AustralieFrV1, Main, Exploration, bibRecord, 002C54

Imputation of KIR Types from SNP Variation Data

Identifieur interne : 002C54 ( Main/Exploration ); précédent : 002C53; suivant : 002C55

Imputation of KIR Types from SNP Variation Data

Auteurs : Damjan Vukcevic [Australie] ; James A. Traherne [Royaume-Uni] ; Sigrid N Ss [Norvège] ; Eva Ellinghaus [Allemagne] ; Yoichiro Kamatani [France, Japon] ; Alexander Dilthey [Royaume-Uni] ; Mark Lathrop [Canada, France] ; Tom H. Karlsen [Norvège] ; Andre Franke [Allemagne] ; Miriam Moffatt [Royaume-Uni] ; William Cookson [Royaume-Uni] ; John Trowsdale [Royaume-Uni] ; Gil Mcvean [Royaume-Uni] ; Stephen Sawcer [Royaume-Uni] ; Stephen Leslie [Australie]

Source :

American Journal of Human Genetics [ 0002-9297 ] ; 2015.

RBID : PMC:4596914

Descripteurs français

English descriptors

KwdEn :
- Asthma (genetics), Case-Control Studies, Cohort Studies, DNA Copy Number Variations (genetics), Dermatitis, Atopic (genetics), Europe, Family, Female, Genetic Predisposition to Disease, Genotype, High-Throughput Nucleotide Sequencing, Humans, Male, Polymorphism, Single Nucleotide (genetics), Receptors, KIR (classification), Receptors, KIR (genetics), Sequence Analysis, DNA.
MESH :
- chemical , classification : Receptors, KIR.
- chemical , genetics : Receptors, KIR.
- geographic : Europe.
- genetics : Asthma, DNA Copy Number Variations, Dermatitis, Atopic, Polymorphism, Single Nucleotide.
- Case-Control Studies, Cohort Studies, Family, Female, Genetic Predisposition to Disease, Genotype, High-Throughput Nucleotide Sequencing, Humans, Male, Sequence Analysis, DNA.

Abstract

Large population studies of immune system genes are essential for characterizing their role in diseases, including autoimmune conditions. Of key interest are a group of genes encoding the killer cell immunoglobulin-like receptors (KIRs), which have known and hypothesized roles in autoimmune diseases, resistance to viruses, reproductive conditions, and cancer. These genes are highly polymorphic, which makes typing expensive and time consuming. Consequently, despite their importance, KIRs have been little studied in large cohorts. Statistical imputation methods developed for other complex loci (e.g., human leukocyte antigen [HLA]) on the basis of SNP data provide an inexpensive high-throughput alternative to direct laboratory typing of these loci and have enabled important findings and insights for many diseases. We present KIR^∗IMP, a method for imputation of KIR copy number. We show that KIR^∗IMP is highly accurate and thus allows the study of KIRs in large cohorts and enables detailed investigation of the role of KIRs in human disease.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4596914

DOI: 10.1016/j.ajhg.2015.09.005
PubMed: 26430804
PubMed Central: 4596914

Affiliations:

