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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Comparison of mRNA Splicing Assay Protocols across Multiple Laboratories: Recommendations for Best Practice in Standardized Clinical Testing</title><author><name sortKey="Whiley, Phillip J" sort="Whiley, Phillip J" uniqKey="Whiley P" first="Phillip J." last="Whiley">Phillip J. Whiley</name><affiliation><nlm:aff id="A1">Genetics & Computational Biology Division, Queensland Institute of Medical Research, Brisbane, Queensland, Australia</nlm:aff></affiliation><affiliation><nlm:aff id="A2">School of Chemistry and Molecular Biosciences, the University of Queensland, Queensland, Australia</nlm:aff></affiliation></author><author><name sortKey="De La Hoya, Miguel" sort="De La Hoya, Miguel" uniqKey="De La Hoya M" first="Miguel" last="De La Hoya">Miguel De La Hoya</name><affiliation><nlm:aff id="A3">Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain</nlm:aff></affiliation></author><author><name sortKey="Thomassen, Mads" sort="Thomassen, Mads" uniqKey="Thomassen M" first="Mads" last="Thomassen">Mads Thomassen</name><affiliation><nlm:aff id="A4">Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark</nlm:aff></affiliation></author><author><name sortKey="Becker, Alexandra" sort="Becker, Alexandra" uniqKey="Becker A" first="Alexandra" last="Becker">Alexandra Becker</name><affiliation><nlm:aff id="A5">Center for Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany</nlm:aff></affiliation><affiliation><nlm:aff id="A6">Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany</nlm:aff></affiliation></author><author><name sortKey="Brandao, Rita" sort="Brandao, Rita" uniqKey="Brandao R" first="Rita" last="Brandão">Rita Brandão</name><affiliation><nlm:aff id="A7">Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands</nlm:aff></affiliation></author><author><name sortKey="Pedersen, Inge Sokilde" sort="Pedersen, Inge Sokilde" uniqKey="Pedersen I" first="Inge Sokilde" last="Pedersen">Inge Sokilde Pedersen</name><affiliation><nlm:aff id="A8">Section of Molecular Diagnostics, Department of Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark</nlm:aff></affiliation></author><author><name sortKey="Montagna, Marco" sort="Montagna, Marco" uniqKey="Montagna M" first="Marco" last="Montagna">Marco Montagna</name><affiliation><nlm:aff id="A9">Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV—IRCCS, Padua, Italy</nlm:aff></affiliation></author><author><name sortKey="Menendez, Mireia" sort="Menendez, Mireia" uniqKey="Menendez M" first="Mireia" last="Menéndez">Mireia Menéndez</name><affiliation><nlm:aff id="A10">Genetic Diagnosis Unit, Hereditary Cancer Program, Institut Català d’Oncologia, Barcelona, Spain</nlm:aff></affiliation></author><author><name sortKey="Quiles, Francisco" sort="Quiles, Francisco" uniqKey="Quiles F" first="Francisco" last="Quiles">Francisco Quiles</name><affiliation><nlm:aff id="A10">Genetic Diagnosis Unit, Hereditary Cancer Program, Institut Català d’Oncologia, Barcelona, Spain</nlm:aff></affiliation></author><author><name sortKey="Gutierrez Enriquez, Sara" sort="Gutierrez Enriquez, Sara" uniqKey="Gutierrez Enriquez S" first="Sara" last="Gutiérrez-Enríquez">Sara Gutiérrez-Enríquez</name><affiliation><nlm:aff id="A11">Oncogenetics Laboratory, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Institut de Recerca, University Hospital Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain</nlm:aff></affiliation></author><author><name sortKey="De Leeneer, Kim" sort="De Leeneer, Kim" uniqKey="De Leeneer K" first="Kim" last="De Leeneer">Kim De Leeneer</name><affiliation><nlm:aff id="A12">Center for Medical Genetics, Ghent University Hospital, De Pintelaan, Ghent, Belgium</nlm:aff></affiliation></author><author><name sortKey="Tenes, Anna" sort="Tenes, Anna" uniqKey="Tenes A" first="Anna" last="Tenés">Anna Tenés</name><affiliation><nlm:aff id="A11">Oncogenetics Laboratory, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Institut de Recerca, University Hospital Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain</nlm:aff></affiliation></author><author><name sortKey="Montalban, Gemma" sort="Montalban, Gemma" uniqKey="Montalban G" first="Gemma" last="Montalban">Gemma Montalban</name><affiliation><nlm:aff id="A11">Oncogenetics Laboratory, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Institut de Recerca, University Hospital Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain</nlm:aff></affiliation></author><author><name sortKey="Tserpelis, Demis" sort="Tserpelis, Demis" uniqKey="Tserpelis D" first="Demis" last="Tserpelis">Demis Tserpelis</name><affiliation><nlm:aff id="A7">Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands</nlm:aff></affiliation></author><author><name sortKey="Yoshimatsu, Toshio" sort="Yoshimatsu, Toshio" uniqKey="Yoshimatsu T" first="Toshio" last="Yoshimatsu">Toshio Yoshimatsu</name><affiliation><nlm:aff id="A13">Department of Medicine, the University of Chicago Medical Center, Chicago, IL</nlm:aff></affiliation></author><author><name sortKey="Tirapo, Carole" sort="Tirapo, Carole" uniqKey="Tirapo C" first="Carole" last="Tirapo">Carole Tirapo</name><affiliation><nlm:aff id="A14">Service de Génétique et U830, Institut Curie, et Université Paris Descartes, Sorbonne Paris Cité, Paris, France</nlm:aff></affiliation></author><author><name sortKey="Raponi, Michela" sort="Raponi, Michela" uniqKey="Raponi M" first="Michela" last="Raponi">Michela Raponi</name><affiliation><nlm:aff id="A15">Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK</nlm:aff></affiliation></author><author><name sortKey="Caldes, Trinidad" sort="Caldes, Trinidad" uniqKey="Caldes T" first="Trinidad" last="Caldes">Trinidad Caldes</name><affiliation><nlm:aff