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AMP v. Myriad - Judge Sweet's opinion, as HTML, pp. 121-135 | 348 comments | Create New Account
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AMP v. Myriad Genetics - Judge Sweet's opinion pp. 79-121, in HTML
Authored by: macliam on Tuesday, April 09 2013 @ 05:51 PM EDT

According to Myriad the majority of academic researchers operating laboratories (as opposed to Clinical Laboratory Improvement Amendments (“CLIA”)-certified laboratories) do not believe that they should share test results with subjects outside of the standard clinical setting. Reilly Decl. ¶¶ 57-59.

As the declarations submitted by the parties make clear, there exists a sharp dispute concerning the impact of patents directed to isolated DNA on genetic research and consequently the health of society. As with the dispute concerning the effect of the patents-in-suit on BRCA1/2 genetic testing, the resolution of these disputes of fact and policy are not possible within the context of these motions.

IV. THE PATENTS

A. Summary of the Patents

The subjects of this declaratory judgment action are fifteen claims contained in seven patents issued by the

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USPTO:25 claims 1, 2, 5, 6, 7, and 20 of U.S. patent 5,747,282 (the “'282 patent”); claims l, 6, and 7 of U.S. patent 5,837,492 (the “'492 patent”); c1aim 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,OOl (the “'001 patent”); claim 1 of U.S. patent 5,753,QQl (the “'441 patent”); and claims l and 2 of U.S. patent 6,033,857 (the “'857 patent”).26

The claims-in-suit may be divided into two types of claims: composition claims and method, or process, claims. Independent claim 1 of the '282 patent is representative of the group of composition claims and claims:

An isolated DNA coding for a BRCA1 polypeptide, said polypeptide having the amino acid sequence set forth in sEQ ID NO:2.

This claim is therefore directed to an isolated DNA

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molecule possessing a nucleotide sequence that translates into the BRCA1 protein. Because most amino acids can result from the translation of more than one DNA codon, multiple DNA sequences correspond to the nucleotide sequence claimed by this claim. Claim 2 of the '282 patent is dependent on claim 1 but contains an additional limitation that identifies the specific BRCA1 nucleotide sequence of the claimed DNA.27. Claims 5 and 6 of the '282 patent are directed to fragments as short as 15 nucleotides of the DNA molecules claimed in claims 1 and 2 of the '282 patent.28 Finally, claim 7 of the '282 patent and claim 1 of the '473 patent are directed to isolated DNA possessing one of the specified mutant BRCA1 gene sequences.29

Claims 1, 6, and 7 of the '492 patent are also

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composition claims covering isolated DNA molecules containing certain specified nucleotide sequences relating to the BRCA2 gene. Claim 1 is directed to an isolated DNA molecule encoding the BRCA2 protein.30 Like claim 1 of the '282 patent, claim 1 of the '492 patent is directed to multiple possible DNA sequences as a result of the redundancy of the DNA codons. Claim 6 of the '492 patent, however, is considerably broader than claim 1 and is directed to any DNA nucleotide encoding any mutant BRCA2 protein that is associated with a predisposition to breast cancer.31 Claim 7 of the '492 patent depends on claim 6 but is restricted to the mutated forms of the BRCA2 nucleotide sequence set forth in the specification.32 As a result of the breadth of these composition claims, they reach isolated BRCA1/2 DNA obtained from any human being.

Claim 1 of the '999 patent is representative of the group of method claims. It claims:

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A method for detecting a germline alteration in a BRCA1 gene, said alteration selected from a group consisting of the alterations set forth in Tables 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 sequence of BRCA1 cDNA made from mRNA from said human sample with the proviso that said germline alteration is not a deletion of 4 nucleotides corresponding to base numbers 4184-4187 of SEQ ID NO:1.

Thus, claim 1 of the '999 patent covers the process of identifying the existence of certain specific mutations in the BRCAl gene by “analyzing” the sequence of the BRCA1 DNA, RNA, or cDNA made from BRCA1 RNA obtained from a human sample.

Most of the remaining method claims-in-suit are similarly structured and directed to the comparison of gene sequences. Claim 1 of the '001 patent claims a method for determining whether a human tumor sample contains a mutation in the BRCA1 gene by “comparing” the sequence of the BRCA1 gene from the tumor with the sequence of the BRCA1 gene from a non-tumor sample from the same person.33

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Claim 1 of the '441 patent and claim 1 of the '857 are both directed to the same process, differing only as to whether the claimed method is directed to BRCA1 ('441) or BRCA2 ('857). Both of these independent claims are directed to the process of determining whether an individual has inherited an altered BRCA1 or BRCA2 gene by “comparing” the individual's BRCA1 or BRCA2 gene sequence with the wild-type BRCA1 or BRCA2 gene sequence.34 Claim 2 of the '857 patent covers a method for determining whether an individual has a predisposition for breast cancer by “comparing” the individual's BRCA2 gene sequence with the known wild-type BRCA2 gene sequence.35

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Finally, claim 20 of the '282 patent claims a method for determining the effectiveness of a potential cancer therapeutic comprising growing cells carrying an altered BRCA1 gene known to cause cancer in the presence and absence Of a potential Cancer therapeutic, comparing the growth rates of the cells, and concluding that a slower growth rate in the presence of the potential therapeutic indicates that it is indeed a cancer therapeutic.36

B. Construction of the Claims37

1. Legal Standard

Before considering the patent-eligibility of a patent claim, the disputed terms in the claims must be

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construed in order ensure the scope of the claims is accurately assessed. See, e.g., Datamize, LLC v. Plumtree Software, Inc., 417 F.3d 1342, 1354 (Fed. Cir. 2005) (“[A] utility patent protects ‘any new and useful process, machine, manufacture, or composition of matter, or any new or useful improvement thereof,' 35 U.S.C. § 101 (2000), the scope of which is defined by the patent's written claims.”). Courts are charged with interpreting disputed claim terms as a matter of law. Markman v. Westview Instruments, Inc., 517 U.S. 370, 384-85 (1996).

In interpreting the meaning of claim terms, “words of a claim are generally given their ordinary and customary meaning” to a person of ordinary skill in the art at the time of invention (i.e., the effective filing date of the patent application). Phillips v. AWH Corp., 415 F.3d 1303, 1312-13 (Fed. Cir. 2005) (internal citations and quotation marks omitted). “Importantly, the person of ordinary skill in the art is deemed to read the claim term not only in the context of the particular claim in which the disputed term appears, but in the context of the entire patent, including the specification.” Id. at 1313. Thus, the Federal Circuit has emphasized the importance of “intrinsic” evidence in claim construction: the words of

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the claim themselves, the written description in the patent's specification, and, when necessary, the history of the patent application's prosecution before the USPTO. Id. at 1314-17.

The process of claim construction begins with the language of the claims themselves. The language of the claim is what the patentee chose to use to “‘particularly point[] out and distinctly claim[] the subject matter which the applicant regards as his invention.‘” Id. at 1311-12 (quoting 35 U.S.C. § 112, ¶ 2). Thus, “the claims themselves provide substantial guidance as to the meaning of particular claim terms.” Id. at 1314. In addition to the particular claim being examined, the context provided by other claims may be helpful as well. “For example, the presence of a dependent claim that adds a particular limitation gives rise to a presumption that the limitation in question is not present in the independent claim.” Id. at 1314-15.

Claim language must also be read in the context of the specification. Id. at 1315. As the Federal Circuit has made clear, “claims, of course, do not stand alone. Rather, they are part of ‘a fully integrated written

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instrument,' consisting principally of a specification that concludes with the claims.” Id. (quoting Markman v. Westview Instruments, Inc., 52 F.3d 967, 978 (Fed. Cir. 1995)). “For that reason, claims ‘must be read in view of the specification, of which they are a part.’” Id. (quoting Markman, 52 F.3d at 979). The specification “is always highly relevant to the claim construction analysis. Usually it is dispositive; it is the single best guide to the meaning of a disputed term.” Id. (quoting Vitronics Corp. v. Conceptronic, Inc., 90 F.3d 1576, 1582 (Fed, Cir. 1996)). Moreover, when the patentee “act[s] as his or her own lexicographer” and includes an explicit definition of a claim term in the specification, that definition is dispositive over any ordinary meaning. Id. at 1319 (internal citation and quotation marks omitted); see also Digital Biometrics, Inc. v. Identix, Inc., 149 F.3d 1335, 1344 (Fed. Cir. 1998).

In relying on the specification to interpret claim terms, the Federal Circuit has also “repeatedly warned against confining the claims” to the embodiments described in the specification. Phillips, 415 F.3d at 1323. The mistake of “reading a limitation from the written description into the claims” is “one of the

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cardinal sins of patent law.'' Id. at 1320 (quoting Scimed Life SyS., Inc. v. Advanced Cardiovascular SyS., Inc., 242 F.3d 1337, 1340 (Fed. Cir. 2001)).

