Abstract
Although the spliceogenic nature of the BRCA2 c.68-7T > A variant has been demonstrated, its association with cancer risk remains controversial. In this study, we accurately quantified by real-time PCR and digital PCR (dPCR), the BRCA2 isoforms retaining or missing exon 3. In addition, the combined odds ratio for causality of the variant was estimated using genetic and clinical data, and its associated cancer risk was estimated by case-control analysis in 83,636 individuals. Co-occurrence in trans with pathogenic BRCA2 variants was assessed in 5,382 families. Exon 3 exclusion rate was 4.5-fold higher in variant carriers (13%) than controls (3%), indicating an exclusion rate for the c.68-7T > A allele of approximately 20%. The posterior probability of pathogenicity was 7.44 × 10−115. There was neither evidence for increased risk of breast cancer (OR 1.03; 95% CI 0.86–1.24) nor for a deleterious effect of the variant when co-occurring with pathogenic variants. Our data provide for the first time robust evidence of the nonpathogenicity of the BRCA2 c.68-7T > A. Genetic and quantitative transcript analyses together inform the threshold for the ratio between functional and altered BRCA2 isoforms compatible with normal cell function. These findings might be exploited to assess the relevance for cancer risk of other BRCA2 spliceogenic variants.
Original language | English (US) |
---|---|
Pages (from-to) | 729-741 |
Number of pages | 13 |
Journal | Human mutation |
Volume | 39 |
Issue number | 5 |
DOIs | |
State | Published - May 2018 |
Keywords
- BRCA2
- digital PCR
- multifactorial likelihood analysis
- quantitative real-time PCR
- spliceogenic variants
ASJC Scopus subject areas
- Genetics
- Genetics(clinical)
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The BRCA2 c.68-7T > A variant is not pathogenic : A model for clinical calibration of spliceogenicity. / kConFab/AOCS Investigators.
In: Human mutation, Vol. 39, No. 5, 05.2018, p. 729-741.Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - The BRCA2 c.68-7T > A variant is not pathogenic
T2 - A model for clinical calibration of spliceogenicity
AU - kConFab/AOCS Investigators
AU - Colombo, Mara
AU - Lòpez-Perolio, Irene
AU - Meeks, Huong D.
AU - Caleca, Laura
AU - Parsons, Michael T.
AU - Li, Hongyan
AU - De Vecchi, Giovanna
AU - Tudini, Emma
AU - Foglia, Claudia
AU - Mondini, Patrizia
AU - Manoukian, Siranoush
AU - Behar, Raquel
AU - Garcia, Encarna B.Gómez
AU - Meindl, Alfons
AU - Montagna, Marco
AU - Niederacher, Dieter
AU - Schmidt, Ane Y.
AU - Varesco, Liliana
AU - Wappenschmidt, Barbara
AU - Bolla, Manjeet K.
AU - Dennis, Joe
AU - Michailidou, Kyriaki
AU - Wang, Qin
AU - Aittomäki, Kristiina
AU - Andrulis, Irene L.
AU - Anton-Culver, Hoda
AU - Arndt, Volker
AU - Beckmann, Matthias W.
AU - Beeghly-Fadel, Alicia
AU - Benitez, Javier
AU - Boeckx, Bram
AU - Bogdanova, Natalia V.
AU - Bojesen, Stig E.
AU - Bonanni, Bernardo
AU - Brauch, Hiltrud
AU - Brenner, Hermann
AU - Burwinkel, Barbara
AU - Chang-Claude, Jenny
AU - Conroy, Don M.
AU - Couch, Fergus J.
AU - Cox, Angela
AU - Cross, Simon S.
AU - Czene, Kamila
AU - Devilee, Peter
AU - Dörk, Thilo
AU - Eriksson, Mikael
AU - Fasching, Peter A.
AU - Figueroa, Jonine
AU - Fletcher, Olivia
AU - Olson, Janet E.
