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Morra A, Mavaddat N, Muranen TA, Ahearn TU, Allen J, Andrulis IL, Auvinen P, Becher H, Behrens S, Blomqvist C, Bojesen SE, Bolla MK, Brauch H, Camp NJ, Carvalho S, Castelao JE, Cessna MH, Chang-Claude J, Chenevix-Trench G, Czene K, Decker B, Dennis J, Dörk T, Dorling L, Dunning AM, Ekici AB, Eriksson M, Evans DG, Fasching PA, Figueroa JD, Flyger H, Gago-Dominguez M, García-Closas M, Geurts-Giele WRR, Giles GG, Guénel P, Gündert M, Hahnen E, Hall P, Hamann U, Harrington PA, He W, Heikkilä P, Hooning MJ, Hoppe R, Howell A, Humphreys K, Jakubowska A, Jung AY, Keeman R, Kristensen VN, Lubiński J, Mannermaa A, Manoochehri M, Manoukian S, Margolin S, Mavroudis D, Milne RL, Mulligan AM, Newman WG, Park-Simon TW, Peterlongo P, Pharoah PDP, Rhenius V, Saloustros E, Sawyer EJ, Schmutzler RK, Shah M, Spurdle AB, Tomlinson I, Truong T, van Veen EM, Vreeswijk MPG, Wang Q, Wendt C, Yang XR, Nevanlinna H, Devilee P, Easton DF, Schmidt MK. The impact of coding germline variants on contralateral breast cancer risk and survival. Am J Hum Genet 2023; 110:475-486. [PMID: 36827971 PMCID: PMC10027471 DOI: 10.1016/j.ajhg.2023.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 02/01/2023] [Indexed: 02/25/2023] Open
Abstract
Evidence linking coding germline variants in breast cancer (BC)-susceptibility genes other than BRCA1, BRCA2, and CHEK2 with contralateral breast cancer (CBC) risk and breast cancer-specific survival (BCSS) is scarce. The aim of this study was to assess the association of protein-truncating variants (PTVs) and rare missense variants (MSVs) in nine known (ATM, BARD1, BRCA1, BRCA2, CHEK2, PALB2, RAD51C, RAD51D, and TP53) and 25 suspected BC-susceptibility genes with CBC risk and BCSS. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated with Cox regression models. Analyses included 34,401 women of European ancestry diagnosed with BC, including 676 CBCs and 3,449 BC deaths; the median follow-up was 10.9 years. Subtype analyses were based on estrogen receptor (ER) status of the first BC. Combined PTVs and pathogenic/likely pathogenic MSVs in BRCA1, BRCA2, and TP53 and PTVs in CHEK2 and PALB2 were associated with increased CBC risk [HRs (95% CIs): 2.88 (1.70-4.87), 2.31 (1.39-3.85), 8.29 (2.53-27.21), 2.25 (1.55-3.27), and 2.67 (1.33-5.35), respectively]. The strongest evidence of association with BCSS was for PTVs and pathogenic/likely pathogenic MSVs in BRCA2 (ER-positive BC) and TP53 and PTVs in CHEK2 [HRs (95% CIs): 1.53 (1.13-2.07), 2.08 (0.95-4.57), and 1.39 (1.13-1.72), respectively, after adjusting for tumor characteristics and treatment]. HRs were essentially unchanged when censoring for CBC, suggesting that these associations are not completely explained by increased CBC risk, tumor characteristics, or treatment. There was limited evidence of associations of PTVs and/or rare MSVs with CBC risk or BCSS for the 25 suspected BC genes. The CBC findings are relevant to treatment decisions, follow-up, and screening after BC diagnosis.
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Affiliation(s)
- Anna Morra
- The Netherlands Cancer Institute, Division of Molecular Pathology, Plesmanlaan 121, 1066 Amsterdam, the Netherlands.
| | - Nasim Mavaddat
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Taru A Muranen
- University of Helsinki, Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | - Thomas U Ahearn
- National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA
| | - Jamie Allen
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Fred A. Litwin Center for Cancer Genetics, Toronto, ON, Canada; University of Toronto, Department of Molecular Genetics, Toronto, ON, Canada
| | - Päivi Auvinen
- University of Eastern Finland, Translational Cancer Research Area, Kuopio, Finland; University of Eastern Finland, Institute of Clinical Medicine, Oncology, Kuopio, Finland; Kuopio University Hospital, Department of Oncology, Cancer Center, Kuopio, Finland
| | - Heiko Becher
- University Medical Center Hamburg-Eppendorf, Institute of Medical Biometry and Epidemiology, Hamburg, Germany
| | - Sabine Behrens
- German Cancer Research Center, Division of Cancer Epidemiology, Heidelberg, Germany
| | - Carl Blomqvist
- University of Helsinki, Department of Oncology, Helsinki University Hospital, Helsinki, Finland
| | - Stig E Bojesen
- Copenhagen University Hospital, Copenhagen General Population Study, Herlev and Gentofte Hospital, Herlev, Denmark; Copenhagen University Hospital, Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Herlev, Denmark; University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Manjeet K Bolla
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany; University of Tübingen, iFIT-Cluster of Excellence, Tübingen, Germany; German Cancer Consortium and German Cancer Research Center, Partner Site Tübingen, Tübingen, Germany
| | - Nicola J Camp
- University of Utah, Department of Internal Medicine and Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Sara Carvalho
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Jose E Castelao
- Instituto de Investigación Sanitaria Galicia Sur, Xerencia de Xestion Integrada de Vigo-SERGAS, Oncology and Genetics Unit, Vigo, Spain
| | | | - Jenny Chang-Claude
- German Cancer Research Center, Division of Cancer Epidemiology, Heidelberg, Germany; University Medical Center Hamburg-Eppendorf, Cancer Epidemiology Group, University Cancer Center Hamburg, Hamburg, Germany
| | - Georgia Chenevix-Trench
- QIMR Berghofer Medical Research Institute, Department of Genetics and Computational Biology, Brisbane, QLD, Australia
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- Oslo University Hospital-Radiumhospitalet, Department of Cancer Genetics, Institute for Cancer Research, Oslo, Norway; University of Oslo, Institute of Clinical Medicine, Faculty of Medicine, Oslo, Norway; Vestre Viken Hospital, Department of Research, Drammen, Norway; Oslo University Hospital, Department of Tumor Biology, Institute for Cancer Research, Oslo, Norway; Oslo University Hospital-Radiumhospitalet, Department of Oncology, Division of Surgery, Cancer and Transplantation Medicine, Oslo, Norway; Akershus University Hospital, Department of Oncology, Lørenskog, Norway; Oslo University Hospital, Oslo Breast Cancer Research Consortium, Oslo, Norway; Oslo University Hospital and University of Oslo, Department of Medical Genetics, Oslo, Norway; The Arctic University of Norway, Department of Community Medicine, Tromsø, Norway; The Arctic University of Norway, Core Facility for Biobanking, Tromsø, Norway