Courts may also utilize the prosecution history which “consists of the complete record of the proceedings before the PTO and includes the prior art cited during the examination of the patent.… [T]he prosecution history can often inform the meaning of the claim language by demonstrating how the inventor understood the invention and whether the inventor limited the invention in the course of prosecution, making the claim scope narrower than it would otherwise be.” Id. at 1317 (internal citations omitted). However, the prosecution history “often lacks the clarity of the specification and thus is less useful for claim construction purposes,” Id.

Lastly, courts may rely on extrinsic evidence such as dictionaries, treatises, and expert testimony, which may serve to provide a source of “accepted meaning of terms used in various fields of science and technology,” or by providing “background on the technology at issue.” Id. at 1317-18. However, such “extrinsic” evidence is “less significant than the intrinsic record in determining the

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legally operative meaning of the claim language.” Id. at 1317 (internal citations and quotation marks omitted). The use of extrinsic evidence may not be used to contradict the meaning of the claim terms as evidenced by the intrinsic evidence. Id. at 1317-19; see also Biagro W. Sales, Inc. v. Grow More, Inc., 423 F.3d 1296, 1302 (Fed. Cir. 2005).

2. Resolution of the disputed claim terms

a. “DNA” and “isolated DNA”

The parties approach the terms “DNA” and “isolated DNA” from opposing perspectives.38 Plaintiffs contend that the term “DNA” means “a sequence of nucleic acids, also referred to as nucleotides” and therefore constitutes a “nucleotide sequence” or a “polynucleotide.” Pl. Br. at 10.39. Myriad disputes Plaintiffs' definition of

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“DNA” insofar as Plaintiffs' definition suggests that the term “DNA” refers merely to information, that is, “a description of the linear order of nucleotide units that make up the polynucleotide.” Myriad Br. at 15. Myriad instead argues that “DNA” refers to “a real and tangible molecule, a chemical composition made up of deoxyribonucleotides linked by a phosphodiester backbone.” Myriad Br. at 14.

As its name implies, DNA, or deoxyribonucleic acid, is an acid—a tangible, Chemical Compound. As Myriad correctly notes, the specifications make clear that “DNA,” as used in the patents, refers to the physical manifestation of the acid, one that may be “substantially separated from other cellular components which naturally accompany a gene.“ '473 patent, col. 19:8-9; '282 patent, col. 19:10-11; '492 patent, col. 17:64-65. Despite the description of the term “DNA” set forth in the briefs, this understanding of the meaning of “DNA” is shared by both plaintiffs' and Myriad's declarants. See Kay ¶ 125; Linck ¶ 45; Schlessinger ¶ 12; Grody ¶ lO; Leonard ¶ 30.

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The term “isolated DNA” is defined by Plaintiffs as “a fragment of DNA substantially separated from other cellular components and other DNA.” Pl. Br. at 10. Myriad disputes Plaintiffs' definition insofar as it implies that fragments of DNA exist free-floating in the cell, separate from other cellular components, such as proteins and the other DNA in the chromosome. Myriad Br. at 16. The patent specifications expressly define “isolated DNA” as a DNA molecule “which is substantially separated from other cellular components which naturally accompany a native human sequence [such as] human genome sequences and proteins” and “includes recombinant or cloned DNA isolates and chemically synthesized analogs or analogs biologically synthesized by heterologous systems.” '473 patent, col. 19:6-15; '282 patent, col. 19:8-18; '492 patent, col. 17:62-18:S.

“Isolated DNA” is therefore construed to refer to a segment of DNA nucleotides existing separate from other cellular components normally associated with native DNA, including proteins and other DNA sequences comprising the remainder of the genome, and includes both DNA originating from a cell as well as DNA synthesized through chemical or heterologous biological means.

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b. “BRCA1” and “BRCA2”

Plaintiffs define the term “BRCA1” as “a articular fragment of DNA found on chromosome 17 that relates to a person's predisposition to develop breast and ovarian cancer.” Pl. Br. at 11. Similarly, Plaintiffs define the te rm “BRCA2'' as “a particular fragment of DNA found on chromosome 13 that relate[s] to a person's predisposition to develop breast and ovarian cancer.” Pl. Br. at 14. hs with Plaintiffs' proposed definition of “isolated DNA,” Myriad argues that these definitions are inconsistent with the patents' definition of “BRCAl” and “BRCA2” as “cancer-predisposing gene[s], some alleles of which cause susceptibility to breast and ovarian cancers” because they suggest that the BRACl and BRCA2 genes are not integrated into a chromosome, but are broken, detached, or otherwise easily removed from their respective chromosomes. Myriad Br. at 16.

The specifications of the patents-in-suit define the terms “BRCAl” and “BRCA2” as “a human breast cancer predisposing gene … some alleles of which cause

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susceptibility to cancer, in particular breast and ovarian cancer.” 1282 patent, col. 4:33-36; see also '282 patent, col. 1:22-23; '492 patent, col. 1:20-21, 4:28-29. Further, neither party disputes that “genes” refer to segments of DNA incorporated into chromosomes.

“BRCA1” is therefore construed to refer to a human gene, normally integrated into chromosome 17, some alleles of which cause susceptibility to breast and ovarian cancer. Similarly, “BRCA2” is construed to refer to a human gene, normally integrated into chromosome 13, some alleles of which cause susceptibility to breast and ovarian cancer.

V. CONCLUSIONS OF LAW

The Summary Judgment Standard

Summary judgment is granted only where there exists no genuine issue of material fact and the moving arty is entitled to judgment as a matter of law. Fed. R. Civ. P. 56(c); see Celotex Corp. v. Catrett, 477 U.S. 317, 322-23 (1986); SCS Commc'ns, Inc. v. Herrick Co., 360 F.3d 329, 338 (2d Cir. 2004). The courts do not try issues of

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fact on a motion for Summary Judgment, but, rather, determine “whether the evidence presents a sufficient disagreement to require submission to a jury or whether it is so one-sided that one party must prevail as a matter of law.” Anderson v. Liberty Lobby, Inc., 477 U.S. 242, 251-52 (1986).

“The party seeking summary judgment bears the burden of establishing that no genuine issue of material fact exists and that the undisputed facts establish [itsJ right to judgment as a matter of law.” Rodriguez v. City of New York, 72 F.3d 1051, 1060-61 (2d Cir. 1995). In determining whether a genuine issue of material fact exists, a court must resolve all ambiguities and draw all reasonable inferences against the moving party. See Matsushita Elec. Indus. Co. v. 2enith Radio Corp., 475 U.S. 574, 587-88 (1986); Gibbs-Alfano v. Burton, 281 F.3d 12, 18 (2d Cir. 2002). However, “the non-moving party may not rely simply on conclusory allegations or speculation to avoid summary judgment, but instead must offer evidence to show that its version of the events is not wholly fanciful.” Morris v. Lindau, 196 F.3d 102, 109 (2d Cir. 1999) (internal quotation marks omitted).

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Summary judgment is appropriate where the moving party has shown that “little or no evidence may be found in support of the nonmoving party's case. When no rational jury could find in favor of the no nm oving party because the evidence to support its case is so slight, there is no genuine issue of material fact and a grant of summary judgment is proper.” Gallo v. Prudential Residential Servs., L.P., 22 F.3d 1219, 1223-24 (2d Cir. 1994) (internal citations omitted).

B. 35 U.S.C. § 101 and Its Scope

Section 101 of Title 35, United States Code, provides:

Whoever invents or discovers any new and Useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefore, subject to the conditions and requirements of this title.

In interpreting this language, the Supreme Court has observed that “Congress plainly contemplated that the patent laws would be given wide scope.” Diamond v.

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Chakrabarty, 447 U.S. 303, 308 (1980); see also J.E.M. Ag Supply, Inc. v. Pioneer Hi-Bred Int'l, Inc., 534 U.S. 124, 131 (2001) (“[W]e are mindful that this Court has already spoken clearly concerning the broad scope and applicability of § 101.”).

However, this broad reading of § 101 and statutory patent eligibility is not without limits. “The Supreme Court has recognized that scientific principles and laws of nature, even when for the first time discovered, have existed throughout time, define the relationship of man to his environment, and, as a consequence, ought not to be the subject of exclusive rights to any one person.” In re Meyer, 688 F.2d 789, 795 (C.C.P.A. 1982) (citing Leroy v. Tatham, 55 U.S. 155, 175 (1852)). Specifically, the Supreme Court has recognized three categories of subject- matter that fall outside the scope of sect; lOl: “The laws of nature, physical phenomena, and abstract ideas have been held not patentable.” Chakrabarty, 447 U.S. at 309; see also Diamond v. Diehr, 450 U.S. 175, 185 (1981). “The rule that the discovery of a law of nature cannot be patented rests, not on the notion that natural phenomena are not processes, but rather on the more fundamental understanding that they are not the kind of ‘discovery’ that the statute

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was enacted to protect.” Parker v. Flook, 431 U.S. 584, 593 (1918).