id="A3">Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain</nlm:aff></affiliation></author><author><name sortKey="Blanco, Ana" sort="Blanco, Ana" uniqKey="Blanco A" first="Ana" last="Blanco">Ana Blanco</name><affiliation><nlm:aff id="A16">Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain</nlm:aff></affiliation></author><author><name sortKey="Santamari A, Marta" sort="Santamari A, Marta" uniqKey="Santamari A M" first="Marta" last="Santamari A">Marta Santamari A</name><affiliation><nlm:aff id="A17">Grupo de Medicina Xenómica—USC, University of Santiago de Compostela, CIBERER, IDIS, Santiago de Compostela, Spain</nlm:aff></affiliation></author><author><name sortKey="Guidugli, Lucia" sort="Guidugli, Lucia" uniqKey="Guidugli L" first="Lucia" last="Guidugli">Lucia Guidugli</name><affiliation><nlm:aff id="A18">Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, NY</nlm:aff></affiliation></author><author><name sortKey="De Garibay, Gorka Ruiz" sort="De Garibay, Gorka Ruiz" uniqKey="De Garibay G" first="Gorka Ruiz" last="De Garibay">Gorka Ruiz De Garibay</name><affiliation><nlm:aff id="A3">Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain</nlm:aff></affiliation></author><author><name sortKey="Wong, Ming" sort="Wong, Ming" uniqKey="Wong M" first="Ming" last="Wong">Ming Wong</name><affiliation><nlm:aff id="A19">Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff></affiliation></author><author><name sortKey="Tancredi, Mariella" sort="Tancredi, Mariella" uniqKey="Tancredi M" first="Mariella" last="Tancredi">Mariella Tancredi</name><affiliation><nlm:aff id="A20">Istituto di Anatomia Patologica, Università di Pisa, Pisa, Italy</nlm:aff></affiliation></author><author><name sortKey="Fachal, Laura" sort="Fachal, Laura" uniqKey="Fachal L" first="Laura" last="Fachal">Laura Fachal</name><affiliation><nlm:aff id="A16">Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain</nlm:aff></affiliation></author><author><name sortKey="Ding, Yuan Chun" sort="Ding, Yuan Chun" uniqKey="Ding Y" first="Yuan Chun" last="Ding">Yuan Chun Ding</name><affiliation><nlm:aff id="A21">Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA</nlm:aff></affiliation></author><author><name sortKey="Kruse, Torben" sort="Kruse, Torben" uniqKey="Kruse T" first="Torben" last="Kruse">Torben Kruse</name><affiliation><nlm:aff id="A4">Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark</nlm:aff></affiliation></author><author><name sortKey="Lattimore, Vanessa" sort="Lattimore, Vanessa" uniqKey="Lattimore V" first="Vanessa" last="Lattimore">Vanessa Lattimore</name><affiliation><nlm:aff id="A22">Department of Pathology' University of Otago, Christchurch, New Zealand</nlm:aff></affiliation></author><author><name sortKey="Kwong, Ava" sort="Kwong, Ava" uniqKey="Kwong A" first="Ava" last="Kwong">Ava Kwong</name><affiliation><nlm:aff id="A23">Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China</nlm:aff></affiliation></author><author><name sortKey="Chan, Tsun Leung" sort="Chan, Tsun Leung" uniqKey="Chan T" first="Tsun Leung" last="Chan">Tsun Leung Chan</name><affiliation><nlm:aff id="A23">Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China</nlm:aff></affiliation></author><author><name sortKey="Colombo, Mara" sort="Colombo, Mara" uniqKey="Colombo M" first="Mara" last="Colombo">Mara Colombo</name><affiliation><nlm:aff id="A24">Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy</nlm:aff></affiliation></author><author><name sortKey="De Vecchi, Giovanni" sort="De Vecchi, Giovanni" uniqKey="De Vecchi G" first="Giovanni" last="De Vecchi">Giovanni De Vecchi</name><affiliation><nlm:aff id="A24">Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy</nlm:aff></affiliation></author><author><name sortKey="Caligo, Maria" sort="Caligo, Maria" uniqKey="Caligo M" first="Maria" last="Caligo">Maria Caligo</name><affiliation><nlm:aff id="A19">Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff></affiliation></author><author><name sortKey="Baralle, Diana" sort="Baralle, Diana" uniqKey="Baralle D" first="Diana" last="Baralle">Diana Baralle</name><affiliation><nlm:aff id="A15">Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK</nlm:aff></affiliation></author><author><name sortKey="Lazaro, Conxi" sort="Lazaro, Conxi" uniqKey="Lazaro C" first="Conxi" last="Lázaro">Conxi Lázaro</name><affiliation><nlm:aff id="A10">Genetic Diagnosis Unit, Hereditary Cancer Program, Institut Català d’Oncologia, Barcelona, Spain</nlm:aff></affiliation></author><author><name sortKey="Couch, Fergus" sort="Couch, Fergus" uniqKey="Couch F" first="Fergus" last="Couch">Fergus Couch</name><affiliation><nlm:aff id="A17">Grupo de Medicina Xenómica—USC, University of Santiago de Compostela, CIBERER, IDIS, Santiago de Compostela, Spain</nlm:aff></affiliation></author><author><name sortKey="Radice, Paolo" sort="Radice, Paolo" uniqKey="Radice P" first="Paolo" last="Radice">Paolo Radice</name><affiliation><nlm:aff id="A24">Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy</nlm:aff></affiliation></author><author><name sortKey="Southey, Melissa C" sort="Southey, Melissa C" uniqKey="Southey M" first="Melissa C." last="Southey">Melissa C. Southey</name><affiliation><nlm:aff id="A18">Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, NY</nlm:aff></affiliation></author><author><name sortKey="Neuhausen, Susan" sort="Neuhausen, Susan" uniqKey="Neuhausen S" first="Susan" last="Neuhausen">Susan Neuhausen</name><affiliation><nlm:aff id="A21">Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA</nlm:aff></affiliation></author><author><name sortKey="Houdayer, Claude" sort="Houdayer, Claude" uniqKey="Houdayer C" first="Claude" last="Houdayer">Claude Houdayer</name><affiliation><nlm:aff id="A14">Service de Génétique et U830, Institut Curie, et Université Paris Descartes, Sorbonne Paris Cité, Paris, France</nlm:aff></affiliation></author><author><name