{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,28]],"date-time":"2026-06-28T11:01:34Z","timestamp":1782644494392,"version":"3.54.5"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The transition\/transversion (Ti\/Tv) ratio and heterozygous\/nonreference-homozygous (het\/nonref-hom) ratio have been commonly computed in genetic studies as a quality control (QC) measurement. Additionally, these two ratios are helpful in our understanding of the patterns of DNA sequence evolution.<\/jats:p>\n               <jats:p>Results: To thoroughly understand these two genomic measures, we performed a study using 1000 Genomes Project (1000G) released genotype data ( N = 1092). An additional two datasets ( N = 581 and N = 6) were used to validate our findings from the 1000G dataset. We compared the two ratios among continental ancestry, genome regions and gene functionality. We found that the Ti\/Tv ratio can be used as a quality indicator for single nucleotide polymorphisms inferred from high-throughput sequencing data. The Ti\/Tv ratio varies greatly by genome region and functionality, but not by ancestry. The het\/nonref-hom ratio varies greatly by ancestry, but not by genome regions and functionality. Furthermore, extreme guanine + cytosine content (either high or low) is negatively associated with the Ti\/Tv ratio magnitude. Thus, when performing QC assessment using these two measures, care must be taken to apply the correct thresholds based on ancestry and genome region. Failure to take these considerations into account at the QC stage will bias any following analysis.<\/jats:p>\n               <jats:p>Contact: \u00a0yan.guo@vanderbilt.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu668","type":"journal-article","created":{"date-parts":[[2014,10,9]],"date-time":"2014-10-09T01:49:44Z","timestamp":1412819384000},"page":"318-323","source":"Crossref","is-referenced-by-count":167,"title":["Genome measures used for quality control are dependent on gene function and ancestry"],"prefix":"10.1093","volume":"31","author":[{"given":"Jing","family":"Wang","sequence":"first","affiliation":[{"name":"1 Center for Quantitative Sciences and 2 Department of Medicine and 3 Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37212, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leon","family":"Raskin","sequence":"additional","affiliation":[{"name":"1 Center for Quantitative Sciences and 2 Department of Medicine and 3 Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37212, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David C.","family":"Samuels","sequence":"additional","affiliation":[{"name":"1 Center for Quantitative Sciences and 2 Department of Medicine and 3 Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37212, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Shyr","sequence":"additional","affiliation":[{"name":"1 Center for Quantitative Sciences and 2 Department of Medicine and 3 Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37212, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Guo","sequence":"additional","affiliation":[{"name":"1 Center for Quantitative Sciences and 2 Department of Medicine and 3 Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37212, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,10,8]]},"reference":[{"key":"2023020116161342900_btu668-B1","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nature11632","article-title":"An integrated map of genetic variation from 1,092 human genomes","volume":"491","author":"Abecasis","year":"2012","journal-title":"Nature"},{"key":"2023020116161342900_btu668-B2","doi-asserted-by":"crossref","first-page":"R68","DOI":"10.1186\/gb-2011-12-7-r68","article-title":"Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities","volume":"12","author":"Bainbridge","year":"2011","journal-title":"Genome Biol."},{"key":"2023020116161342900_btu668-B3","doi-asserted-by":"crossref","first-page":"e72","DOI":"10.1093\/nar\/gks001","article-title":"Summarizing and correcting the GC content bias in high-throughput sequencing","volume":"40","author":"Benjamini","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023020116161342900_btu668-B4","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"Consortium","year":"2012","journal-title":"Nature"},{"key":"2023020116161342900_btu668-B5","doi-asserted-by":"crossref","first-page":"e105","DOI":"10.1093\/nar\/gkn425","article-title":"Substantial biases in ultra-short read data sets from high-throughput DNA sequencing","volume":"36","author":"Dohm","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2023020116161342900_btu668-B6","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/nature09534","article-title":"A map of human genome variation from population-scale sequencing","volume":"467","author":"Durbin","year":"2010","journal-title":"Nature"},{"key":"2023020116161342900_btu668-B7","doi-asserted-by":"crossref","first-page":"886","DOI":"10.1038\/ng.2344","article-title":"Exome sequencing of extreme phenotypes identifies DCTN4 as a modifier of chronic \n              Pseudomonas aeruginosa\n               infection in cystic fibrosis","volume":"44","author":"Emond","year":"2012","journal-title":"Nat. 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