{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,7]],"date-time":"2026-02-07T16:27:33Z","timestamp":1770481653213,"version":"3.49.0"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Determination of the relative copy number of single-nucleotide sequence variants (SNVs) within a DNA sample is a frequent experimental goal. Various methods can be applied to this problem, although hybridization-based approaches tend to suffer from high-setup cost and poor adaptability, while others (such as pyrosequencing) may not be accessible to all laboratories. The potential to extract relative copy number information from standard dye-terminator electropherograms has been little explored, yet this technology is cheap and widely accessible. Since several biologically important loci have paralogous copies that interfere with genotyping, and which may also display copy number variation (CNV), there are many situations in which determination of the relative copy number of SNVs is desirable.<\/jats:p>\n               <jats:p>Results: We have developed a desktop application, QSVanalyzer, which allows high-throughput quantification of the proportions of DNA sequences containing SNVs. In reconstruction experiments, QSVanalyzer accurately estimated the known relative proportions of SNVs. By analyzing a large panel of genomic DNA samples, we demonstrate the ability of the software to analyze not only common biallelic SNVs, but also SNVs within a locus at which gene conversion between four genomic paralogs operates, and within another that is subject to CNV.<\/jats:p>\n               <jats:p>Availability and Implementation: QSVanalyzer is freely available at http:\/\/dna.leeds.ac.uk\/qsv\/. It requires the Microsoft .NET framework version 2.0, which can be installed on all Microsoft operating systems from Windows 98 onwards.<\/jats:p>\n               <jats:p>Contact: \u00a0msjimc@leeds.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp583","type":"journal-article","created":{"date-parts":[[2009,10,10]],"date-time":"2009-10-10T01:23:47Z","timestamp":1255137827000},"page":"3244-3250","source":"Crossref","is-referenced-by-count":98,"title":["Inferring relative proportions of DNA variants from sequencing electropherograms"],"prefix":"10.1093","volume":"25","author":[{"given":"I. M.","family":"Carr","sequence":"first","affiliation":[{"name":"Leeds Institute of Molecular Medicine, Wellcome Trust Brenner Building, University of Leeds, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK"}]},{"given":"J. I.","family":"Robinson","sequence":"additional","affiliation":[{"name":"Leeds Institute of Molecular Medicine, Wellcome Trust Brenner Building, University of Leeds, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK"}]},{"given":"R.","family":"Dimitriou","sequence":"additional","affiliation":[{"name":"Leeds Institute of Molecular Medicine, Wellcome Trust Brenner Building, University of Leeds, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK"}]},{"given":"A. F.","family":"Markham","sequence":"additional","affiliation":[{"name":"Leeds Institute of Molecular Medicine, Wellcome Trust Brenner Building, University of Leeds, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK"}]},{"given":"A. W.","family":"Morgan","sequence":"additional","affiliation":[{"name":"Leeds Institute of Molecular Medicine, Wellcome Trust Brenner Building, University of Leeds, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK"}]},{"given":"D. T.","family":"Bonthron","sequence":"additional","affiliation":[{"name":"Leeds Institute of Molecular Medicine, Wellcome Trust Brenner Building, University of Leeds, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK"}]}],"member":"286","published-online":{"date-parts":[[2009,10,9]]},"reference":[{"key":"2023013112145272100_B1","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1038\/nature04489","article-title":"Copy number polymorphism in FCGR3 predisposes to glomerulonephritis in rats and humans","volume":"439","author":"Aitman","year":"2006","journal-title":"Nature"},{"key":"2023013112145272100_B2","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1093\/nar\/28.2.605","article-title":"Measurement of locus copy number by hybridisation with amplifiable probes","volume":"28","author":"Armour","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023013112145272100_B3","doi-asserted-by":"crossref","first-page":"e19","DOI":"10.1093\/nar\/gkl1089","article-title":"Accurate, high-throughput typing of copy number variation using paralogue ratios from dispersed repeats","volume":"35","author":"Armour","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023013112145272100_B4","doi-asserted-by":"crossref","first-page":"954","DOI":"10.1086\/420796","article-title":"Novel PMS2 pseudogenes can conceal recessive mutations causing a distinctive childhood cancer syndrome","volume":"74","author":"De Vos","year":"2004","journal-title":"Am. 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