Le document en format XML

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<author><name sortKey="Dilthey, Alexander" sort="Dilthey, Alexander" uniqKey="Dilthey A" first="Alexander" last="Dilthey">Alexander Dilthey</name>
<affiliation wicri:level="4"><nlm:aff id="aff10">Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN</wicri:regionArea>
<orgName type="university">Université d'Oxford</orgName>
<placeName><settlement type="city">Oxford</settlement>
<region type="nation">Angleterre</region>
<region type="région" nuts="1">Oxfordshire</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Lathrop, Mark" sort="Lathrop, Mark" uniqKey="Lathrop M" first="Mark" last="Lathrop">Mark Lathrop</name>
<affiliation wicri:level="1"><nlm:aff id="aff11">McGill University and Génome Québec Innovation Centre, Montreal, 740 Dr. Penfield Avenue, Room 7104, Montreal, QC H3A 0G1, Canada</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>McGill University and Génome Québec Innovation Centre, Montreal, 740 Dr. Penfield Avenue, Room 7104, Montreal, QC H3A 0G1</wicri:regionArea>
<wicri:noRegion>QC H3A 0G1</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="aff8">Fondation Jean Dausset, Centre d’Etude du Polymorphisme Humain, 27 Rue Juliette Dodu, 75010 Paris, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Fondation Jean Dausset, Centre d’Etude du Polymorphisme Humain, 27 Rue Juliette Dodu, 75010 Paris</wicri:regionArea>
<wicri:noRegion>75010 Paris</wicri:noRegion>
<placeName><settlement type="city">Paris</settlement>
<region type="région" nuts="2">Île-de-France</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Karlsen, Tom H" sort="Karlsen, Tom H" uniqKey="Karlsen T" first="Tom H." last="Karlsen">Tom H. Karlsen</name>
<affiliation wicri:level="1"><nlm:aff id="aff5">Research Institute of Internal Medicine, Department of Cancer Medicine, Surgery, and Transplantation, Oslo University Hospital Rikshospitalet, Postboks 4950, Nydalen, 0424 Oslo, Norway</nlm:aff>
<country xml:lang="fr">Norvège</country>
<wicri:regionArea>Research Institute of Internal Medicine, Department of Cancer Medicine, Surgery, and Transplantation, Oslo University Hospital Rikshospitalet, Postboks 4950, Nydalen, 0424 Oslo</wicri:regionArea>
<placeName><settlement type="city">Oslo</settlement>
<region nuts="2">Østlandet</region>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="aff12">K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Postboks 1171, Blindern, 0318 Oslo, Norway</nlm:aff>
<country xml:lang="fr">Norvège</country>
<wicri:regionArea>K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Postboks 1171, Blindern, 0318 Oslo</wicri:regionArea>
<placeName><settlement type="city">Oslo</settlement>
<region nuts="2">Østlandet</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Franke, Andre" sort="Franke, Andre" uniqKey="Franke A" first="Andre" last="Franke">Andre Franke</name>
<affiliation wicri:level="3"><nlm:aff id="aff7">Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Schittenhelmstraße 12, 24105 Kiel, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Schittenhelmstraße 12, 24105 Kiel</wicri:regionArea>
<placeName><region type="land" nuts="2">Schleswig-Holstein</region>
<settlement type="city">Kiel</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Moffatt, Miriam" sort="Moffatt, Miriam" uniqKey="Moffatt M" first="Miriam" last="Moffatt">Miriam Moffatt</name>
<affiliation wicri:level="1"><nlm:aff id="aff13">National Heart and Lung Institute, Imperial College London, Royal Brompton Campus, Dovehouse Street, London SW3 6LY, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>National Heart and Lung Institute, Imperial College London, Royal Brompton Campus, Dovehouse Street, London SW3 6LY</wicri:regionArea>
<wicri:noRegion>London SW3 6LY</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Cookson, William" sort="Cookson, William" uniqKey="Cookson W" first="William" last="Cookson">William Cookson</name>
<affiliation wicri:level="1"><nlm:aff id="aff13">National Heart and Lung Institute, Imperial College London, Royal Brompton Campus, Dovehouse Street, London SW3 6LY, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>National Heart and Lung Institute, Imperial College London, Royal Brompton Campus, Dovehouse Street, London SW3 6LY</wicri:regionArea>
<wicri:noRegion>London SW3 6LY</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Trowsdale, John" sort="Trowsdale, John" uniqKey="Trowsdale J" first="John" last="Trowsdale">John Trowsdale</name>
<affiliation wicri:level="4"><nlm:aff id="aff3">Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY</wicri:regionArea>
<orgName type="university">Université de Cambridge</orgName>
<placeName><settlement type="city">Cambridge</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Angleterre de l'Est</region>
</placeName>
</affiliation>
<affiliation wicri:level="4"><nlm:aff id="aff4">Division of Immunology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Division of Immunology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP</wicri:regionArea>
<orgName type="university">Université de Cambridge</orgName>
