Extensive Variation in the Mutation Rate Between and Within Human Genes Associated with Mendelian Disease.
Identifieur interne : 001F17 ( Main/Exploration ); précédent : 001F16; suivant : 001F18Extensive Variation in the Mutation Rate Between and Within Human Genes Associated with Mendelian Disease.
Auteurs : Thomas Smith [Royaume-Uni] ; Gladys Ho [Australie] ; John Christodoulou [Australie] ; Elizabeth Ann Price [Royaume-Uni] ; Zerrin Onadim [Royaume-Uni] ; Marion Gauthier-Villars [France] ; Catherine Dehainault [France] ; Claude Houdayer [France] ; Beatrice Parfait [France] ; Rick Van Minkelen [Pays-Bas] ; Dietmar Lohman [Allemagne] ; Adam Eyre-Walker [Royaume-Uni]Source :
- Human mutation [ 1098-1004 ] ; 2016.
Descripteurs français
- KwdFr :
- Algorithmes, Codon non-sens, Humains, Hétérogénéité génétique, Ilots CpG, Neurofibromine-1 (génétique), Protéine-2 de liaison au CpG méthylé (génétique), Protéines de liaison à la protéine du rétinoblastome (génétique), Prédisposition génétique à une maladie (génétique), Taux de mutation, Ubiquitin-protein ligases (génétique).
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Methyl-CpG-Binding Protein 2, Neurofibromin 1, Retinoblastoma Binding Proteins, Ubiquitin-Protein Ligases.
- chemical : Codon, Nonsense.
- genetics : Genetic Predisposition to Disease.
- Algorithms, CpG Islands, Genetic Heterogeneity, Humans, Mutation Rate.
Abstract
We have investigated whether the mutation rate varies between genes and sites using de novo mutations (DNMs) from three genes associated with Mendelian diseases (RB1, NF1, and MECP2). We show that the relative frequency of mutations at CpG dinucleotides relative to non-CpG sites varies between genes and relative to the genomic average. In particular we show that the rate of transition mutation at CpG sites relative to the rate of non-CpG transversion is substantially higher in our disease genes than amongst DNMs in general; the rate of CpG transition can be several hundred-fold greater than the rate of non-CpG transversion. We also show that the mutation rate varies significantly between sites of a particular mutational type, such as non-CpG transversion, within a gene. We estimate that for all categories of sites, except CpG transitions, there is at least a 30-fold difference in the mutation rate between the 10% of sites with the highest and lowest mutation rates. However, our best estimate is that the mutation rate varies by several hundred-fold variation. We suggest that the presence of hypermutable sites may be one reason certain genes are associated with disease.
DOI: 10.1002/humu.22967
PubMed: 26857394
Affiliations:
- Allemagne, Australie, France, Pays-Bas, Royaume-Uni
- Angleterre, Grand Londres, Hollande-Méridionale, Nouvelle-Galles du Sud, Sussex de l'Est, Île-de-France
- Brighton, Falmer, Londres, Paris, Rotterdam, Sydney
- Université Paris-Descartes, Université du Sussex
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last="Ho">Gladys Ho</name><affiliation wicri:level="3"><nlm:affiliation>NSW Centre for Rett Syndrome Research, Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>NSW Centre for Rett Syndrome Research, Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney</wicri:regionArea><placeName><settlement type="city">Sydney</settlement><region type="état">Nouvelle-Galles du Sud</region></placeName></affiliation></author><author><name sortKey="Christodoulou, John" sort="Christodoulou, John" uniqKey="Christodoulou J" first="John" last="Christodoulou">John Christodoulou</name><affiliation wicri:level="3"><nlm:affiliation>NSW Centre for Rett Syndrome Research, Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>NSW Centre for Rett Syndrome Research, Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney</wicri:regionArea><placeName><settlement type="city">Sydney</settlement><region type="état">Nouvelle-Galles du Sud</region></placeName></affiliation></author><author><name sortKey="Price, Elizabeth Ann" sort="Price, Elizabeth Ann" uniqKey="Price E" first="Elizabeth Ann" last="Price">Elizabeth Ann Price</name><affiliation wicri:level="3"><nlm:affiliation>Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, The Royal London Hospital, 80 Newark Street, London, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, The Royal London Hospital, 80 Newark Street, London</wicri:regionArea><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Onadim, Zerrin" sort="Onadim, Zerrin" uniqKey="Onadim Z" first="Zerrin" last="Onadim">Zerrin Onadim</name><affiliation wicri:level="3"><nlm:affiliation>Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, The Royal London