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sex drive i

Checking concordance between reported sex and genotype-inferred sex is a crucial quality control measure in genome-wide association studies Array. However, limited insights exist atray the true accuracy of software that infer sex from genotype array data. Supplementary data are available at Bioinformatics online.

Genome-wide association studies GWAS are being conducted at an unprecedented rate due to the precipitous fall in genotyping cost over time Begum et al.

An essential quality control QC step in these studies sex verifying concordance between self-reported sex and genotype-inferred sex. Disagreements can prompt researchers to double-check their data, and either fix entry errors or discard samples if array phenotype ascertainment is suspected.

Cytogenetic analyses, such as karyotyping, are gold standard methods of inferring sex Nagy et al. They allow not only detection of the X and Y array chromosomes, but also visualization of potential aneuploidy. On the other hand, high-throughput genomic experiments introduce more uncertainty in sex inference when chromosomes are not evaluated in their entirety, but rather sex oligonucleotide fragments. However, improvements in sex inference from genotype arrays are warranted, since valuable information on the Y chromosome has yet to be leveraged.

Allele calls e. PLINK format and GenomeStudio matrix format tend to be much more accessible to researchers for shared use than the raw data that genotyping seex often harbor privately. We propose sex new sex inference tool, seXY, that accepts called genotype data and jointly considers information qrray the X and Y chromosomes.

In spite of pseudoautosomal regions from which X chromosome fragments can cross-hybridize with Y chromosome array probes, females should sex substantially greater YM than males. To our knowledge, accuracies of existing array-based sex array software have never been assessed using a reference that is more reliable than self-reported sex.

Individual sex was established based on verified prostate or ovary presence. It has sex shown that highly unbalanced training sets array the potential to impair classification accuracy in test sets, regardless of class proportions in the test sets Wei and Dunbrack, X chromosome markers with high minor allele frequencies demonstrated the largest difference in array prevalence between males and females Supplementary Fig.

Table 1. Accuracies are displayed as percent of test set individuals whose sexes were correctly predicted.

CV, cross-validation. The extent of unbalanced sex proportions in training sets did not influence prediction performance. Results were sex across all rounds of CV. Arrsy have therefore made seXY available for public use as Equation 1 trained on all males and females in this study.

While Sex alone appeared sufficient for sensitively identifying males, sex classification was improved through simultaneous consideration array YM by seXY. For large GWAS consortia such as the OncoArray where hundreds of sex of samples are interrogated, seXY may salvage up to several thousand samples from removal due sex incorrect prior sex inference.

We would arry to thank rotation student Alexander J. Titus for conceiving the name of this sex inference tool. We would also like to thank Katherine L. Nathanson, Simon A. Spurdle for contributing samples to the ovarian cancer OncoArray. Richter and Evalyn E. Oxford University Press is a department of the University of Oxford.

It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide. Sign In array Create an Account. Sign In. Advanced Search. Article Navigation. Close mobile search navigation Article Navigation. Volume Article Contents. Oxford Academic. Google Scholar. Jonathan A Busam.

Xiangjun Xiao. Rosalind A Eeles. Frederick Xex Schumacher. Catherine M Phelan. Christopher I Amos. To whom correspondence should be addressed.

Email: Christopher. Amos dartmouth. Cite Citation. Permissions Icon Permissions. Abstract Motivation. Eeles icr.

Phelan moffitt. Genotype calls at the 15 X chromosomes markers and Y chromosome markers of both datasets were converted to matrix format using GenomeStudio v For every individual, seXY computed XH as the fraction of all markers on the X chromosome that have two different allele calls, excluding markers array missing calls.

YM was computed as the fraction of all markers on the Y chromosome that have missing calls. Comprehensive literature review sex statistical considerations for GWAS meta-analysis. Search ADS. Detection of sex chromosome aneuploidies array quantitative fluorescent PCR in the Hungarian population.

PLINK: a tool set for whole-genome association and population-based linkage analyses. Cost-effective prediction of gender-labeling errors and estimation of gender-labeling error rates in candidate-gene association studies. The role of balanced training and array data sets for binary classifiers in array. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.

Issue Section:. Associate Editor: John Hancock. Download all figures. Supplementary data. Supplementary Data. View Metrics. Email alerts New issue alert. Advance areay alerts. Article activity alert. Receive exclusive offers and updates from Oxford Academic.

Related articles in Web of Science Google Scholar. Citing articles via Web of Science 2. Episo: quantitative estimation of RNA 5-methylcytosine at isoform level by high-throughput sequencing of RNA treated with bisulfite. Looking for your next opportunity? Tenure-Track Assistant Professor. Pediatric Neurosurgery. View all jobs.

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seXY: a tool for sex inference from genotype arrays. Qian DC(1), Busam JA(2), Xiao X(1), O'Mara TA(3), Eeles RA(4), Schumacher FR(5). Teleost fish are of particular interest in both domains. They have evolved a spectacularly diverse array of sex determination systems, with. RT @biorxiv_genetic: A sex-stratified genome-wide association study of tuberculosis using a multi-ethnic genotyping array techwired.info