A high-performance computing toolset for relatedness and principal component analysis of SNP data

Bioinformatics

Volumn 28, Issue 24, 2012, Pages 3326-3328

  Zheng, Xiuwen ^a   Levine, David ^a   Shen, Jess ^a   Gogarten, Stephanie M ^a   Laurie, Cathy ^a   Weir, Bruce S ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER PROGRAM; GENETIC ASSOCIATION; HUMAN; PRINCIPAL COMPONENT ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; GENOME-WIDE ASSOCIATION STUDY; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS; SOFTWARE;

EID: 84870820953     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts606     Document Type: Article

References (12)

1. 1000 Genomes Project Consortium. (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061-1073.
2. Cardon, L.R. and Palmer, L.J. (2003) Population stratification and spurious allelic association. Lancet, 361, 598-604.
3. Choi, Y. et al. (2009) Case-control association testing in the presence of unknown relationships. Genet Epidemiol., 33, 668-678.
4. Cornelis, M.C. et al. (2010) The gene, environment association studies consortium (GENEVA): maximizing the knowledge obtained from gwas by collaboration across studies of multiple conditions. Genet Epidemiol., 34, 364-372.
5. Danecek, P. et al. (2011) The variant call format and vcftools. Bioinformatics, 27, 2156-2158.
6. Gogarten, S.M. et al. (2012) GWASTools: an R/Bioconductor package for quality control and analysis of genome-wide association studies. Bioinformatics [Epub ahead of print, doi:10.1093/bioinformatics/bts610, October 10, 2012].
7. Laurie, C.C. et al. (2010) Quality control and quality assurance in genotypic data for genome-wide association studies. Genet Epidemiol., 34, 591-602.
8. Milligan, B.G. (2003) Maximum-likelihood estimation of relatedness. Genetics, 163, 1153-1167.
9. Price, A.L. et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet., 38, 904-909.
10. Price, A.L. et al. (2010) New approaches to population stratification in genome-wide association studies. Nat. Rev. Genet., 11, 459-463.
11. Purcell, S. et al. (2007) Plink: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet., 81, 559-575.
12. Zhu, X. et al. (2008) A unified association analysis approach for family and unrelated samples correcting for stratification. Am. J. Hum. Genet., 82, 352-365.