| | - Kamila Czene
- Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Stockholm, Sweden
| | - Brennan Decker
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK; Foundation Medicine, Inc, Pathology, Cambridge, MA, USA
| | - Joe Dennis
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Thilo Dörk
- Hannover Medical School, Gynaecology Research Unit, Hannover, Germany
| | - Leila Dorling
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Alison M Dunning
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge, UK
| | - Arif B Ekici
- Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Institute of Human Genetics, Erlangen, Germany
| | - Mikael Eriksson
- Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Stockholm, Sweden
| | - D Gareth Evans
- University of Manchester, Manchester Academic Health Science Centre, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester, UK; St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester, UK
| | - Peter A Fasching
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Jonine D Figueroa
- National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA; The University of Edinburgh, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK; The University of Edinburgh, Cancer Research UK Edinburgh Centre, Edinburgh, UK
| | - Henrik Flyger
- Copenhagen University Hospital, Department of Breast Surgery, Herlev and Gentofte Hospital, Herlev, Denmark
| | - Manuela Gago-Dominguez
- Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela, Complejo Hospitalario Universitario de Santiago, SERGAS, Genomic Medicine Group, International Cancer Genetics and Epidemiology Group, Santiago de Compostela, Spain; University of California San Diego, Moores Cancer Center, La Jolla, CA, USA
| | - Montserrat García-Closas
- National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA
| | | | - Graham G Giles
- Cancer Council Victoria, Cancer Epidemiology Division, Melbourne, VIC, Australia; The University of Melbourne, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Melbourne, VIC, Australia; Monash University, Precision Medicine, School of Clinical Sciences at Monash Health, Clayton, VIC, Australia
| | - Pascal Guénel
- INSERM, University Paris-Saclay, Center for Research in Epidemiology and Population Health, Team Exposome and Heredity, Villejuif, France
| | - Melanie Gündert
- German Cancer Research Center, Molecular Epidemiology Group, C080, Heidelberg, Germany; University of Heidelberg, Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg, Heidelberg, Germany; Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Diabetes Research, Neuherberg, Germany
| | - Eric Hahnen
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Familial Breast and Ovarian Cancer, Cologne, Germany; Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Integrated Oncology, Cologne, Germany
| | - Per Hall
- Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Stockholm, Sweden; Södersjukhuset, Department of Oncology, Stockholm, Sweden
| | - Ute Hamann
- German Cancer Research Center, Molecular Genetics of Breast Cancer, Heidelberg, Germany
| | - Patricia A Harrington
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge, UK
| | - Wei He
- Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Stockholm, Sweden
| | - Päivi Heikkilä
- University of Helsinki, Department of Pathology, Helsinki University Hospital, Helsinki, Finland
| | - Maartje J Hooning
- Erasmus MC Cancer Institute, Department of Medical Oncology, Rotterdam, the Netherlands
| | - Reiner Hoppe
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany; University of Tübingen, Tübingen, Germany
| | - Anthony Howell
- University of Manchester, Division of Cancer Sciences, Manchester, UK
| | - Keith Humphreys
- Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Stockholm, Sweden
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- Peter MacCallum Cancer Center, Research Department, Melbourne, VIC, Australia; The University of Melbourne, Sir Peter MacCallum Department of Oncology, Melbourne, VIC, Australia
| | - Anna Jakubowska
- Pomeranian Medical University, Department of Genetics and Pathology, International Hereditary Cancer Center, Szczecin, Poland; Pomeranian Medical University, Independent Laboratory of Molecular Biology and Genetic Diagnostics, Szczecin, Poland
| | - Audrey Y Jung
- German Cancer Research Center, Division of Cancer Epidemiology, Heidelberg, Germany
| | - Renske Keeman
- The Netherlands Cancer Institute, Division of Molecular Pathology, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Vessela N Kristensen
- University of Oslo, Institute of Clinical Medicine, Faculty of Medicine, Oslo, Norway; Oslo University Hospital and University of Oslo, Department of Medical Genetics, Oslo, Norway
| | - Jan Lubiński
- Pomeranian Medical University, Department of Genetics and Pathology, International Hereditary Cancer Center, Szczecin, Poland
| | - Arto Mannermaa
- University of Eastern Finland, Translational Cancer Research Area, Kuopio, Finland; University of Eastern Finland, Institute of Clinical Medicine, Pathology and Forensic Medicine, Kuopio, Finland; Kuopio University Hospital, Biobank of Eastern Finland, Kuopio, Finland
| | - Mehdi Manoochehri
- German Cancer Research Center, Molecular Genetics of Breast Cancer, Heidelberg, Germany
| | - Siranoush Manoukian
- Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Unit of Medical Genetics, Department of Medical Oncology and Hematology, Milan, Italy
| | - Sara Margolin
- Södersjukhuset, Department of Oncology, Stockholm, Sweden; Karolinska Institutet, Department of Clinical Science and Education, Södersjukhuset, Stockholm, Sweden
| | - Dimitrios Mavroudis
- University Hospital of Heraklion, Department of Medical Oncology, Heraklion, Greece
| | - Roger L Milne