N1 - Funding Information: HEBON: The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON) consists of the following Collaborating Centers: Netherlands Cancer Institute (coordinating center), Amsterdam, NL: M.A. Rookus, F.B.L. Hogervorst, F.E. van Leeuwen, L.E. van der Kolk, M.K. Schmidt, N.S. Russell, J.L. de Lange, R. Wijnands; Erasmus Medical Center, Rotterdam, NL: J.M. Collée, A.M.W. van den Ouwe-land, M.J. Hooning, C. Seynaeve, C.H.M. van Deurzen, I.M. Obdeijn; Leiden University Medical Center, NL: C.J. van Asperen, J.T. Wijnen, R.A.E.M. Tollenaar, P. Devilee, T.C.T.E.F. van Cronenburg; Radboud University Nijmegen Medical Center, NL: C.M. Kets, A.R. Mensenkamp; University Medical Center Utrecht, NL: M.G.E.M. Ausems, R.B. van der Luijt, C.C. van der Pol; Amsterdam Medical Center, NL: C.M. Aalfs, T.A.M. van Os; VU University Medical Center, Amsterdam, NL: J.J.P. Gille, Q. Waisfisz, H.E.J. Meijers-Heijboer; Maastricht University Medical Center, NL: E.B. Gómez-Garcia, M.J. Blok; University of Gronin-gen, NL: J.C. Oosterwijk, A.H. van der Hout, M.J. Mourits, G.H. de Bock; The Netherlands Comprehensive Cancer Organisation (IKNL): S. Siesling, J.Verloop; The nationwide network and registry of histo-and cytopathology in The Netherlands (PALGA): L.I.H. Overbeek. HEBON thanks the study participants and the registration teams of IKNL and PALGA for part of the data collection. The HEBON study is supported by the Dutch Cancer Society grants NKI1998-1854, NKI2004-308, NKI2007-3756, the Netherlands Organisation of Scientific Research grant NWO 91109024, the Pink Ribbon grants 110005 and 2014-187.WO76, the BBMRI grant NWO 184.021.007/CP46 and the Tran-scan grant JTC 2012 Cancer 12-054. Funding Information: the NHMRC Senior Research Fellowship Scheme; Spanish Instituto de Salud Carlos III funding, an initiative of the Spanish Ministry of Economy and Innovation partially supported by European Regional Development FEDER Funds; Associazione Italiana per la Ricerca sul Cancro, Grant/Award Number: N◦15547 to P.R.; the Cancer Council Queensland; NHMRC Project grant scheme Funding Information: We thank Bent Ejlertsen, Department of Oncology, and Anne-Marie Gerdes, Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark for recruitment and genetic counselling of breast cancer patients. ABCFS: Maggie Angelakos, Judi Maskiell, Gillian Dite. ABCS: Blood bank Sanquin, The Netherlands. BBCS: Eileen Williams, Elaine Ryder-Mills, Kara Sargus. BIGGS: Niall McInerney, Gabrielle Colleran, Andrew Rowan, Angela Jones. BSUCH: Peter Bugert, Medical Faculty Mannheim. CGPS: staff and participants of the Copenhagen General Population Study, and Dorthe Uldall Andersen, Maria Birna Arnadottir, Anne Bank, Dorthe Kjeldg?rd Hansen for the excellent technical assistance. The Danish Cancer Biobank is acknowledged for providing infrastructure for the collection of blood samples for the cases. CNIO-BCS: Guillermo Pita, Charo Alonso, Nuria ?lvarez, Pilar Zamora, Primitiva Menendez, the Human Genotyping-CEGEN Unit (CNIO). CTS: the CTS Steering Committee includes Leslie Bernstein, James Lacey, Sophia Wang, Huiyan Ma, and Jessica Clague DeHart at the Beckman Research Institute of City of Hope, Dennis Deapen, Rich Pinder, and Eunjung Lee at the University of Southern California, Pam Horn-Ross, Peggy Reynolds, Christina Clarke Dur and David Nelson at the Cancer Prevention Institute of California, Argyrios Ziogas, and Hannah Park at the University of California Irvine, and Fred Schumacher at Case Western University. ESTHER: Hartwig Ziegler, Sonja Wolf, Volker Hermann, Christa Stegmaier, Katja