Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

A test for Hardy-Weinberg equilibrium on the X chromosome for sex-biased admixed populations

Daniel Backenroth, Shai Carmi
doi: https://doi.org/10.1101/552794
Daniel Backenroth
1Braun School of Public Health and community medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Shai Carmi
1Braun School of Public Health and community medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

Genome-wide scans for deviations from Hardy-Weinberg equilibrium (HWE) are commonly applied to detect genotyping errors. In contrast to the autosomes, genotype frequencies on the X chromosome do not reach HWE within a single generation. Instead, if allele frequencies in males and females initially differ, they oscillate for a few generations towards equilibrium. Several populations world-wide have experienced recent sex-biased admixture, namely, their male and female founders differed in ancestry and thus in allele frequencies. Sex-biased admixture makes testing for HWE difficult on X, because deviations are naturally expected, even under random mating post-admixture and error-free genotyping. In this paper, we develop a likelihood ratio test and a χ2 test that detect deviations from HWE on X while allowing for natural deviations due to sex-biased admixture. We demonstrate by simulations that our tests are powerful for detecting deviations due to non-random mating, while at the same time they do not reject the null under historical sex-biased admixture and random mating thereafter. We also demonstrate that when applied to 1000 Genomes project populations (e.g., as a quality control step), our tests reject fewer SNPs (among those showing frequency differences between the sexes) than other tests.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
Back to top
PreviousNext
Posted February 17, 2019.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
A test for Hardy-Weinberg equilibrium on the X chromosome for sex-biased admixed populations
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
A test for Hardy-Weinberg equilibrium on the X chromosome for sex-biased admixed populations
Daniel Backenroth, Shai Carmi
bioRxiv 552794; doi: https://doi.org/10.1101/552794
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
A test for Hardy-Weinberg equilibrium on the X chromosome for sex-biased admixed populations
Daniel Backenroth, Shai Carmi
bioRxiv 552794; doi: https://doi.org/10.1101/552794

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genetics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3585)
  • Biochemistry (7539)
  • Bioengineering (5494)
  • Bioinformatics (20724)
  • Biophysics (10292)
  • Cancer Biology (7946)
  • Cell Biology (11609)
  • Clinical Trials (138)
  • Developmental Biology (6584)
  • Ecology (10161)
  • Epidemiology (2065)
  • Evolutionary Biology (13573)
  • Genetics (9511)
  • Genomics (12811)
  • Immunology (7900)
  • Microbiology (19490)
  • Molecular Biology (7632)
  • Neuroscience (41969)
  • Paleontology (307)
  • Pathology (1254)
  • Pharmacology and Toxicology (2189)
  • Physiology (3258)
  • Plant Biology (7017)
  • Scientific Communication and Education (1293)
  • Synthetic Biology (1946)
  • Systems Biology (5417)
  • Zoology (1112)