Automated SNP Genotype Clustering Algorithm to Improve Data Completeness in High-Throughput SNP Genotyping Datasets from Custom Arrays

Genomics, Proteomics and Bioinformatics

Volumn 5, Issue 3-4, 2007, Pages 256-259

  Smith, Edward M ^a   Littrell, Jack ^a   Olivier, Michael ^a  

^a MEDICAL COLLEGE OF WISCONSIN   (United States)

Author keywords

algorithm; clustering; SNP genotyping

Indexed keywords

ALGORITHM; ARTICLE; CHROMOSOME ANALYSIS; CLUSTER ANALYSIS; GENOTYPE; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; CLUSTER ANALYSIS; DATABASES, NUCLEIC ACID; GENOTYPE; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 38949093567     PISSN: 16720229     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1672-0229(08)60014-5     Document Type: Article

References (13)

1. Liu W.M., et al. Algorithms for large-scale genotyping microarrays. Bioinformatics 19 (2003) 2397-2403
2. Huentelman M.J., et al. SNiPer: improved SNP genotype calling for Affymetrix 10K GeneChip microarray data. BMC Genomics 6 (2005) 149
3. Lamy P., et al. Genotyping and annotation of Affymetrix SNP arrays. Nucleic Acids Res. 34 (2006) e100
4. Hua J., et al. SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays. Bioinformatics 23 (2007) 57-63
5. Rabbee N., and Speed T.P. A genotype calling algorithm for Affymetrix SNP arrays. Bioinformatics 22 (2006) 7-12
6. Xiao Y., et al. A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microar- rays. Bioinformatics 23 (2007) 1459-1467
7. Hardenbol P., et al. Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat. Biotechnol. 21 (2003) 673-678
8. Hardenbol P., et al. Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay. Genome Res. 15 (2005) 269-275
9. Kissebah A.H., et al. Quantitative trait loci on chromosomes 3 and 17 influence phenotypes of the metabolic syndrome. Proc. Natl. Acad. Sci. USA 97 (2000) 14478-14483
10. Sonnenberg G.E., et al. Genetic determinants of obesity-related lipid traits. J. Lipid Res. 45 (2004) 610-615
11. Smith E.M., et al. Comparison of linkage disequilibrium patterns between the HapMap CEPH samples and a family-based cohort of Northern European descent. Genomics 88 (2006) 407-414
12. Olivier M., et al. High-throughput genotyping of single nucleotide polymorphisms using new biplex invader technology. Nucleic Acids Res. 30 (2002) e53
13. McPeek M.S., et al. Best linear unbiased allele- frequency estimation in complex pedigrees. Biometrics 60 (2004) 359-367