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Next-generation sequencing for the diagnosis of hereditary breast and ovarian cancer using genomic capture targeting multiple candidate genes

Identifieur interne : 000327 ( Main/Exploration ); précédent : 000326; suivant : 000328

Next-generation sequencing for the diagnosis of hereditary breast and ovarian cancer using genomic capture targeting multiple candidate genes

Auteurs : Laurent Castéra [France] ; Sophie Krieger [France] ; Antoine Rousselin [France] ; Angélina Legros [France] ; Jean-Jacques Baumann [France] ; Olivia Bruet [France] ; Baptiste Brault [France] ; Robin Fouillet [France] ; Nicolas Goardon [France] ; Olivier Letac [France] ; Stéphanie Baert-Desurmont [France] ; Julie Tinat [France] ; Odile Bera [France] ; Catherine Dugast [France] ; Pascaline Berthet [France] ; Florence Polycarpe [France] ; Valérie Layet [France] ; Agnes Hardouin [France] ; Thierry Frébourg [France] ; Dominique Vaur [France]

Source :

RBID : PMC:4200427

English descriptors

Abstract

To optimize the molecular diagnosis of hereditary breast and ovarian cancer (HBOC), we developed a next-generation sequencing (NGS)-based screening based on the capture of a panel of genes involved, or suspected to be involved in HBOC, on pooling of indexed DNA and on paired-end sequencing in an Illumina GAIIx platform, followed by confirmation by Sanger sequencing or MLPA/QMPSF. The bioinformatic pipeline included CASAVA, NextGENe, CNVseq and Alamut-HT. We validated this procedure by the analysis of 59 patients' DNAs harbouring SNVs, indels or large genomic rearrangements of BRCA1 or BRCA2. We also conducted a blind study in 168 patients comparing NGS versus Sanger sequencing or MLPA analyses of BRCA1 and BRCA2. All mutations detected by conventional procedures were detected by NGS. We then screened, using three different versions of the capture set, a large series of 708 consecutive patients. We detected in these patients 69 germline deleterious alterations within BRCA1 and BRCA2, and 4 TP53 mutations in 468 patients also tested for this gene. We also found 36 variations inducing either a premature codon stop or a splicing defect among other genes: 5/708 in CHEK2, 3/708 in RAD51C, 1/708 in RAD50, 7/708 in PALB2, 3/708 in MRE11A, 5/708 in ATM, 3/708 in NBS1, 1/708 in CDH1, 3/468 in MSH2, 2/468 in PMS2, 1/708 in BARD1, 1/468 in PMS1 and 1/468 in MLH3. These results demonstrate the efficiency of NGS in performing molecular diagnosis of HBOC. Detection of mutations within other genes than BRCA1 and BRCA2 highlights the genetic heterogeneity of HBOC.


Url:
DOI: 10.1038/ejhg.2014.16
PubMed: 24549055
PubMed Central: 4200427


Affiliations:


Links toward previous steps (curation, corpus...)