- Cancer Council Victoria, Cancer Epidemiology Division, Melbourne, VIC, Australia; The University of Melbourne, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Melbourne, VIC, Australia; Monash University, Precision Medicine, School of Clinical Sciences at Monash Health, Clayton, VIC, Australia
| | - Anna Marie Mulligan
- University of Toronto, Department of Laboratory Medicine and Pathobiology, Toronto, ON, Canada; University Health Network, Laboratory Medicine Program, Toronto, ON, Canada
| | - William G Newman
- University of Manchester, Manchester Academic Health Science Centre, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester, UK; St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester, UK
| | | | - Paolo Peterlongo
- IFOM ETS - the AIRC Institute of Molecular Oncology, Genome Diagnostics Program, Milan, Italy
| | - Paul D P Pharoah
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK; University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge, UK
| | - Valerie Rhenius
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge, UK
| | | | - Elinor J Sawyer
- King's College London, School of Cancer & Pharmaceutical Sciences, Comprehensive Cancer Centre, Guy's Campus, London, UK
| | - Rita K Schmutzler
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Familial Breast and Ovarian Cancer, Cologne, Germany; Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Integrated Oncology, Cologne, Germany; Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Molecular Medicine Cologne, Cologne, Germany
| | - Mitul Shah
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge, UK
| | - Amanda B Spurdle
- QIMR Berghofer Medical Research Institute, Population Health Program, Brisbane, QLD, Australia
| | - Ian Tomlinson
- University of Birmingham, Institute of Cancer and Genomic Sciences, Birmingham, UK; University of Oxford, Wellcome Trust Centre for Human Genetics and Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Thérèse Truong
- INSERM, University Paris-Saclay, Center for Research in Epidemiology and Population Health, Team Exposome and Heredity, Villejuif, France
| | - Elke M van Veen
- University of Manchester, Manchester Academic Health Science Centre, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester, UK; St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester, UK
| | - Maaike P G Vreeswijk
- Leiden University Medical Center, Department of Human Genetics, Leiden, the Netherlands
| | - Qin Wang
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Camilla Wendt
- Södersjukhuset, Department of Oncology, Stockholm, Sweden; Karolinska Institutet, Department of Clinical Science and Education, Södersjukhuset, Stockholm, Sweden
| | - Xiaohong R Yang
- National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA
| | - Heli Nevanlinna
- University of Helsinki, Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | - Peter Devilee
- Leiden University Medical Center, Department of Human Genetics, Leiden, the Netherlands; Leiden University Medical Center, Department of Pathology, Leiden, the Netherlands
| | - Douglas F Easton
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK; University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge, UK
| | - Marjanka K Schmidt
- The Netherlands Cancer Institute, Division of Molecular Pathology, Plesmanlaan 121, 1066 Amsterdam, the Netherlands; The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Division of Psychosocial Research and Epidemiology, Amsterdam, the Netherlands.
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2
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Dumont M, Weber-Lassalle N, Joly-Beauparlant C, Ernst C, Droit A, Feng BJ, Dubois S, Collin-Deschesnes AC, Soucy P, Vallée M, Fournier F, Lemaçon A, Adank MA, Allen J, Altmüller J, Arnold N, Ausems MGEM, Berutti R, Bolla MK, Bull S, Carvalho S, Cornelissen S, Dufault MR, Dunning AM, Engel C, Gehrig A, Geurts-Giele WRR, Gieger C, Green J, Hackmann K, Helmy M, Hentschel J, Hogervorst FBL, Hollestelle A, Hooning MJ, Horváth J, Ikram MA, Kaulfuß S, Keeman R, Kuang D, Luccarini C, Maier W, Martens JWM, Niederacher D, Nürnberg P, Ott CE, Peters A, Pharoah PDP, Ramirez A, Ramser J, Riedel-Heller S, Schmidt G, Shah M, Scherer M, Stäbler A, Strom TM, Sutter C, Thiele H, van Asperen CJ, van der Kolk L, van der Luijt RB, Volk AE, Wagner M, Waisfisz Q, Wang Q, Wang-Gohrke S, Weber BHF, Devilee P, Tavtigian S, Bader GD, Meindl A, Goldgar DE, Andrulis IL, Schmutzler RK, Easton DF, Schmidt MK, Hahnen E, Simard J. Uncovering the Contribution of Moderate-Penetrance Susceptibility Genes to Breast Cancer by Whole-Exome Sequencing and Targeted Enrichment Sequencing of Candidate Genes in Women of European Ancestry. Cancers (Basel) 2022; 14:cancers14143363. [PMID: 35884425 PMCID: PMC9317824 DOI: 10.3390/cancers14143363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 01/27/2023] Open
Abstract
Rare variants in at least 10 genes, including BRCA1, BRCA2, PALB2, ATM, and CHEK2, are associated with increased risk of breast cancer; however, these variants, in combination with common variants identified through genome-wide association studies, explain only a fraction of the familial aggregation of the disease. To identify further susceptibility genes, we performed a two-stage whole-exome sequencing study. In the discovery stage, samples from 1528 breast cancer cases enriched for breast cancer susceptibility and 3733 geographically matched unaffected controls were sequenced. Using five different filtering and gene prioritization strategies, 198 genes were selected for further validation. These genes, and a panel of 32 known or suspected breast cancer susceptibility genes, were assessed in a validation set of 6211 cases and 6019 controls for their association with risk of breast cancer overall, and by estrogen receptor (ER) disease subtypes, using gene burden tests applied to loss-of-function and rare missense variants. Twenty genes showed nominal evidence of association (p-value < 0.05) with either overall or subtype-specific breast cancer. Our study had the statistical power to detect susceptibility genes with effect sizes similar to ATM, CHEK2, and PALB2, however, it was underpowered to identify genes in which susceptibility variants are rarer or confer smaller effect sizes. Larger sample sizes would be required in order to identify such genes.
