A genotype calling algorithm for the Illumina BeadArray platform

Bioinformatics

Volumn 23, Issue 20, 2007, Pages 2741-2746

  Teo, Yik Y ^a,b   Inouye, Michael ^b   Small, Kerrin S ^a,b   Gwilliam, Rhian ^b   Deloukas, Panagiotis ^b   Kwiatkowski, Dominic P ^a,b   Clark, Taane G ^a,b  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BIOINFORMATICS; COMPUTER LANGUAGE; COMPUTER PROGRAM; CONTROLLED STUDY; DNA HYBRIDIZATION; DNA MICROARRAY; GENETIC ALGORITHM; GENOTYPE; MATHEMATICAL MODEL; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 35748941336     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm443     Document Type: Article

References (17)

1. Affymetrix Inc (2006) BRLMM: An improved genotype calling method for the GenChip Human Mapping 500K Array Set. http://www.affymetrix.com/support/ technical/whitepapers/brlmm_whitepaper.pdf
2. Bolstad,B.M. et al. (2003) A comparison of normalization methods for high density of oligonucleotide array data based on variance and bias. Bioinformatics, 19, 185-193.
3. Carvalho,B. et al. (2007) Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics 8, 485-499.
4. Di,X. et al. (2005) Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays. Bioinformatics, 21, 1958-1963.
5. Gudmundsson,J. et al. (2007) Genome-wide association study identifies a second prostate cancer susceptibility variantat 8q24. Nat. Genet., 39, 631-637.
6. Gunderson,K.L. et al. (2006) Whole-genome genotyping of haplotype tag single nucleotide polymorphisms. Pharmacogenomics, 7, 641-648.
7. Kermani,B.G (2005) Artificial intelligence and global normalization methods for genotyping. US Patent 20060224529.
8. Moorhead,M. et al. (2006) Optimal genotype determination in highly multiplexed SNP data. Eur. J. Hum. Genet., 14, 207-215.
9. Plagnol,V. et al. (2007) A method to address differential bias in genotyping in large-scale association studies. PLoS Genet., 3 e74.
10. Rabbee,N. and Speed,T.P (2006) A genotype calling algorithm for Affymetrix SNP arrays. Bioinformatics, 1, 7-12.
11. Rioux,J.D. et al. (2007) Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy n disease pathogenesis. Nat. Genet., 39, 596-604.
12. Saxena,R. et al. (2007) Genome-wide association analysis identifies loci for Type 2 diabetes and triglyceride levels. Science 316, 1341-1336.
13. Scott,L.J. et al. (2007) A genome-wide association study of Type 2 diabetes in Finns detects multiple susceptibility variants. Science 316, 1341-1345.
14. Steemers,F.J. et al. (2007) Whole genome, genotyping technologies on the BeadArray platform. Biotechnol. J., 2, 41-49.
15. The Wellcome, Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of-seven common diseases and 3000 shared controls. Nature, 447, 661-678.
16. Xiao,Y. et al. (2007) A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays. Bioinformatics, 27, 1459-1467.
17. Yeager,M. et al. (2007) Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat. Genet., 39 645-649.