Le document en format XML

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<title xml:lang="en" level="a" type="main">Next-generation sequencing for the diagnosis of hereditary breast and ovarian cancer using genomic capture targeting multiple candidate genes</title>
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<name sortKey="Baumann, Jean Jacques" sort="Baumann, Jean Jacques" uniqKey="Baumann J" first="Jean-Jacques" last="Baumann">Jean-Jacques Baumann</name>
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<name sortKey="Goardon, Nicolas" sort="Goardon, Nicolas" uniqKey="Goardon N" first="Nicolas" last="Goardon">Nicolas Goardon</name>
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<institution>Department of Cancer Biology and Genetics, CLCC François Baclesse</institution>
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<institution>Department of Genetics, University Hospital</institution>
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</author>
<author>
<name sortKey="Tinat, Julie" sort="Tinat, Julie" uniqKey="Tinat J" first="Julie" last="Tinat">Julie Tinat</name>
<affiliation wicri:level="1">
<nlm:aff id="aff2">
<institution>Inserm U1079</institution>
, Rouen,
<country>France</country>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff4">
<institution>Department of Genetics, University Hospital</institution>
, Rouen,
<country>France</country>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Bera, Odile" sort="Bera, Odile" uniqKey="Bera O" first="Odile" last="Bera">Odile Bera</name>
<affiliation wicri:level="1">
<nlm:aff id="aff5">
<institution>Department of Genetics, University Hospital</institution>
, Fort-de-France,
<country>France</country>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Dugast, Catherine" sort="Dugast, Catherine" uniqKey="Dugast C" first="Catherine" last="Dugast">Catherine Dugast</name>
<affiliation wicri:level="1">
<nlm:aff id="aff6">
<institution>Department of Genetics, University Hospital</institution>
, Rennes,
<country>France</country>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Berthet, Pascaline" sort="Berthet, Pascaline" uniqKey="Berthet P" first="Pascaline" last="Berthet">Pascaline Berthet</name>
<affiliation wicri:level="1">
<nlm:aff id="aff7">
<institution>Department of Genetics, CLCC François Baclesse</institution>
, Caen,
<country>France</country>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Polycarpe, Florence" sort="Polycarpe, Florence" uniqKey="Polycarpe F" first="Florence" last="Polycarpe">Florence Polycarpe</name>
<affiliation wicri:level="1">
<nlm:aff id="aff7">
<institution>Department of Genetics, CLCC François Baclesse</institution>
, Caen,
<country>France</country>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Layet, Valerie" sort="Layet, Valerie" uniqKey="Layet V" first="Valérie" last="Layet">Valérie Layet</name>
<affiliation wicri:level="1">
<nlm:aff id="aff8">
<institution>Department of Genetics, Jacques Monod Hospital</institution>
, Le Havre,
<country>France</country>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Hardouin, Agnes" sort="Hardouin, Agnes" uniqKey="Hardouin A" first="Agnes" last="Hardouin">Agnes Hardouin</name>
<affiliation wicri:level="1">
<nlm:aff id="aff1">
<institution>Department of Cancer Biology and Genetics, CLCC François Baclesse</institution>
, Caen,
<country>France</country>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff2">
<institution>Inserm U1079</institution>
, Rouen,
<country>France</country>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Frebourg, Thierry" sort="Frebourg, Thierry" uniqKey="Frebourg T" first="Thierry" last="Frébourg">Thierry Frébourg</name>
<affiliation wicri:level="1">
<nlm:aff id="aff2">
<institution>Inserm U1079</institution>
, Rouen,
<country>France</country>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff4">
<institution>Department of Genetics, University Hospital</institution>
, Rouen,
<country>France</country>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff9">
<institution>Rouen University, IRIB</institution>
, Rouen,
<country>France</country>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author>
<name sortKey="Vaur, Dominique" sort="Vaur, Dominique" uniqKey="Vaur D" first="Dominique" last="Vaur">Dominique Vaur</name>
<affiliation wicri:level="1">
<nlm:aff id="aff1">
<institution>Department of Cancer Biology and Genetics, CLCC François Baclesse</institution>