sortKey="Fackenthal, Jim" sort="Fackenthal, Jim" uniqKey="Fackenthal J" first="Jim" last="Fackenthal">Jim Fackenthal</name><affiliation><nlm:aff id="A13">Department of Medicine, the University of Chicago Medical Center, Chicago, IL</nlm:aff></affiliation></author><author><name sortKey="Van Overeem Hansen, Thomas" sort="Van Overeem Hansen, Thomas" uniqKey="Van Overeem Hansen T" first="Thomas" last="Van Overeem Hansen">Thomas Van Overeem Hansen</name><affiliation><nlm:aff id="A25">Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark</nlm:aff></affiliation></author><author><name sortKey="Vega, Ana" sort="Vega, Ana" uniqKey="Vega A" first="Ana" last="Vega">Ana Vega</name><affiliation><nlm:aff id="A16">Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain</nlm:aff></affiliation></author><author><name sortKey="Diez, Orland" sort="Diez, Orland" uniqKey="Diez O" first="Orland" last="Diez">Orland Diez</name><affiliation><nlm:aff id="A11">Oncogenetics Laboratory, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Institut de Recerca, University Hospital Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain</nlm:aff></affiliation></author><author><name sortKey="Blok, Rien" sort="Blok, Rien" uniqKey="Blok R" first="Rien" last="Blok">Rien Blok</name><affiliation><nlm:aff id="A7">Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands</nlm:aff></affiliation></author><author><name sortKey="Claes, Kathleen" sort="Claes, Kathleen" uniqKey="Claes K" first="Kathleen" last="Claes">Kathleen Claes</name><affiliation><nlm:aff id="A12">Center for Medical Genetics, Ghent University Hospital, De Pintelaan, Ghent, Belgium</nlm:aff></affiliation></author><author><name sortKey="Wappenschmidt, Barbara" sort="Wappenschmidt, Barbara" uniqKey="Wappenschmidt B" first="Barbara" last="Wappenschmidt">Barbara Wappenschmidt</name><affiliation><nlm:aff id="A5">Center for Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany</nlm:aff></affiliation><affiliation><nlm:aff id="A6">Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany</nlm:aff></affiliation></author><author><name sortKey="Walker, Logan" sort="Walker, Logan" uniqKey="Walker L" first="Logan" last="Walker">Logan Walker</name><affiliation><nlm:aff id="A22">Department of Pathology' University of Otago, Christchurch, New Zealand</nlm:aff></affiliation></author><author><name sortKey="Spurdle, Amanda B" sort="Spurdle, Amanda B" uniqKey="Spurdle A" first="Amanda B." last="Spurdle">Amanda B. Spurdle</name><affiliation><nlm:aff id="A1">Genetics & Computational Biology Division, Queensland Institute of Medical Research, Brisbane, Queensland, Australia</nlm:aff></affiliation></author><author><name sortKey="Brown, Melissa A" sort="Brown, Melissa A" uniqKey="Brown M" first="Melissa A." last="Brown">Melissa A. Brown</name><affiliation><nlm:aff id="A2">School of Chemistry and Molecular Biosciences, the University of Queensland, Queensland, Australia</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24212087</idno><idno type="pmc">4351044</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351044</idno><idno type="RBID">PMC:4351044</idno><idno type="doi">10.1373/clinchem.2013.210658</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">002164</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">002164</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Comparison of mRNA Splicing Assay Protocols across Multiple Laboratories: Recommendations for Best Practice in Standardized Clinical Testing</title><author><name sortKey="Whiley, Phillip J" sort="Whiley, Phillip J" uniqKey="Whiley P" first="Phillip J." last="Whiley">Phillip J. Whiley</name><affiliation><nlm:aff id="A1">Genetics & Computational Biology Division, Queensland Institute of Medical Research, Brisbane, Queensland, Australia</nlm:aff></affiliation><affiliation><nlm:aff id="A2">School of Chemistry and Molecular Biosciences, the University of Queensland, Queensland, Australia</nlm:aff></affiliation></author><author><name sortKey="De La Hoya, Miguel" sort="De La Hoya, Miguel" uniqKey="De La Hoya M" first="Miguel" last="De La Hoya">Miguel De La Hoya</name><affiliation><nlm:aff id="A3">Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain</nlm:aff></affiliation></author><author><name sortKey="Thomassen, Mads" sort="Thomassen, Mads" uniqKey="Thomassen M" first="Mads" last="Thomassen">Mads Thomassen</name><affiliation><nlm:aff id="A4">Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark</nlm:aff></affiliation></author><author><name sortKey="Becker, Alexandra" sort="Becker, Alexandra" uniqKey="Becker A" first="Alexandra" last="Becker">Alexandra Becker</name><affiliation><nlm:aff id="A5">Center for Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany</nlm:aff></affiliation><affiliation><nlm:aff id="A6">Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany</nlm:aff></affiliation></author><author><name sortKey="Brandao, Rita" sort="Brandao, Rita" uniqKey="Brandao R" first="Rita" last="Brandão">Rita Brandão</name><affiliation><nlm:aff id="A7">Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands</nlm:aff></affiliation></author><author><name sortKey="Pedersen, Inge Sokilde" sort="Pedersen, Inge Sokilde" uniqKey="Pedersen I" first="Inge Sokilde" last="Pedersen">Inge Sokilde Pedersen</name><affiliation><nlm:aff id="A8">Section of Molecular Diagnostics, Department of Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark</nlm:aff></affiliation></author><author><name sortKey="Montagna, Marco" sort="Montagna, Marco" uniqKey="Montagna M" first="Marco" last="Montagna">Marco Montagna</name><affiliation><nlm:aff id="A9">Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV—IRCCS, Padua, Italy</nlm:aff></affiliation></author><author><name sortKey="Menendez, Mireia" sort="Menendez, Mireia" uniqKey="Menendez