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Affiliation(s)
- Martine Dumont
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Nana Weber-Lassalle
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (N.W.-L.); (C.E.); (R.K.S.); (E.H.)
| | - Charles Joly-Beauparlant
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Corinna Ernst
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (N.W.-L.); (C.E.); (R.K.S.); (E.H.)
| | - Arnaud Droit
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Bing-Jian Feng
- Department of Dermatology, University of Utah, Salt Lake City, UT 84103, USA; (B.-J.F.); (D.E.G.)
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA;
| | - Stéphane Dubois
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Annie-Claude Collin-Deschesnes
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Penny Soucy
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Maxime Vallée
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Frédéric Fournier
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Audrey Lemaçon
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Muriel A. Adank
- Family Cancer Clinic, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (M.A.A.); (F.B.L.H.); (L.v.d.K.)
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (J.A.); (H.T.)
| | - Norbert Arnold
- Institute of Clinical Molecular Biology, Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, 24105 Kiel, Germany;
| | - Margreet G. E. M. Ausems
- Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center Utrecht, 3584 Utrecht, The Netherlands;
| | - Riccardo Berutti
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; (R.B.); (T.M.S.)
| | - Manjeet K. Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
| | - Shelley Bull
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; (S.B.); (J.G.); (G.D.B.); (I.L.A.)
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
| | - Sten Cornelissen
- Division of Molecular Pathology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (S.C.); (R.K.); (M.K.S.)
| | - Michael R. Dufault
- Precision Medicine and Computational Biology, Sanofi Genzyme, Cambridge, MA 02142, USA;
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (A.M.D.); (C.L.); (M.S.)
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, 04107 Leipzig, Germany;
| | - Andrea Gehrig
- Centre of Familial Breast and Ovarian Cancer, Department of Medical Genetics, Institute of Human Genetics, University of Würzburg, 97074 Würzburg, Germany;
| | | | - Christian Gieger
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; (C.G.); (A.P.)
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany
| | - Jessica Green
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; (S.B.); (J.G.); (G.D.B.); (I.L.A.)
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - Karl Hackmann
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany;
| | - Mohamed Helmy
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada;
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138632, Singapore
- Department of Computer Science, Lakehead University, Thunder Bay, ON P7B 5E1, Canada
| | - Julia Hentschel
- Institute of Human Genetics, University Leipzig, 04103 Leipzig, Germany;
| | - Frans B. L. Hogervorst
- Family Cancer Clinic, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (M.A.A.); (F.B.L.H.); (L.v.d.K.)
| | - Antoinette Hollestelle
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 Rotterdam, The Netherlands; (A.H.); (M.J.H.); (J.W.M.M.)
| | - Maartje J. Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 Rotterdam, The Netherlands; (A.H.); (M.J.H.); (J.W.M.M.)
| | - Judit Horváth
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany;
| | - M. Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center, 3015 Rotterdam, The Netherlands;
| | - Silke Kaulfuß
- Institute of Human Genetics, University Medical Center Göttingen, 37075 Göttingen, Germany;
| | - Renske Keeman
- Division of Molecular Pathology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (S.C.); (R.K.); (M.K.S.)
| | - Da Kuang
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada;
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada;
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (A.M.D.); (C.L.); (M.S.)
| | - Wolfgang Maier
- German Center for Neurodegenerative Diseases (DZNE), Department of Neurodegenerative Diseases and Geriatric Psychiatry, Medical Faculty, University Hospital Bonn, 53127 Bonn, Germany;
| | - John W. M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 Rotterdam, The Netherlands; (A.H.); (M.J.H.); (J.W.M.M.)
| | - Dieter Niederacher
- Department of Gynecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany;
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne (CMMC), Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany;
| | - Claus-Eric Ott
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 13353 Berlin, Germany;
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; (C.G.); (A.P.)
- Department of Epidemiology, Institute for Medical Information Processing, Biometry and Epidemiology, Medical Faculty, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Paul D. P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (A.M.D.); (C.L.); (M.S.)
| | - Alfredo Ramirez
- Division for Neurogenetics and Molecular Psychiatry, Medical Faculty, University of Cologne, 50937 Cologne, Germany;
| | - Juliane Ramser
- Division of Gynaecology and Obstetrics, Klinikum Rechts der Isar der Technischen Universität München, 81675 Munich, Germany; (J.R.); (A.M.)
| | - Steffi Riedel-Heller
- Institute of Social Medicine, Occupational Health and Public Health, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany;
| | - Gunnar Schmidt
- Institute of Human Genetics, Hannover Medical School, 30625 Hannover, Germany;
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (A.M.D.); (C.L.); (M.S.)
| | - Martin Scherer
- Department of Primary Medical Care, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany;
| | - Antje Stäbler
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany;
| | - Tim M. Strom
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; (R.B.); (T.M.S.)
| | - Christian Sutter
- Institute of Human Genetics, University Hospital Heidelberg, 69120 Heidelberg, Germany;
| | - Holger Thiele
- Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (J.A.); (H.T.)
| | - Christi J. van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, 2333 Leiden, The Netherlands; (C.J.v.A.); (R.B.v.d.L.)
| | - Lizet van der Kolk
- Family Cancer Clinic, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (M.A.A.); (F.B.L.H.); (L.v.d.K.)
| | - Rob B. van der Luijt
- Department of Clinical Genetics, Leiden University Medical Center, 2333 Leiden, The Netherlands; (C.J.v.A.); (R.B.v.d.L.)
