A note on exact tests of Hardy-Weinberg equilibrium.

By Janis E. Wigginton, David J. Cutler, Gonçalo R. Abecasis. American Journal of Human Genetics, 2005

1,541 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/b85062ef403007f1337f0d93167f6901224cbbb0

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In Genetics

Citations in the corpus

The MBOAT7-TMC4 Variant rs641738 Increases Risk of Nonalcoholic Fatty Liver Disease in Individuals of European Descent (2016, positive): “The MBOAT7/TMC4 was recently identified as a locus involved in alcoholic cirrhosis 33 .”
An 18-kDa Translocator Protein (TSPO) polymorphism explains differences in binding affinity of the PET radioligand PBR28 (2011, methodology): “All samples were duplicated on each plate as a quality control measure.”
PEDSTATS: descriptive statistics, graphics and quality assessment for gene mapping data (2005, background): “A summary of affected, unaffected and discordant pairs can also be produced, and may help guide decisions on whether a dataset contains sufficient information for an affected relative pair analysis to be carried out (Risch, 1990; Whittemore and Halpern, 1994 ).”
Web-Based, Participant-Driven Studies Yield Novel Genetic Associations for Common Traits (2010, methodology): “SNPs with a call rate under 98% were excluded from analysis, as were those with minor allele frequency under 0 : 5% or a p-value for Hardy-Weinberg equilibrium (using the test from [49] within all the northern Europeans in the database) under 10 { 10 .”
Genome-wide association study identifies variants in the ABO locus associated with susceptibility to pancreatic cancer (2009, neutral): “Deviation from Hardy-Weinberg proportions were teste”
Genome-wide association study of alcohol dependence (2009, background): “These findings and those of the intergenic SNPs are provided in Table 1, Table 2, eTable 4, and eTable 5.(51) Figures 3, 4, and 5 show P values of the SNPs located in ±1-Mb intervals around the most significant findings at 2q35, 5q32, and Xp22.”
Reliable ABC model choice via random forests (2014, methodology): “istance between two consecutive SNPs is 1 kb in order to minimize linkage disequilibrium between SNPs, and (iv) SNP loci showing signicant deviation from Hardy-Weinberg equilibrium at a 1% threshold Wigginton et al. (2005) in at least one of the four populations have been removed (35 SNP loci involv”
Second-generation PLINK: rising to the challenge of larger and richer datasets (2014, methodology): “PLINK 1.0 used the SNP-HWE algorithm in a paper by Wigginton et al. [13] to execute this test.”
SNPs in KCNQ1 are associated with susceptibility to type 2 diabetes in East Asian and European populations (2008, methodology): “We performed HWE test according to a method previously describe”
A tutorial on statistical methods for population association studies (2006, methodology): “The Pearson test is easy to compute, but the χ 2 approximation can be poor when there are low genotype counts, and it is better to use a Fisher exact test, which does not rely on the χ 2 approximatio”
High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios (2021, positive): “To filter the SNV/INDEL call set for haplotype phasing, we first annotated the call set with HWE exact test p-values (Wigginton et al., 2005), stratified by super-population, using the BCFtools fill-tags plugin (Li, 2011).”
Genome-Wide Association Scan Shows Genetic Variants in the FTO Gene Are Associated with Obesity-Related Traits (2007, methodology): “Our initial analysis focused on evaluating the additive effects of 362,129 SNPs (Table S1) that passed quality control checks [27,28].”