M" first="Mireia" last="Menéndez">Mireia Menéndez</name><affiliation><nlm:aff id="A10">Genetic Diagnosis Unit, Hereditary Cancer Program, Institut Català d’Oncologia, Barcelona, Spain</nlm:aff></affiliation></author><author><name sortKey="Quiles, Francisco" sort="Quiles, Francisco" uniqKey="Quiles F" first="Francisco" last="Quiles">Francisco Quiles</name><affiliation><nlm:aff id="A10">Genetic Diagnosis Unit, Hereditary Cancer Program, Institut Català d’Oncologia, Barcelona, Spain</nlm:aff></affiliation></author><author><name sortKey="Gutierrez Enriquez, Sara" sort="Gutierrez Enriquez, Sara" uniqKey="Gutierrez Enriquez S" first="Sara" last="Gutiérrez-Enríquez">Sara Gutiérrez-Enríquez</name><affiliation><nlm:aff id="A11">Oncogenetics Laboratory, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Institut de Recerca, University Hospital Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain</nlm:aff></affiliation></author><author><name sortKey="De Leeneer, Kim" sort="De Leeneer, Kim" uniqKey="De Leeneer K" first="Kim" last="De Leeneer">Kim De Leeneer</name><affiliation><nlm:aff id="A12">Center for Medical Genetics, Ghent University Hospital, De Pintelaan, Ghent, Belgium</nlm:aff></affiliation></author><author><name sortKey="Tenes, Anna" sort="Tenes, Anna" uniqKey="Tenes A" first="Anna" last="Tenés">Anna Tenés</name><affiliation><nlm:aff id="A11">Oncogenetics Laboratory, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Institut de Recerca, University Hospital Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain</nlm:aff></affiliation></author><author><name sortKey="Montalban, Gemma" sort="Montalban, Gemma" uniqKey="Montalban G" first="Gemma" last="Montalban">Gemma Montalban</name><affiliation><nlm:aff id="A11">Oncogenetics Laboratory, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Institut de Recerca, University Hospital Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain</nlm:aff></affiliation></author><author><name sortKey="Tserpelis, Demis" sort="Tserpelis, Demis" uniqKey="Tserpelis D" first="Demis" last="Tserpelis">Demis Tserpelis</name><affiliation><nlm:aff id="A7">Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands</nlm:aff></affiliation></author><author><name sortKey="Yoshimatsu, Toshio" sort="Yoshimatsu, Toshio" uniqKey="Yoshimatsu T" first="Toshio" last="Yoshimatsu">Toshio Yoshimatsu</name><affiliation><nlm:aff id="A13">Department of Medicine, the University of Chicago Medical Center, Chicago, IL</nlm:aff></affiliation></author><author><name sortKey="Tirapo, Carole" sort="Tirapo, Carole" uniqKey="Tirapo C" first="Carole" last="Tirapo">Carole Tirapo</name><affiliation><nlm:aff id="A14">Service de Génétique et U830, Institut Curie, et Université Paris Descartes, Sorbonne Paris Cité, Paris, France</nlm:aff></affiliation></author><author><name sortKey="Raponi, Michela" sort="Raponi, Michela" uniqKey="Raponi M" first="Michela" last="Raponi">Michela Raponi</name><affiliation><nlm:aff id="A15">Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK</nlm:aff></affiliation></author><author><name sortKey="Caldes, Trinidad" sort="Caldes, Trinidad" uniqKey="Caldes T" first="Trinidad" last="Caldes">Trinidad Caldes</name><affiliation><nlm:aff id="A3">Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain</nlm:aff></affiliation></author><author><name sortKey="Blanco, Ana" sort="Blanco, Ana" uniqKey="Blanco A" first="Ana" last="Blanco">Ana Blanco</name><affiliation><nlm:aff id="A16">Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain</nlm:aff></affiliation></author><author><name sortKey="Santamari A, Marta" sort="Santamari A, Marta" uniqKey="Santamari A M" first="Marta" last="Santamari A">Marta Santamari A</name><affiliation><nlm:aff id="A17">Grupo de Medicina Xenómica—USC, University of Santiago de Compostela, CIBERER, IDIS, Santiago de Compostela, Spain</nlm:aff></affiliation></author><author><name sortKey="Guidugli, Lucia" sort="Guidugli, Lucia" uniqKey="Guidugli L" first="Lucia" last="Guidugli">Lucia Guidugli</name><affiliation><nlm:aff id="A18">Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, NY</nlm:aff></affiliation></author><author><name sortKey="De Garibay, Gorka Ruiz" sort="De Garibay, Gorka Ruiz" uniqKey="De Garibay G" first="Gorka Ruiz" last="De Garibay">Gorka Ruiz De Garibay</name><affiliation><nlm:aff id="A3">Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain</nlm:aff></affiliation></author><author><name sortKey="Wong, Ming" sort="Wong, Ming" uniqKey="Wong M" first="Ming" last="Wong">Ming Wong</name><affiliation><nlm:aff id="A19">Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff></affiliation></author><author><name sortKey="Tancredi, Mariella" sort="Tancredi, Mariella" uniqKey="Tancredi M" first="Mariella" last="Tancredi">Mariella Tancredi</name><affiliation><nlm:aff id="A20">Istituto di Anatomia Patologica, Università di Pisa, Pisa, Italy</nlm:aff></affiliation></author><author><name sortKey="Fachal, Laura" sort="Fachal, Laura" uniqKey="Fachal L" first="Laura" last="Fachal">Laura Fachal</name><affiliation><nlm:aff id="A16">Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain</nlm:aff></affiliation></author><author><name sortKey="Ding, Yuan Chun" sort="Ding, Yuan Chun" uniqKey="Ding Y" first="Yuan Chun" last="Ding">Yuan Chun Ding</name><affiliation><nlm:aff id="A21">Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA</nlm:aff></affiliation></author><author><name sortKey="Kruse, Torben" sort="Kruse, Torben" uniqKey="Kruse T" first="Torben" last="Kruse">Torben Kruse</name><affiliation><nlm:aff id="A4">Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark</nlm:aff></affiliation></author><author><name sortKey="Lattimore, Vanessa" sort="Lattimore, Vanessa" uniqKey="Lattimore V" first="Vanessa" last="Lattimore">Vanessa Lattimore</name><affiliation><nlm:aff