Methods for high throughput genotyping

Details Methods for high throughput genotyping Methods for high throughput genotyping

2011-08-02

2011-08-02

Brusca, John S (Department: 1631)

Data processing: measuring, calibrating, or testing

Measurement system in a specific environment

Biological or biochemical

C435S006120, C700S001000

Reexamination Certificate

active

07991564

ABSTRACT:
Methods for genotyping polymorphisms using allele specific probes are disclosed. A training set is used to generate a model for each polymorphism to be interrogated. The training set is used to obtain an estimate of the asymmetry between an intensity measurement for a first allele and an intensity measurement for a second allele of the same polymorphism. The intensity measurement obtained for a test sample is adjusted using the estimate of asymmetry prior to using the intensity measurements to make a genotyping call. In preferred embodiments the adjustment is applied to polymorphisms that have a likelihood of being heterozygous that is above a specified threshold.

REFERENCES:
patent: 5143854 (1992-09-01), Pirrung et al.
patent: 5242974 (1993-09-01), Holmes
patent: 5252743 (1993-10-01), Barrett et al.
patent: 5324633 (1994-06-01), Fodor et al.
patent: 5384261 (1995-01-01), Winkler et al.
patent: 5405783 (1995-04-01), Pirrung et al.
patent: 5412087 (1995-05-01), McGall et al.
patent: 5424186 (1995-06-01), Fodor et al.
patent: 5451683 (1995-09-01), Barrett et al.
patent: 5482867 (1996-01-01), Barrett et al.
patent: 5491074 (1996-02-01), Aldwin et al.
patent: 5527681 (1996-06-01), Holmes
patent: 5541061 (1996-07-01), Fodor et al.
patent: 5547839 (1996-08-01), Dower et al.
patent: 5550215 (1996-08-01), Holmes
patent: 5571639 (1996-11-01), Hubbell et al.
patent: 5578832 (1996-11-01), Trulson et al.
patent: 5593839 (1997-01-01), Hubbell et al.
patent: 5624711 (1997-04-01), Sundberg et al.
patent: 5631734 (1997-05-01), Stern et al.
patent: 5795716 (1998-08-01), Chee
patent: 5800992 (1998-09-01), Fodor et al.
patent: 5831070 (1998-11-01), Pease et al.
patent: 5834758 (1998-11-01), Trulson et al.
patent: 5837832 (1998-11-01), Chee et al.
patent: 5856092 (1999-01-01), Dale et al.
patent: 5856101 (1999-01-01), Hubbell et al.
patent: 5858659 (1999-01-01), Sapolsky et al.
patent: 5871928 (1999-02-01), Fodor et al.
patent: 5889165 (1999-03-01), Fodor et al.
patent: 5902723 (1999-05-01), Dower et al.
patent: 5936324 (1999-08-01), Montagu
patent: 5959098 (1999-09-01), Goldberg et al.
patent: 5968740 (1999-10-01), Fodor et al.
patent: 5974164 (1999-10-01), Chee
patent: 5981185 (1999-11-01), Matson et al.
patent: 5981956 (1999-11-01), Stern
patent: 6013449 (2000-01-01), Hacia et al.
patent: 6020135 (2000-02-01), Levine et al.
patent: 6025601 (2000-02-01), Trulson et al.
patent: 6033860 (2000-03-01), Lockhart et al.
patent: 6040138 (2000-03-01), Lockhart et al.
patent: 6040193 (2000-03-01), Winkler et al.
patent: 6045996 (2000-04-01), Cronin et al.
patent: 6090555 (2000-07-01), Fiekowsky et al.
patent: 6136269 (2000-10-01), Winkler et al.
patent: 6141096 (2000-10-01), Stern et al.
patent: 6147205 (2000-11-01), McGall et al.
patent: 6177248 (2001-01-01), Oliner et al.
patent: 6185030 (2001-02-01), Overbeck
patent: 6197506 (2001-03-01), Fodor et al.
patent: 6201639 (2001-03-01), Overbeck
patent: 6218803 (2001-04-01), Montagu et al.
patent: 6225625 (2001-05-01), Pirrung et al.
patent: 6262216 (2001-07-01), McGall
patent: 6269846 (2001-08-01), Overbeck et al.
patent: 6284460 (2001-09-01), Fodor et al.
patent: 6300063 (2001-10-01), Lipshutz et al.
patent: 6309822 (2001-10-01), Fodor et al.
patent: 6310189 (2001-10-01), Fodor et al.
patent: 6333179 (2001-12-01), Matsuzaki et al.
patent: 6361947 (2002-03-01), Dong et al.
patent: 6368799 (2002-04-01), Chee
patent: 6428752 (2002-08-01), Montagu
patent: 6872529 (2005-03-01), Su
patent: 2005/0123971 (2005-06-01), Di et al.
patent: 2005/0164270 (2005-07-01), Balaban et al.
patent: 2005/0208555 (2005-09-01), Raimond et al.
patent: 2005/0222777 (2005-10-01), Kaushikkar
patent: 2005/0227244 (2005-10-01), Matsuzaki et al.
patent: 2005/0250151 (2005-11-01), Mei et al.
patent: 2005/0287575 (2005-12-01), Di et al.
patent: WO 99/36760 (1999-07-01), None
patent: WO 99/47964 (1999-09-01), None
patent: WO 00/58516 (2000-10-01), None
patent: WO01/58593 (2001-08-01), None
Hua et al. SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays Bioinformatics vol. 23, pp. 57-63 (2006).
U.S. Appl. No. 09/536,841, filed Mar. 27, 2000, Fan et al.
U.S. Appl. No. 60/319,253, filed May 17, 2002, Dong et al.
U.S. Appl. No. 60/364,731, filed Mar. 15, 2002, Weiner et al.
U.S. Appl. No. 60/744,002, filed Mar. 30, 2006, Cawley et al.
AFFYMETRIX, BRLMM: An Improved Genotype Calling Method for the Genechip Human Mapping 500K Array set, revision date Apr. 14, 2006.
Di et al, Bioinformatics 21:1958 21:1958-1963 (2005).
Fan et al, Cold Spring Harb. Symp. Quant. Biol. 68:69-78 (2003).
Fan et al, Genome Research 10:853-60 (2000).
Gunderson et al, Nat. Genet. 37, 549-554 (2005).
Hardenbol et al, Nature Biotech, 21:673-678 (2003).
Lovmar et al, Quantitative evaluation by minisequencing and microarrays reveals accurate multiplexed SNP genotyping if whole genome amplified DNA, Nucleic Acids Research vol. 31, paper e129, pp. 1-9 (2003).
Pastinen et al, Genome Research 10:1031 (2000).
Rabbee and Speed, Bioinformatics 22:7-12 (2006).
Synaven, Nat. Genet. Suppl: S5-10(2005).

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