De Novo Occurrence of a Variant in ARL3 and Apparent Autosomal Dominant Transmission of Retinitis Pigmentosa
Identifieur interne : 008011 ( Ncbi/Checkpoint ); précédent : 008010; suivant : 008012De Novo Occurrence of a Variant in ARL3 and Apparent Autosomal Dominant Transmission of Retinitis Pigmentosa
Auteurs : Samuel P. Strom [États-Unis] ; Michael J. Clark [États-Unis] ; Ariadna Martinez [États-Unis] ; Sarah Garcia [États-Unis] ; Amira A. Abelazeem [Égypte] ; Anna Matynia [États-Unis] ; Sachin Parikh [États-Unis] ; Lori S. Sullivan [États-Unis] ; Sara J. Bowne [États-Unis] ; Stephen P. Daiger [États-Unis] ; Michael B. Gorin [États-Unis]Source :
- PLoS ONE [ 1932-6203 ] ; 2016.
Abstract
Retinitis pigmentosa is a phenotype with diverse genetic causes. Due to this genetic heterogeneity, genome-wide identification and analysis of protein-altering DNA variants by exome sequencing is a powerful tool for novel variant and disease gene discovery. In this study, exome sequencing analysis was used to search for potentially causal DNA variants in a two-generation pedigree with apparent dominant retinitis pigmentosa.
Variant identification and analysis of three affected members (mother and two affected offspring) was performed via exome sequencing. Parental samples of the index case were used to establish inheritance. Follow-up testing of 94 additional retinitis pigmentosa pedigrees was performed via retrospective analysis or Sanger sequencing.
A total of 136 high quality coding variants in 123 genes were identified which are consistent with autosomal dominant disease. Of these, one of the strongest genetic and functional candidates is a c.269A>G (p.Tyr90Cys) variant in
Url:
DOI: 10.1371/journal.pone.0150944
PubMed: 26964041
PubMed Central: 4786330
Affiliations:
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Clark</name><affiliation wicri:level="2"><nlm:aff id="aff002"><addr-line>Personalis Inc., Menlo Park, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Personalis Inc., Menlo Park, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Martinez, Ariadna" sort="Martinez, Ariadna" uniqKey="Martinez A" first="Ariadna" last="Martinez">Ariadna Martinez</name><affiliation wicri:level="2"><nlm:aff id="aff003"><addr-line>Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Garcia, Sarah" sort="Garcia, Sarah" uniqKey="Garcia S" first="Sarah" last="Garcia">Sarah Garcia</name><affiliation wicri:level="2"><nlm:aff id="aff002"><addr-line>Personalis Inc., Menlo Park, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Personalis Inc., Menlo Park, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Abelazeem, Amira A" sort="Abelazeem, Amira A" uniqKey="Abelazeem A" first="Amira A." last="Abelazeem">Amira A. Abelazeem</name><affiliation wicri:level="1"><nlm:aff id="aff004"><addr-line>Research Institute of Ophthalmology, Cairo, Egypt</addr-line></nlm:aff><country xml:lang="fr">Égypte</country><wicri:regionArea>Research Institute of Ophthalmology, Cairo</wicri:regionArea><wicri:noRegion>Cairo</wicri:noRegion></affiliation></author><author><name sortKey="Matynia, Anna" sort="Matynia, Anna" uniqKey="Matynia A" first="Anna" last="Matynia">Anna Matynia</name><affiliation wicri:level="2"><nlm:aff id="aff005"><addr-line>Jules Stein Eye Institute and Department of Ophthalmology, University of California Los Angeles, Los Angeles, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Jules Stein Eye Institute and Department of Ophthalmology, University of California Los Angeles, Los Angeles, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Parikh, Sachin" sort="Parikh, Sachin" uniqKey="Parikh S" first="Sachin" last="Parikh">Sachin Parikh</name><affiliation wicri:level="2"><nlm:aff id="aff005"><addr-line>Jules Stein Eye Institute and Department of Ophthalmology, University of California Los Angeles, Los Angeles, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Jules Stein Eye Institute and Department of Ophthalmology, University of California Los Angeles, Los Angeles, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Sullivan, Lori S" sort="Sullivan, Lori S" uniqKey="Sullivan L" first="Lori S." last="Sullivan">Lori S. 