id="A22">Department of Pathology' University of Otago, Christchurch, New Zealand</nlm:aff></affiliation></author><author><name sortKey="Kwong, Ava" sort="Kwong, Ava" uniqKey="Kwong A" first="Ava" last="Kwong">Ava Kwong</name><affiliation><nlm:aff id="A23">Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China</nlm:aff></affiliation></author><author><name sortKey="Chan, Tsun Leung" sort="Chan, Tsun Leung" uniqKey="Chan T" first="Tsun Leung" last="Chan">Tsun Leung Chan</name><affiliation><nlm:aff id="A23">Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China</nlm:aff></affiliation></author><author><name sortKey="Colombo, Mara" sort="Colombo, Mara" uniqKey="Colombo M" first="Mara" last="Colombo">Mara Colombo</name><affiliation><nlm:aff id="A24">Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy</nlm:aff></affiliation></author><author><name sortKey="De Vecchi, Giovanni" sort="De Vecchi, Giovanni" uniqKey="De Vecchi G" first="Giovanni" last="De Vecchi">Giovanni De Vecchi</name><affiliation><nlm:aff id="A24">Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy</nlm:aff></affiliation></author><author><name sortKey="Caligo, Maria" sort="Caligo, Maria" uniqKey="Caligo M" first="Maria" last="Caligo">Maria Caligo</name><affiliation><nlm:aff id="A19">Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia</nlm:aff></affiliation></author><author><name sortKey="Baralle, Diana" sort="Baralle, Diana" uniqKey="Baralle D" first="Diana" last="Baralle">Diana Baralle</name><affiliation><nlm:aff id="A15">Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK</nlm:aff></affiliation></author><author><name sortKey="Lazaro, Conxi" sort="Lazaro, Conxi" uniqKey="Lazaro C" first="Conxi" last="Lázaro">Conxi Lázaro</name><affiliation><nlm:aff id="A10">Genetic Diagnosis Unit, Hereditary Cancer Program, Institut Català d’Oncologia, Barcelona, Spain</nlm:aff></affiliation></author><author><name sortKey="Couch, Fergus" sort="Couch, Fergus" uniqKey="Couch F" first="Fergus" last="Couch">Fergus Couch</name><affiliation><nlm:aff id="A17">Grupo de Medicina Xenómica—USC, University of Santiago de Compostela, CIBERER, IDIS, Santiago de Compostela, Spain</nlm:aff></affiliation></author><author><name sortKey="Radice, Paolo" sort="Radice, Paolo" uniqKey="Radice P" first="Paolo" last="Radice">Paolo Radice</name><affiliation><nlm:aff id="A24">Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy</nlm:aff></affiliation></author><author><name sortKey="Southey, Melissa C" sort="Southey, Melissa C" uniqKey="Southey M" first="Melissa C." last="Southey">Melissa C. Southey</name><affiliation><nlm:aff id="A18">Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, NY</nlm:aff></affiliation></author><author><name sortKey="Neuhausen, Susan" sort="Neuhausen, Susan" uniqKey="Neuhausen S" first="Susan" last="Neuhausen">Susan Neuhausen</name><affiliation><nlm:aff id="A21">Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA</nlm:aff></affiliation></author><author><name sortKey="Houdayer, Claude" sort="Houdayer, Claude" uniqKey="Houdayer C" first="Claude" last="Houdayer">Claude Houdayer</name><affiliation><nlm:aff id="A14">Service de Génétique et U830, Institut Curie, et Université Paris Descartes, Sorbonne Paris Cité, Paris, France</nlm:aff></affiliation></author><author><name sortKey="Fackenthal, Jim" sort="Fackenthal, Jim" uniqKey="Fackenthal J" first="Jim" last="Fackenthal">Jim Fackenthal</name><affiliation><nlm:aff id="A13">Department of Medicine, the University of Chicago Medical Center, Chicago, IL</nlm:aff></affiliation></author><author><name sortKey="Van Overeem Hansen, Thomas" sort="Van Overeem Hansen, Thomas" uniqKey="Van Overeem Hansen T" first="Thomas" last="Van Overeem Hansen">Thomas Van Overeem Hansen</name><affiliation><nlm:aff id="A25">Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark</nlm:aff></affiliation></author><author><name sortKey="Vega, Ana" sort="Vega, Ana" uniqKey="Vega A" first="Ana" last="Vega">Ana Vega</name><affiliation><nlm:aff id="A16">Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain</nlm:aff></affiliation></author><author><name sortKey="Diez, Orland" sort="Diez, Orland" uniqKey="Diez O" first="Orland" last="Diez">Orland Diez</name><affiliation><nlm:aff id="A11">Oncogenetics Laboratory, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Institut de Recerca, University Hospital Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain</nlm:aff></affiliation></author><author><name sortKey="Blok, Rien" sort="Blok, Rien" uniqKey="Blok R" first="Rien" last="Blok">Rien Blok</name><affiliation><nlm:aff id="A7">Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands</nlm:aff></affiliation></author><author><name sortKey="Claes, Kathleen" sort="Claes, Kathleen" uniqKey="Claes K" first="Kathleen" last="Claes">Kathleen Claes</name><affiliation><nlm:aff id="A12">Center for Medical Genetics, Ghent University Hospital, De Pintelaan, Ghent, Belgium</nlm:aff></affiliation></author><author><name sortKey="Wappenschmidt, Barbara" sort="Wappenschmidt, Barbara" uniqKey="Wappenschmidt B" first="Barbara" last="Wappenschmidt">Barbara Wappenschmidt</name><affiliation><nlm:aff id="A5">Center for Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany</nlm:aff></affiliation><affiliation><nlm:aff id="A6">Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany</nlm:aff></affiliation></author><author><name sortKey="Walker, Logan" sort="Walker, Logan" uniqKey="Walker L" first="Logan" last="Walker">Logan Walker</name><affiliation><nlm:aff id="A22">Department of Pathology' University of Otago, Christchurch, New Zealand</nlm:aff></affiliation></author><author><name sortKey="Spurdle, Amanda B" sort="Spurdle, Amanda B" uniqKey="Spurdle A" first="Amanda B." last="Spurdle">Amanda B. Spurdle</name><affiliation><nlm:aff id="A1">Genetics & Computational Biology Division, Queensland Institute of Medical Research, Brisbane, Queensland, Australia</nlm:aff></affiliation></author><author><name sortKey="Brown, Melissa A" sort="Brown, Melissa A" uniqKey="Brown M" first="Melissa A." last="Brown">Melissa A. Brown</name><affiliation><nlm:aff id="A2">School of Chemistry and Molecular Biosciences, the University of Queensland, Queensland, Australia</nlm:aff></affiliation></author></analytic><series><title level="j">Clinical chemistry</title><idno type="ISSN">0009-9147</idno><idno type="eISSN">1530-8561</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec id="S1"><title>Background</title><p id="P1">Accurate evaluation of unclassified sequence variants in cancer predisposition genes is essential for clinical management and depends on a multifactorial analysis of clinical, genetic, pathologic, and bioinformatic variables and assays of transcript length and abundance. The integrity of assay data in turn relies on appropriate assay design, interpretation, and reporting.</p></sec><sec id="S2"><title>Methods</title><p id="P2">We conducted a multicenter investigation to compare mRNA splicing assay protocols used by members of the ENIGMA (Evidence-Based Network for the Interpretation of Germline Mutant Alleles) consortium. We compared similarities and differences in results derived from analysis of a panel of breast cancer 1, early onset (<italic>BRCA1</italic>) and breast cancer 2, early onset (<italic>BRCA2</italic>) gene variants known to alter splicing (<italic>BRCA1</italic>: c.135-1G>T, c.591C>T, c.594-2A>C, c.671-2A>G, and c.5467+5G>C and <italic>BRCA2</italic>: c.426-12_8delGTTTT, c.7988A>T, c.8632+1G>A, and c.9501+3A>T). Differences in protocols were then assessed to determine which elements were critical in reliable assay design.</p></sec><sec id="S3"><title>Results</title><p id="P3">PCR primer design strategies, PCR conditions, and product detection methods, combined with a prior knowledge of expected alternative transcripts, were the key factors for accurate splicing assay results. For example, because of the position of primers and PCR extension times, several isoforms associated with <italic>BRCA1</italic>, c.594-2A>C and c.671-2A>G, were not detected by many sites. Variation was most evident for the detection of low-abundance transcripts (e.g., <italic>BRCA2</italic> c.8632+1G>A Δ19,20 and <italic>BRCA1</italic> c.135-1g>t Δ5q and Δ3). Detection of low-abundance transcripts was sometimes addressed by using more analytically sensitive detection methods (e.g., <italic>BRCA2</italic> c.426-12_8delGTTTT ins18bp).</p></sec><sec id="S4"><title>Conclusions</title><p id="P4">We provide recommendations for best practice and raise key issues to consider when designing mRNA assays for evaluation of unclassified sequence variants.</p></sec></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">9421549</journal-id><journal-id journal-id-type="pubmed-jr-id">2992</journal-id><journal-id journal-id-type="nlm-ta">Clin Chem</journal-id><journal-id journal-id-type="iso-abbrev">Clin. Chem.</journal-id><journal-title-group><journal-title>Clinical chemistry</journal-title></journal-title-group><issn pub-type="ppub">0009-9147</issn><issn pub-type="epub">1530-8561</issn></journal-meta><article-meta><article-id pub-id-type="pmid">24212087</article-id><article-id pub-id-type="pmc">4351044</article-id><article-id pub-id-type="doi">10.1373/clinchem.2013.210658</article-id><article-id pub-id-type="manuscript">NIHMS666445</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Comparison of mRNA Splicing Assay Protocols across Multiple Laboratories: Recommendations for Best Practice in Standardized Clinical Testing</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Whiley</surname><given-names>Phillip J.</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>de la Hoya</surname><given-names>Miguel</given-names></name><xref ref-type="aff" rid="A3">3</xref></contrib><contrib contrib-type="author"><name><surname>Thomassen</surname><given-names>Mads</given-names></name><xref ref-type="aff" rid="A4">4</xref></contrib><contrib contrib-type="author"><name><surname>Becker</surname><given-names>Alexandra</given-names></name><xref ref-type="aff" rid="A5">5</xref><xref ref-type="aff" rid="A6">6</xref></contrib><contrib contrib-type="author"><name><surname>Brandão</surname><given-names>Rita</given-names></name><xref ref-type="aff" rid="A7">7</xref></contrib><contrib contrib-type="author"><name><surname>Pedersen</surname><given-names>Inge Sokilde</given-names></name><xref ref-type="aff" rid="A8">8</xref></contrib><contrib contrib-type="author"><name><surname>Montagna</surname><given-names>Marco</given-names></name><xref ref-type="aff" rid="A9">9</xref></contrib><contrib contrib-type="author"><name><surname>Menéndez</surname><given-names>Mireia</given-names></name><xref ref-type="aff" rid="A10">10</xref></contrib><contrib contrib-type="author"><name><surname>Quiles</surname><given-names>Francisco</given-names></name><xref ref-type="aff" rid="A10">10</xref></contrib><contrib contrib-type="author"><name><surname>Gutiérrez-Enríquez</surname><given-names>Sara</given-names></name><xref ref-type="aff" rid="A11">11</xref></contrib><contrib contrib-type="author"><name><surname>De Leeneer</surname><given-names>Kim</given-names></name><xref ref-type="aff" rid="A12">12</xref></contrib><contrib contrib-type="author"><name><surname>Tenés</surname><given-names>Anna</given-names></name><xref ref-type="aff" rid="A11">11</xref></contrib><contrib contrib-type="author"><name><surname>Montalban</surname><given-names>Gemma</given-names></name><xref ref-type="aff" rid="A11">11</xref></contrib><contrib contrib-type="author"><name><surname>Tserpelis</surname><given-names>Demis</given-names></name><xref