The exclusion of products of nature40 as patentable subject matter under § 101 also reflects the Supreme Court's recognition that ‘[p]henomena of nature, though just discovered, mental processes, and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work.” Gottschalk v. Benson, 409 U.S. 63, 67 (1912). Thus, as Justice Breyer has observed, “the reason for this exclusion is that sometimes too much patent protection can impede rather than ‘promote the Progress of Science and useful Arts,’ the constitutional objective of patent and copyright protection.” Lab. Corp. of Am. Holdings v. Metabolite Labs., Inc., 548 U.S, 124, 126-21 (2006) (Breyer, J.,

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dissenting) (quoting U.S. Const., Art. I, § 8, cl. 8.) (emphasis in original). For these reasons, “manifestations of laws of nature [are] free to all men and reserved exclusively to none.” Funk Bros. Seed Co. v. Kalo Inoculant Co., 333 U.S. 127, 130 (1948).

The inquiry into an invention's patent eligibility is a fundamental one, and as such, “[t]he ob1igation to determine what type of discovery is sought to be patented must precede the determination of whether that discovery is, in fact, new or obvious.” Flook, 437 U.S. at 593; see also In re Bilski, 545 F.3d 943, 950 (Fed. Cir. 2008) (en banc), cert. granted, 129 S. Ct. 2735 (2009) (”Whether a claim is drawn to patent-eligible subject matter under § lOl is a threshold inquiry, and any claim of an application failing the requirements of § 101 must be rejected even if it meets all of the other legal requirements of patentability.” (citing In re Comiskey, 499 F.3d 1365, 1372 (Fed. Cir. 2007)); Prometheus Labs. v. Mayo Collaborative Servs., 581 F.3d 1336, 1343 (Fed. Cir. 2009) (noting that in determining patent eligibility, “it is improper to consider whether a claimed element or step in a process is novel or nonobvious, since such considerations are separate requirements set forth in 35 U.S.C. §§ 102 and

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103, respectively.” (citing Bilski, 545 F.3d at 958)). Consistent with this approach, the courts have rejected patent claims even when the purported invention was highly beneficial or novel, or the research and work that went into identifying it was costly or time-consuming. See, e.g., Funk Bros., 333 U.S. at 130; Am. Fruit Growers, Inc. v. Brodgex Co., 283 U.S. 1, 11-13 (1931); Gen. Elec. Co. v_ De Forest Radio Co., 28 F.2d 641, 642-43 (3d Cir. 1928).

The distinction between the § 101 inquiry into patentable subject matter and the other requirements for patentability set forth in Title 35 is of particular importance in evaluating the authorities cited by the parties and the arguments presented. The discussion of § 101 in In re Bergy, 596 F.2d 952 (C.C.P.A. 1979) by the late Honorable Giles S. Rich, one of the authors of the 1952 Patent Act, is particularly informative in clarifying the proper scope of a § 10l analysis. There, Judge Rich stated what considerations were salient—and importantly, what considerations were not—in a § 101 analysis:

Section lOl states three requirements: novelty, utility, and statutory subject matter. The understanding that these three requirements are separate and distinct is long-standing and has been universally accepted.… Thus, the questions of whether a particular invention is

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novel or useful are questions wholly apart from whether the invention falls into a category of statutory subject matter. Of the three requirements stated in § 101, only two, utility and statutory subject matter, are applied under § 101. As we shall show, in 1952 Congress voiced its intent to consider the novelty of an invention under § 102 where it is first made clear what the statute means by “new,” notwithstanding the fact that this requirement is first named in § 101.

Id. at 960-61 (emphasis added). Judge Rich further cautioned that “statements in the older cases must be handled with care lest the terms used in their reasoning clash with the reformed terminology of the present statute; lack of meticulous care may lead to distorted legal conclusions.” Id. at 959. The Supreme Court subsequently affirmed this understanding of the § 101 analysis in Diehr, noting that while it had been argued that “novelty is an appropriate consideration under § 101,” “[t]he question … of whether a particular invention is novel is ‘wholly apart from whether from whether the invention falls into a category of statutory subject matter.’” 450 U.S. at 189-90 (quoting Bergy, 596 F.2d at 961); see also _Bilski, 545 F.3d at 958 (“So here, it is irrelevant to the § 101 analysis whether Applicants' claimed process is novel or non- obvious.”).

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dissenting) (quoting U.S. Const., Art. I, § 8, cl. 8.) (emphasis in original). For these reasons, “manifestations of laws of nature [are] free to all men and reserved exclusively to none.” Funk Bros. Seed Co. v. Kalo Inoculant Co., 333 U.S. 127, 130 (1948).

The inquiry into an invention's patent eligibility is a fundamental one, and as such, “[t]he ob1igation to determine what type of discovery is sought to be patented must precede the determination of whether that discovery is, in fact, new or obvious.” Flook, 437 U.S. at 593; see also In re Bilski, 545 F.3d 943, 950 (Fed. Cir. 2008) (en banc), cert. granted, 129 S. Ct. 2735 (2009) (”Whether a claim is drawn to patent-eligible subject matter under § lOl is a threshold inquiry, and any claim of an application failing the requirements of § 101 must be rejected even if it meets all of the other legal requirements of patentability.” (citing In re Comiskey, 499 F.3d 1365, 1372 (Fed. Cir. 2007)); Prometheus Labs. v. Mayo Collaborative Servs., 581 F.3d 1336, 1343 (Fed. Cir. 2009) (noting that in determining patent eligibility, “it is improper to consider whether a claimed element or step in a process is novel or nonobvious, since such considerations are separate requirements set forth in 35 U.S.C. §§ 102 and

102

As noted, the issue presented by the instant motions with regpect to the composition claims is whether or not claims directed to isolated DNA containing naturally-occurring sequences fall within the products of nature exception to § 101. Based upon the reasons set forth below, it is concluded that the composition claims- in-suit are excepted.

1. Consideration of the merits of Plaintiffs' challenge is appropriate.

Myriad offers several arguments for why this Court should not engage the substance of Plaintiffs' claims, but should instead dismiss them out of hand. Foremost among them is Myriad's assertion that Plaintiffs' claims should be dismissed in light of the “carefully considered policy of the USPTO,” which is “entitled to great respect from the courts.” Myriad Br. at 26. In so arguing, Myriad notes the presumption of validity afforded to patents, see 35 U.S.C. § 282, and the USPTO's prior consideration of the eligibility of gene-related patents, see Utility Examination Guidelines 66 Fed. Reg. 1092, 1092-99 (Jan. 5, 2001), as well as the Supreme Court's statements in J.E.M. Ag Supply, 534 U.S. 124.

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The Federal Circuit has previously held that it owes no deference to USPTO legal determinations. See, e.g., Arnold P'Ship v. Dudas, 362 F.3d 1338, 1340 (Fed. Cir. 2004) (“This court reviews statutory interpretation, the central issue in this case, without deference.”). While Congress has created a presumption of validity for issued patents, approximately 40% of patents challenged in the courts have been found invalid, demonstrating that this presumption is far from absolute. See Institute for Intellectual Property & Information Law, University of Houston Law Center, Patstats.org, Full Calendar Year 2008 Report, http://www.patstats.org/2008_Full_Year_Posting.rev3.htm (indicating that 40% of all validity determinations in federal court in 2008 found the challenged patent invalid); Paul F. Morgan & Bruce Stoner, Reexamination v. Litigation — Making Intelligent Decisions in Challenging Patent Validity, 86 J. Pat. & Trademark Off. Soc'y 441-461 (2004) (citing USPTO statistics showing that 74% of patents previously issued by the Patent Office and later challenged through the reexamination process were either canceled or changed by the USPTO). Moreover, the lack of Congressional action to specifically prohibit gene patents in response to the USPTO's prior grant of such patents does not preclude

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their review by the courts. For example, in Bilski, 545 F.3d 943, the Federal Circuit set out a test for the patentability of method claims that potentially will invalidate thousands of patents on business method patents, degpite Congress' silence concerning the patentability of such methods. Finally, while the Supreme Court in J.E.M. Ag Supply noted the USPTO's practice of issuing patents on sexually reproducing plants in concluding that such plants represented patentable subject matter under § 101, that passing observation was neither dispositive nor central to the Court's holding and does not establish a rule of judicial deference to the USPTO's practices. See J.E.M. Ag _Supply, 534 U.S. at 144-45. Indeed, the judicial deference urged by Myriad is difficult to reconcile with the courts' consideration of the substantive issues presented in cases such as Chakrabarty and indeed, J.E.M. Ag Supply itself.