- Department of Medical Genetics, University Medical Center, 3584 Utrecht, The Netherlands
| | - Alexander E. Volk
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany;
| | - Michael Wagner
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, 53127 Bonn, Germany;
| | - Quinten Waisfisz
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 Amsterdam, The Netherlands;
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
| | - Shan Wang-Gohrke
- Department of Gynaecology and Obstetrics, University of Ulm, 89081 Ulm, Germany;
| | - Bernhard H. F. Weber
- Institute of Human Genetics, Regensburg University, 93053 Regensburg, Germany;
- Institute of Clinical Human Genetics, University Hospital Regensburg, 93053 Regensburg, Germany
| | | | | | - Peter Devilee
- Department of Pathology, Department of Human Genetics, Leiden University Medical Center, 2333 Leiden, The Netherlands;
| | - Sean Tavtigian
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA;
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Gary D. Bader
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; (S.B.); (J.G.); (G.D.B.); (I.L.A.)
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada;
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada;
- Department of Computer Science, University of Toronto, Toronto, ON M5S 3E1, Canada
- Princess Margaret Research Institute, University Health Network, Toronto, ON M5G 0A3, Canada
| | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Klinikum Rechts der Isar der Technischen Universität München, 81675 Munich, Germany; (J.R.); (A.M.)
| | - David E. Goldgar
- Department of Dermatology, University of Utah, Salt Lake City, UT 84103, USA; (B.-J.F.); (D.E.G.)
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA;
| | - Irene L. Andrulis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; (S.B.); (J.G.); (G.D.B.); (I.L.A.)
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - Rita K. Schmutzler
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (N.W.-L.); (C.E.); (R.K.S.); (E.H.)
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (A.M.D.); (C.L.); (M.S.)
| | - Marjanka K. Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (S.C.); (R.K.); (M.K.S.)
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (N.W.-L.); (C.E.); (R.K.S.); (E.H.)
| | - Jacques Simard
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
- Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec, QC G1V 0A6, Canada
- Correspondence: ; Tel.: +418-654-2264
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3
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Roepman P, de Bruijn E, van Lieshout S, Schoenmaker L, Boelens MC, Dubbink HJ, Geurts-Giele WRR, Groenendijk FH, Huibers MMH, Kranendonk MEG, Roemer MGM, Samsom KG, Steehouwer M, de Leng WWJ, Hoischen A, Ylstra B, Monkhorst K, van der Hoeven JJM, Cuppen E. Clinical Validation of Whole Genome Sequencing for Cancer Diagnostics. J Mol Diagn 2021; 23:816-833. [PMID: 33964451 DOI: 10.1016/j.jmoldx.2021.04.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/17/2021] [Accepted: 04/12/2021] [Indexed: 02/08/2023] Open
Abstract
Whole genome sequencing (WGS) using fresh-frozen tissue and matched blood samples from cancer patients may become the most complete genetic tumor test. With the increasing availability of small biopsies and the need to screen more number of biomarkers, the use of a single all-inclusive test is preferable over multiple consecutive assays. To meet high-quality diagnostics standards, we optimized and clinically validated WGS sample and data processing procedures, resulting in a technical success rate of 95.6% for fresh-frozen samples with sufficient (≥20%) tumor content. Independent validation of identified biomarkers against commonly used diagnostic assays showed a high sensitivity (recall; 98.5%) and precision (positive predictive value; 97.8%) for detection of somatic single-nucleotide variants and insertions and deletions (across 22 genes), and high concordance for detection of gene amplification (97.0%; EGFR and MET) as well as somatic complete loss (100%; CDKN2A/p16). Gene fusion analysis showed a concordance of 91.3% between DNA-based WGS and an orthogonal RNA-based gene fusion assay. Microsatellite (in)stability assessment showed a sensitivity of 100% with a precision of 94%, and virus detection (human papillomavirus), an accuracy of 100% compared with standard testing. In conclusion, whole genome sequencing has a >95% sensitivity and precision compared with routinely used DNA techniques in diagnostics, and all relevant mutation types can be detected reliably in a single assay.
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Affiliation(s)
- Paul Roepman
- Hartwig Medical Foundation, Amsterdam, the Netherlands.
| | | | | | | | - Mirjam C Boelens
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | | | - Floris H Groenendijk
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Manon M H Huibers
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Margaretha G M Roemer
- Department of Pathology, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Kris G Samsom
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marloes Steehouwer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Department Internal Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Bauke Ylstra
- Department of Pathology, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Kim Monkhorst
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, the Netherlands; Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, the Netherlands
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4
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Radonic T, Geurts-Giele WRR, Samsom KG, Roemen GMJM, von der Thüsen JH, Thunnissen E, Meijssen IC, Sleddens HFBM, Dinjens WNM, Boelens MC, Weijers K, Speel EJM, Finn SP, O'Brien C, van Wezel T, Cohen D, Monkhorst K, Roepman P, Dubbink HJ. RET Fluorescence In Situ Hybridization Analysis Is a Sensitive but Highly Unspecific Screening Method for RET Fusions in Lung Cancer. J Thorac Oncol 2021; 16:798-806. [PMID: 33588111 DOI: 10.1016/j.jtho.2021.01.1619] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 01/09/2021] [Accepted: 01/19/2021] [Indexed: 12/31/2022]
Abstract
INTRODUCTION RET gene fusions are established oncogenic drivers in 1% of NSCLC. Accurate detection of advanced patients with RET fusions is essential to ensure optimal therapy choice. We investigated the performance of fluorescence in situ hybridization (FISH) as a diagnostic test for detecting functional RET fusions. METHODS Between January 2016 and November 2019, a total of 4873 patients with NSCLC were routinely screened for RET fusions using either FISH (n = 2858) or targeted RNA next-generation sequencing (NGS) (n = 2015). If sufficient material was available, positive cases were analyzed by both methods (n = 39) and multiple FISH assays (n = 17). In an independent cohort of 520 patients with NSCLC, whole-genome sequencing data were investigated for disruptive structural variations and functional fusions in the RET and compared with ALK and ROS1 loci. RESULTS FISH analysis revealed RET rearrangement in 48 of 2858 cases; of 30 rearranged cases double tested with NGS, only nine had a functional RET fusion. RNA NGS yielded RET fusions in 14 of 2015 cases; all nine cases double tested by FISH had RET locus rearrangement. Of these 18 verified RET fusion cases, 16 had a split signal and two a complex rearrangement by FISH. By whole-genome sequencing, the prevalence of functional fusions compared with all disruptive events was lower in the RET (4 of 9, 44%) than the ALK (27 of 34, 79%) and ROS1 (9 of 12, 75%) loci. CONCLUSIONS FISH is a sensitive but unspecific technique for RET screening, always requiring a confirmation using an orthogonal technique, owing to frequently occurring RET rearrangements not resulting in functional fusions in NSCLC.
