Hardy–Weinberg quality control

I. GOMES; A. COLLINS; C. LONJOU; N. S. THOMAS; J. WILKINSON; M. WATSON; N. MORTON

doi:10.1046/j.1469-1809.1999.6360535.x

Abstract

An efficient test of deviation from Hardy–Weinberg frequencies with one degree of freedom was applied to 44 marker loci in a genome scan, and 7 loci had a significant excess of apparent homozygotes (χ2(1) > 6) suggestive of typing error. In this example evidence for linkage did not increase when outliers were censored. Statistical quality control is an essential part of genotyping, and the effect of mistyping and map error should be considered in evaluating any genome scan.

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Lonjou, C. Barnes, K. Chen, H. Cookson, W. O. C. M. Deichmann, K. A. Hall, I. P. Holloway, J. W. Laitinen, T. Palmer, L. J. Wjst, M. and Morton, N. E. 2000. A first trial of retrospective collaboration for positional cloning in complex inheritance: Assay of the cytokine region on chromosome 5 by the Consortium on Asthma Genetics (COAG). Proceedings of the National Academy of Sciences, Vol. 97, Issue. 20, p. 10942.

Rodríguez, Santiago Visedo, Guillermo and Zapata, Carlos 2001. Detection of errors in dinucleotide repeat typing by nondenaturing electrophoresis. ELECTROPHORESIS, Vol. 22, Issue. 13, p. 2656.

Zapata, Carlos Núñez, Concepción and Velasco, Teresa 2002. Distribution of Nonrandom Associations Between Pairs of Protein Loci Along the Third Chromosome ofDrosophila melanogaster. Genetics, Vol. 161, Issue. 4, p. 1539.

Maniatis, N. Collins, A. Xu, C.-F. McCarthy, L. C. Hewett, D. R. Tapper, W. Ennis, S. Ke, X. and Morton, N. E. 2002. The first linkage disequilibrium (LD) maps: Delineation of hot and cold blocks by diplotype analysis. Proceedings of the National Academy of Sciences, Vol. 99, Issue. 4, p. 2228.

Schick, James H. Iyengar, Sudha K. Klein, Barbara E. Klein, Ronald Reading, Karlie Liptak, Rachel Millard, Christopher Lee, Kristine E. Tomany, Sandra C. Moore, Emily L. Fijal, Bonnie A. and Elston, Robert C. 2003. A Whole-Genome Screen of a Quantitative Trait of Age-Related Maculopathy in Sibships from the Beaver Dam Eye Study. The American Journal of Human Genetics, Vol. 72, Issue. 6, p. 1412.

BONIN, A. BELLEMAIN, E. BRONKEN EIDESEN, P. POMPANON, F. BROCHMANN, C. and TABERLET, P. 2004. How to track and assess genotyping errors in population genetics studies. Molecular Ecology, Vol. 13, Issue. 11, p. 3261.

Rodríguez, Santiago Chen, Xiao‐he and Day, Ian N. M. 2004. Typing dinucleotide repeat loci using microplate array diagonal gel electrophoresis: Proof of principle. ELECTROPHORESIS, Vol. 25, Issue. 7-8, p. 975.

Wiencke, Kristine Louka, Andrew Sverre Spurkland, Anne Vatn, Morten the IBSEN study group Schrumpf, Erik and Boberg, Kirsten Muri 2004. Association of matrix metalloproteinase-1 and -3 promoter polymorphisms with clinical subsets of Norwegian primary sclerosing cholangitis patients. Journal of Hepatology, Vol. 41, Issue. 2, p. 209.

Zhang, Weihua Collins, Andrew Gibson, Jane Tapper, William J. Hunt, Sarah Deloukas, Panos Bentley, David R. and Morton, Newton E. 2004. Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps. Proceedings of the National Academy of Sciences, Vol. 101, Issue. 52, p. 18075.

Maier, L. M. Cooper, J. D. Walker, N. Smyth, D. J. and Todd, J. A. 2005. Comment to: Biason-Lauber A, Boehm B, Lang-Muritano M et al. (2005) Association of childhood type 1 diabetes mellitus with a variant of PAX4: possible link to beta cell regenerative capacity. Diabetologia 48:900–905. Diabetologia, Vol. 48, Issue. 10, p. 2180.

Scapoli, C Trombelli, L Mamolini, E and Collins, A 2005. Linkage disequilibrium analysis of case–control data: an application to generalized aggressive periodontitis. Genes & Immunity, Vol. 6, Issue. 1, p. 44.

Chen, John J Duan, Tao Single, Richard Mather, Kristie and Thomson, Glenys 2005. Hardy-Weinberg Testing of a Single Homozygous Genotype. Genetics, Vol. 170, Issue. 3, p. 1439.

Wittke-Thompson, Jacqueline K. Pluzhnikov, Anna and Cox, Nancy J. 2005. Rational Inferences about Departures from Hardy-Weinberg Equilibrium. The American Journal of Human Genetics, Vol. 76, Issue. 6, p. 967.

Gibson, Jane Tapper, William Zhang, Weihua Morton, Newton and Collins, Andrew 2005. Cosmopolitan linkage disequilibrium maps. Human Genomics, Vol. 2, Issue. 1, p. 20.

Salanti, Georgia Amountza, Georgia Ntzani, Evangelia E and Ioannidis, John P A 2005. Hardy–Weinberg equilibrium in genetic association studies: an empirical evaluation of reporting, deviations, and power. European Journal of Human Genetics, Vol. 13, Issue. 7, p. 840.

Tapper, W. Collins, A. Gibson, J. Maniatis, N. Ennis, S. and Morton, N. E. 2005. A map of the human genome in linkage disequilibrium units. Proceedings of the National Academy of Sciences, Vol. 102, Issue. 33, p. 11835.

Lai, Hung-Cheng Chu, Chi-Ming Lin, Ya-Wen Chang, Cheng-Chang Nieh, Shin Yu, Mu-Hsien and Chu, Tang-Yuan 2005. Matrix metalloproteinase 1 gene polymorphism as a prognostic predictor of invasive cervical cancer. Gynecologic Oncology, Vol. 96, Issue. 2, p. 314.

HOFFMAN, J. I. and AMOS, W. 2005. Microsatellite genotyping errors: detection approaches, common sources and consequences for paternal exclusion. Molecular Ecology, Vol. 14, Issue. 2, p. 599.

Pompanon, François Bonin, Aurélie Bellemain, Eva and Taberlet, Pierre 2005. Genotyping errors: causes, consequences and solutions. Nature Reviews Genetics, Vol. 6, Issue. 11, p. 847.

Yong Zou, Guang and Donner, Allan 2006. The Merits of Testing Hardy‐Weinberg Equilibrium in the Analysis of Unmatched Case‐Control Data: A Cautionary Note. Annals of Human Genetics, Vol. 70, Issue. 6, p. 923.

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Hardy–Weinberg quality control

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