title: seXY: a tool for sex inference from genotype arrays.
abstract: Checking concordance between reported sex and genotype-inferred sex is a crucial quality control measure in genome-wide association studies (GWAS). However, limited insights exist regarding the true accuracy of software that infer sex from genotype array data.
  
  
  
  We present seXY, a logistic regression model trained on both X chromosome heterozygosity and Y chromosome missingness, that consistently demonstrated >99.5% sex inference accuracy in cross-validation for 889 males and 5,361 females enrolled in prostate cancer and ovarian cancer GWAS. Compared to PLINK, one of the most popular tools for sex inference in GWAS that assesses only X chromosome heterozygosity, seXY achieved marginally better male classification and 3% more accurate female classification.
  
  
  
  https://github.com/Christopher-Amos-Lab/seXY.
  
  
  
  Christopher.I.Amos@dartmouth.edu.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biomedical Data Science, Dartmouth Geisel School of Medicine, Lebanon, NH 03756, USA.
authors.forename: David C
authors.initials: DC
authors.lastname: Qian
authors.affiliation: Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA.
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Busam
authors.affiliation: Department of Biomedical Data Science, Dartmouth Geisel School of Medicine, Lebanon, NH 03756, USA.
authors.forename: Xiangjun
authors.initials: X
authors.lastname: Xiao
authors.affiliation: Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.
authors.forename: Tracy A
authors.initials: TA
authors.lastname: O'Mara
authors.affiliation: Division of Genetics and Epidemiology, Institute of Cancer Research, London SW7 3RP, UK.
authors.forename: Rosalind A
authors.initials: RA
authors.lastname: Eeles
authors.affiliation: Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA.
authors.forename: Frederick R
authors.initials: FR
authors.lastname: Schumacher
authors.affiliation: Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL 33612, USA.
authors.forename: Catherine M
authors.initials: CM
authors.lastname: Phelan
authors.affiliation: Department of Biomedical Data Science, Dartmouth Geisel School of Medicine, Lebanon, NH 03756, USA.
authors.forename: Christopher I
authors.initials: CI
authors.lastname: Amos
mesh_terms: D002877:Chromosomes, Human; D005260:Female; D055106:Genome-Wide Association Study / Q000379:methods*; D006801:Humans; D008297:Male; D011786:Quality Control; D012730:Sex Chromosomes; D012732:Sex Determination Analysis / Q000379:methods*; D012984:Software