<placeName><settlement type="city">Cambridge</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Angleterre de l'Est</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Mcvean, Gil" sort="Mcvean, Gil" uniqKey="Mcvean G" first="Gil" last="Mcvean">Gil Mcvean</name>
<affiliation wicri:level="4"><nlm:aff id="aff10">Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN</wicri:regionArea>
<orgName type="university">Université d'Oxford</orgName>
<placeName><settlement type="city">Oxford</settlement>
<region type="nation">Angleterre</region>
<region type="région" nuts="1">Oxfordshire</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Sawcer, Stephen" sort="Sawcer, Stephen" uniqKey="Sawcer S" first="Stephen" last="Sawcer">Stephen Sawcer</name>
<affiliation wicri:level="4"><nlm:aff id="aff14">Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ</wicri:regionArea>
<orgName type="university">Université de Cambridge</orgName>
<placeName><settlement type="city">Cambridge</settlement>
<region type="country">Angleterre</region>
<region type="région" nuts="1">Angleterre de l'Est</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Leslie, Stephen" sort="Leslie, Stephen" uniqKey="Leslie S" first="Stephen" last="Leslie">Stephen Leslie</name>
<affiliation wicri:level="1"><nlm:aff id="aff1">Statistical Genetics, Murdoch Childrens Research Institute, Parkville, VIC 3052, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Statistical Genetics, Murdoch Childrens Research Institute, Parkville, VIC 3052</wicri:regionArea>
<wicri:noRegion>VIC 3052</wicri:noRegion>
</affiliation>
<affiliation wicri:level="4"><nlm:aff id="aff2">School of Mathematics and Statistics, University of Melbourne, Parkville, VIC 3010, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Mathematics and Statistics, University of Melbourne, Parkville, VIC 3010</wicri:regionArea>
<orgName type="university">Université de Melbourne</orgName>
<placeName><settlement type="city">Melbourne</settlement>
<region type="état">Victoria (État)</region>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j">American Journal of Human Genetics</title>
<idno type="ISSN">0002-9297</idno>
<idno type="eISSN">1537-6605</idno>
<imprint><date when="2015">2015</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Asthma (genetics)</term>
<term>Case-Control Studies</term>
<term>Cohort Studies</term>
<term>DNA Copy Number Variations (genetics)</term>
<term>Dermatitis, Atopic (genetics)</term>
<term>Europe</term>
<term>Family</term>
<term>Female</term>
<term>Genetic Predisposition to Disease</term>
<term>Genotype</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Humans</term>
<term>Male</term>
<term>Polymorphism, Single Nucleotide (genetics)</term>
<term>Receptors, KIR (classification)</term>
<term>Receptors, KIR (genetics)</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN</term>
<term>Asthme (génétique)</term>
<term>Eczéma atopique (génétique)</term>
<term>Europe</term>
<term>Famille</term>
<term>Femelle</term>
<term>Génotype</term>
<term>Humains</term>
<term>Mâle</term>
<term>Polymorphisme de nucléotide simple (génétique)</term>
<term>Prédisposition génétique à une maladie</term>
<term>Récepteurs KIR ()</term>
<term>Récepteurs KIR (génétique)</term>
<term>Séquençage nucléotidique à haut débit</term>
<term>Variations de nombre de copies de segment d'ADN (génétique)</term>
<term>Études cas-témoins</term>
<term>Études de cohortes</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="classification" xml:lang="en"><term>Receptors, KIR</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Receptors, KIR</term>
</keywords>
<keywords scheme="MESH" type="geographic" xml:lang="en"><term>Europe</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Asthma</term>
<term>DNA Copy Number Variations</term>
<term>Dermatitis, Atopic</term>
<term>Polymorphism, Single Nucleotide</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Asthme</term>
<term>Eczéma atopique</term>
<term>Polymorphisme de nucléotide simple</term>
<term>Récepteurs KIR</term>
<term>Variations de nombre de copies de segment d'ADN</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Case-Control Studies</term>
<term>Cohort Studies</term>
<term>Family</term>
<term>Female</term>
<term>Genetic Predisposition to Disease</term>
<term>Genotype</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Humans</term>
<term>Male</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term>
<term>Europe</term>
<term>Famille</term>
<term>Femelle</term>
<term>Génotype</term>
<term>Humains</term>
<term>Mâle</term>
<term>Prédisposition génétique à une maladie</term>
<term>Récepteurs KIR</term>
<term>Séquençage nucléotidique à haut débit</term>
<term>Études cas-témoins</term>
