Claims for Patent: 7,981,609

Summary for Patent: 7,981,609

Title:	Methods for identifying and using SNP panels
Abstract:	Described are methods for identifying single nucleotide polymorphism (SNPs) that are useful for analyzing genetic samples, and for using said SNPs to determine genetic identity of samples.
Inventor(s):	Rubin; Mark A. (Cambridge, MA), Demichelis; Francesca (Cambridge, MA), Garraway; Levi A. (Newton, MA), Sellers; William R. (Brookline, MA)
Assignee:	The Brigham and Women\'s Hospital, Inc. (Boston, MA) Dana-Farber Cancer Institute, Inc. (Boston, MA)
Application Number:	11/811,149
Patent Litigation and PTAB cases:	See patent lawsuits and PTAB cases for patent 7,981,609
Patent Claims:	1. A method for identifying at least one single nucleotide polymorphism (SNP) useful for analyzing a genetic sample, the method comprising: (a) obtaining a population of selected genetic samples; (b) separating the population of genetic samples into a first subpopulation of genetic samples comprising a portion of the genetic samples and a second subpopulation comprising the remaining genetic samples; (c) analyzing the genotype at each SNP of a plurality of SNPs for each genetic sample in the first subpopulation of genetic samples to determine for each SNP analyzed: i) N.sub.aa, the number of genetic samples in which the SNP is homozygous for a first allele, ii) N.sub.bb, the number of genetic samples in which the SNP is homozygous for a second allele, and iii) N.sub.ab, the number of genetic samples in which the SNP is heterozygous for a first and a second allele; (d) for the genetic samples in the first subpopulation, ranking each SNP of the plurality of SNPs by how nearly the ratio N.sub.aa:N.sub.bb:N.sub.ab matches the ratio 1:1:2 to provide a ranking of SNPs; (e) analyzing the genotype at each SNP in the plurality of SNPs for each genetic sample in the second subpopulation of genetic samples to determine for each SNP: i) N'.sub.aa, the number of genetic samples in which the SNP is homozygous for a first allele, ii) N'.sub.bb, the number of genetic samples in which the SNP is homozygous for a second allele, and iii) N'.sub.ab, the number of genetic samples in which the SNP is heterozygous for a first and a second allele; (f) for the genetic samples in the second subpopulation, determining how closely the ratio N'.sub.aa:N'.sub.bb:N'.sub.ab matches the ratio 1:1:2 to provide a score for each SNP; (g) designating a SNP that both ranks above a pre-determined cut-off in the ranking when analyzed in the first subpopulation and has a score above a pre-determined score when analyzed in the second subpopulation as a candidate SNP; (h) repeating steps (b)-(g) at least two times, each time designating one or more SNPs as a candidate SNP to generate at least two groups of candidate SNPs; and (i) identifying a SNP designated as a candidate SNP at least two times as a SNP useful for analyzing a genetic sample. 2. The method of claim 1, wherein steps (b)-(g) are repeated at least 10 times and wherein a SNP designated as a candidate SNP at least 4 times is identified as a SNP useful for analyzing genetic samples. 3. The method of claim 1, wherein steps (b)-(g) are repeated at least 100 times and wherein a SNP designated as a candidate SNP at least 40 times is identified as a SNP useful for analyzing genetic samples. 4. The method of claim 1, wherein steps (b)-(g) are repeated at least 500 times and wherein a SNP designated as a candidate SNP at least 200 times is identified as a SNP useful for analyzing genetic samples. 5. The method of claim 1, wherein the method is used to identify at least 10 SNPs useful for distinguishing genetic samples. 6. A method for identifying a panel of SNPs useful for analyzing a genetic sample, the method comprising: (a) using the method of claim 1 to identify a plurality of SNPs useful for analyzing a genetic sample; (b) excluding at least one of the plurality of SNPs; and (c) identifying the remaining SNPs as a panel of SNPs useful for analyzing a genetic sample. 7. The method of claim 6, wherein at least one SNP located in an intron is excluded. 8. The method of claim 6, wherein at least one SNP located in a region subject to loss of heterozygosity is excluded. 9. The method of claim 6, wherein at least one SNP having a heterozygosity rate that differs more than 2% between Caucasian and Asian populations is excluded. 10. The method of claim 6, wherein at least one SNP having a heterozygosity rate that differs more than 2% between Caucasian and African American populations is excluded. 11. The method of claim 6, wherein at least one SNP having a heterozygosity rate that differs more than 2% between Asian and African American populations is excluded. 12. A method for analyzing a genetic sample, the method comprising: (a) obtaining a first genetic sample; (b) analyzing the genotype of the genetic sample at each SNP in a set of SNPs identified as useful for analyzing genetic samples, wherein each SNP in the set of SNPs was identified using the method of claim 1; and (b) comparing the genotype of the genetic sample at each SNP in the set of SNPs to the genotype of a second genetic sample at each SNP in the set of SNPs to determine if the first and second genetic samples are the same or different.

Details for Patent 7,981,609

Applicant	Tradename	Biologic Ingredient	Dosage Form	BLA	Approval Date	Patent No.	Expiredate
Merck Sharp & Dohme Corp.	INTRON A	interferon alfa-2b	For Injection	103132	06/04/1986		2026-06-09
Merck Sharp & Dohme Corp.	INTRON A	interferon alfa-2b	For Injection	103132			2026-06-09
Merck Sharp & Dohme Corp.	INTRON A	interferon alfa-2b	Injection	103132			2026-06-09