ref-type="aff" rid="A7">7</xref></contrib><contrib contrib-type="author"><name><surname>Yoshimatsu</surname><given-names>Toshio</given-names></name><xref ref-type="aff" rid="A13">13</xref></contrib><contrib contrib-type="author"><name><surname>Tirapo</surname><given-names>Carole</given-names></name><xref ref-type="aff" rid="A14">14</xref></contrib><contrib contrib-type="author"><name><surname>Raponi</surname><given-names>Michela</given-names></name><xref ref-type="aff" rid="A15">15</xref></contrib><contrib contrib-type="author"><name><surname>Caldes</surname><given-names>Trinidad</given-names></name><xref ref-type="aff" rid="A3">3</xref></contrib><contrib contrib-type="author"><name><surname>Blanco</surname><given-names>Ana</given-names></name><xref ref-type="aff" rid="A16">16</xref></contrib><contrib contrib-type="author"><name><surname>Santamariña</surname><given-names>Marta</given-names></name><xref ref-type="aff" rid="A17">17</xref></contrib><contrib contrib-type="author"><name><surname>Guidugli</surname><given-names>Lucia</given-names></name><xref ref-type="aff" rid="A18">18</xref></contrib><contrib contrib-type="author"><name><surname>de Garibay</surname><given-names>Gorka Ruiz</given-names></name><xref ref-type="aff" rid="A3">3</xref></contrib><contrib contrib-type="author"><name><surname>Wong</surname><given-names>Ming</given-names></name><xref ref-type="aff" rid="A19">19</xref></contrib><contrib contrib-type="author"><name><surname>Tancredi</surname><given-names>Mariella</given-names></name><xref ref-type="aff" rid="A20">20</xref></contrib><contrib contrib-type="author"><name><surname>Fachal</surname><given-names>Laura</given-names></name><xref ref-type="aff" rid="A16">16</xref></contrib><contrib contrib-type="author"><name><surname>Ding</surname><given-names>Yuan Chun</given-names></name><xref ref-type="aff" rid="A21">21</xref></contrib><contrib contrib-type="author"><name><surname>Kruse</surname><given-names>Torben</given-names></name><xref ref-type="aff" rid="A4">4</xref></contrib><contrib contrib-type="author"><name><surname>Lattimore</surname><given-names>Vanessa</given-names></name><xref ref-type="aff" rid="A22">22</xref></contrib><contrib contrib-type="author"><name><surname>Kwong</surname><given-names>Ava</given-names></name><xref ref-type="aff" rid="A23">23</xref></contrib><contrib contrib-type="author"><name><surname>Chan</surname><given-names>Tsun Leung</given-names></name><xref ref-type="aff" rid="A23">23</xref></contrib><contrib contrib-type="author"><name><surname>Colombo</surname><given-names>Mara</given-names></name><xref ref-type="aff" rid="A24">24</xref></contrib><contrib contrib-type="author"><name><surname>De Vecchi</surname><given-names>Giovanni</given-names></name><xref ref-type="aff" rid="A24">24</xref></contrib><contrib contrib-type="author"><name><surname>Caligo</surname><given-names>Maria</given-names></name><xref ref-type="aff" rid="A19">19</xref></contrib><contrib contrib-type="author"><name><surname>Baralle</surname><given-names>Diana</given-names></name><xref ref-type="aff" rid="A15">15</xref></contrib><contrib contrib-type="author"><name><surname>Lázaro</surname><given-names>Conxi</given-names></name><xref ref-type="aff" rid="A10">10</xref></contrib><contrib contrib-type="author"><name><surname>Couch</surname><given-names>Fergus</given-names></name><xref ref-type="aff" rid="A17">17</xref></contrib><contrib contrib-type="author"><name><surname>Radice</surname><given-names>Paolo</given-names></name><xref ref-type="aff" rid="A24">24</xref></contrib><contrib contrib-type="author"><name><surname>Southey</surname><given-names>Melissa C.</given-names></name><xref ref-type="aff" rid="A18">18</xref></contrib><contrib contrib-type="author"><name><surname>Neuhausen</surname><given-names>Susan</given-names></name><xref ref-type="aff" rid="A21">21</xref></contrib><contrib contrib-type="author"><name><surname>Houdayer</surname><given-names>Claude</given-names></name><xref ref-type="aff" rid="A14">14</xref></contrib><contrib contrib-type="author"><name><surname>Fackenthal</surname><given-names>Jim</given-names></name><xref ref-type="aff" rid="A13">13</xref></contrib><contrib contrib-type="author"><name><surname>Van Overeem Hansen</surname><given-names>Thomas</given-names></name><xref ref-type="aff" rid="A25">25</xref></contrib><contrib contrib-type="author"><name><surname>Vega</surname><given-names>Ana</given-names></name><xref ref-type="aff" rid="A16">16</xref></contrib><contrib contrib-type="author"><name><surname>Diez</surname><given-names>Orland</given-names></name><xref ref-type="aff" rid="A11">11</xref></contrib><contrib contrib-type="author"><name><surname>Blok</surname><given-names>Rien</given-names></name><xref ref-type="aff" rid="A7">7</xref></contrib><contrib contrib-type="author"><name><surname>Claes</surname><given-names>Kathleen</given-names></name><xref ref-type="aff" rid="A12">12</xref></contrib><contrib contrib-type="author"><name><surname>Wappenschmidt</surname><given-names>Barbara</given-names></name><xref ref-type="aff" rid="A5">5</xref><xref ref-type="aff" rid="A6">6</xref></contrib><contrib contrib-type="author"><name><surname>Walker</surname><given-names>Logan</given-names></name><xref ref-type="aff" rid="A22">22</xref></contrib><contrib contrib-type="author"><name><surname>Spurdle</surname><given-names>Amanda B.</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Brown</surname><given-names>Melissa A.