<term>Études de cohortes</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>Large population studies of immune system genes are essential for characterizing their role in diseases, including autoimmune conditions. Of key interest are a group of genes encoding the killer cell immunoglobulin-like receptors (KIRs), which have known and hypothesized roles in autoimmune diseases, resistance to viruses, reproductive conditions, and cancer. These genes are highly polymorphic, which makes typing expensive and time consuming. Consequently, despite their importance, KIRs have been little studied in large cohorts. Statistical imputation methods developed for other complex loci (e.g., human leukocyte antigen [HLA]) on the basis of SNP data provide an inexpensive high-throughput alternative to direct laboratory typing of these loci and have enabled important findings and insights for many diseases. We present KIR<sup>∗</sup>
IMP, a method for imputation of KIR copy number. We show that KIR<sup>∗</sup>
IMP is highly accurate and thus allows the study of KIRs in large cohorts and enables detailed investigation of the role of KIRs in human disease.</p>
</div>
</front>
</TEI>
<affiliations><list><country><li>Allemagne</li>
<li>Australie</li>
<li>Canada</li>
<li>France</li>
<li>Japon</li>
<li>Norvège</li>
<li>Royaume-Uni</li>
</country>
<region><li>Angleterre</li>
<li>Angleterre de l'Est</li>
<li>Oxfordshire</li>
<li>Schleswig-Holstein</li>
<li>Victoria (État)</li>
<li>Île-de-France</li>
<li>Østlandet</li>
</region>
<settlement><li>Cambridge</li>
<li>Kiel</li>
<li>Melbourne</li>
<li>Oslo</li>
<li>Oxford</li>
<li>Paris</li>
</settlement>
<orgName><li>Université d'Oxford</li>
<li>Université de Cambridge</li>
<li>Université de Melbourne</li>
</orgName>
</list>
<tree><country name="Australie"><noRegion><name sortKey="Vukcevic, Damjan" sort="Vukcevic, Damjan" uniqKey="Vukcevic D" first="Damjan" last="Vukcevic">Damjan Vukcevic</name>
</noRegion>
<name sortKey="Leslie, Stephen" sort="Leslie, Stephen" uniqKey="Leslie S" first="Stephen" last="Leslie">Stephen Leslie</name>
<name sortKey="Leslie, Stephen" sort="Leslie, Stephen" uniqKey="Leslie S" first="Stephen" last="Leslie">Stephen Leslie</name>
<name sortKey="Vukcevic, Damjan" sort="Vukcevic, Damjan" uniqKey="Vukcevic D" first="Damjan" last="Vukcevic">Damjan Vukcevic</name>
</country>
<country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Traherne, James A" sort="Traherne, James A" uniqKey="Traherne J" first="James A." last="Traherne">James A. Traherne</name>
</region>
<name sortKey="Cookson, William" sort="Cookson, William" uniqKey="Cookson W" first="William" last="Cookson">William Cookson</name>
<name sortKey="Dilthey, Alexander" sort="Dilthey, Alexander" uniqKey="Dilthey A" first="Alexander" last="Dilthey">Alexander Dilthey</name>
<name sortKey="Mcvean, Gil" sort="Mcvean, Gil" uniqKey="Mcvean G" first="Gil" last="Mcvean">Gil Mcvean</name>
<name sortKey="Moffatt, Miriam" sort="Moffatt, Miriam" uniqKey="Moffatt M" first="Miriam" last="Moffatt">Miriam Moffatt</name>
<name sortKey="Sawcer, Stephen" sort="Sawcer, Stephen" uniqKey="Sawcer S" first="Stephen" last="Sawcer">Stephen Sawcer</name>
<name sortKey="Traherne, James A" sort="Traherne, James A" uniqKey="Traherne J" first="James A." last="Traherne">James A. Traherne</name>
<name sortKey="Trowsdale, John" sort="Trowsdale, John" uniqKey="Trowsdale J" first="John" last="Trowsdale">John Trowsdale</name>
<name sortKey="Trowsdale, John" sort="Trowsdale, John" uniqKey="Trowsdale J" first="John" last="Trowsdale">John Trowsdale</name>
</country>
<country name="Norvège"><region name="Østlandet"><name sortKey="N Ss, Sigrid" sort="N Ss, Sigrid" uniqKey="N Ss S" first="Sigrid" last="N Ss">Sigrid N Ss</name>
</region>
<name sortKey="Karlsen, Tom H" sort="Karlsen, Tom H" uniqKey="Karlsen T" first="Tom H." last="Karlsen">Tom H. Karlsen</name>
<name sortKey="Karlsen, Tom H" sort="Karlsen, Tom H" uniqKey="Karlsen T" first="Tom H." last="Karlsen">Tom H. Karlsen</name>
<name sortKey="N Ss, Sigrid" sort="N Ss, Sigrid" uniqKey="N Ss S" first="Sigrid" last="N Ss">Sigrid N Ss</name>
</country>
<country name="Allemagne"><region name="Schleswig-Holstein"><name sortKey="Ellinghaus, Eva" sort="Ellinghaus, Eva" uniqKey="Ellinghaus E" first="Eva" last="Ellinghaus">Eva Ellinghaus</name>
</region>
<name sortKey="Franke, Andre" sort="Franke, Andre" uniqKey="Franke A" first="Andre" last="Franke">Andre Franke</name>
</country>
<country name="France"><region name="Île-de-France"><name sortKey="Kamatani, Yoichiro" sort="Kamatani, Yoichiro" uniqKey="Kamatani Y" first="Yoichiro" last="Kamatani">Yoichiro Kamatani</name>
</region>
<name sortKey="Lathrop, Mark" sort="Lathrop, Mark" uniqKey="Lathrop M" first="Mark" last="Lathrop">Mark Lathrop</name>
</country>
<country name="Japon"><noRegion><name sortKey="Kamatani, Yoichiro" sort="Kamatani, Yoichiro" uniqKey="Kamatani Y" first="Yoichiro" last="Kamatani">Yoichiro Kamatani</name>
</noRegion>
</country>
<country name="Canada"><noRegion><name sortKey="Lathrop, Mark" sort="Lathrop, Mark" uniqKey="Lathrop M" first="Mark" last="Lathrop">Mark Lathrop</name>
</noRegion>
</country>
</tree>
</affiliations>
</record>

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Serveur d'exploration sur les relations entre la France et l'Australie

Imputation of KIR Types from SNP Variation Data

Imputation of KIR Types from SNP Variation Data

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	Serveur d'exploration sur les relations entre la France et l'Australie
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