The problem with
claim 6 is that it is so broad that it includes products of
nature (the BRCA1 exons) and portions of other genes; its
validity is not salvaged because it includes some species
that are not natural. Accordingly, I would hold claim 6
unpatentable.

The other claim to a short segment of DNA, claim 5 of
the ’282 patent, is breathtakingly broad. That claim
covers any segment of the DNA defined by claim 1, pro-
vided that the segment is at least 15 nucleotides long.
Claim 1, in turn, covers any isolated DNA that codes for
the BRCA1 polypeptide. Thus, claim 5 would cover not
only the isolated BRCA1 gene in each of its numerous
molecular variations, but also any sub-sequence of those
molecules, including portions that fall in the undefined
range of those molecules denoted “vvvvvvvvvvvvv.” Claim
5 would therefore be unpatentable for the same reasons
as claim 1 and claim 6.

Of course, in light of its breadth, claim 5 of the ’282
patent is likely to be invalid on other grounds, and thus a
ruling as to patent eligibility with respect to that claim
may be superfluous. Nonetheless, it is important to
consider the effects of such broad patent claims on the
biotechnology industry. While Myriad has emphasized
the biotechnology industry’s need of patent protection to
encourage and reward research in this difficult and
important field, there is another side to the coin. Broad
19 ASSOCIATION FOR MOLECULAR v. PTO

claims to genetic material present a significant obstacle to
the next generation of innovation in genetic medicine—
multiplex tests and whole-genome sequencing. New
technologies are being developed to sequence many genes
or even an entire human genome rapidly, but firms devel-
oping those technologies are encountering a thicket of
patents. Secretary’s Advisory Comm. on Genetics,
Health, and Society, Dep’t of Health & Human Servs.,
Gene Patents and Licensing Practices and Their Impact on
Patient Access to Genetic Tests 49-62 (2010). In order to
sequence an entire genome, a firm would have to license
thousands of patents from many different licensors. See
id. at 50-51. Even if many of those patents include claims
that are invalid for anticipation or obviousness, the costs
involved in determining the scope of all of those patents
could be prohibitive. See id. at 51-52; Rebecca S.
Eisenberg, Noncompliance, Nonenforcement, Nonproblem?
Rethinking the Anticommons in Biomedical Research, 45
Hou. L. Rev. 1059, 1076-1080 (2008) (concluding that
existing studies “have focused relatively little attention on
downstream product development” and that interviews
accompanying those studies suggest that, though smaller
than initially feared, the costs associated with the patent
thicket are “quite real in the calculations of product-
developing firms”).

My colleagues assign significant weight to the fact
that since 2001 the PTO has had guidelines in place that
have allowed patents on entire human genes. They
conclude that those guidelines, and the PTO’s earlier
practice, are entitled to deference from this court as to the
question whether patents to isolated human genes consti-
tute patent-eligible subject matter. I think the PTO’s
practice and guidelines are not entitled to significant
weight, for several reasons.
ASSOCIATION FOR MOLECULAR v. PTO 20

First, as we have recognized, the PTO lacks substan-
tive rulemaking authority as to issues such as patentabil-
ity. Animal Legal Def. Fund v. Quigg, 932 F.2d 920, 930
(Fed. Cir. 1991). In areas of patent scope, we owe defer-
ence only commensurate with “the thoroughness of its
consideration and the validity of its reasoning.” Merck &
Co. v. Kessler, 80 F.3d 1543, 1550 (Fed. Cir. 1996). The
comments that the PTO issued at the time of its 2001
guidelines in response to suggestions that isolated human
genes were not patentable are, frankly, perfunctory. See
John M. Conley & Roberte Makowski, Back to the Future:
Rethinking the Product of Nature Doctrine as a Barrier to
Biotechnology Patents, 85 J. Pat. & Trademark Off. Soc’y
301 (2003). Because those comments, at least on their
face, do not reflect thorough consideration and study of
the issue, I do not regard them as worthy of much weight
in the analysis of this complex question.

Second, whatever force the PTO’s views on the issue
of patent eligibility may have had in the past has, at the
very least, been substantially undermined by the position
the government has taken in this case. The Department
of Justice has twice filed a brief on behalf of the United
States in this court taking the position that Myriad’s gene
claims (other than the cDNA claims) are not patent-
eligible. Although the PTO did not “sign” the brief on
either occasion and we are left to guess about the status
of any possible continuing inter-agency disagreements
about the issue, the Department of Justice speaks for the
Executive Branch, and the PTO is part of the Executive
Branch, so it is fair to conclude that the Executive Branch
has modified its position from the one taken by the PTO
in its 2001 guidelines and, informally, before that.

Finally, prior to the Supreme Court’s decision in
Chakrabarty, the PTO had determined that microorgan-
21 ASSOCIATION FOR MOLECULAR v. PTO

isms were not subject to patenting, but the Supreme
Court gave no indication that it regarded that view as
entitled to deference. Moreover, the Court gave short
shrift to the Commissioner’s contention (which was made
the lead argument in the government’s brief in that case)
that the patentability of life-forms was an issue that
should be left to Congress. Citing Marbury v. Madison, 5
U.S. (1 Cranch) 137 (1803), the Court explained that
“Congress has performed its constitutional role in defin-
ing patentable subject matter in § 101; we perform ours in
construing the language Congress has employed.” Chak-
rabarty, 477 U.S. at 315. We have the same responsibility
and should not shy away from deciding the issues of law
that the parties have brought to us. Although my col-
leagues believe our analysis of the legal question in this
case should be influenced by purported expectations of the
inventing community based on the PTO’s past practice of
issuing patents on human genes, that is in effect to give
the PTO lawmaking authority that Congress has not
accorded it. 6 There is no collective right of adverse pos-
session to intellectual property, and we should not create
one. Our role is to interpret the law that Congress has
written in accordance with the governing precedents. I
would do so and would affirm the district court’s rulings
as to the BRCA gene and BRCA gene segment claims.

6 Because the asserted reliance interest is based on
PTO practice and not on prior judicial decisions, this case
is not analogous to Warner Jenkinson Co. v. Hilton Davis
Chemical Co., 520 U.S. 17 (1997), or Festo Corp. v.
Shoketsu Kinzoku Kogyo Kabushiki Co., 535 U.S. 722
(2002), where the expectations of the inventing commu-
nity were based on longstanding Supreme Court prece-
dent.