Hospital, 80 Newark Street, London, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, The Royal London Hospital, 80 Newark Street, London</wicri:regionArea><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Gauthier Villars, Marion" sort="Gauthier Villars, Marion" uniqKey="Gauthier Villars M" first="Marion" last="Gauthier-Villars">Marion Gauthier-Villars</name><affiliation wicri:level="3"><nlm:affiliation>Service de Génétique, Institut Curie, Paris, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Service de Génétique, Institut Curie, Paris</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author><author><name sortKey="Dehainault, Catherine" sort="Dehainault, Catherine" uniqKey="Dehainault C" first="Catherine" last="Dehainault">Catherine Dehainault</name><affiliation wicri:level="3"><nlm:affiliation>Service de Génétique, Institut Curie, Paris, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Service de Génétique, Institut Curie, Paris</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author><author><name sortKey="Houdayer, Claude" sort="Houdayer, Claude" uniqKey="Houdayer C" first="Claude" last="Houdayer">Claude Houdayer</name><affiliation wicri:level="3"><nlm:affiliation>Service de Génétique, Institut Curie, Paris, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Service de Génétique, Institut Curie, Paris</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author><author><name sortKey="Parfait, Beatrice" sort="Parfait, Beatrice" uniqKey="Parfait B" first="Beatrice" last="Parfait">Beatrice Parfait</name><affiliation wicri:level="4"><nlm:affiliation>EA7331, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>EA7331, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, Paris</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Paris</settlement><settlement type="city">Paris</settlement></placeName><orgName type="university">Université Paris-Descartes</orgName></affiliation></author><author><name sortKey="Van Minkelen, Rick" sort="Van Minkelen, Rick" uniqKey="Van Minkelen R" first="Rick" last="Van Minkelen">Rick Van Minkelen</name><affiliation wicri:level="3"><nlm:affiliation>Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, Netherlands.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Clinical Genetics, Erasmus Medical Center, Rotterdam</wicri:regionArea><placeName><settlement type="city">Rotterdam</settlement><region nuts="2" type="province">Hollande-Méridionale</region></placeName></affiliation></author><author><name sortKey="Lohman, Dietmar" sort="Lohman, Dietmar" uniqKey="Lohman D" first="Dietmar" last="Lohman">Dietmar Lohman</name><affiliation wicri:level="1"><nlm:affiliation>Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen</wicri:regionArea><wicri:noRegion>Essen</wicri:noRegion><wicri:noRegion>Essen</wicri:noRegion><wicri:noRegion>Essen</wicri:noRegion></affiliation></author><author><name sortKey="Eyre Walker, Adam" sort="Eyre Walker, Adam" uniqKey="Eyre Walker A" first="Adam" last="Eyre-Walker">Adam Eyre-Walker</name><affiliation wicri:level="4"><nlm:affiliation>School of Life Sciences, University of Sussex, Brighton, United Kingdom.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>School of Life Sciences, University of Sussex, Brighton</wicri:regionArea><orgName type="university">Université du Sussex</orgName><placeName><settlement type="city">Brighton</settlement><settlement type="town">Falmer</settlement><region type="nation">Angleterre</region><region nuts="2" type="region">Sussex de l'Est</region></placeName></affiliation></author></analytic><series><title level="j">Human mutation</title><idno type="eISSN">1098-1004</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Codon, Nonsense</term><term>CpG Islands</term><term>Genetic Heterogeneity</term><term>Genetic Predisposition to Disease (genetics)</term><term>Humans</term><term>Methyl-CpG-Binding Protein 2 (genetics)</term><term>Mutation Rate</term><term>Neurofibromin 1 (genetics)</term><term>Retinoblastoma Binding Proteins (genetics)</term><term>Ubiquitin-Protein Ligases (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Codon non-sens</term><term>Humains</term><term>Hétérogénéité génétique</term><term>Ilots CpG</term><term>Neurofibromine-1 (génétique)</term><term>Protéine-2 de liaison au CpG méthylé (génétique)</term><term>Protéines de liaison à la protéine du rétinoblastome (génétique)</term><term>Prédisposition génétique à une maladie (génétique)</term><term>Taux de mutation</term><term>Ubiquitin-protein ligases (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Methyl-CpG-Binding Protein 2</term><term>Neurofibromin 1</term><term>Retinoblastoma