Ex Parte Sproles et al

Patent Trial and Appeal BoardApr 29, 2013

11937896 (P.T.A.B. Apr. 29, 2013)

UNITED STATES PATENT AND TRADEMARK OFFICE UNITED STATES DEPARTMENT OF COMMERCE United States Patent and Trademark Office Address: COMMISSIONER FOR PATENTS P.O. Box 1450 Alexandria, Virginia 22313-1450 www.uspto.gov APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO. 11/937,896 11/09/2007 Dean I. Sproles 78372/2010 2699 7590 04/29/2013 Iverson Genetic Diagnostics, Inc. c/o Dean Sproles 19805 North Creek Parkway, Suite 200 Bothell, WA 98011 EXAMINER BRUSCA, JOHN S ART UNIT PAPER NUMBER 1631 MAIL DATE DELIVERY MODE 04/29/2013 PAPER Please find below and/or attached an Office communication concerning this application or proceeding. The time period for reply, if any, is set in the attached communication. PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE __________ BEFORE THE PATENT TRIAL AND APPEAL BOARD __________ Ex parte DEAN I. SPROLES and ROY L. SWANK __________ Appeal 2013-000615 Application 11/937,896 Technology Center 1600 __________ Before JACQUELINE WRIGHT BONILLA, ULRIKE W. JENKS, and SHERIDAN K. SNEDDEN, Administrative Patent Judges. SNEDDEN, Administrative Patent Judge. DECISION ON APPEAL This is an appeal under 35 U.S.C. § 134 involving claims to a method for assessing a genetic expression of multiple sclerosis. The Examiner has rejected the claims as obvious. We have jurisdiction under 35 U.S.C. § 6(b). We affirm. Appeal 2013-000615 Application 11/937,896 2 STATEMENT OF THE CASE Appellants’ invention relates to “to transcriptional detection of single nucleotide polymorphisms (SNP) and insertion/deletion (I/D) genetic polymorphisms through a proportional analysis of RNA sequences detected through fluorescence hybridization on a custom manufactured microarray gene expression platform” (Specification 10, ¶ [0029]). Claims 21-36 are on appeal. Claim 21, the only independent claim on appeal, is representative and reads as follows (emphasis added): 21. A method for assessing a genetic expression of multiple sclerosis, comprising: a) obtaining at least one sample of genetic material from each of a plurality of people exhibiting a potential for developing multiple sclerosis; b) isolating strands of genetic sequences from each sample from a); c) for each sample from each person, separating at least one strand of genetic sequence from the strands from b), wherein said at least one strand of genetic sequence is identified by a specific genetic sequence associated with multiple sclerosis; d) grouping said at least one strand of genetic sequence from each sample from c), wherein all strands in each group are identified by a specific genetic sequence and are grouped across each sample from each person; e) determining a first correlation between a first genetic sample and a first genetic sequence associated with multiple sclerosis and determining a second correlation between a second genetic sample and a second genetic sequence associated with multiple sclerosis; f) determining a third correlation between the first and second correlations of e) g) collecting data about the first, second and third correlations into a client computer; and h) transmitting the data from g) to a server computer. Appeal 2013-000615 Application 11/937,896 3 The claims stand rejected as follows: I. Claims 21-25 and 27-36 under 35 U.S.C. § 103(a) as being unpatentable over the combination of Gödde, 1 Ardlie, 2 and Huff 3 as evidenced by Wang. 4 II. Claim 26 under 35 U.S.C. § 103(a) as being unpatentable over the combination of Gödde, Ardlie, Huff, and Leyva 5 as evidenced by Wang. The same issue is dispositive for each rejection. Issue The Examiner finds that “Göode et al. shows correlations between SNPs and multiple sclerosis, and the measurement of the SNPs in genetic samples, and further shows that three SNPs are likely to be inherited together as a haplotype, which is a correlation of SNPs that correlate with multiple sclerosis” (Ans. 9). The Examiner relies on Wang “to show that the hybridization process of Göode [sic] et al. inherently performs separation of 1 Gödde et al., Association of the HLA region with multiple sclerosis as confirmed by a genome screen using > 10,000 SNPs on DNA chips, 83 J. MOL. MED. 486-494 (2005). 2 Ardlie et al., Patterns of Linkage Disequilibrium in the Human Genome, 3 NATURE REVIEWS GENETICS 299-309 (2002). 3 Huff, US 6,760,731 B2, issued Jul. 6, 2004. 4 Wang et al., Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymorphisms in the Human Genome, 280 SCIENCE 1077 -1082 (1998). 5 Leyva et al., IFNAR1 and IFNAR2 polymorphisms confer susceptibility to multiple sclerosis but not to interferon-beta treatment response, 163 JOURNAL OF NEUROIMMUNOLOGY 165-171 (2005). Appeal 2013-000615 Application 11/937,896 4 strands” as required by claim 21 (id. at 8-9). That is, the “[h]ybridization of strands to different regions of a microarray by virtue of the presence of different probes at each microarray region results in separation and grouping of strands in the sample between the different probes on the microarray according to their sequence” (id. at 9). The issue presented is: Does the evidence of record support the Examiner’s finding that the combined prior art renders obvious a genetic assessment method involving separating and grouping strands of genetic sequences according to a specific genetic sequence as recited in claim 21? Findings of Fact The following findings of fact (“FF”) are supported by a preponderance of the evidence of record. FF1. Gödde discloses the results of a multiple sclerosis (MS) genome screen where “[t]wo hundred individual DNA (pop1) were screened, each using 11,555 SNP markers on DNA chips” (Gödde 489, right column). FF2. “More than 500 SNPs revealed significant differences between cases and controls before Bonferroni correction” (id. at Abstract). FF3. “Highly significant association was evidenced for loci rs23951 66, rs2213584, rs2395182 and rs2227139 located in the immediate vicinity of the HLA-DRA gene” (id. at 491, left column). Principles of Law “[T]he examiner bears the initial burden, on review