</given-names></name><xref ref-type="aff" rid="A2">2</xref><on-behalf-of>on behalf of the ENIGMA consortium</on-behalf-of></contrib></contrib-group><aff id="A1"><label>1</label>Genetics & Computational Biology Division, Queensland Institute of Medical Research, Brisbane, Queensland, Australia</aff><aff id="A2"><label>2</label>School of Chemistry and Molecular Biosciences, the University of Queensland, Queensland, Australia</aff><aff id="A3"><label>3</label>Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain</aff><aff id="A4"><label>4</label>Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark</aff><aff id="A5"><label>5</label>Center for Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany</aff><aff id="A6"><label>6</label>Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany</aff><aff id="A7"><label>7</label>Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands</aff><aff id="A8"><label>8</label>Section of Molecular Diagnostics, Department of Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark</aff><aff id="A9"><label>9</label>Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV—IRCCS, Padua, Italy</aff><aff id="A10"><label>10</label>Genetic Diagnosis Unit, Hereditary Cancer Program, Institut Català d’Oncologia, Barcelona, Spain</aff><aff id="A11"><label>11</label>Oncogenetics Laboratory, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Institut de Recerca, University Hospital Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain</aff><aff id="A12"><label>12</label>Center for Medical Genetics, Ghent University Hospital, De Pintelaan, Ghent, Belgium</aff><aff id="A13"><label>13</label>Department of Medicine, the University of Chicago Medical Center, Chicago, IL</aff><aff id="A14"><label>14</label>Service de Génétique et U830, Institut Curie, et Université Paris Descartes, Sorbonne Paris Cité, Paris, France</aff><aff id="A15"><label>15</label>Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK</aff><aff id="A16"><label>16</label>Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain</aff><aff id="A17"><label>17</label>Grupo de Medicina Xenómica—USC, University of Santiago de Compostela, CIBERER, IDIS, Santiago de Compostela, Spain</aff><aff id="A18"><label>18</label>Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, NY</aff><aff id="A19"><label>19</label>Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia</aff><aff id="A20"><label>20</label>Istituto di Anatomia Patologica, Università di Pisa, Pisa, Italy</aff><aff id="A21"><label>21</label>Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA</aff><aff id="A22"><label>22</label>Department of Pathology' University of Otago, Christchurch, New Zealand</aff><aff id="A23"><label>23</label>Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China</aff><aff id="A24"><label>24</label>Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy</aff><aff id="A25"><label>25</label>Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark</aff><author-notes><corresp id="FN1"><label>*</label>Address correspondence to this author at: The University of Queensland, St. Lucia, Qld, 4072, Australia. <email>melissa.brown@uq.edu.au</email></corresp></author-notes><pub-date pub-type="nihms-submitted"><day>25</day><month>2</month><year>2015</year></pub-date><pub-date pub-type="epub"><day>08</day><month>11</month><year>2013</year></pub-date><pub-date pub-type="ppub"><month>2</month><year>2014</year></pub-date><pub-date pub-type="pmc-release"><day>05</day><month>3</month><year>2015</year></pub-date><volume>60</volume><issue>2</issue><fpage>341</fpage><lpage>352</lpage><pmc-comment>elocation-id from pubmed: 10.1373/clinchem.2013.210658</pmc-comment>
<permissions><copyright-statement>© 2013 American Association for Clinical Chemistry</copyright-statement><copyright-year>2013</copyright-year></permissions><abstract><sec id="S1"><title>Background</title><p id="P1">Accurate evaluation of unclassified sequence variants in cancer predisposition genes is essential for clinical management and depends on a multifactorial analysis of clinical, genetic, pathologic, and bioinformatic variables and assays of transcript length and abundance. The integrity of assay data in turn relies on appropriate assay design, interpretation, and reporting.</p></sec><sec id="S2"><title>Methods</title><p id="P2">We conducted a multicenter investigation to compare mRNA splicing assay protocols used by members of the ENIGMA (Evidence-Based Network for the Interpretation of Germline Mutant Alleles) consortium. We compared similarities and differences in results derived from analysis of a panel of breast cancer 1, early onset (<italic>BRCA1</italic>) and breast cancer 2, early onset (<italic>BRCA2</italic>) gene variants known to alter splicing (<italic>BRCA1</italic>: c.135-1G>T, c.591C>T, c.594-2A>C, c.671-2A>G, and c.5467+5G>C and <italic>BRCA2</italic>: c.426-12_8delGTTTT, c.7988A>T, c.8632+1G>A, and c.9501+3A>T). Differences in protocols were then assessed to determine which elements were critical in reliable assay design.</p></sec><sec id="S3"><title>Results</title><p id="P3">PCR primer design strategies, PCR conditions, and product detection methods, combined with a prior knowledge of expected alternative transcripts, were the key factors for accurate splicing assay results. For example, because of the position of primers and PCR extension times, several isoforms associated with <italic>BRCA1</italic>, c.594-2A>C and c.671-2A>G, were not detected by many sites. Variation was most evident for the detection of low-abundance transcripts (e.g., <italic>BRCA2</italic> c.8632+1G>A Δ19,20 and <italic>BRCA1</italic> c.135-1g>t Δ5q and Δ3). Detection of low-abundance transcripts was sometimes addressed by using more analytically sensitive detection methods (e.g., <italic>BRCA2</italic> c.426-12_8delGTTTT ins18bp).</p></sec><sec id="S4"><title>Conclusions</title><p id="P4">We provide recommendations for best practice and raise key issues to consider when designing mRNA assays for evaluation of unclassified sequence variants.</p></sec></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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