Moreover, in the absence of a § 101 challenge to patent validity, the fact that courts have previously upheld the validity of patents directed to biological products in response to § 102 and/or § 103 challenges has no bearing on the present inquiry. See e.g., In re Kubin, 561 F.3d 1351 (Fed. Cir. 2009) (considering obviousness of claims); In re O'Farrell, 853 F.2d 894 (Fed. Cir. 1988)

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(same). The Patent Act sets out patent invalidity as an issue to be raised by the parties, see 35 U.S.C. § 282, and it would be erroneous to treat a case involving DNA-related patents as holding that isolated human genes constitute patentable subject matter under § 101. Were that the case, the Supreme Court could have proceeded with its consideration of Metabolite Labs., after it granted certiorari and the parties and amici had fully briefed the issue of patentable subject matter eligibility, rather than dismissing certiorari as improvidently granted based on the parties' failure to raise the § lOl issue below. 548 U.S. 124.

Finally, Myriad's suggestion that invalidating the patents-in-suit would constitute an unconstitutional taking in violation of the Fifth Amendment of the Constitution or a violation of the United States' obligations under the Agreement on Trade-Related Aspects of Intellectual Property Rights (“TRIPS”) is unpersuasive. Myriad's novel takings argument runs counter to a long history of invalidation of patent claims by the courts and is unsupported by legal precedent. Similarly, Articles 8.1 and 27.3 of TRIPS permit governments to incorporate public health concerns into their intellectual property laws and

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to exclude from patentability diagnostic, therapeutic, or surgical methods as well as particular inventions on the grounds of public interest. As a result, invalidation of the patents-in-suit would constitute neither a constitutional violation nor a conflict with the United States' treaty obligations.

2. Patentable subject matter must be “markedly different” from a product of nature

Supreme Court precedent has established that products of nature do not constitute patentable subject matter absent a change that results in the creation of a fundamentally new product. In American Fruit Growers, the Supreme Court rejected patent claims covering fruit whose skin had been treated with mold-resistant borax acknowledging that the “complete article is not found in nature,” and “treatment, labor and manipulation” went into producing the fruit, the Court nonetheless held that the fruit did not become an “article of manufacture” unless it “possesses a new or distinctive form, quality, or property” compared to the naturally-occurring article.41 283 U.S. at 11. The Court went on to observe:

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Manufacture implies a change, but every change is not manufacture, and yet every change in an article is the result of treatment, labor, and manipulation. But something more is necessary.… There must be transformation; a new and different article must emerge having a distinctive name, character, or use.

Id. at 12-13 (quoting Annheuser-Busch Brewing Ass'n v. United States, 207 U.S. 556, 562 (1908)) (internal citation and quotation marks omitted).

Similarly, in Funk Brothers, the Supreme Court considered whether a mixture of several naturally-occurring species of bacteria was patentable.42 333 U.S. at 128-31. Each species of bacteria in the mixture could extract nitrogen from the air for plant usage. While the patent holder had created a mixture by selecting and testing for strains of bacteria that did not mutually inhibit one

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another, the Court concluded that the patent holder “did not create a state of inhibition or of non-inhibition in the bacteria. Their qualities are the work of nature. Those qualities are of course not patentable.” Id. at 130.

Most recently, the Supreme Court addressed the application of § 101 to product claims in Diamond v. Chakrabarty, 447 U.S. 303. In Chakrabarty, the Court considered whether a “live, human-made micro-organism is patentable subject matter under 35 U.S.C. § 101.” Id. at 305. The microorganism in question was a bacterium that had been genetically engineered to break down multiple components of crude oil and possessed considerable utility in the treatment of oil spills. Id. In concluding that the man-made bacterial strain was patentable, the Court observed that the claim “is not to a hitherto unknown natural phenomenon, but to a nonnaturally occurring manufacture or composition of matter—a product of human ingenuity ‘having a distinctive name, character [and] use.’” Id. at 309-10 (quoting Hartranft v. Wiegmann, 121 U.S. 609, 615 (1887)). The Court went on to contrast the Chakrabarty bacterium with the bacterial mixture at issue in Funk Brothers, stating that in Chakrabarty's case, “the patentee has produced a new bacterium with markedly

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different characteristics from any found in nature and one having the potential for significant utility. His discovery is not nature's handiwork, but his own.…” Id. at 310.43 This requirement that an invention possess “markedly different characteristics” for purposes of § 101 reflects the oft-repeated requirement that an invention have “a new or distinctive form, quality, or property” from a product of nature. Am. Fruit Growers, 283 U.S. at 11; In re Merz, 97 F.2d 599, 601 (C.C.P.A. 1935) (“[M]ere purification of known materials does not result in a patentable product,” unless “the product obtained in such a case had properties and characteristics which were different in kind from those of the known product rather than in degree.”).

Courts have also specifically held that “purification” of a natural compound, without more, is insufficient to render a product of nature patentable. In The American Wood-Paper Co. v. The Fibre Disintearating Co., 90 U.S. (23 Wall.) 566 (1874), the Supreme Court held

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that refined cellulose, consisting of purified pulp derived from wood and vegetable, was unpatentable because it was “an extract obtained by the decomposition or disintegration of material substance.” Id. at 593. As the Court observed:

There are many things well known and valuable in medicine or in the arts which may be extracted from divers[e] substances. But the extract is the same, no matter from what it has been taken A process to obtain it from a subject from which it has never been taken may be the creature of invention, but the thing itself when obtained cannot be called a new manufacture.

Id. at 593-94.44 Similarly, in Cochrane v. Badische Anilin & Soda Fabrik, 111 U.S. 293 (1884), the Court rejected a patent on an artificial version of a natural red dye called alizarine that was produced by manipulating another compound through acid, heat, water or distillation. See generally, _id. Although the artificial version of the dye was of a brighter hue than the naturally occurring dye, the Court concluded that “[c]alling it artificial alizarine did not make it a new composition of matter, and patentable as such.…” Id. at 311 (citing Am. Wood-Paper, 90 U.S. (23 Wall.) at 593).

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In General Electric, 28 F.2d at 642, the Third Circuit Court of hppeals considered the patentability of purified tungsten, which possessed superior characteristics and utility over its brittle, naturally-occurring form. The court first noted that “[i]f it is a natural thing then clearly, even if [the patentee] was the first to uncover it and bring it into view, he cannot have a patent for it because a patent cannot be aHarded for a discovery or for a product of nature, or for a chemical element.” Id. The court went on to state:

Naturally He inquire who created pure tungsten. Coolidge? No. It existed in nature and doubtless has existed there for centuries. The fact that no one before Coolidge found it there does not negative its origin or existence.

The second part of the claim reads: “Having ductility and high tensile strength.” Did Coolidge give those qualities to “substantially pure tungsten”? We think not for it is now conceded that tungsten pure is ductile cold. If it possess that quality now it is certain that it possessed it always.

Id. at 643. The Court of Customs and Patent Appeals (“C.C.P.A.“), the precursor to the Federal Circuit Court of

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Appeals,45 subsequently relied on General Electric in rejecting patents claiming purified uraniwn and vanadium. See In re Marden, 47 F.2d 957, 957-58 (C.C.P.A. 1931) (“Marden I”); In re Marden, 47 F.2d 958, 1059 (C.C.P.A. 1931) (“Marden II”) (“The quality of purity of vanadium or its ductility is a quality of a natural product and as such is not patentable.”). Similarly, in Ex Parte Latimer, the Patent Commissioner refused to allow a patent on pine needle fibers that were better suited for textile production, even though it was necessary to remove the needle from its sheath and other resinous material. 1889 Dec. Comm'r Pat. 123, 125 (1889) (“Nature made them so and not the process by which they are taken from the leaf or needle.”).

Myriad argues that purification of “‘naturally occurring’ compounds that ‘do not exist in nature in pure form’ renders such compounds patent-eligible.” Myriad Br. at 21 (quoting In re Bergstrom, 427 F.2d 1394, 1401 (C.C.P.A. 1970)). However, Myriad cites no Supreme Court

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authority that would rebut the authorities presented by Plaintiffs, nor do the cited cases support Myriad's position.