Butterbach. GC-HBOC: Stefanie Engert, Heide Hellebrand, Sandra Kr?ber and LIFE - Leipzig Research Centre for Civilization Diseases (Markus Loeffler, Joachim Thiery, Matthias N?chter, Ronny Baber). GENICA Network: Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University of T?bingen, Germany [HB, Wing-Yee Lo, Christina Justenhoven], German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) [HB], Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Germany [Yon-Dschun Ko, Christian Baisch], Institute of Pathology, University of Bonn, Germany [Hans-Peter Fischer], Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany [UH], Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bochum, Germany [Thomas Br?ning, Beate Pesch, Sylvia Rabstein, Anne Lotz]; and Institute of Occupational Medicine and Maritime Medicine, University Medical Center Hamburg-Eppendorf, Germany [Volker Harth]. HEBCS: Sofia Khan, Johanna Kiiski, Carl Blomqvist, Rainer Fagerholm, Kirsimari Aaltonen, Karl von Smitten, Irja Erkkil?. HMBCS: Peter Hillemanns, Hans Christiansen and Johann H. Karstens. KBCP: Eija My?h?nen, Helena Kemil?inen. kConFab/AOCS: Heather Thorne, Eveline Niedermayr, all the kConFab research nurses and staff, the heads and staff of the Family Cancer Clinics, and the Clinical Follow Up Study (which has received funding from the NHMRC, the National Breast Cancer Foundation, Cancer Australia, and the National Institute of Health (USA)) for their contributions to this resource, and the many families who contribute to kConFab. LMBC: Gilian Peuteman, Thomas Van Brussel, EvyVanderheyden and Kathleen Corthouts. MARIE: Petra Seibold, Dieter Flesch-Janys, Judith Heinz, Nadia Obi, Alina Vrieling, Sabine Behrens, Ursula Eilber, Muhabbet Celik, Til Olchers and Stefan Nickels. MBCSG: Bernard Peissel, Jacopo Azzollini, Daniela Zaffaroni and Milena Mariani of the Fondazione IRCCS Istituto Nazionale dei Tumori (INT); Monica Barile and Irene Feroce of the Istituto Europeo di Oncologia (IEO) and the personnel of the Cogentech Cancer Genetic Test Laboratory. MYBRCA: study partcipants and research staff (particularly Patsy Ng, Nurhidayu Hassan, Yoon Sook-Yee, Daphne Lee, Lee Sheau Yee, Phuah Sze Yee and Norhashimah Hassan) for their contributions and commitment to this study. NBHS: study partcipants and research staff for their contributions and commitment to this study. OBCS: Arja Jukkola-Vuorinen, Mervi Grip, Saila Kauppila, Meeri Otsukka, Leena Keskitalo and Kari Mononen for their contributions to this study. OFBCR: Teresa Selander and Nayana Weerasooriya. ORIGO: E. Krol-Warmerdam, and J. Blom for patient accrual, administering questionnaires, and managing clinical information. The LUMC survival data were retrieved from the Leiden hospital-based cancer registry system (ONCDOC) with the help of Dr. J. Molenaar. PBCS: Louise Brinton, Mark Sherman, Neonila Szeszenia-Dabrowska, Beata Peplonska, Witold Zatonski, Pei Chao, Michael Stagner. pKARMA: the Swedish Medical Research Counsel. RBCS: Petra Bos, Jannet Blom, Ellen Crepin, Elisabeth Huijskens, Anja Kromwijk-Nieuwlaat, Annette Heemskerk, the Erasmus MC Family Cancer Clinic. SASBAC: the Swedish Medical Research Counsel. SBCS: Sue Higham, Helen Cramp, Dan Connley, Ian Brock, Sabapathy Balasubramanian and Malcolm W.R. Reed. SEARCH: the SEARCH and EPIC teams. SGBCC: the participants and research coordinator Ms Tan Siew Li. SZBCS: Ewa Putresza. UKBGS: Breast Cancer Now and the Institute of Cancer Research for support and funding of the Breakthrough Generations Study, and the study participants, study staff, and the doctors, nurses