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Major sex differences in allele frequencies for X chromosomal variants in both the 1000 Genomes Project and gnomAD

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  • Zhong Wang
  • Lei Sun
  • Andrew D Paterson

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

Suggested Citation

  • Zhong Wang & Lei Sun & Andrew D Paterson, 2022. "Major sex differences in allele frequencies for X chromosomal variants in both the 1000 Genomes Project and gnomAD," PLOS Genetics, Public Library of Science, vol. 18(5), pages 1-35, May.
    • Handle: RePEc:plo:pgen00:1010231
    DOI: 10.1371/journal.pgen.1010231
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    1. Charles A. Tilford & Tomoko Kuroda-Kawaguchi & Helen Skaletsky & Steve Rozen & Laura G. Brown & Michael Rosenberg & John D. McPherson & Kristine Wylie & Mandeep Sekhon & Tamara A. Kucaba & Robert H. W, 2001. "A physical map of the human Y chromosome," Nature, Nature, vol. 409(6822), pages 943-945, February.
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