Myriad has relied heavily on the holding of the Honorable Learned Hand in Parke-Davis & Co. v. H.K. Mulford Co. 189 F.2d 95 (S.D.N.Y. 1911).46 In Parke-Davis, Judge Land considered a challenge to the validity of a patent

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claiming an adrenaline compound that had been isolated and purified from animal suprarenal glands. Id. at 97. It had been known that suprarenal glands in powdered form had hemostatic, blood-pressure-raising and astringent properties, but could not be used for those purposes in gross form. The isolated adrenaline, however, possessed the desired therapeutic properties and could be administered to humans.

Although Myriad argues that the holding in Parke-Davis establishes that the purification of a natural product necessarily renders it patentable, the opinion, read closely, fails to support such a conclusion. The question before the court in Parke-Davis was one of novelty (a modern-day § 102 question), not of patentable subject matter (the § lOl question before this Court). In framing the issue, Judge Hand observed that, “[the validity of the claims] is attacked, first, because they are anticipated in the art; and second, for a number of technical grounds which I shall take up in turn.” Id. at 101 (emphasis added). He went on to conclude that the patented purified extract was not, in fact, different from the prior art “only for a degree of purity,” but rather was a different chemical substance from that found in the prior art. Id.

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at 103 (observing that “no one had ever isolated a substance [adrenaline] which was not in salt form” and that “the [claimed] base [form of adrenaline] was an original production of [the patentee's]”). Thus, Judge Hand held that the purified adrenaline was not anticipated by the prior art, namely, the ground paradrenal gland that was known to possess certain beneficial properties. See Merck & Co. v. Olin Mathieson Chem. Corp., 253 F.2d 156, 162 (4th Cir. 1958) (“It was further held [in Parke-Davis] that the invention was not anticipated, though the principle was known to exist in the suprarenal glands.”).

Only after concluding that the claimed purified adrenaline was novel over the prior art did Judge Hand Offer, as dicta, the statement to Which Myriad cites: “But, even if it were merely an extracted product without change, there is no rule that such products are not patentable.” Id. at 103. While the accuracy of this statement at the time was written is dubious in light of American Wood-Paper (to which Judge Hand did not cite) it is certainly no longer good law in light of subsequent Supreme Court cases, which, as noted above, require that a claimed invention possess “markedly different characteristics” over products existing in nature in order for it to constitute patentable

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subject matter.47 Chakrabarty, 447 U.S. at 310; see also Funk Bros., 333 U.S. at 130-32. By the same token, Judge Hand's suggestion that a claimed invention was patentable since it was a “new thing commercially and therapeutically,” Parke-Davis, 189 F.2d at 103, is firmly contradicted by subsequent case law establishing that “it is improper to consider whether a claimed element or step in a process is novel or nonobvious, since such congiderations are separate requirements” when evaluating whether a claim is patent-eligible subject matter. Prometheus, 581 F.3d at 1343; see also Bergy, 596 F.2d at 960-61. Such an approach would also be inconsistent with the Supreme Court's rejection of the patentability of the commercially useful mixture of bacteria in Funk Brothers, the refined cellulose in American Wood-Paper, and the electromagnetic communication devices in O'Reilly v. Morse, 56 U.S. (15 How.) 62 (1853).

The distinction between considerations of novelty and patentable subject matter similarly undermines Myriad's reliance on Bergstrom and In re Kratz, 592 F.2d 1169 (C.C.P.A. 1979), both of which presented issues of novelty

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and anticipation rather than the question of patentable subject matter. In Bergstrom, the C.C.P.A. considered an appeal from a rejection by the Board of Patent and Interferences (“BPAI”) of a patent claiming the purified rostaglandins PGE2 and PGE3 that had been extracted from human or animal prostate glands. 427 F.2d at 1398. Although the BPAI cited § 101 in its rejection, the C.C.P.A. recognized the issue as a § 102 question of novelty. Id. at 1400 (“Tested by the conventional evidentiary criteria or ‘conditions for patentability’ relevant to the present factual situation which Congress has expressed in the various provisions of 35 U.S.C. § 102, appellants are undoubtedly correct, for the Patent Office has not been able to … establish that the claimed subject matter lacks 'novelty.’”); see also id. at 1401 (“[T]he fundamental error in the board's position, as we see it, is the analysis and answer it gave to the sole issue it accurately posed - whether the claimed pure materials are novel as compared with the less pure materials of the reference.” (internal citation and uotation marks omitted)). Indeed, the C.C.P.A. itself has subsequently recognized that Bergstrom is properly viewed as a case concerning novelty. Bergy, 596 F.2d at 961 (“Our research has disclosed only two instances in which

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rejections for lack of novelty were made by the PTO under § 101.… In In re Berastrom we in effect treated the rejection as if it had been made under § 102, obServing in the process that ‘The word “new” in § 101 is defined and to be construed in accordance with the provisions of § 102.’” (internal citation omitted)).

Kratz examined the rejection of a patent claiming a substantially purified chemical compound naturally occurring in strawberries, called 2-methyl-2-pentenoic acid (“2M2PA”). 592 F.2d at 1170. The patentee had appealed from the BPAI's determination that the purified compound was obvious over the prior art under § 103. See _id. Although there was some discussion about whether the composition claimed was a naturally-occurring compound, the C.C.P.A. did not view the question before it as a § 101 inquiry. Instead, the court treated the appeal as a question of novelty and anticipation pursuant to § 102.48 See, e.g., id. at 1174 (“It should be clear that an

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anticipation rejection in such a case is necessarily based on a dual footing.”).49

Finally, Merck & Co., Inc. v. Olin Mathieson Chem. Corp., 253 F.2d 156, cited by Myriad, is entirely consistent with the principle set forth in Funk Brothers and American Fruit Growers that something derived from a product of nature must “possess a new or distinctive form, quality, or property” in order to become patentable subject matter. Am. Fruit Growers, 283 U.S. at 11. In Merck, the Fourth Circuit considered the validity of a patent claiming a Vitamin B12 composition useful for treating pernicious anemia. Id. at 157. Although naturally occurring Vitamin B12 produced in cows had known therapeutic properties and was commercially available, the court found the purified B12 Compositipn, which was obtained from a microorganism, patentable. In upholding the validity of the patent, the court held:

Every slight step in purification does not produce a new product. What is gained may be the

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old product, but with a greater degree of purity. Alpha alumina purified is still alpha alumina, In re Ridgway, 76 F.2d 602,[] and ultramarine from which floatable impurities have been removed is still ultramarine, In re Merz, 97 F.2d 599 …

Id. at 163. Because the court concluded that the purified B12 was more than a “mere advance in the degree of purity of a known product,” it determined that the claimed invention was entitled to patent protection. Id. at 164.

In sum, the clear line of Supreme Court precedent and accompanying lower court authorities, stretching from American Wood-Paper through to Chakrabarty, establishes that purification of a product of nature, without more, cannot transform it into patentable subject matter. Rather, the purified product must pogsess “markedly different characteristics” in order to satisfy the requirements of § 101.

3. The claimed isolated DNA is not “markedly different” from native DNA

The question thus presented by Plaintiffs' challenge to the composition claims is whether the isolated DNA claimed by Myriad possesses “markedly different

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NOTES

25 The USPTO granted these patents pursuant to a formal written policy that permits the patenting of “isolated and purified” DNA encoding human genes and pursuant to a practice that permits such DNA patents and the patenting of correlations created by nature between natural elements of the body and a predisposition to disease. See Utility Examination Guidelines, 66 Fed. Reg. 1,093 (Jan. 5, 2001).

26 For purposes of understanding what the claim terms would have meant to a person of ordinary skill in the art at the time of the application for the patents, an application date of August 1994 is presumed for the '282, '473, '999, '001, and '441 patents and December 1995 for the '492 and '857 patents.

27 Claim 2 of the '282 patent reads: “The isolated DNA of claim 1, wherein said DNA has the nucleotide sequence get forth in SEQ ID NO:1.”

28 Claim 5 of the '282 patent claims: “An isolated DNA having at least 15 nucleotides of the DNA of claim 1.” Claim 6 of the '282 patent reads: “An isolated DNA having at least 15 nucleotides of the DNA of claim 2.”

29 Claim 7 of the '282 patent reads: “An isolated DNA selected from the group consisting of: (a) a DNA having the nucleotide sequence get forth in SEQ ID NO:1 having T at nucleotide position 4056; (b) a DNA having the nucleotide sequence set forth in SEQ ID NO:1 having an extra C at nucleotide position 5385; (c) a DNA having the nucleotide sequence set forth in SEQ ID NO:1 having G at nucleotide position 5443; and (d) a DNA having the nucleotide sequence set forth in SEQ ID NO:1 having 11 base pairs at nucleotide positions 189-199 deleted.” Claim 1 of the '473 patent reads: “An isolated DNA comprising an altered BRCA1 DNA having at least one of the alterations set forth in Tableg 12A, 14, 18 or 19 with the proviso that the alteration is not a deletion of four nucleotides corre9ponding to base numbers 4184-4187 in SEQ. ID. NO:1.”

