MixupMapper: Correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects

Bioinformatics

Volumn 27, Issue 15, 2011, Pages 2104-2111

  Westra, Harm Jan ^a   Jansen, Ritsert C ^b   Fehrmann, Rudolf S N ^a   te Meerman, Gerard J ^a   van Heel, David ^c   Wijmenga, Cisca ^a   Franke, Lude ^a,c  

^a UNIVERSITY MEDICAL CENTER GRONINGEN   (Netherlands)

^b UNIVERSITY OF GRONINGEN   (Netherlands)

^c QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; GENE EXPRESSION PROFILING; GENETIC ASSOCIATION; GENOMICS; GENOTYPE; HUMAN; LABORATORY DIAGNOSIS; METHODOLOGY; PHENOTYPE; QUANTITATIVE TRAIT LOCUS; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; GENE EXPRESSION PROFILING; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; GENOTYPE; HUMANS; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; SENSITIVITY AND SPECIFICITY; SPECIMEN HANDLING;

EID: 79960426031     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr323     Document Type: Article

References (29)

1. Barrett,J.C. et al. (2009) Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nat. Genet., 41, 703-707.
2. Breitling,R. et al. (2008) Genetical genomics: spotlight on QTL hotspots PLoS Genet., 4, e1000232.
3. Benovoy,D. et al. (2008) Effect of polymorphisms within probe-target sequences on olignonucleotide microarray experiments. Nucleic Acids Res., 36, 4417-4423.
4. Bullaughey, K. et al. (2009) Expression quantitative trait loci detected in cell lines are often present in primary tissues, Hum Mol Genet, 18, 4296-4303.
5. Buyske,S. et al. (2009) When a case is not a case: effects of phenotype misclassification on power and sample size requirements for the transmission disequilibrium test with affected child trios. Hum. Hered., 67, 287-292.
6. Choy,E. et al. (2008) Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. PLoS Genet., 4, e1000287.
7. Dubois,P.C. et al. (2010) Multiple common variants for celiac disease influencing immune gene expression. Nat. Genet., 42, 295-302.
8. Franke,A. et al. (2010) Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat. Genet., 42, 1118-1125.
9. Gordon,D. and Finch,S.J. (2004) Consequences of error. In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley & Sons, Ltd.
10. Heap,G.A. et al. (2009) Complex nature of SNP genotype effects on gene expression in primary human leucocytes. BMC Med Genomics, 2, 1.
11. Heinzen,E.L. et al. (2008) Tissue-specific genetic control of splicing: implications for the study of complex traits. PLoS Biol, 6, e1.
12. Hindorff,L.A. et al. (2009) Potential etiologic and functional implications of genomewide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA, 106, 9362-9367.
13. Ho,L. and Lange,E. (2010) Using public control genotype data to increase power and decrease cost of case-control genetic association studies. Hum. Genet., 128, 597-608.
14. Jansen,R.C. and Nap,J.P. (2001) Genetical genomics: the added value from segregation. Trends Genet., 17, 388-391.
15. Lango Allen,H. et al. (2010) Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature, 467, 832-838.
16. Leek,J.T. and Storey,J.D. (2007) Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet., 3, 1724-1735.
17. Manolio,T.A. et al. (2009) Finding the missing heritability of complex diseases. Nature, 461, 747-753.
18. McCarthy,M.I. and Hirschhorn,J.N. (2008) Genome-wide association studies: potential next steps on a genetic journey. Hum. Mol. Genet., 17, R156-R165.
19. Park,J.H. et al. (2010) Estimation of effect size distribution from genome-wide association studies and implications for future discoveries. Nat. Genet., 42, 570-575.
20. Samuels,D.C. et al. (2009) Detecting new neurodegenerative disease genes: does phenotype accuracy limit the horizon? Trends Genet., 25, 486-488.
21. Speliotes,E.K. et al. (2010) Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat. Genet., 42, 937-948.
22. Stranger,B.E. et al. (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science, 315, 848-853.
23. Sulem,P. et al. (2007) Genetic determinants of hair, eye and skin pigmentation in Europeans. Nat. Genet., 39, 1443-1452.
24. Teslovich,T.M. et al. (2010) Biological, clinical and population relevance of 95 loci for blood lipids. Nature, 466, 707-713.
25. Voight,B.F. et al. (2010) Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat. Genet., 42, 579-589.
26. Webster,J.A. et al. (2009) Genetic control of human brain transcript expression in Alzheimer disease. Am. J. Hum. Genet., 84, 445-458.
27. Yip,S.P. (2002) Sequence variation at the human ABO locus. Ann. Hum. Genet., 66, 1-27.
28. Zhang,W. et al. (2009) Identification of common genetic variants that account for transcript isoform variation between human populations. Hum. Genet., 125, 81-93.
29. Zheng,G. and Tian,X. (2005) The impact of diagnostic error on testing genetic association in case-control studies. Stat. Med., 24, 869-882.