Challenges in Whole Exome Sequencing: An Example from Hereditary Deafness
Identifieur interne : 004462 ( Main/Exploration ); précédent : 004461; suivant : 004463Challenges in Whole Exome Sequencing: An Example from Hereditary Deafness
Auteurs : Asli Sirmaci [États-Unis] ; Yvonne J. K. Edwards [États-Unis] ; Hatice Akay [Turquie] ; Mustafa Tekin [États-Unis, Turquie]Source :
- PLoS ONE [ 1932-6203 ] ; 2012.
Abstract
Whole exome sequencing provides unprecedented opportunities to identify causative DNA variants in rare Mendelian disorders. Finding the responsible mutation via traditional methods in families with hearing loss is difficult due to a high degree of genetic heterogeneity. In this study we combined autozygosity mapping and whole exome sequencing in a family with 3 affected children having nonsyndromic hearing loss born to consanguineous parents. Two novel missense homozygous variants, c.508C>A (p.H170N) in
Url:
DOI: 10.1371/journal.pone.0032000
PubMed: 22363784
PubMed Central: 3283682
Affiliations:
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Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff2"><addr-line>Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation></author><author><name sortKey="Edwards, Yvonne J K" sort="Edwards, Yvonne J K" uniqKey="Edwards Y" first="Yvonne J. K." last="Edwards">Yvonne J. K. Edwards</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff2"><addr-line>Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation></author><author><name sortKey="Akay, Hatice" sort="Akay, Hatice" uniqKey="Akay H" first="Hatice" last="Akay">Hatice Akay</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Radiodiagnostics Unit, Veni Vidi Hospital, Diyarbakir, Turkey</addr-line></nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Radiodiagnostics Unit, Veni Vidi Hospital, Diyarbakir</wicri:regionArea><wicri:noRegion>Diyarbakir</wicri:noRegion></affiliation></author><author><name sortKey="Tekin, Mustafa" sort="Tekin, Mustafa" uniqKey="Tekin M" first="Mustafa" last="Tekin">Mustafa Tekin</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff2"><addr-line>Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Division of Pediatric Genetics, Ankara University School of Medicine, Ankara, Turkey</addr-line></nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Division of Pediatric Genetics, Ankara University School of Medicine, Ankara</wicri:regionArea><wicri:noRegion>Ankara</wicri:noRegion></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Whole exome sequencing provides unprecedented opportunities to identify causative DNA variants in rare Mendelian disorders. Finding the responsible mutation via traditional methods in families with hearing loss is difficult due to a high degree of genetic heterogeneity. In this study we combined autozygosity mapping and whole exome sequencing in a family with 3 affected children having nonsyndromic hearing loss born to consanguineous parents. Two novel missense homozygous variants, c.508C>A (p.H170N) in <italic>GIPC3</italic> and c.1328C>T (p.T443M) in <italic>ZNF57</italic>, were identified in the same ∼6 Mb autozygous region on chromosome 19 in affected members of the family. Both variants co-segregated with the phenotype and were absent in 335 ethnicity-matched controls. Biallelic <italic>GIPC3</italic> mutations have recently been reported to cause autosomal recessive nonsyndromic sensorineural hearing loss. Thus we conclude that the hearing loss in the family described in this report is caused by a novel missense mutation in <italic>GIPC3</italic>. Identified variant in <italic>GIPC3</italic> had a low read depth, which was initially filtered out during the analysis leaving <italic>ZNF57</italic> as the only potential causative gene. This study highlights some of the challenges in the analyses of whole exome data in the bid to establish the true causative variant in Mendelian disease.