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Strom</name><affiliation wicri:level="2"><nlm:aff id="aff001"><addr-line>Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Clark, Michael J" sort="Clark, Michael J" uniqKey="Clark M" first="Michael J." last="Clark">Michael J. Clark</name><affiliation wicri:level="2"><nlm:aff id="aff002"><addr-line>Personalis Inc., Menlo Park, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Personalis Inc., Menlo Park, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Martinez, Ariadna" sort="Martinez, Ariadna" uniqKey="Martinez A" first="Ariadna" last="Martinez">Ariadna Martinez</name><affiliation wicri:level="2"><nlm:aff id="aff003"><addr-line>Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Garcia, Sarah" sort="Garcia, Sarah" uniqKey="Garcia S" first="Sarah" last="Garcia">Sarah Garcia</name><affiliation wicri:level="2"><nlm:aff id="aff002"><addr-line>Personalis Inc., Menlo Park, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Personalis Inc., Menlo Park, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Abelazeem, Amira A" sort="Abelazeem, Amira A" uniqKey="Abelazeem A" first="Amira A." last="Abelazeem">Amira A. Abelazeem</name><affiliation wicri:level="1"><nlm:aff id="aff004"><addr-line>Research Institute of Ophthalmology, Cairo, Egypt</addr-line></nlm:aff><country xml:lang="fr">Égypte</country><wicri:regionArea>Research Institute of Ophthalmology, Cairo</wicri:regionArea><wicri:noRegion>Cairo</wicri:noRegion></affiliation></author><author><name sortKey="Matynia, Anna" sort="Matynia, Anna" uniqKey="Matynia A" first="Anna" last="Matynia">Anna Matynia</name><affiliation wicri:level="2"><nlm:aff id="aff005"><addr-line>Jules Stein Eye Institute and Department of Ophthalmology, University of California Los Angeles, Los Angeles, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Jules Stein Eye Institute and Department of Ophthalmology, University of California Los Angeles, Los Angeles, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Parikh, Sachin" sort="Parikh, Sachin" uniqKey="Parikh S" first="Sachin" last="Parikh">Sachin Parikh</name><affiliation wicri:level="2"><nlm:aff id="aff005"><addr-line>Jules Stein Eye Institute and Department of Ophthalmology, University of California Los Angeles, Los Angeles, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Jules Stein Eye Institute and Department of Ophthalmology, University of California Los Angeles, Los Angeles, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Sullivan, Lori S" sort="Sullivan, Lori S" uniqKey="Sullivan L" first="Lori S." last="Sullivan">Lori S. Sullivan</name><affiliation wicri:level="2"><nlm:aff id="aff006"><addr-line>Human Genetics Center, University of Texas Health Science Center, Houston, Texas, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Human Genetics Center, University of Texas Health Science Center, Houston, Texas</wicri:regionArea><placeName><region type="state">Texas</region></placeName></affiliation></author><author><name sortKey="Bowne, Sara J" sort="Bowne, Sara J" uniqKey="Bowne S" first="Sara J." last="Bowne">Sara J. Bowne</name><affiliation wicri:level="2"><nlm:aff id="aff006"><addr-line>Human Genetics Center, University of Texas Health Science Center, Houston, Texas, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Human Genetics Center, University of Texas Health Science Center, Houston, Texas</wicri:regionArea><placeName><region type="state">Texas</region></placeName></affiliation></author><author><name sortKey="Daiger, Stephen P" sort="Daiger, Stephen P" uniqKey="Daiger S" first="Stephen P." last="Daiger">Stephen P. Daiger</name><affiliation wicri:level="2"><nlm:aff id="aff006"><addr-line>Human Genetics Center, University of Texas Health Science Center, Houston, Texas, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Human Genetics Center, University of Texas Health Science Center, Houston, Texas</wicri:regionArea><placeName><region type="state">Texas</region></placeName></affiliation></author><author><name sortKey="Gorin, Michael B" sort="Gorin, Michael