Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays

Bioinformatics

Volumn 21, Issue 9, 2005, Pages 1958-1963

  Di, Xiaojun ^a   Matsuzaki, Hajime ^a   Webster, Teresa A ^a   Hubbell, Earl ^a   Liu, Guoying ^a   Dong, Shoulian ^a   Bartell, Dan ^a   Huang, Jing ^a   Chiles, Richard ^a   Yang, Geoffrey ^a   Shen, Mei Mei ^a   Kulp, David ^a   Kennedy, Giulia C ^a   Mei, Rui ^a   Jones, Keith W ^a   Cawley, Simon ^a  

^a Thermo Fisher Scientific   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE;

ACCURACY; ANALYTIC METHOD; ANALYTICAL ERROR; ARTICLE; CLASSIFICATION; CONTROLLED STUDY; GENE PROBE; GENETIC ALGORITHM; GENETIC LINKAGE; GENETIC MODEL; GENETIC SCREENING; GENETIC SELECTION; GENOTYPE; HUMAN; MOLECULAR HYBRIDIZATION; MULTIGENE FAMILY; POPULATION GENETICS; PRIORITY JOURNAL; PROTEIN MICROARRAY; QUALITY CONTROL; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS;

EID: 20844440702     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti275     Document Type: Article

References (22)

1. Brooks,A.J. (1999) The essence of SNPS. Gene, 234, 177-186.
2. Cutler,D.J. et al. (2001) High-throughput variation detection and genotyping using microarrays. Genome Res., 11, 1913-1925.
3. Dong,S. et al. (2001) Flexible use of high-density oligonucleotide arrays for single-nucleotide polymorphism discovery and validation. Genome Res., 11, 1418-1424.
4. Fan,J. et al. (2000) Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. Genome Res., 10, 853-860.
5. Fodor,S.P. et al. (1991) Light-directed, spatially addressable parallel chemical synthesis. Science, 251, 767-773.
6. Fodor,S.P. et al. (1993) Multiplexed biochemical assays with biological chips. Nature, 364, 555-556.
7. HapMap (2003) The international hapmap consortium. Nature, 426, 789-796.
8. Hollander,M. and Wolfe,D. (1999) Nonparametric Statistical Methods, 2nd edn. Wiley, NY.
9. Hubbell,E., Webster,T. and Matsuzaki,H. (2004) Quickly choosing choice snps for chips. Poster presentation. In Proceedings of RECOMB 2004, San Diego, CA.
10. Kennedy,G. et al. (2003) Large scale genotyping of complex DNA. Nat. Biotechnol., 21, 1233-1237.
11. Koed,K. et al. (2005) High-density single nucleotide polymorphism array defines novel stage and location-dependent allelic imbalances in human bladder tumors. Cancer Res., 65, 34-45.
12. Liu,W.-M. et al. (2003) Algorithms for large scale genotyping microarrays. Bioinformatics, 19, 2397-2403.
13. Liu,W.-M. et al. (2001) Rank-based algorithms for analysis of microarrays. Proc. SPIE, 4266, 56-57.
14. Matsuzaki,H. et al. (2004a) Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat. Methods, 1, 109-111.
15. Matsuzaki,H. et al. (2004b) Parallel genotyping of over 10,000 SNPs using a one primer assay on a high density oligonucleotide array. Genome Res., 14, 414-425.
16. Middleton,F.A. et al. (2004) Genomewide Linkage Analysis of Bipolar Disorder by Use of a High-Density Single-Nucleotide-Polymorphism (SNP) Genotyping Assay: A Comparison with Microsatellite Marker Assays and Finding of Significant Linkage to Chromosome 6q22. Am. J. Hum. Genet., 74, 886-897.
17. Pease,A.C. et al. (1993) Light-generated oligonucleotide arrays for rapid dna sequence analysis. Proc. Natl. Acad. Sci. USA, 91, 555-556.
18. Puffenberger,E.G. et al. (2004) Mapping of sudden infant death with dysgenesis of the testes syndrome (SIDDT) by a SNP genome scan and identification of TSPYLloss of function. PNAS, 101, 11689-11694.
19. Ranch,A. et al. (2004) Molecular karyotyping using an SNP array for genomewide genotyping. J. Med. Genet., 41, 916-922.
20. Sellick,G.S. et al. (2003) A novel gene for neonatal diabetes maps to chromosome 1Op12.1-p13. Diabetes, 52, 2636-2638.
21. Shrimpton,A.E. et al. (2004) A HOX Gene Mutation in a Family with Isolated Congenital Vertical Talus and Charcot-Marie-Tooth Disease. Am. J. Hum. Genet., 75, 92-96.
22. Woods,C.G. et al. (2004) A new method for autozygosity mapping using single nucleotide polymorphisms (SNPS) and EXCLUDEAR. J. Med. Genet., 41, e101.