30 Claim 1 of the '492 patent reads: “An isolated DNA molecule coding for a BRCA2 polypeptide, said DNA molecule comprising a nucleic acid sequence encoding the amino acid sequence set forth in SEQ ID NO:2.”

31 Claim 6 of the '492 patent reads: “An isolated DNA molecule coding for a mutated form of the BRCA2 polypeptide set forth in SEQ ID NO:2, wherein said mutated form of the BRCA2 polypeptide is associated with susceptibility to cancer.”

32 32 claim 7 of the '492 patent reads: “The isolated DNA molecule of claim 6, wherein the DNA molecule comprises a mutated nucleotide gequence set forth in SEQ ID cNO:1.”

33 Claim 1 of the '001 patent reads: “A method for screening a tumor semple from a human subject for a somatic alteration in a BRCA1 gene in said tumor which comprises gene comparing a first sequence selected form [sic] the group consisting of a BRCA1 gene from said tumor 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 DNA 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 alteration in the BRCA1 gene in said tumor sample.”

34 Claim 1 of the '441 patent reads: “A method for screening germline of a human subject for an alteration of a BRCA1 gene which comprises comparing germline sequence of a BRCA1 gene or BRCA1 RNA from a tissue samp1e from said subject or a sequence of BRCA1 cDNA made from mRNA from said sample with germline sequences of wild-type BRCA1 gene, wild- type BRCA1 RNA or wild-type BRCA1 cDNA, wherein a difference in the sequence of the BRCA1 gene, BRCA1 RNA or BRCA1 cDNA of the subject from wild-type indicates an alteration in the BRCA1 gene in said subject.” Claim 1 of the '857 patent claims: “A method for identifying a mutant BRCA2 nucleotide sequence in a suspected mutant BRCA2 allele which comprises comparing the nucleotide sequence of the suspected mutant BRCA2 allele with the wild-type BRCA2 nucleotide sequence, wherein a difference between the suspected mutant and the wild-type sequences identifies a mutant BRCA2 nucleotide sequence.”

35 Claim 2 of the '857 patent reads: “A method for diagnosing a predisposition for breast cancer in a human subject which comprises comparing the germline sequence of the BRCA2 gene or the sequence of its mRNA in a tissue sample from said subject with the germline sequence of the wild-type BRCA2 gene or the sequence of its mRNA, wherein an alteration in the germline sequence of the BRCA2 gene or the sequence of its mRNA of the subject indicates a predisposition to said cancer.”

36 Claim 20 of the '282 patent reads: “A method for screening potential cancer therapeutics which comprises: growing a transformed eukaryotic host cell containing an altered BRCA1 gene causing cancer n the presence of a compound suspected of being a cancer therapeutic, growing said transformed eukaryotic host cell in the absence of said compound, determining the 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 comparing the growth rate of said host cells, wherein a slower rate of growth of said host cell in the presence of said compound is indicative of a cancer therapeutic.”

37 In addition to the claim terms discussed below, the parties also dispute the proper interpretation of the method claims—i.e., whether they may be construed to encompass certain transformative steps. Because this issue is broader in scope than simple claim term definition, it is addressed infra in Section VII.D.

38 The degree to which the parties actually disagree on the meaning of the discussed claim terms is unclear; however, to the extent some digagreement has been noted by the parties, this section seeks to resolve them.

39 For purposes of this opinion, “Pl. Br.” refers to Plaintiffs' Memorandum of Law in Support of Motion for Summary Judgment; “Myriad Br.” refers to Myriad Defendants' Memorandum of Law (l) in Support of Their Motion for Summary Judgment and (2) in Opposition to Plaintiffs' Motion for Summary Judgment; “Pl. Reply” refers to the Memorandum of Law (l) in Further Support of Plaintiffs' Motion for Summary Judgment ngainst All Defendants and (2) in Opposition to the Myriad Defendants' Motion for Summary Judgment and (3) in Opposition to Defendant United States Patent and Trademark Office's Motion for Judgment on the Pleadings; “Myriad Reply” refers to Myriad Defendants' Memorandum in Reply to Plaintiffs' Opposition to Myriad Defendants' Motion for Summary Judgment; and “USPTO Reply” refers to the Reply Memorandwn of Law in Further Support of Defendant United States Patent and Trademark Office's Motion for Judgment on the Pleadings and in Opposition to Plaintiffs' Motion for Summary Judgment.

40 Myriad distinguishes between “laws of nature,” ”natural phenomena,” and “abstract ideas,” which it concedes are not patentable, and “products of nature,” for which it appears to argue no prohibition to patentability exists. Although the digtinction between these two categories is unclear, it is well established that “products of nature” are not patentable. See e.g., Chakrabarty, 447 U.S. at 13 (stating that relevant distinction for § 101 patentability is “between products of nature, whether living or not, and human-made inventions”); Gen. Elec. Co. v. De Forest Radio Co., 28 F.2d 641, 642 (3d Cir. 1928) (noting that “a patent cannot be awarded for a discovery or for a product of nature, or for a chemical element”); In re Marden, 47 F.2d 957, 957 (C.C.P.A. 1931) (concluding that “[u]ranium is a product of nature, and the appellant is not entitled to a patent on the same, or upon any of the inherent natural qualities of that metal”); In re Marden, 47 F.2d 958, 959 (C.C.P.A. 1931) (stating that “pure 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.”).

41 Myriad argues that American Fruit Growers was decided on novelty grounds, rather than subject matter patentability. See Myriad Br. at 26. However, the Court's novelty discussion was restricted to its analysis of the process claims. Am. Fruit Growers, 283 U.S. at 13-14 (“If it be assumed that the process claims under consideration cover an invention, we think this lacked novelty when application was made for the patent August 13, 1923”). In contrast, its rejection of the composition claims was based on an analysis of subject matter patentability. See id. at 11 (“Is an orange, the rind of which has become impregnated with borax, through immersion in a solution, and thereby resistant to blue mold decay, a ‘manufacture,’ or manufactured article, within the meaning of section 31, title 35, U.S. Code?”).

42 Myriad suggests that the Supreme Court's holding in Funk Brothers was premised on an obviousness determination, rather than patentable subject matter. Subsequent Supreme Court opinions, however, have treated the holding in Funk Brothers as a statement of patentable subject matter. See Chakrabarty, 447 U.S. at 309-lO; F1ook, 437 U.S. at 591-92; Benson, 409 U.S. at 67-68.

43 Although Chakrabarty is often cited for the proposition that “anything under the sun that is made by man” is patentable, id. at 309, that phrase is a misleading quotation from the legislative history of the Patent Act of 1952. The full quote clearly acknowledges the statutory limitations to patentable subject matter: “A person may have ‘invented’ a machine or a manufacture, which may include anything under the sun made by man, but it ig not necessarily patentable under section 101 unless the conditions of the title are fulfilled.” H.R. Rep. No. 1923, 82d Cong., 2d Sess. 6 (1952).

44 Given the posture of the challenge to the patent's validity, the Court rested its holding on the fact that the patent in question was invalid as non-novel. Id.

45 The decisions of the C.C.P.A. remain binding precedent in patent cases. See South CorD. v. Untted States, 690 F.2d J368, 1370-71 (Fed. Cir. 19B2) (en banc) (adopting “[t]hat body of law represented by the holdings of … the Court of Customs and Patent Appeals&rellip; as “precedent” for the then-new Federal Circuit so as to “continu[el the stability in those areas of the law previously within the jurisdiction of our predecessor courts”).

46 The invocation of Judge Hand is frequently practiced in this Circuit. See, e.g.,United States v. Rigas, 583 F.3d 108, 121 n.3 (2d Cir. 2009) (quoting Learned Hand for the proposition that appellate cour

[ Reply to This | Parent | # ]

AMP v. Myriad Genetics - extracts from Judge Sweet's opinion, as HTML
Authored by: PJ on Tuesday, April 09 2013 @ 08:04 PM EDT
Just so you know, the ACLU has an entire page of documents on this case, including the one you worked on, and you can copy and paste them

It's here.