Binding Proteins</term><term>Ubiquitin-Protein Ligases</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Codon, Nonsense</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genetic Predisposition to Disease</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Neurofibromine-1</term><term>Protéine-2 de liaison au CpG méthylé</term><term>Protéines de liaison à la protéine du rétinoblastome</term><term>Prédisposition génétique à une maladie</term><term>Ubiquitin-protein ligases</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>CpG Islands</term><term>Genetic Heterogeneity</term><term>Humans</term><term>Mutation Rate</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Codon non-sens</term><term>Humains</term><term>Hétérogénéité génétique</term><term>Ilots CpG</term><term>Taux de mutation</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We have investigated whether the mutation rate varies between genes and sites using de novo mutations (DNMs) from three genes associated with Mendelian diseases (RB1, NF1, and MECP2). We show that the relative frequency of mutations at CpG dinucleotides relative to non-CpG sites varies between genes and relative to the genomic average. In particular we show that the rate of transition mutation at CpG sites relative to the rate of non-CpG transversion is substantially higher in our disease genes than amongst DNMs in general; the rate of CpG transition can be several hundred-fold greater than the rate of non-CpG transversion. We also show that the mutation rate varies significantly between sites of a particular mutational type, such as non-CpG transversion, within a gene. We estimate that for all categories of sites, except CpG transitions, there is at least a 30-fold difference in the mutation rate between the 10% of sites with the highest and lowest mutation rates. However, our best estimate is that the mutation rate varies by several hundred-fold variation. We suggest that the presence of hypermutable sites may be one reason certain genes are associated with disease.</div></front></TEI><affiliations><list><country><li>Allemagne</li><li>Australie</li><li>France</li><li>Pays-Bas</li><li>Royaume-Uni</li></country><region><li>Angleterre</li><li>Grand Londres</li><li>Hollande-Méridionale</li><li>Nouvelle-Galles du Sud</li><li>Sussex de l'Est</li><li>Île-de-France</li></region><settlement><li>Brighton</li><li>Falmer</li><li>Londres</li><li>Paris</li><li>Rotterdam</li><li>Sydney</li></settlement><orgName><li>Université Paris-Descartes</li><li>Université du Sussex</li></orgName></list><tree><country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Smith, Thomas" sort="Smith, Thomas" uniqKey="Smith T" first="Thomas" last="Smith">Thomas Smith</name></region><name sortKey="Eyre Walker, Adam" sort="Eyre Walker, Adam" uniqKey="Eyre Walker A" first="Adam" last="Eyre-Walker">Adam Eyre-Walker</name><name sortKey="Onadim, Zerrin" sort="Onadim, Zerrin" uniqKey="Onadim Z" first="Zerrin" last="Onadim">Zerrin Onadim</name><name sortKey="Price, Elizabeth Ann" sort="Price, Elizabeth Ann" uniqKey="Price E" first="Elizabeth Ann" last="Price">Elizabeth Ann Price</name></country><country name="Australie"><region name="Nouvelle-Galles du Sud"><name sortKey="Ho, Gladys" sort="Ho, Gladys" uniqKey="Ho G" first="Gladys" last="Ho">Gladys Ho</name></region><name sortKey="Christodoulou, John" sort="Christodoulou, John" uniqKey="Christodoulou J" first="John" last="Christodoulou">John Christodoulou</name></country><country name="France"><region name="Île-de-France"><name sortKey="Gauthier Villars, Marion" sort="Gauthier Villars, Marion" uniqKey="Gauthier Villars M" first="Marion" last="Gauthier-Villars">Marion Gauthier-Villars</name></region><name sortKey="Dehainault, Catherine" sort="Dehainault, Catherine" uniqKey="Dehainault C" first="Catherine" last="Dehainault">Catherine Dehainault</name><name sortKey="Houdayer, Claude" sort="Houdayer, Claude" uniqKey="Houdayer C" first="Claude" last="Houdayer">Claude Houdayer</name><name sortKey="Parfait, Beatrice" sort="Parfait, Beatrice" uniqKey="Parfait B" first="Beatrice" last="Parfait">Beatrice Parfait</name></country><country name="Pays-Bas"><region name="Hollande-Méridionale"><name sortKey="Van Minkelen, Rick" sort="Van Minkelen, Rick" uniqKey="Van Minkelen R" first="Rick" last="Van Minkelen">Rick Van Minkelen</name></region></country><country name="Allemagne"><noRegion><name sortKey="Lohman, Dietmar" sort="Lohman, Dietmar" uniqKey="Lohman D" first="Dietmar" last="Lohman">Dietmar Lohman</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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