A simple and fast two-locus quality control test to detect false positives due to batch effects in genome-wide association studies
Article first published online: 22 NOV 2010
© 2010 Wiley-Liss, Inc.
Volume 34, Issue 8, pages 854–862, December 2010
How to Cite
Lee, S. H., Nyholt, D. R., Macgregor, S., Henders, A. K., Zondervan, K. T., Montgomery, G. W. and Visscher, P. M. (2010), A simple and fast two-locus quality control test to detect false positives due to batch effects in genome-wide association studies. Genet. Epidemiol., 34: 854–862. doi: 10.1002/gepi.20541
- Issue published online: 22 NOV 2010
- Article first published online: 22 NOV 2010
- Manuscript Accepted: 9 SEP 2010
- Manuscript Revised: 28 JUL 2010
- Manuscript Received: 10 JUN 2010
- Wellcome Trust Case-Control Consortium.
- 2006. Identification of probable genotyping errors by consideration of haplotypes. Eur J Hum Genet 14:450–458. , , , , , , .
- 2009. On quality control measures in genome-wide association studies: a test to assess the genotyping quality of individual probands in family-based association studies and an application to the HapMap data. PLoS Genet 5:e1000572. , , .
- 2010. Quantitative trait loci for CD4:CD8 lymphocyte ratio are associated with risk of type 1 diabetes and HIV-1 immune control. Am J Hum Genet 86:88–92. , , , , , , , , , , , , , , , , , , , , , .
- 2009. Missing call bias in high-throughput genotyping. BMC Genomics 10:106. , , , , , .
- 2008. Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies. PLoS Genet 4:e1000130. , , , .
- 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18:337–338. .
- 2008. Predicting unobserved phenotypes for complex traits from whole-genome SNP data. PLoS Genet 4:e1000231. , , , , .
- 2006. The impact of missing and erroneous genotypes on tagging SNP selection and power of subsequent association tests. Hum Hered 61:31–44. , , .
- 2009. Finding the missing heritability of complex diseases. Nature 461:747–753. , , , , , , , , , , , , , , , , , , , , , , , , , , .
- 2009. Impact of genotyping errors on the type I error rate and the power of haplotype-based association methods. BMC Genet 10:3. , , , , .
- 2010. A variant in LIN28B is associated with 2D:4D finger-length ratio, a putative retrospective biomarker of prenatal testosterone exposure. Am J Hum Genet 86:519–525. , , , , , , , , , , , , , , , , .
- 2003. Undetected genotyping errors cause apparent overtransmission of common alleles in the transmission/disequilibrium test. Am J Hum Genet 72:598–610. , , .
- 2008. How to interpret a genome-wide association study. J Am Med Assoc 299:1335–1344. , .
- 2006. WHAP: haplotype-based association analysis. Bioinformatics 23:255–256. , , .
- 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81:559–575. , , , , , , , , , , .
- 2002. The international endogene study: a collection of families for genetic research in endometriosis. Fertil Steril 78:679–685. , , , , , , , .
- 2005. Genomewide linkage study in 1,176 affected sister pair families identifies a significant susceptibility locus for endometriosis on chromosome 10q26. Am J Hum Genet 77:365–376. , , , , , , , , , , , , , , , , .
- 2008. Sizing up human height variation. Nat Genet 40:489–490. .
- 2006. Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings. PLoS Genet 2:e41. , , , , , , , .
- 2007. Prediction of individual genetic risk to disease from genome-wide association studies. Genome Res 17:1520–1528. , , .
- WTCCC. 2007. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447:661–678.
- 2006. Contrasting linkage-disequilibrium patterns between cases and controls as a novel association-mapping method. Am J Hum Genet 78:737–746. , , .