B" uniqKey="Gorin M" first="Michael B." last="Gorin">Michael B. Gorin</name><affiliation wicri:level="2"><nlm:aff id="aff005"><addr-line>Jules Stein Eye Institute and Department of Ophthalmology, University of California Los Angeles, Los Angeles, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Jules Stein Eye Institute and Department of Ophthalmology, University of California Los Angeles, Los Angeles, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec id="sec001"><title>Background</title><p>Retinitis pigmentosa is a phenotype with diverse genetic causes. Due to this genetic heterogeneity, genome-wide identification and analysis of protein-altering DNA variants by exome sequencing is a powerful tool for novel variant and disease gene discovery. In this study, exome sequencing analysis was used to search for potentially causal DNA variants in a two-generation pedigree with apparent dominant retinitis pigmentosa.</p></sec><sec id="sec002"><title>Methods</title><p>Variant identification and analysis of three affected members (mother and two affected offspring) was performed via exome sequencing. Parental samples of the index case were used to establish inheritance. Follow-up testing of 94 additional retinitis pigmentosa pedigrees was performed via retrospective analysis or Sanger sequencing.</p></sec><sec id="sec003"><title>Results and Conclusions</title><p>A total of 136 high quality coding variants in 123 genes were identified which are consistent with autosomal dominant disease. Of these, one of the strongest genetic and functional candidates is a c.269A>G (p.Tyr90Cys) variant in <italic>ARL3</italic>. Follow-up testing established that this variant occurred <italic>de novo</italic> in the index case. No additional putative causal variants in <italic>ARL3</italic> were identified in the follow-up cohort, suggesting that if <italic>ARL3</italic> variants can cause adRP it is an extremely rare phenomenon.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Haim, M" uniqKey="Haim M">M Haim</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fahim, At" uniqKey="Fahim A">AT Fahim</name></author><author><name sortKey="Daiger, Sp" uniqKey="Daiger S">SP Daiger</name></author><author><name sortKey="Weleber, Rg" uniqKey="Weleber R">RG Weleber</name></author><author><name sortKey="Pagon, Ra" uniqKey="Pagon R">RA Pagon</name></author><author><name sortKey="Adam, Mp" uniqKey="Adam M">MP Adam</name></author><author><name sortKey="Bird, Td" uniqKey="Bird T">TD Bird</name></author><author><name sortKey="Dolan, Cr" uniqKey="Dolan C">CR Dolan</name></author><author><name sortKey="Fong, Ct" uniqKey="Fong C">CT 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Strom</name></region><name sortKey="Bowne, Sara J" sort="Bowne, Sara J" uniqKey="Bowne S" first="Sara J." last="Bowne">Sara J. Bowne</name><name sortKey="Clark, Michael J" sort="Clark, Michael J" uniqKey="Clark M" first="Michael J." last="Clark">Michael J. Clark</name><name sortKey="Daiger, Stephen P" sort="Daiger, Stephen P" uniqKey="Daiger S" first="Stephen P." last="Daiger">Stephen P. Daiger</name><name sortKey="Garcia, Sarah" sort="Garcia, Sarah" uniqKey="Garcia S" first="Sarah" last="Garcia">Sarah Garcia</name><name sortKey="Gorin, Michael B" sort="Gorin, Michael B" uniqKey="Gorin M" first="Michael B." last="Gorin">Michael B. Gorin</name><name sortKey="Martinez, Ariadna" sort="Martinez, Ariadna" uniqKey="Martinez A" first="Ariadna" last="Martinez">Ariadna Martinez</name><name sortKey="Matynia, Anna" sort="Matynia, Anna" uniqKey="Matynia A" first="Anna" last="Matynia">Anna Matynia</name><name sortKey="Parikh, Sachin" sort="Parikh, Sachin" uniqKey="Parikh S" first="Sachin" last="Parikh">Sachin Parikh</name><name sortKey="Sullivan, Lori S" sort="Sullivan, Lori S" uniqKey="Sullivan L" first="Lori S." last="Sullivan">Lori S. Sullivan</name></country><country name="Égypte"><noRegion><name sortKey="Abelazeem, Amira A" sort="Abelazeem, Amira A" uniqKey="Abelazeem A" first="Amira A." last="Abelazeem">Amira A. Abelazeem</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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