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Ariosa Diagnostics v. Verinata Health, Inc.

United States Court of Appeals, Federal Circuit

November 16, 2015

ARIOSA DIAGNOSTICS, Appellant
v.
VERINATA HEALTH, INC., Appellee

Appeals from the United States Patent and Trademark Office, Patent Trial and Appeal Board in Nos. IPR2013-00276, IPR2013-00277.

MARK A. LEMLEY, Durie Tangri LLP, San Francisco, CA, argued for appellant. Also represented by DARALYN JEANNINE DURIE, ALEXANDRA HELEN MOSS; GREG GARDELLA, Oblon, Spivak, McClelland, Maier & Neustadt, LLP, Alexandria VA.

EDWARD R. REINES, Weil, Gotshal & Manges LLP, Redwood Shores, CA, argued for appellee. Also represented by DEREK C. WALTER, ANANT N. PRADHAN; MICHAEL T. ROSATO, Wilson, Sonsini, Goodrich & Rosati, PC, Seattle, WA.

Before PROST, Chief Judge, WALLACH, and TARANTO, Circuit Judges.

OPINION

Taranto, Circuit Judge.

Verinata Health, Inc. owns U.S. Patent No. 8,318,430, which describes and claims methods of noninvasive prenatal testing for the presence of fetal chromosomal abnormalities. In particular, the methods may identify " aneuploidy," i.e., the presence of an abnormal number of copies of a chromosome--say, three rather than the normal two for chromosome 21, an abnormality that characterizes Down Syndrome. The methods involve obtaining blood samples from several pregnant women; isolating from the samples genomic DNA molecules not contained in cells; choosing particular DNA sequences--some on a chromosome of concern, some not; indexing by maternal source the chromosomes or regions containing those sequences; amplifying (making many copies of) the group of chromosomes or regions; performing massively parallel sequencing on the resulting pool; using the indexing to count, for a particular maternal source, the number of sequences from chromosomes of concern versus the number from reference chromosomes or regions; and determining based on the comparison whether there are fetal chromosomal abnormalities, such as an extra copy of a chromosome of concern.

Ariosa Diagnostics, Inc. petitioned the Patent Trial and Appeal Board for inter partes review of claims 1-18 and, in a separate petition, claims 19-30, challenging the claims for obviousness under 35 U.S.C. § 103. The Board concluded that Ariosa had not met its burden of proving that claims 1-18 and 19-30 would have been obvious. Ariosa Diagnostics v. Verinata Health, Inc., IPR2013-276, 2014 WL 5454541 (PTAB Oct. 23, 2014); Ariosa Diagnostics v. Verinata Health, Inc., IPR2013-277, 2014 WL 5454542 (PTAB Oct. 23, 2014). We vacate the decisions and remand for further consideration because of one matter that the Board's language suggests it did not sufficiently consider.[1]

Background

Verinata and Ariosa are competitors in the relatively new field of noninvasive prenatal diagnostics, which includes testing for fetal chromosomal abnormalities. For many years, prenatal chromosomal testing required invasive, high-risk procedures, such as amniocentesis. Noninvasive tests, based on the combination of ultrasound observation and measurement of biochemical markers in blood samples drawn from the pregnant woman, suffered from low accuracy--in a matter where accuracy is very important. The 1997 discovery of cellfree fetal DNA circulating in maternal blood suggested the possibility of superior noninvasive tests, but turning the possibility into a reality presented significant challenges.

One challenge involved the proportion of the total amount of cell-free DNA in maternal blood that came from the fetus. That proportion is typically less than 10 percent. Some scientists seeking to use the 1997 discovery focused on distinguishing fetal DNA from maternal DNA in a blood sample. By separating fetal from maternal DNA, or determining the particular fetal/maternal ratio of cell-free DNA, certain counting methods could try to discern which fetus-specific chromosomes had an abnormal number of copies.

Verinata's '430 patent, with a priority date of January 2010, does not rely on separating fetal from maternal cellfree DNA or, even, determining the fetal/maternal ratio of cell-free DNA. '430 patent, col. 5, lines 63-65. Rather, the '430 patent describes a counting technique applied to an overall pool of DNA segments, selected for comparing a chromosome of concern (say, chromosome 21) with a reference chromosome (or chromosomal region), making the comparison by identifying the respective DNA sequences. Fetal aneuploidy (in the case of, for example, three versus two copies of a chromosome) may be determined by comparing the number of sequences generated from the chromosome of concern with the number of sequences generated from a reference chromosome--counting copies from all cell-free DNA, whether fetal or maternal. Id., col. 13, lines 59-64. But because cell-free fetal DNA is such a small proportion of total cell-free DNA, the elevation in the target-sequence count will be small in an overall sample; and for the numerical elevation to be significant and sufficiently reliable for prenatal testing, a large sample must be created and sequenced. The '430 patent describes doing so by amplifying the target and reference sequences, pooling samples from several women and indexing them for later identification, and using massively parallel sequencing. '430 patent, col. 1, lines 41-48; id., col. 6, lines 20-27; id., col. 12, lines 56-63.

Claim 1 of the patent states:

1. A method for determining a presence or absence of a fetal aneuploidy in a fetus for each of a plurality of maternal blood samples obtained from a plurality of different pregnant women, said maternal blood samples comprising fetal and maternal cell-free genomic DNA, said method comprising:
(a) obtaining a fetal and maternal cell-free genomic DNA sample from each of the plurality of maternal blood samples;
(b) selectively enriching a plurality of non-random polynucleotide sequences of each fetal and maternal cell-free genomic DNA sample of (a) to generate a library derived from each fetal and maternal cell-free genomic DNA sample of enriched and indexed fetal and maternal non-random polynucleotide sequences, wherein each library of enriched and indexed fetal and maternal non-random polynucleotide sequences includes an indexing nucleotide sequence which identifies a maternal blood sample of the plurality of maternal blood samples,
wherein said plurality of non-random polynucleotide sequences comprises at least 100 different non-random polynucleotide sequences selected from a first chromosome tested for being aneuploid and at least 100 different non-random polynucleotide sequences selected from a reference chromosome, wherein the first chromosome tested for being aneuploid and the reference chromosome are different, and wherein each of said plurality of non-random polynucleotide sequences is from 10 to 1000 nucleotide bases in length,
(c) pooling the libraries generated in (b) to produce a pool of enriched and indexed fetal and maternal ...

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