[ Reply to This | Parent | # ]

AMP v. Myriad Genetics - Judge Sweet's opinion, repost of p.102
Authored by: macliam on Wednesday, April 10 2013 @ 03:25 PM EDT

Accordingly, in considering whether the patents- in-suit comply with § 101, the proper analysis requires detemining (l) whether the claimed invention possesses utility; and (2) whether the claimed invention constitutes statutory subject matter, that is, whether it is a “process, machine, manufacture, or composition of matter, or any new and useful improvement thereof,” 35 U.S.C. § 101, or whether the claimed invention instead falls within the judicially created “products of nature” exception to patentable subject matter, i.e., “laws of nature, natural phenomenon, and abstract ideas,” Chakrabarty, 447 U.S. at 309. In contrast, the question of whether an invention is “new” or “novel” over the prior art is a question addressed by § 102 and falls outside of the scope of the present § 101 analysis. Because it is undisputed that the claimed compositions and methods possess utility, the sole task of this Court is to resolve whether the claimed compositions and methods constitute statutory subject matter or fall within the judicially created products of nature exception to patentable subject matter.

C. The Composition Claims Are Invalid Under 35 U.S.C. § 101

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[ Reply to This | Parent | # ]

AMP v. Myriad - Judge Sweet's opinion, as HTML, pp. 121-135
Authored by: macliam on Wednesday, April 10 2013 @ 03:30 PM EDT
old product, but with a greater degree of purity. Alpha alumina purified is still alpha alumina, In re Ridgway, 76 F.2d 602,[] and ultramarine from which floatable impurities have been removed is still ultramarine, In re Merz, 97 F.2d 599 …

Id. at 163. Because the court concluded that the purified B12 was more than a “mere advance in the degree of purity of a known product,” it determined that the claimed invention was entitled to patent protection. Id. at 164.

In sum, the clear line of Supreme Court precedent and accompanying lower court authorities, stretching from American Wood-Paper through to Chakrabarty, establishes that purification of a product of nature, without more, cannot transform it into patentable subject matter. Rather, the purified product must pogsess “markedly different characteristics” in order to satisfy the requirements of § 101.

3. The claimed isolated DNA is not “markedly different” from native DNA

The question thus presented by Plaintiffs' challenge to the composition claims is whether the isolated DNA claimed by Myriad possesses “markedly different

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characteristics” from a product of nature.50 Chakrabarty, 447 U.S. at 310. In support of its position, Myriad cites several differences between the isolated DNA claimed in the patents and the native DNA found within human cells. None, however, establish the subject matter patentability of isolated BRCA1/2 DNA.

The central premise of Myriad's argument that the claimed DNA is “markedly different” from DNA found in nature is the assertion that “[i]solated DNA molecules should be treated no differently than other chemical compounds for patent eligibility,” Myriad Br. at 26, and that the alleged “difference in the structural and functional properties of isolated DNA” render the claimed DNA patentable subject matter, Myriad Br. at 31.

Myriad's focus on the chemical nature of DNA, however, fails to acknowledge the unique characteristics of DNA that differentiate it from other chemical compounds. As Myriad's expert Dr. Joseph Straus observed: “Genes are of double nature: On the one hand, they are chemical substances or molecules. On the other hand, they are

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physical carriers of information, i.e., where the actual biological function of this information is coding for proteins. Thus, inherently genes are multifunctional.” Straus Decl ¶ 20; see also The Cell at 98, 104 (“Today the idea that DNA carries genetic information in its long chain of nucleotides is so fundamental to biological thought that it is sometimes difficult to realize the enormous intellectual gap that it filled.… DNA is relatively inert chemically.”); Kevin Davies & Michael White, Breakthrough: The Race to Find the Breast Cancer Gene 166 (1996) (noting that Myriad Genetics' April 1994 press release described itself as a “genetic information business”) . This informational quality is unique among the chemical compounds found in our bodies, and it would be erroneous to view DNA as “no different[]” than other chemicals previously the subject of patents.51

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Myriad's argument that all chemical compounds, such as the adrenaline at issue in Parke-Davis, necessarily conveys some information ignores the biological realities of DNA in comparison to other chemical compounds in the body. The information encoded in DNA is not information about its own molecular structure incidental to its biological function, as is the case with adrenaline or other chemicals found in the body. Rather, the information encoded by DNA reflects its primary biological function: directing the synthesis of other molecules in the body - namely, proteins, “biological molecules of enormous importance” which “catalyze biochemical reactions” and constitute the “major structural materials of the animal body.” O'Farrell, 854 F.2d at 895-96. DNA, and in particular the ordering of its nucleotides, therefore serves as the physical embodiment of laws of nature—those that define the construction of the human body. Any “information” that may be embodied by adrenaline and similar molecules serves no comparable function, and none of the declarations submitted by Myriad support such a conclusion. Consequently, the use of simple analogies comparing DNA with chemical compounds previously the subject of patents cannot replace consideration of the distinctive characteristics of DNA.

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In light of DNA's unique qualities as a physical embodiment of information, none of the structural and functional differences cited by Myriad between native BRCAI/2 DNA and the isolated BRCAI/2 DNA claimed in the patents-in-suit render the claimed DNA “markedly different.” This conclusion is driven by the overriding importance of DNA's nucleotide sequence to both its natural biological function as well as the utility associated with DNA in its isolated form. The preservation of this defining characteristic of DNA in its native and isolated forms mandates the conclusion that the challenged composition claims are directed to unpatentable products of nature.

Myriad argues that the § 101 inquiry into the subject matter patentability of isolated DNA should focus exclusively on the differences alleged to exist between native and isolated DNA, rather than considering the similarities that exist between the two forms of DNA. See, e.g., Myriad Reply at 8-9 (“[T]he observation that isolated DNA and native DNA share this single property [i.e. the same protein coding sequences] is irrelevant to the critical issue of whether there are differences in their

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properties. It is the differences that are legally relevant to the novelty inquiry under Section 101, not the properties held in common.” (emphasis in original)); Myriad Br. at 8. Setting aside the fact that considerations such as novelty are irrelevant for § 101 purposes, see Bergy, 596 F.2d at 960-61, Myriad offers no authorities supporting such an approach. To the contrary, the Supreme Court has held that “[i]n determining the eligibility of [a] claimed process for patent protection under § 101, [the] claims must be considered as a whole.” Diehr, 450 U.S. at 188. Similarly, the Federal Circuit has expressly held that “[i]n the final analysis under § 101, the claimed invention, as a whole, must be evaluated for what it is.” In re Grams, 888 F.2d 835, 839 (Fed. Cir. 1989) (quoting In re Abele, 684 F.2d 902, 907 (C.C.P.A. 1982)).

Were Myriad's approach the law, it is difficult to discern how any invention could fail the test. For example, the bacterial mixture in Funk Brothers was unquestionably different from any preexisting bacterial mixture; yet the Supreme Court recognized that a patent directed to the mixture, considered as a whole, did no more than patent “the handiwork of nature.” 333 U.S. at 131. There will almost inevitably be some identifiable

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differences between a claimed invention and a product of nature; the appropriate § 101 inquiry is whether, considering the claimed invention as a whole, it is sufficiently distinct in its fundamental characteristics from natural phenomena to possess the required “distinctive name, character, [and] use.” Chakrabarty, 447 U.S. at 309-10.

None of Myriad's arguments establish the distinctive nature of the claimed DNA. Myriad's argument that association of chromosomal proteins with native DNA establishes the existence of “structural differences” between native and isolated DNA relies on an incorrect comparison between isolated DNA and chromatin, which are indeed different insofar as chromatin includes chromosomal proteins normally associated with DNA. The proper comparison is between the claimed isolated DNA and the corresponding native DNA, and the presence or absence of chromosomal proteins merely constitutes a difference in purity that cannot serve to establish subject matter patentability. See Gen. Elec., 28 F.2d at 642-43; Marden I, 47 F.2d at 957-58; Marden II, 47 F.2d at 1059.

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Myriad also attempts to rely on its assertion that native DNA contains intron sequences that are absent in the claimed BRCAI/2 DNA. However, some of the claims, such as claim 1 of the '282 patent, are directed broadly to DNA “coding for a BRCA1 polypeptide.” Native BRCA1 DNA, by definition, encodes the BRCA1 protein; thus claim 1 of the '282 patent would cover purified BRCA1 DNA possessing the exact same structure found in the human cell, introns and all.52 See also '492 patent, claim 1 (similarly claiming isolated DNA “coding for a BRCA2 polypeptide”). In addition, several of the composition claims are directed to isolated DNA containing as few as 15 nucleotides of the BRCA1 coding sequence, see, e. g., '282 patent, claims 5 & 6, and at least some of these short DNA sequences will be found within a single exon of the native BRCA1 gene sequence. See Adam Pavlicek, et al., Evolution of the Tumor Suppressor BRCA1 Locus in Primates: Implications for Cancer Predisposition, 13 Human Molecular Genetics 2737, 2737 (2004) (noting BRCA1 exons range from 37 to 3427 nucleotides in length). Therefore, for these small DNA fragments, the existence of introns in native BRCA1 DNA is completely irrelevant to the question of structural

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differences when comparing these short DNA molecules with native BRCAI DNA.