and other health care providers and health information sources who have contributed to the study. We acknowledge NHS funding to the Royal Marsden/ICR NIHR Biomedical Research Centre. HEBON: The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON) consists of the following Collaborating Centers: Netherlands Cancer Institute (coordinating center), Amsterdam, NL: M.A. Rookus, F.B.L. Hogervorst, F.E. van Leeuwen, L.E. van der Kolk, M.K. Schmidt, N.S. Russell, J.L. de Lange, R. Wijnands; Erasmus Medical Center, Rotterdam, NL: J.M. Coll?e, A.M.W. van den Ouweland, M.J. Hooning, C. Seynaeve, C.H.M. van Deurzen, I.M. Obdeijn; Leiden University Medical Center, NL: C.J. van Asperen, J.T. Wijnen, R.A.E.M. Tollenaar, P. Devilee, T.C.T.E.F. van Cronenburg; Radboud University Nijmegen Medical Center, NL: C.M. Kets, A.R. Mensenkamp; University Medical Center Utrecht, NL: M.G.E.M. Ausems, R.B. van der Luijt, C.C. van der Pol; Amsterdam Medical Center, NL: C.M. Aalfs, T.A.M. van Os; VU University Medical Center, Amsterdam, NL: J.J.P. Gille, Q. Waisfisz, H.E.J. Meijers-Heijboer; Maastricht University Medical Center, NL: E.B. G?mez-Garcia, M.J. Blok; University of Groningen, NL: J.C. Oosterwijk, A.H. van der Hout, M.J. Mourits, G.H. de Bock; The Netherlands Comprehensive Cancer Organisation (IKNL): S. Siesling, J.Verloop; The nationwide network and registry of histo- and cytopathology in The Netherlands (PALGA): L.I.H. Overbeek. HEBON thanks the study participants and the registration teams of IKNL and PALGA for part of the data collection. The HEBON study is supported by the Dutch Cancer Society grants NKI1998-1854, NKI2004-308, NKI2007-3756, the Netherlands Organisation of Scientific Research grant NWO 91109024, the Pink Ribbon grants 110005 and 2014-187.WO76, the BBMRI grant NWO 184.021.007/CP46 and the Transcan grant JTC 2012 Cancer 12-054. We thank Cristina Lecchi (Dipartimento di Medicina Veterinaria, Universit? di Milano, Milano, Italy) for technical advices. Funding Information: ABCFS: Maggie Angelakos, Judi Maskiell, Gillian Dite. ABCS: Blood bank Sanquin, The Netherlands. BBCS: Eileen Williams, Elaine Ryder-Mills, Kara Sargus. BIGGS: Niall McInerney, Gabrielle Colleran, Andrew Rowan, Angela Jones. BSUCH: Peter Bugert, Medical Faculty Mannheim. CGPS: staff and participants of the Copenhagen General Population Study, and Dorthe Uldall Andersen, Maria Birna Arnadot-tir, Anne Bank, Dorthe Kjeldgård Hansen for the excellent technical assistance. The Danish Cancer Biobank is acknowledged for providing infrastructure for the collection of blood samples for the cases. CNIO-BCS: Guillermo Pita, Charo Alonso, Nuria Álvarez, Pilar Zamora, Prim-itiva Menendez, the Human Genotyping-CEGEN Unit (CNIO). CTS: the CTS Steering Committee includes Leslie Bernstein, James Lacey, Sophia Wang, Huiyan Ma, and Jessica Clague DeHart at the Beckman Research Institute of City of Hope, Dennis Deapen, Rich Pinder, and Eunjung Lee at the University of Southern California, Pam Horn-Ross, Peggy Reynolds, Christina Clarke Dur and David Nelson at the Cancer Prevention Institute of California, Argyrios Zio-gas, and Hannah Park at the University of California Irvine, and Fred Schumacher at Case Western University. ESTHER: Hartwig Ziegler, Sonja Wolf, Volker Hermann, Christa Stegmaier, Katja Butterbach. GC-HBOC: Stefanie Engert, Heide Hellebrand, Sandra Kröber and LIFE - Leipzig Research Centre for Civilization Diseases (Markus Loef-fler, Joachim Thiery, Matthias Nüchter, Ronny Baber). GENICA Network: Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University of Tübingen, Germany [HB, Wing-Yee Lo, Christina Justenhoven], German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) [HB], Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Kranken-haus, Bonn, Germany [Yon-Dschun Ko, Christian Baisch], Institute of Pathology, University of Bonn, Germany [Hans-Peter Fischer], Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany [UH], Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bochum, Germany [Thomas Brüning, Beate Pesch, Sylvia Rabstein, Anne Lotz]; and Institute of Occupational Medicine and Maritime Medicine, University Medical Center Hamburg-Eppendorf, Germany [Volker Harth]. HEBCS: Sofia Khan, Johanna Kiiski, Carl Blomqvist, Rainer Fagerholm, Kirsimari Aal-tonen, Karl von Smitten, Irja Erkkilä. HMBCS: Peter Hillemanns, Hans Christiansen and Johann H. Karstens. KBCP: Eija Myöhänen, Helena Kemiläinen. kConFab/AOCS: Heather Thorne, Eveline Niedermayr, all the kConFab research nurses and staff, the heads and staff of the Family Cancer Clinics, and the Clinical Follow Up Study (which has received funding from the NHMRC, the National Breast Cancer Foundation, Cancer Australia, and the National Institute of Health (USA)) for their contributions to this resource, and the many families who contribute to kConFab. LMBC: Gilian Peuteman, Thomas Van Brussel, Evy-Vanderheyden and Kathleen Corthouts. MARIE: Petra Seibold, Dieter Flesch-Janys, Judith Heinz, Nadia Obi, Alina Vrieling, Sabine Behrens, Ursula Eilber, Muhabbet Celik, Til Olchers and Stefan Nickels. MBCSG: Bernard Peissel, Jacopo Azzollini, Daniela Zaffaroni and Milena Mari-ani of the Fondazione IRCCS Istituto Nazionale dei Tumori (INT); Monica Barile and Irene Feroce of the Istituto Europeo di Oncologia (IEO) and the personnel of the Cogentech Cancer Genetic Test Laboratory. MYBRCA: study partcipants and research staff (particularly Patsy Ng, Nurhidayu Hassan, Yoon Sook-Yee, Daphne Lee, Lee Sheau Yee, Phuah Sze Yee and Norhashimah Hassan) for their contributions and commitment to this study. NBHS: study partcipants and research staff for their contributions and commitment to this study. OBCS:ArjaJukkola-Vuorinen, Mervi Grip, Saila Kauppila, Meeri Otsukka, Leena Keskitalo and Kari Mononen for their contributions to this study. OFBCR: Teresa Selander and Nayana Weerasooriya. ORIGO: E. Krol-Warmerdam, and J. Blom for patient accrual, administering questionnaires, and managing clinical information. The LUMC survival data were retrieved from the Leiden hospital-based cancer registry system (ONCDOC) with the help of Dr. J. Molenaar. PBCS: Louise Brinton, Mark Sherman, Neonila Szeszenia-Dabrowska, Beata Peplonska, Witold Zatonski, Pei Chao, Michael Stagner. pKARMA: the Swedish Medical Research Counsel. RBCS: Petra Bos, Jannet Blom, Ellen Crepin, Elisabeth Huijskens, Anja Kromwijk-Nieuwlaat, Annette Heemskerk, the Erasmus MC Family Cancer Clinic. SASBAC: the Swedish Medical Research Counsel. SBCS: Sue Higham, Helen Cramp, Dan Connley, Ian Brock, Sabapathy Bal-asubramanian and Malcolm W.R. Reed. SEARCH: the SEARCH and EPIC teams. SGBCC: the participants and research coordinator Ms Tan Siew Li. SZBCS: Ewa Putresza. UKBGS: Breast Cancer Now and the Institute of Cancer Research for support and funding of the Break-through Generations Study, and the study participants, study staff, and the doctors, nurses and other health care providers and health information sources who have contributed to the study. We acknowledge NHS funding to the Royal Marsden/ICR NIHR Biomedical Research Centre. Publisher Copyright: © 2018 The Authors. Human Mutation published by Wiley Periodicals, Inc.