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Friedman, Tb" uniqKey="Friedman T">TB Friedman</name></author><author><name sortKey="Griffith, Aj" uniqKey="Griffith A">AJ Griffith</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Morton, Cc" uniqKey="Morton C">CC Morton</name></author><author><name sortKey="Nance, We" uniqKey="Nance W">WE Nance</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Becker, J" uniqKey="Becker J">J Becker</name></author><author><name sortKey="Semler, O" uniqKey="Semler O">O Semler</name></author><author><name sortKey="Gilissen, C" uniqKey="Gilissen C">C Gilissen</name></author><author><name sortKey="Li, Y" uniqKey="Li Y">Y Li</name></author><author><name sortKey="Bolz, Hj" uniqKey="Bolz 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Ray</name></author><author><name sortKey="Hildebrand, Ms" uniqKey="Hildebrand M">MS Hildebrand</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Doyle, Da" uniqKey="Doyle D">DA Doyle</name></author><author><name sortKey="Lee, A" uniqKey="Lee A">A Lee</name></author><author><name sortKey="Lewis, J" uniqKey="Lewis J">J Lewis</name></author><author><name sortKey="Kim, E" uniqKey="Kim E">E Kim</name></author><author><name sortKey="Sheng, M" uniqKey="Sheng M">M Sheng</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Songyang, Z" uniqKey="Songyang Z">Z Songyang</name></author><author><name sortKey="Fanning, As" uniqKey="Fanning A">AS Fanning</name></author><author><name sortKey="Fu, C" uniqKey="Fu C">C Fu</name></author><author><name sortKey="Xu, J" uniqKey="Xu J">J Xu</name></author><author><name sortKey="Marfatia, Sm" uniqKey="Marfatia S">SM Marfatia</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ahmed, Zm" uniqKey="Ahmed Z">ZM Ahmed</name></author><author><name sortKey="Morell, Rj" uniqKey="Morell R">RJ Morell</name></author><author><name sortKey="Riazuddin, S" uniqKey="Riazuddin S">S Riazuddin</name></author><author><name sortKey="Gropman, A" uniqKey="Gropman A">A Gropman</name></author><author><name sortKey="Shaukat, S" uniqKey="Shaukat S">S Shaukat</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Avraham, Kb" uniqKey="Avraham K">KB Avraham</name></author><author><name sortKey="Hasson, T" uniqKey="Hasson T">T Hasson</name></author><author><name sortKey="Steel, Kp" uniqKey="Steel K">KP Steel</name></author><author><name sortKey="Kingsley, Dm" uniqKey="Kingsley D">DM Kingsley</name></author><author><name sortKey="Russell, Lb" uniqKey="Russell L">LB Russell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Reed, Bc" uniqKey="Reed B">BC Reed</name></author><author><name sortKey="Cefalu, C" uniqKey="Cefalu C">C Cefalu</name></author><author><name sortKey="Bellaire, Bh" uniqKey="Bellaire B">BH Bellaire</name></author><author><name sortKey="Cardelli, Ja" uniqKey="Cardelli J">JA Cardelli</name></author><author><name sortKey="Louis, T" uniqKey="Louis T">T Louis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rehman, Au" uniqKey="Rehman A">AU Rehman</name></author><author><name sortKey="Gul, K" uniqKey="Gul K">K Gul</name></author><author><name sortKey="Morell, Rj" uniqKey="Morell R">RJ Morell</name></author><author><name sortKey="Lee, K" uniqKey="Lee K">K Lee</name></author><author><name sortKey="Ahmed, Zm" uniqKey="Ahmed Z">ZM Ahmed</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Turquie</li><li>États-Unis</li></country><region><li>Floride</li></region></list><tree><country name="États-Unis"><region name="Floride"><name sortKey="Sirmaci, Asli" sort="Sirmaci, Asli" uniqKey="Sirmaci A" first="Asli" last="Sirmaci">Asli Sirmaci</name></region><name sortKey="Edwards, Yvonne J K" sort="Edwards, Yvonne J K" uniqKey="Edwards Y" first="Yvonne J. K." last="Edwards">Yvonne J. K. Edwards</name><name sortKey="Edwards, Yvonne J K" sort="Edwards, Yvonne J K" uniqKey="Edwards Y" first="Yvonne J. K." last="Edwards">Yvonne J. K. Edwards</name><name sortKey="Sirmaci, Asli" sort="Sirmaci, Asli" uniqKey="Sirmaci A" first="Asli" last="Sirmaci">Asli Sirmaci</name><name sortKey="Tekin, Mustafa" sort="Tekin, Mustafa" uniqKey="Tekin M" first="Mustafa" last="Tekin">Mustafa Tekin</name><name sortKey="Tekin, Mustafa" sort="Tekin, Mustafa" uniqKey="Tekin M" first="Mustafa" last="Tekin">Mustafa Tekin</name></country><country name="Turquie"><noRegion><name sortKey="Akay, Hatice" sort="Akay, Hatice" uniqKey="Akay H" first="Hatice" last="Akay">Hatice Akay</name></noRegion><name sortKey="Tekin, Mustafa" sort="Tekin, Mustafa" uniqKey="Tekin M" first="Mustafa" last="Tekin">Mustafa Tekin</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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