ArticlePLoS genetics2022
Major sex differences in allele frequencies for X chromosomal variants in both the 1000 Genomes Project and gnomAD.
Article in PLoS genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Assessing Hardy-Weinberg equilibrium in T2T-aligned 1000 genomes project.PLoS genetics · 2026Article
- Autosomal Type IV Collagen Genes Display Sex Differences in Genetic Risk for Hematuria.Kidney international reports · 2026Article
- Drivers of systemic male-female allele frequency divergence in humans.bioRxiv : the preprint server for biology · 2026Article
- XhetRel: a pipeline for X heterozygosity and relatedness analysis of sequencing data.Bioinformatics advances · 2026Article
- On the analysis of genetic association with long-read sequencing data.PLoS genetics · 2025Article
- Evolutionary divergence between homologous X-Y chromosome genes shapes sex-biased biology.Nature ecology & evolution · 2025Article
- Chromosome X-wide common variant association study in autism spectrum disorder.American journal of human genetics · 2025Article
- The battle of the sexes in humans is highly polygenic.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Chromosome X-Wide Common Variant Association Study (XWAS) in Autism Spectrum Disorder.medRxiv : the preprint server for health sciences · 2024Article
- Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria.Nature communications · 2024Article
- Comprehensive whole-genome analyses of the UK Biobank reveal significant sex differences in both genotype missingness and allele frequency on the X chromosome.Human molecular genetics · 2024Article
- Statistical Learning of Large-Scale Genetic Data: How to Run a Genome-Wide Association Study of Gene-Expression Data Using the 1000 Genomes Project Data.Statistics in biosciences · 2024Article
- The roles of sexual selection and sexual conflict in shaping patterns of genome and transcriptome variation.Nature ecology & evolution · 2023Review
- eXclusionarY: 10 years later, where are the sex chromosomes in GWASs?American journal of human genetics · 2023Review
- The hidden factor: accounting for covariate effects in power and sample size computation for a binary trait.Bioinformatics (Oxford, England) · 2023Article
- Inferring Balancing Selection From Genome-Scale Data.Genome biology and evolution · 2023Review
- Why does the X chromosome lag behind autosomes in GWAS findings?PLoS genetics · 2023Article
- Hemizygosity can reveal variant pathogenicity on the X-chromosome.Human genetics · 2023Article
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3 authors.
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Abstract
An unexpectedly high proportion of SNPs on the X chromosome in the 1000 Genomes Project phase 3 data were identified with significant sex differences in minor allele frequencies (sdMAF). sdMAF persisted for many of these SNPs in the recently released high coverage whole genome sequence of the 1000 Genomes Project that was aligned to GRCh38, and it was consistent between the five super-populations. Among the 245,825 common (MAF>5%) biallelic X-chromosomal SNPs in the phase 3 data presumed to be of high quality, 2,039 have genome-wide significant sdMAF (p-value <5e-8). sdMAF varied by location: non-pseudo-autosomal region (NPR) = 0.83%, pseudo-autosomal regions (PAR1) = 0.29%, PAR2 = 13.1%, and X-transposed region (XTR)/PAR3 = 0.85% of SNPs had sdMAF, and they were clustered at the NPR-PAR boundaries, among others. sdMAF at the NPR-PAR boundaries are biologically expected due to sex-linkage, but have generally been ignored in association studies. For comparison, similar analyses found only 6, 1 and 0 SNPs with significant sdMAF on chromosomes 1, 7 and 22, respectively. Similar sdMAF results for the X chromosome were obtained from the high coverage whole genome sequence data from gnomAD V 3.1.2 for both the non-Finnish European and African/African American samples. Future X chromosome analyses need to take sdMAF into account.
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