{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T00:40:09Z","timestamp":1675298409879},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2016,11,3]],"date-time":"2016-11-03T00:00:00Z","timestamp":1478131200000},"content-version":"vor","delay-in-days":778,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation : During the past 4 years, whole-exome sequencing has become a standard tool for finding rare variants causing Mendelian disorders. In that time, there has also been a proliferation of both sequencing platforms and approaches to analyse their output. This requires approaches to assess the performance of different methods. Traditionally, criteria such as comparison with microarray data or a number of known polymorphic sites have been used. Here we expand such approaches, developing a maximum likelihood framework and using it to estimate the sensitivity and specificity of whole-exome sequencing data.<\/jats:p>\n               <jats:p>Results : Using whole-exome sequencing data for a panel of 19 individuals, we show that estimated sensitivity and specificity are similar to those calculated using microarray data as a reference. We explore the effect of frequency misspecification arising from using an inappropriately selected population and find that, although the estimates are affected, the rankings across procedures remain the same.<\/jats:p>\n               <jats:p>Availability and implementation : An implementation using Perl and R can be found at busso.ncl.ac.uk (Username: igm101; Password: Z1z1nts).<\/jats:p>\n               <jats:p>Contact : Darren.Houniet@ogt.com ; mauro.santibanez-koref@newcastle.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu606","type":"journal-article","created":{"date-parts":[[2014,9,19]],"date-time":"2014-09-19T04:50:41Z","timestamp":1411102241000},"page":"56-61","source":"Crossref","is-referenced-by-count":0,"title":["Using population data for assessing next-generation sequencing performance"],"prefix":"10.1093","volume":"31","author":[{"given":"Darren T.","family":"Houniet","sequence":"first","affiliation":[{"name":"1 Oxford Gene Technology, Begbroke Science Park, Oxford, Oxfordshire, OX5 1PF, 2 Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway NE1 3BZ, Newcastle upon Tyne and 3 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK"}]},{"given":"Thahira J.","family":"Rahman","sequence":"additional","affiliation":[{"name":"1 Oxford Gene Technology, Begbroke Science Park, Oxford, Oxfordshire, OX5 1PF, 2 Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway NE1 3BZ, Newcastle upon Tyne and 3 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK"}]},{"given":"Saeed","family":"Al Turki","sequence":"additional","affiliation":[{"name":"1 Oxford Gene Technology, Begbroke Science Park, Oxford, Oxfordshire, OX5 1PF, 2 Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway NE1 3BZ, Newcastle upon Tyne and 3 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK"}]},{"given":"Matthew E.","family":"Hurles","sequence":"additional","affiliation":[{"name":"1 Oxford Gene Technology, Begbroke Science Park, Oxford, Oxfordshire, OX5 1PF, 2 Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway NE1 3BZ, Newcastle upon Tyne and 3 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK"}]},{"given":"Yaobo","family":"Xu","sequence":"additional","affiliation":[{"name":"1 Oxford Gene Technology, Begbroke Science Park, Oxford, Oxfordshire, OX5 1PF, 2 Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway NE1 3BZ, Newcastle upon Tyne and 3 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK"}]},{"given":"Judith","family":"Goodship","sequence":"additional","affiliation":[{"name":"1 Oxford Gene Technology, Begbroke Science Park, Oxford, Oxfordshire, OX5 1PF, 2 Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway NE1 3BZ, Newcastle upon Tyne and 3 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK"}]},{"given":"Bernard","family":"Keavney","sequence":"additional","affiliation":[{"name":"1 Oxford Gene Technology, Begbroke Science Park, Oxford, Oxfordshire, OX5 1PF, 2 Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway NE1 3BZ, Newcastle upon Tyne and 3 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK"}]},{"given":"Mauro","family":"Santibanez Koref","sequence":"additional","affiliation":[{"name":"1 Oxford Gene Technology, Begbroke Science Park, Oxford, Oxfordshire, OX5 1PF, 2 Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway NE1 3BZ, Newcastle upon Tyne and 3 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK"}]}],"member":"286","published-online":{"date-parts":[[2014,9,17]]},"reference":[{"key":"2023020116154828900_btu606-B1","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1101\/gr.112326.110","article-title":"Dindel: accurate indel calls from short-read data","volume":"21","author":"Albers","year":"2011","journal-title":"Genome Res."},{"key":"2023020116154828900_btu606-B2","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1038\/nrg3031","article-title":"Exome sequencing as a tool for Mendelian disease gene discovery","volume":"12","author":"Bamshad","year":"2011","journal-title":"Nat. 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