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Affiliation(s)
- Teodora Radonic
- Department of Pathology, Cancer Center Amsterdam, Vrije University, Amsterdam University Medical Center, Amsterdam, The Netherlands.
| | - W R R Geurts-Giele
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Kris G Samsom
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Guido M J M Roemen
- Department of Pathology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jan H von der Thüsen
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Erik Thunnissen
- Department of Pathology, Cancer Center Amsterdam, Vrije University, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Isabelle C Meijssen
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Hein F B M Sleddens
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Mirjam C Boelens
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Karin Weijers
- Department of Pathology, Cancer Center Amsterdam, Vrije University, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Ernst Jan M Speel
- Department of Pathology, Maastricht University Medical Center, Maastricht, The Netherlands; School for Oncology and Developmental Biology (GROW), Maastricht, The Netherlands
| | - Stephen P Finn
- Department of Histopathology, St. James's Hospital and Trinity College Dublin, Dublin, Ireland; Cancer Molecular Diagnostics, St. James's Hospital and Trinity College Dublin, Dublin, Ireland; Thoracic Oncology Research Group, Trinity Translational Medical Institute, St. James's Hospital and Trinity College Dublin, Dublin, Ireland
| | - Cathal O'Brien
- Department of Histopathology, St. James's Hospital and Trinity College Dublin, Dublin, Ireland; Cancer Molecular Diagnostics, St. James's Hospital and Trinity College Dublin, Dublin, Ireland; Thoracic Oncology Research Group, Trinity Translational Medical Institute, St. James's Hospital and Trinity College Dublin, Dublin, Ireland
| | - Tom van Wezel
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Danielle Cohen
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Kim Monkhorst
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | - H J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
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5
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Loonen AJM, Huijsmans CJJ, Geurts-Giele WRR, Leeijen C, van der Linden JC, van den Brule AJC. Performance analysis of high-throughput HPV testing on three automated workflows. APMIS 2020; 128:497-505. [PMID: 32562292 DOI: 10.1111/apm.13064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 06/02/2020] [Indexed: 12/29/2022]
Abstract
Primary high-risk human papillomavirus (hrHPV) DNA testing has been introduced in several countries worldwide, including The Netherlands. The objective of this study was to compare three automated workflow procedures for hrHPV testing of which the hrHPV detection assays meet the international guidelines for HPV testing. To mimic a realistic screening situation, we aimed to process 15 000 residual PreservCyt cervical samples in a period of 3 months. During a 3 months period, four technicians were involved in processing 5000 specimens per month on three automated platforms, (1) Qiagen Digene® HC2 HPV DNA test (HC2, signal amplification); (2) Roche Cobas® HPV test (DNA amplification), and (3) Hologic Aptima® HPV test (RNA amplification). We measured and scored general aspects (time-to-results, hands-on-time (HOT)), maintenance, pre-run, run and post-run aspects, inventory (orders, storage), and number of errors on a scale from 1 to 10. As determined for one complete workflow each, maximum processing capacity and HOT were 296 samples and 2 h:55 m, 282 samples and 3 h:20 m, and 264 samples and 4 h:15 m for Aptima, Cobas, and HC2, respectively. The mean throughput time per run was 5 h:51 m for Cobas in which 94 samples could be processed. For Aptima, the mean throughput time per run was 6 h:30 m for 60 samples. Mean throughput time for HC2 is longer since results were provided on day 2. In this study, the fully automated Aptima workflow scores best with a 7.2, followed by Cobas with a score of 7.1 and HC2 with a score of 5.8. Although all HPV tests used in this comparison meet the international test guidelines, the performance (workflow) characteristics of the assays vary widely. A specific choice of a laboratory for high-throughput testing can be different based on the laboratory's demands, but also hands-on-time, time-to-results/ # samples, maintenance, pre-run, run and post-run parameters, consumables, technical support, and number of errors are important operational factors for the selection of a fully automated workflow for hrHPV testing.