PY - 2018/5
Y1 - 2018/5
N2 - Although the spliceogenic nature of the BRCA2 c.68-7T > A variant has been demonstrated, its association with cancer risk remains controversial. In this study, we accurately quantified by real-time PCR and digital PCR (dPCR), the BRCA2 isoforms retaining or missing exon 3. In addition, the combined odds ratio for causality of the variant was estimated using genetic and clinical data, and its associated cancer risk was estimated by case-control analysis in 83,636 individuals. Co-occurrence in trans with pathogenic BRCA2 variants was assessed in 5,382 families. Exon 3 exclusion rate was 4.5-fold higher in variant carriers (13%) than controls (3%), indicating an exclusion rate for the c.68-7T > A allele of approximately 20%. The posterior probability of pathogenicity was 7.44 × 10−115. There was neither evidence for increased risk of breast cancer (OR 1.03; 95% CI 0.86–1.24) nor for a deleterious effect of the variant when co-occurring with pathogenic variants. Our data provide for the first time robust evidence of the nonpathogenicity of the BRCA2 c.68-7T > A. Genetic and quantitative transcript analyses together inform the threshold for the ratio between functional and altered BRCA2 isoforms compatible with normal cell function. These findings might be exploited to assess the relevance for cancer risk of other BRCA2 spliceogenic variants.
AB - Although the spliceogenic nature of the BRCA2 c.68-7T > A variant has been demonstrated, its association with cancer risk remains controversial. In this study, we accurately quantified by real-time PCR and digital PCR (dPCR), the BRCA2 isoforms retaining or missing exon 3. In addition, the combined odds ratio for causality of the variant was estimated using genetic and clinical data, and its associated cancer risk was estimated by case-control analysis in 83,636 individuals. Co-occurrence in trans with pathogenic BRCA2 variants was assessed in 5,382 families. Exon 3 exclusion rate was 4.5-fold higher in variant carriers (13%) than controls (3%), indicating an exclusion rate for the c.68-7T > A allele of approximately 20%. The posterior probability of pathogenicity was 7.44 × 10−115. There was neither evidence for increased risk of breast cancer (OR 1.03; 95% CI 0.86–1.24) nor for a deleterious effect of the variant when co-occurring with pathogenic variants. Our data provide for the first time robust evidence of the nonpathogenicity of the BRCA2 c.68-7T > A. Genetic and quantitative transcript analyses together inform the threshold for the ratio between functional and altered BRCA2 isoforms compatible with normal cell function. These findings might be exploited to assess the relevance for cancer risk of other BRCA2 spliceogenic variants.
KW - BRCA2
KW - digital PCR
KW - multifactorial likelihood analysis
KW - quantitative real-time PCR
KW - spliceogenic variants
UR - http://www.scopus.com/inward/record.url?scp=85044863861&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85044863861&partnerID=8YFLogxK
U2 - 10.1002/humu.23411
DO - 10.1002/humu.23411
M3 - Article
C2 - 29460995
AN - SCOPUS:85044863861
VL - 39
SP - 729
EP - 741
JO - Human Mutation
JF - Human Mutation
SN - 1059-7794
IS - 5
ER -