, Caen,
<country>France</country>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1">
<nlm:aff id="aff2">
<institution>Inserm U1079</institution>
, Rouen,
<country>France</country>
</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
</analytic>
<series>
<title level="j">European Journal of Human Genetics</title>
<idno type="ISSN">1018-4813</idno>
<idno type="eISSN">1476-5438</idno>
<imprint>
<date when="2014">2014</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc>
<textClass>
<keywords scheme="KwdEn" xml:lang="en">
<term>Adult</term>
<term>Aged</term>
<term>BRCA1 Protein (genetics)</term>
<term>BRCA1 Protein (metabolism)</term>
<term>BRCA2 Protein (genetics)</term>
<term>BRCA2 Protein (metabolism)</term>
<term>Breast Neoplasms (diagnosis)</term>
<term>Breast Neoplasms (genetics)</term>
<term>Breast Neoplasms, Male (diagnosis)</term>
<term>Breast Neoplasms, Male (genetics)</term>
<term>Case-Control Studies</term>
<term>Computational Biology</term>
<term>Female</term>
<term>Gene Rearrangement</term>
<term>Genetic Predisposition to Disease</term>
<term>Genetic Testing</term>
<term>Genomics (methods)</term>
<term>High-Throughput Nucleotide Sequencing (methods)</term>
<term>Humans</term>
<term>Male</term>
<term>Middle Aged</term>
<term>Mutation</term>
<term>Ovarian Neoplasms (diagnosis)</term>
<term>Ovarian Neoplasms (genetics)</term>
<term>Reproducibility of Results</term>
<term>Tumor Suppressor Protein p53 (genetics)</term>
<term>Tumor Suppressor Protein p53 (metabolism)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en">
<term>BRCA1 Protein</term>
<term>BRCA2 Protein</term>
<term>Tumor Suppressor Protein p53</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en">
<term>BRCA1 Protein</term>
<term>BRCA2 Protein</term>
<term>Tumor Suppressor Protein p53</term>
</keywords>
<keywords scheme="MESH" qualifier="diagnosis" xml:lang="en">
<term>Breast Neoplasms</term>
<term>Breast Neoplasms, Male</term>
<term>Ovarian Neoplasms</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en">
<term>Breast Neoplasms</term>
<term>Breast Neoplasms, Male</term>
<term>Ovarian Neoplasms</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en">
<term>Genomics</term>
<term>High-Throughput Nucleotide Sequencing</term>
</keywords>
<keywords scheme="MESH" xml:lang="en">
<term>Adult</term>
<term>Aged</term>
<term>Case-Control Studies</term>
<term>Computational Biology</term>
<term>Female</term>
<term>Gene Rearrangement</term>
<term>Genetic Predisposition to Disease</term>
<term>Genetic Testing</term>
<term>Humans</term>
<term>Male</term>
<term>Middle Aged</term>
<term>Mutation</term>
<term>Reproducibility of Results</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front>
<div type="abstract" xml:lang="en">
<p>To optimize the molecular diagnosis of hereditary breast and ovarian cancer (HBOC), we developed a next-generation sequencing (NGS)-based screening based on the capture of a panel of genes involved, or suspected to be involved in HBOC, on pooling of indexed DNA and on paired-end sequencing in an Illumina GAIIx platform, followed by confirmation by Sanger sequencing or MLPA/QMPSF. The bioinformatic pipeline included CASAVA, NextGENe, CNVseq and Alamut-HT. We validated this procedure by the analysis of 59 patients' DNAs harbouring SNVs, indels or large genomic rearrangements of
<italic>BRCA1</italic>
or
<italic>BRCA2</italic>
. We also conducted a blind study in 168 patients comparing NGS
<italic>versus</italic>
Sanger sequencing or MLPA analyses of
<italic>BRCA1</italic>
and
<italic>BRCA2</italic>
. All mutations detected by conventional procedures were detected by NGS. We then screened, using three different versions of the capture set, a large series of 708 consecutive patients. We detected in these patients 69 germline deleterious alterations within
<italic>BRCA1</italic>
and
<italic>BRCA2</italic>
, and 4
<italic>TP53</italic>
mutations in 468 patients also tested for this gene. We also found 36 variations inducing either a premature codon stop or a splicing defect among other genes: 5/708 in
<italic>CHEK2,</italic>
3/708 in
<italic>RAD51C</italic>
, 1/708 in
<italic>RAD50,</italic>
7/708 in
<italic>PALB2</italic>
, 3/708 in
<italic>MRE11A</italic>
, 5/708 in
<italic>ATM</italic>
, 3/708 in
<italic>NBS1</italic>
, 1/708 in
<italic>CDH1</italic>
, 3/468 in
<italic>MSH2</italic>
, 2/468 in
<italic>PMS2</italic>