of the prior art or on any other ground, of presenting a prima facie case of unpatentability. If Appeal 2013-000615 Application 11/937,896 5 that burden is met, the burden of coming forward with evidence or argument shifts to the applicant.” In re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992). “The combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 416 (2007). Analysis Interpretation of “genetic sequence” We begin with claim interpretation, since until a claim is properly interpreted, its scope cannot be compared to the prior art. The method of claim 21 recites the steps of separating and grouping genetic sequences that have been isolated from a sample (e.g., blood sample). The phrase “genetic sequence” is not defined in the Specification, however, the use of “genetic sequence” in the Specification is informative (see, e.g., Specification 14-16, ¶¶ [38]-[43]). The method disclosed in the Specification describes the isolation of genetic material based upon the specific gene sequence of a RNA strand, for example, “a gene sequence associated with a gene expression indicative of a specific MS trait” (id. at ¶ [41]). The strands are grouped, where “[s]uch grouping allows for the assimilation of data on an aggregate level based on various gene expressions” (id. at ¶ [42]) or “aggregate[ion of] information associated with each blood sample ... accomplished through the groupings of similar strands” (id. at ¶ [43]). In light of above disclosure, we find that the Specification supports a finding that the recitation of “grouping said at least one strand of genetic sequence from each sample” in claim 21 refers to the Appeal 2013-000615 Application 11/937,896 6 grouping of the information contained in the genetic sequence obtained from individual samples. Obviousness of Claim 21 over Gödde, Ardlie, Huff and Wang We are not persuaded by Appellants’ contention that the Examiner fails “to show that the prior art teaches separating and grouping strands of genetic sequences according to a specific genetic sequence as recited in claim 21” (App. Br. 18). Rather, we agree with the Examiner that the isolation of genetic material on a DNA chip for the purpose of performing a genotyping analysis of a multiple sclerosis patient population, as suggested by the cited references, inherently involves the separation and grouping of genetic sequence information as recited in claim 21. We are not persuaded by Appellants’ arguments to the contrary and we find no evidence of record that clearly distinguishes the method of the combined references from the claimed method. Appellants further contend that “[t]here is no art of record that teaches or even suggests the concept of establishing a correlation amongst correlations” (id. at 21). We first note that the Specification does not define or use the term “correlation.” Rather, Appellants’ rely on the disclosure at ¶¶ [42] – [44] of the Specification for support of this element of the claim (App. Br. 9-10). Here, we find no meaningful distinction between the method described in these passages of the Specification and the methods involved with association mapping disclosed in the cited prior art. For example, the Specification discloses that “[w]ith any number of associations in place from the groupings, statistical data from the aggregated blood samples based on associations of one blood sample with another may be Appeal 2013-000615 Application 11/937,896 7 extrapolated” (Specification at 16, ¶ [44]). In comparison, Gödde discloses a highly significant association for loci located in the immediate vicinity of the HLA-DRA gene (Gödde at 491, left column), suggesting that a marker in the HLA region may be used to determine susceptibility of MS (see, Ans. 4). Furthermore, to the extent that the claims encompass the association of multiple genetic sequences to MS or the association of a genetic sequence to other genetic sequences, Ardlie discloses the use of genetic patterns as a mapping tool. Specifically, Ardlie explains the analysis involved with linkage disequilibrium (LD) mapping, where LD is the non-random association of alleles at adjacent loci. When a particular allele at one locus is found together on the same chromosome with a specific allele at a second locus – more often than expected if the loci were segregating independently in a population – the loci are in disequilibrium. (Ardlie at 300). Ardlie suggests that “association studies offer substantially greater power for mapping common disease genes than do traditional linkage studies, and that LD can offer a shortcut to genome-wide association studies” (id. at 299). In view of these disclosures of Gödde and Ardlie, we find the prior art to teach or suggest the recited correlations, as interpreted in view of the Specification. Appellants have pointed to no evidence of record that clearly distinguishes the claimed correlations from association mapping techniques disclosed in the combined cited art. In view of the above, we find that the Examiner has set forth a prima facie case of obviousness that has not been adequately rebutted by Appellants. The Examiner has provided a rational basis for combining the Appeal 2013-000615 Application 11/937,896 8 cited references, where the proposed modifications address each disputed element of claim 21 and are supported by the evidence on this record. Conclusion of Law The preponderance of evidence on this record supports the Examiner’s finding that combined prior art renders claim 21 obvious. Claims 21-25 and 27-36 fall with claim 21. 37 C.F.R. § 41.37(c)(1)(vii). II. The Examiner rejected claim 26 under 35 U.S.C. § 103(a) as being unpatentable over the combination of Gödde, Ardlie, Huff, and Leyva as evidenced by Wang. Appellants argue that claim 26 is allowable by virtue of its dependence on claim 21 without providing additional argument or evidence (App. Br. 24). Thus, for the same reasons discussed above, Appellants arguments do not persuade us that the Examiner has erred in concluding that claim 26 is obvious over Gödde, Ardlie, Huff, Leyva and Wang. SUMMARY We affirm all rejections on appeal. AFFIRMED cdc