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Affiliation(s)
- Anne J M Loonen
- Pathologie-DNA, Lab for Molecular Diagnostics, Location Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands.,Department of Applied Natural Sciences, Section Diagnostics and Test Development, Fontys University of Applied Sciences, Eindhoven, The Netherlands
| | - Cornelis J J Huijsmans
- Pathologie-DNA, Lab for Molecular Diagnostics, Location Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands
| | | | - Cindy Leeijen
- Pathologie-DNA, Lab for Molecular Diagnostics, Location Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands
| | - Johannes C van der Linden
- Pathologie-DNA, Lab for Molecular Diagnostics, Location Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands
| | - Adriaan J C van den Brule
- Pathologie-DNA, Lab for Molecular Diagnostics, Location Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands
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6
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Pruis MA, Geurts-Giele WRR, von der TJH, Meijssen IC, Dinjens WNM, Aerts JGJV, Dingemans AMC, Lolkema MP, Paats MS, Dubbink HJ. Highly accurate DNA-based detection and treatment results of MET exon 14 skipping mutations in lung cancer. Lung Cancer 2019; 140:46-54. [PMID: 31862577 DOI: 10.1016/j.lungcan.2019.11.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/01/2019] [Accepted: 11/14/2019] [Indexed: 12/15/2022]
Abstract
OBJECTIVES The oncogenic MET exon 14 skipping mutation (METex14del) is described to drive 1.3 %-5.7 % of non-small-cell lung cancer (NSCLC) and multiple studies with cMET inhibitors show promising clinical responses. RNA-based analysis seems most optimal for METex14del detection, however, acquiring sufficient RNA material is often problematic. An alternative is DNA-based analysis, but commercially available DNA-based panels only detect up to 63 % of known METex14del alterations. The goal of this study is to describe an optimized DNA-based diagnostic test for METex14del in NSCLC, including clinical features and follow-up of patients treated with cMET-targeted therapy and consequent resistance mechanisms. MATERIAL AND METHODS Routinely processed diagnostic pathology non-squamous NSCLC specimens were investigated by a custom-made DNA-based targeted amplicon-based next generation sequencing (NGS) panel, which includes 4 amplicons for METex14del detection. Retrospectively, histopathological characteristics and clinical follow up were investigated for advanced non-squamous NSCLC with METex14del. RESULTS In silico analysis showed that our NGS panel is able to detect 96 % of reported METex14 alterations. METex14del was found in 2 % of patients with non-squamous NSCLC tested for therapeutic purposes. In total, from May 2015 - Sep 2018, METex14del was found in 46 patients. Thirty-six of these patients had advanced non-squamous NSCLC, they were predominantly elderly (76.5 years [53-90]), male (25/36) and (ex)-smokers (23/36). Five patients received treatment with crizotinib (Pfizer Oncology), in a named patient based program, disease control was achieved for 4/5 patients (3 partial responses, 1 stable disease) and one patient had a mixed response. Two patients developed a MET D1228N mutation during crizotinib treatment, inducing a resistance mechanism to crizotinib. CONCLUSIONS This study shows that METex14del can be reliably detected by routine DNA NGS analysis. Although a small cohort, patients responded well to targeted treatment, underlining the need for routine testing of METex14del in advanced non-squamous NSCLC to guarantee optimal personalized treatment.
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Affiliation(s)
- M A Pruis
- Department of Pulmonary Diseases, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - W R R Geurts-Giele
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Thüsen J H von der
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - I C Meijssen
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - W N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - J G J V Aerts
- Department of Pulmonary Diseases, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - A M C Dingemans
- Department of Pulmonary Diseases, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Department of Pulmonary Diseases, Maastricht UMC +, Maastricht, the Netherlands
| | - M P Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - M S Paats
- Department of Pulmonary Diseases, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - H J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
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7
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Eijkelenboom A, Tops BBJ, van den Berg A, van den Brule AJC, Dinjens WNM, Dubbink HJ, Ter Elst A, Geurts-Giele WRR, Groenen PJTA, Groenendijk FH, Heideman DAM, Huibers MMH, Huijsmans CJJ, Jeuken JWM, van Kempen LC, Korpershoek E, Kroeze LI, de Leng WWJ, van Noesel CJM, Speel EJM, Vogel MJ, van Wezel T, Nederlof PM, Schuuring E, Ligtenberg MJL. Recommendations for the clinical interpretation and reporting of copy number gains using gene panel NGS analysis in routine diagnostics. Virchows Arch 2019; 474:673-680. [PMID: 30888490 PMCID: PMC6581937 DOI: 10.1007/s00428-019-02555-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/14/2019] [Accepted: 03/03/2019] [Indexed: 01/09/2023]
Abstract
Next-generation sequencing (NGS) panel analysis on DNA from formalin-fixed paraffin-embedded (FFPE) tissue is increasingly used to also identify actionable copy number gains (gene amplifications) in addition to sequence variants. While guidelines for the reporting of sequence variants are available, guidance with respect to reporting copy number gains from gene-panel NGS data is limited. Here, we report on Dutch consensus recommendations obtained in the context of the national Predictive Analysis for THerapy (PATH) project, which aims to optimize and harmonize routine diagnostics in molecular pathology. We briefly discuss two common approaches to detect gene copy number gains from NGS data, i.e., the relative coverage and B-allele frequencies. In addition, we provide recommendations for reporting gene copy gains for clinical purposes. In addition to general QC metrics associated with NGS in routine diagnostics, it is recommended to include clinically relevant quantitative parameters of copy number gains in the clinical report, such as (i) relative coverage and estimated copy numbers in neoplastic cells, (ii) statistical scores to show significance (e.g., z-scores), and (iii) the sensitivity of the assay and restrictions of NGS-based detection of copy number gains. Collectively, this information can guide clinical and analytical decisions such as the reliable detection of high-level gene amplifications and the requirement for additional in situ assays in case of borderline results or limited sensitivity.
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Affiliation(s)
- Astrid Eijkelenboom
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Bastiaan B J Tops
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Anke van den Berg
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Arja Ter Elst
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Willemina R R Geurts-Giele
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Floris H Groenendijk
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Daniëlle A M Heideman
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Manon M H Huibers
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | | - Léon C van Kempen
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Esther Korpershoek
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Leonie I Kroeze
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Carel J M van Noesel
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ernst-Jan M Speel
- Department of Pathology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Maartje J Vogel
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Petra M Nederlof
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ed Schuuring
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands. .,Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands.
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8
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Jansen AML, Crobach S, Geurts-Giele WRR, van den Akker BEWM, Garcia MV, Ruano D, Nielsen M, Tops CMJ, Wijnen JT, Hes FJ, van Wezel T, Dinjens WNM, Morreau H. Distinct Patterns of Somatic Mosaicism in the APC Gene in Neoplasms From Patients With Unexplained Adenomatous Polyposis. Gastroenterology 2017; 152:546-549.e3. [PMID: 27816598 DOI: 10.1053/j.gastro.2016.10.040] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/21/2016] [Accepted: 10/23/2016] [Indexed: 12/02/2022]
Abstract
We investigated the presence and patterns of mosaicism in the APC gene in patients with colon neoplasms not associated with any other genetic variants; we performed deep sequence analysis of APC in at least 2 adenomas or carcinomas per patient. We identified mosaic variants in APC in adenomas from 9 of the 18 patients with 21 to approximately 100 adenomas. Mosaic variants of APC were variably detected in leukocyte DNA and/or non-neoplastic intestinal mucosa of these patients. In a comprehensive sequence analysis of 1 patient, we found no evidence for mosaicism in APC in non-neoplastic intestinal mucosa. One patient was found to carry a mosaic c.4666dupA APC variant in only 10 of 16 adenomas, indicating the importance of screening 2 or more adenomas for genetic variants.