, 1/708 in
<italic>BARD1</italic>
, 1/468 in
<italic>PMS1</italic>
and 1/468 in
<italic>MLH3</italic>
. These results demonstrate the efficiency of NGS in performing molecular diagnosis of HBOC. Detection of mutations within other genes than
<italic>BRCA1</italic>
and
<italic>BRCA2</italic>
highlights the genetic heterogeneity of HBOC.</p>
</div>
</front>
</TEI>
<affiliations>
<list>
<country>
<li>France</li>
</country>
</list>
<tree>
<country name="France">
<noRegion>
<name sortKey="Castera, Laurent" sort="Castera, Laurent" uniqKey="Castera L" first="Laurent" last="Castéra">Laurent Castéra</name>
</noRegion>
<name sortKey="Baert Desurmont, Stephanie" sort="Baert Desurmont, Stephanie" uniqKey="Baert Desurmont S" first="Stéphanie" last="Baert-Desurmont">Stéphanie Baert-Desurmont</name>
<name sortKey="Baert Desurmont, Stephanie" sort="Baert Desurmont, Stephanie" uniqKey="Baert Desurmont S" first="Stéphanie" last="Baert-Desurmont">Stéphanie Baert-Desurmont</name>
<name sortKey="Baumann, Jean Jacques" sort="Baumann, Jean Jacques" uniqKey="Baumann J" first="Jean-Jacques" last="Baumann">Jean-Jacques Baumann</name>
<name sortKey="Bera, Odile" sort="Bera, Odile" uniqKey="Bera O" first="Odile" last="Bera">Odile Bera</name>
<name sortKey="Berthet, Pascaline" sort="Berthet, Pascaline" uniqKey="Berthet P" first="Pascaline" last="Berthet">Pascaline Berthet</name>
<name sortKey="Brault, Baptiste" sort="Brault, Baptiste" uniqKey="Brault B" first="Baptiste" last="Brault">Baptiste Brault</name>
<name sortKey="Bruet, Olivia" sort="Bruet, Olivia" uniqKey="Bruet O" first="Olivia" last="Bruet">Olivia Bruet</name>
<name sortKey="Castera, Laurent" sort="Castera, Laurent" uniqKey="Castera L" first="Laurent" last="Castéra">Laurent Castéra</name>
<name sortKey="Dugast, Catherine" sort="Dugast, Catherine" uniqKey="Dugast C" first="Catherine" last="Dugast">Catherine Dugast</name>
<name sortKey="Fouillet, Robin" sort="Fouillet, Robin" uniqKey="Fouillet R" first="Robin" last="Fouillet">Robin Fouillet</name>
<name sortKey="Frebourg, Thierry" sort="Frebourg, Thierry" uniqKey="Frebourg T" first="Thierry" last="Frébourg">Thierry Frébourg</name>
<name sortKey="Frebourg, Thierry" sort="Frebourg, Thierry" uniqKey="Frebourg T" first="Thierry" last="Frébourg">Thierry Frébourg</name>
<name sortKey="Frebourg, Thierry" sort="Frebourg, Thierry" uniqKey="Frebourg T" first="Thierry" last="Frébourg">Thierry Frébourg</name>
<name sortKey="Goardon, Nicolas" sort="Goardon, Nicolas" uniqKey="Goardon N" first="Nicolas" last="Goardon">Nicolas Goardon</name>
<name sortKey="Hardouin, Agnes" sort="Hardouin, Agnes" uniqKey="Hardouin A" first="Agnes" last="Hardouin">Agnes Hardouin</name>
<name sortKey="Hardouin, Agnes" sort="Hardouin, Agnes" uniqKey="Hardouin A" first="Agnes" last="Hardouin">Agnes Hardouin</name>
<name sortKey="Krieger, Sophie" sort="Krieger, Sophie" uniqKey="Krieger S" first="Sophie" last="Krieger">Sophie Krieger</name>
<name sortKey="Krieger, Sophie" sort="Krieger, Sophie" uniqKey="Krieger S" first="Sophie" last="Krieger">Sophie Krieger</name>
<name sortKey="Krieger, Sophie" sort="Krieger, Sophie" uniqKey="Krieger S" first="Sophie" last="Krieger">Sophie Krieger</name>
<name sortKey="Layet, Valerie" sort="Layet, Valerie" uniqKey="Layet V" first="Valérie" last="Layet">Valérie Layet</name>
<name sortKey="Legros, Angelina" sort="Legros, Angelina" uniqKey="Legros A" first="Angélina" last="Legros">Angélina Legros</name>
<name sortKey="Letac, Olivier" sort="Letac, Olivier" uniqKey="Letac O" first="Olivier" last="Letac">Olivier Letac</name>
<name sortKey="Polycarpe, Florence" sort="Polycarpe, Florence" uniqKey="Polycarpe F" first="Florence" last="Polycarpe">Florence Polycarpe</name>
<name sortKey="Rousselin, Antoine" sort="Rousselin, Antoine" uniqKey="Rousselin A" first="Antoine" last="Rousselin">Antoine Rousselin</name>
<name sortKey="Tinat, Julie" sort="Tinat, Julie" uniqKey="Tinat J" first="Julie" last="Tinat">Julie Tinat</name>
<name sortKey="Tinat, Julie" sort="Tinat, Julie" uniqKey="Tinat J" first="Julie" last="Tinat">Julie Tinat</name>
<name sortKey="Vaur, Dominique" sort="Vaur, Dominique" uniqKey="Vaur D" first="Dominique" last="Vaur">Dominique Vaur</name>
<name sortKey="Vaur, Dominique" sort="Vaur, Dominique" uniqKey="Vaur D" first="Dominique" last="Vaur">Dominique Vaur</name>
</country>
</tree>
</affiliations>
</record>

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