More generally, the fact that the BRCAI/2 cDNA molecules covered by the composition claims-in-suit contain only the protein coding exons and not the introns found in native DNA does not render these cDNAs and their native counterparts “markedly different.” The splice variants represented by these cDNAs are the result of the naturally-occurring splicing of pre-mRNA into mature mRNA. Therefore, not only are the coding sequences contained in the claimed DNA identical to those found in native DNA, the particular arrangement of those coding sequences is the result of the natural phenomena of RNA splicing. Finally, at least in the case of BRCA1, the claimed cDNA sequences are actually found in the human genome in the form of a naturally occurring pseudogene. See Mason Supp. Decl. ¶ 18.53

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Myriad's argument that the functional differences between native and isolated DNA demonstrates that they are “markedly different” relies on the fact that isolated DNA may be used in applications for which native DNA is unsuitable, namely, in “molecular diagnostic tests (e.g., as probes, primers, templates for sequencing reactions), in biotechnological processes (e.g. production of pure BRCA1 and BRCA2 protein), and even in medical treatments (e.g. gene therapy).” Myriad Reply at 9; see also Myriad Br. at 30-32.

Isolated DNA's utility as a primer or a molecular probe (for example, for Southern blots) arises from its ability to “target and interact with other DNA molecules,” that is, the ability of a given DNA molecule to bind exclusively to a specific DNA target sequence. Myriad Br. at 33; see Kay Decl. ¶ 138. Thus, for example, a 24 nucleotide segment of isolated BRCA1 DNA can be used as a primer because it will bind only to its corresponding location in the BRCAl gene. However, the basis for this utility is the fact that the isolated DNA possesses the identical nucleotide sequence as the target DNA sequence,54

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thus allowing target specific hybridization between the DNA primer and the portion of the target DNA molecule possessing the corresponding sequence. Kay Decl. ¶¶ 135-36, 138. In contrast, another 24 nucleotide segment of DNA possessing the same nucleotide composition but a different nucleotide sequence would not have the same utility because it would be unable to hybridize to the proper location in the BRCA1 gene.55 Indeed, Myriad implicitly acknowledges this fact when it states that the usefulness of isolated DNA molecules “is based on their ability to target and interact with other DNA molecules, which is a function of their own individual structure and chemistry.” Myriad Br. at 33 (emphasis added). Therefore, the cited utility of the isolated DNA as a primer or probe is primarily a function of the nucleotide sequence identity between native and isolated BRCA1/2 DNA.

Similarly, the utility of isolated DNA as a sequencing target relies on the preservation of native DNA's nucleotide sequence. Indeed, one need look no further than Myriad's BRACAnalysis testing, which relies on the sequencing of isolated DNA (i.e. the PCR amplified

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exons of BRCA1/2) , to determine the sequence of the corresponding DNA coding sequences found in the cell. The entire premise behind Myriad's genetic testing is that the claimed isolated DNA retains, in all relevant respects, the identical nucleotide sequence found in native DNA. The use of isolated BRCA1/2 DNA in the production of BRCA1/2 proteins or in gene therapy also relies on the identity between the native DNA sequences and the sequences contained in the isolated DNA molecule. Were the isolated BRCA1/2 sequences different in any significant way, the entire point of their use—the production of BRCA1/2 proteins—would be undermined.

While the absence of proteins and other nucleotide sequences is currently required for DNA to be useful for the cited purposes, the purification of native DNA does not alter its essential characteristic—its nucleotide sequence—that is defined by nature and central to both its biological function within the cell and its utility as a research tool in the lab. The requirement that the DNA used be “isolated” is ultimately a technological limitation to the use of DNA in this fashion, and a time may come when the use of DNA for molecular and diagnostic purposes may not require such purification. The

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nucleotide sequence, however, is the defining characteristic of the isolated DNA that will always be required to provide the sequence-specific targeting and protein coding ability that allows isolated DNA to be used for the various applications cited by Myriad. For these reasons, the use of isolated DNA for the various purposes cited by Myriad does not establish the existence of differences “in kind” between native and isolated DNA that would establish the subject matter patentability of what is otherwise a product of nature. See Am. Fruit Growers, 283 U.S. at 11.

Finally, the isolated BRCA1/2 DNA claimed in Myriad's patents bears comparison to the bacterial mixture in Funk Brothers. In explaining why the claimed mixture of bacteria did not constitute an invention, the Court observed that the first part of the claimed invention was the “[d]iscovery of the fact that certain strains of each species of these bacteria can be mixed without harmful effect to the properties of either” which was “a discovery of their qualities of non-inhibition. It is no more than the discovery of some of the handiwork of nature and hence is not patentable.” 33 U.S. at 131. The Court went on to observe that the second part of the claimed invention was

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“[t]he aggregation of select strains of the several species into one product[, ] an application of that newly-discovered natural principle. But however ingenious the discovery of that natural principle may have been, the application of it is hardly more than an advance in the packaging of the inoculants.” Id.

According to Myriad, the invention claimed in its patents required the identification of the specific segments of chromosomes 17 and 13 that correlated with breast and ovarian cancer (BRCA1 and BRCA2) followed by the isolation of these sequences away from other genomic DNA and cellular components. Myriad Reply at 6 (“By identifying these particular BRCA DNAs and isolating them away from other genomic DNA and other cellular components, the inventors created the claimed isolated BRCA DNA molecules.”). Like the discovery of the mutual non-inhibition of the bacteria in Funk Brothers, discovery of this important correlation was a discovery of the handiwork of nature—the natural effect of certain mutations in a particular segment of the human genome. And like the aggregation of bacteria in Funk Brothers, the isolation of the BRCA1 and BRCA2 DNA, while requiring technical skill and considerable labor, was simply the application of

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techniques well-known to those skilled in the art. See Parthasarathy Decl. ¶ 19. The identification of the BRCA1 and BRCA2 gene sequences is unquestionably a valuable scientific achievement for which Myriad deserves recognition, but that is not the same as concluding that it is something for which they are entitled to a patent. See Funk Bros., 33 U.S. at 132 (“[O]nce nature's secret of the non-inhibitive quality of certain strains of the [nitrogen- fixing bacteria] was discovered, the state of the art made the production of a mixed inoculant a simple step. Even though it may have been the product of skill, it certainly was not the product of invention.”).

Because the claimed isolated DNA is not markedly different from native DNA as it exists in nature, it constitutes unpatentable subject matter under 35 U.S.C. § 101.

D. The Method Claims are Invalid Under 35 U.S.C. § 101

“Phenomena of nature, though just discovered, mental processes, and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work.” Benson, 409 U.S. at 67. However,

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NOTES

50 50 The parties do not appear to dispute that isolated DNA claimed in the patents-in-suit are “useful” for purposes of § 101.

51 Myriad and many of the amici suggest that the invalidation of the patents-in-suit will result in the decimation of the biotechnology industry. See, e.g., Myriad Br. at 28-29 (suggesting that a finding that DNA is unpatentable subject matter will invalidate patents to important chemical compounds such as the anticancer drug Taxol (paclitaxel) and leave “little to nothing” of the United States biotechnology industry). The conclusions reached in this opinion concerning the subject matter patentability of isolated DNA, however, are based on the unique properties of DNA that distinguish it from all other chemicals and biological molecules found in nature. As a result, Myriad's predictions for the future of the U.S. biotechnology industry are unfounded.

52 To the extent a claim reads on unpatentable subject matter, the entire claim must be deemed invalid. See Titanium Metals Corp. of Am. v. Banner, 778 F.2d 775, 782 (Fed. Cir. 1985).

53 Native DNA is sometimes methylated, but that methylation is preserved when the DNA is extracted and purified. Nussbaum Decl. ¶ 20. Since the claimed “isolated DNA” includes DNA extracted and purified from the body, methylation of DNA in the body does not distinguish native DNA from the claimed DNA. In addition, DNA in the body also exists in a non-methylated state, just as the synthesized DNA claimed in the patents would not be methylated. More importantly, while methylation affects the transcription of a gene in the body, it does not have any impact on the genetic information contained within the DNA. Indeed, DNA is demethylated and remethylated as it passes from the germline of one generation to the next. Nussbaum Decl. ¶ 28.

54 To be precise, the isolated single-stranded DNA molecule utilized as a primer or probe has the identical sequence as the complementary DNA strand to the DNA strand containing the target DNA sequence. The description in the text is meant to serve as a short-hand description of this relationship.

55 55 The same reasoning applies with respect to the use of isolated DNA as a probe. See Kay Decl. ¶¶ 135-36.

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