ArticleHuman genetics2017
A genome-wide study of Hardy-Weinberg equilibrium with next generation sequence data.
Article in Human genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- Assessing Hardy-Weinberg equilibrium in T2T-aligned 1000 genomes project.PLoS genetics · 2026Article
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- Sequencing and health data resource of children of African ancestry.Genetics in medicine : official journal of the American College of Medical Genetics · 2026Article
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- Impact of GST and TP53 gene polymorphisms on susceptibility to end stage renal disease: A case-control analysis.PloS one · 2026Article
- Association of genotypes at single-nucleotide polymorphisms inIBRO neuroscience reports · 2025Article
- Genomic-Wide Association Markers and Candidate Genes for the High-Protein Trait in Storage Roots of Cassava (Plants (Basel, Switzerland) · 2025Article
- SNP-RFLP Markers for the Study ofEcology and evolution · 2025Article
- Identification and characterization of 17 novel polynucleotide microsatellite markers in Ocypode stimpsoni (Decapoda: Ocypodidae).BMC research notes · 2024Article
- Next-generation data filtering in the genomics era.Nature reviews. Genetics · 2024Review
- Variants rs3804099 and rs3804100 in theInternational journal of molecular sciences · 2024Article
- Influence of Genetic Polymorphisms on the Age at Cancer Diagnosis in a Homogenous Lynch Syndrome Cohort of Individuals Carrying theBiomedicines · 2024Article
- Association between vitamin D metabolism gene polymorphisms and schizophrenia.Biomedical reports · 2024Article
- Genes Involved in Susceptibility to Obesity and Emotional Eating Behavior in a Romanian Population.Nutrients · 2024Article
- Hardy-Weinberg Equilibrium in Meta-Analysis Studies and Large-Scale Genomic Sequencing Era.Asian Pacific journal of cancer prevention : APJCP · 2024Review
- Association ofHeliyon · 2024Article
- Towards pharmacogenomics-guided tuberculosis (TB) therapy: N-acetyltransferase-2 genotypes among TB-infected Kenyans of mixed ethnicity.BMC medical genomics · 2024Article
- Calpain 1 gene expression in liver tissue and the association of novel calpain 1 single-nucleotide polymorphisms (SNPs) with meat quality in Bali cattle.Archives animal breeding · 2024Article
- Pharmacogenetic analysis of inter-ethnic variability in the uptake transporter SLCO1B1 gene in Colombian, Mozambican, and Portuguese populations.BMC medical genomics · 2023Article
- Range-wide population genomics of the spongy moth,Evolutionary applications · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Statistical tests for Hardy-Weinberg equilibrium have been an important tool for detecting genotyping errors in the past, and remain important in the quality control of next generation sequence data. In this paper, we analyze complete chromosomes of the 1000 genomes project by using exact test procedures for autosomal and X-chromosomal variants. We find that the rate of disequilibrium largely exceeds what might be expected by chance alone for all chromosomes. Observed disequilibrium is, in about 60% of the cases, due to heterozygote excess. We suggest that most excess disequilibrium can be explained by sequencing problems, and hypothesize mechanisms that can explain exceptional heterozygosities. We report higher rates of disequilibrium for the MHC region on chromosome 6, regions flanking centromeres and p-arms of acrocentric chromosomes. We also detected long-range haplotypes and areas with incidental high disequilibrium. We report disequilibrium to be related to read depth, with variants having extreme read depths being more likely to be out of equilibrium. Disequilibrium rates were found to be 11 times higher in segmental duplications and simple tandem repeat regions. The variants with significant disequilibrium are seen to be concentrated in these areas. For next generation sequence data, Hardy-Weinberg disequilibrium seems to be a major indicator for copy number variation.
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