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Affiliation(s)
- Anne M L Jansen
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands; Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Stijn Crobach
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Willemina R R Geurts-Giele
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, The Netherlands
| | | | | | - Dina Ruano
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Carli M J Tops
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Juul T Wijnen
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands; Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands.
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9
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Geurts-Giele WRR, Leenen CHM, Dubbink HJ, Meijssen IC, Post E, Sleddens HFBM, Kuipers EJ, Goverde A, van den Ouweland AMW, van Lier MGF, Steyerberg EW, van Leerdam ME, Wagner A, Dinjens WNM. Somatic aberrations of mismatch repair genes as a cause of microsatellite-unstable cancers. J Pathol 2014; 234:548-59. [PMID: 25111426 DOI: 10.1002/path.4419] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 07/28/2014] [Accepted: 08/06/2014] [Indexed: 12/17/2022]
Abstract
Lynch syndrome (LS) is caused by germline mutations in mismatch repair (MMR) genes, resulting in microsatellite-unstable tumours. Approximately 35% of suspected LS (sLS) patients test negative for germline MMR gene mutations, hampering conclusive LS diagnosis. The aim of this study was to investigate somatic MMR gene aberrations in microsatellite-unstable colorectal and endometrial cancers of sLS patients negative for germline MMR gene mutations. Suspected LS cases were selected from a retrospective Clinical Genetics Department diagnostic cohort and from a prospective multicentre population-based study on LS in The Netherlands. In total, microsatellite-unstable tumours of 40 sLS patients (male/female 20/20, median age 57 years) were screened for somatic MMR gene mutations by next-generation sequencing. In addition, loss of heterozygosity (LOH) of the affected MMR genes in these tumours as well as in 68 LS-associated tumours and 27 microsatellite-unstable tumours with MLH1 promoter hypermethylation was studied. Of the sLS cases, 5/40 (13%) tumours had two pathogenic somatic mutations and 16/40 (40%) tumours had a (likely) pathogenic mutation and LOH. Overall, LOH of the affected MMR gene locus was observed in 24/39 (62%) tumours with informative LOH markers. Of the LS cases and the tumours with MLH1 promoter hypermethylation, 39/61 (64%) and 2/21 (10%) tumours, respectively, demonstrated LOH. Half of microsatellite-unstable tumours of sLS patients without germline MMR gene mutations had two (likely) deleterious somatic MMR gene aberrations, indicating their sporadic origin. Therefore, we advocate adding somatic mutation and LOH analysis of the MMR genes to the molecular diagnostic workflow of LS.
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Affiliation(s)
- Willemina R R Geurts-Giele
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Centre, Rotterdam, The Netherlands
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Geurts-Giele WRR, Wolvers-Tettero ILM, Dinjens WNM, Lam KH, Langerak AW. Successive B-cell lymphomas mostly reflect recurrences rather than unrelated primary lymphomas. Am J Clin Pathol 2013; 140:114-26. [PMID: 23765542 DOI: 10.1309/ajcpi14gxnwasvuz] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
OBJECTIVES To address whether successive B-cell lymphomas, diagnosed within a 5- to 15-year interval, are recurrences or unrelated primary lymphomas. METHODS Immunoglobulin heavy and κ light chain gene rearrangements were studied using multiplex polymerase chain reaction fragment assays and sequence analysis in 61 patients. RESULTS Clonal patterns of the multiple lymphomas from 36 patients were determined and classified accordingly: 30 recurrences, 2 possible recurrences, 2 different clones with a common origin, and 2 unrelated primary lymphomas. CONCLUSIONS Regardless of subtype, 89% to 94% of late B-cell lymphoma relapses were recurrences of the primary tumor. Therefore, routinely investigating the possible clonal relationship between successive lymphomas may not be warranted except for specific lymphoma subtypes such as diffuse large B-cell lymphomas.
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Affiliation(s)
| | | | - Winand N. M. Dinjens
- Department of Pathology, Erasmus Medical Center, University Medical Center, Rotterdam, the Netherlands
| | - King H. Lam
- Department of Pathology, Erasmus Medical Center, University Medical Center, Rotterdam, the Netherlands
| | - Anton W. Langerak
- Department of Immunology, Erasmus Medical Center, University Medical Center, Rotterdam, the Netherlands
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11
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Geurts-Giele WRR, Dirkx-van der Velden AW, Bartalits NMMT, Verhoog LC, Hanselaar WEJJ, Dinjens WNM. Molecular diagnostics of a single multifocal non-small cell lung cancer case using targeted next generation sequencing. Virchows Arch 2012; 462:249-54. [PMID: 23262782 DOI: 10.1007/s00428-012-1346-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 11/13/2012] [Accepted: 11/20/2012] [Indexed: 10/27/2022]
Abstract
Histological and molecular subtyping of non-small cell lung cancer (NSCLC) is important for predicting survival and drug response in these patients. Up to 8 % of NSCLC are multifocal and these tumor foci are often clonally related. Multiple foci can however also represent different primary tumors, with prognostic and therapeutic consequences. We describe a patient with multifocal NSCLC from which we obtained tissue from two separate lesions. With routine conventional molecular determinations, the clonal relationship between the two lesions was determined. In addition, targeted next generation sequencing with the Ion Torrent Personal Genome Machine (PGM) was performed to explore the accuracy and additional value of this relatively new technique. The two tumors of this patient showed different activating epidermal growth factor receptor (EGFR) mutations, EGFR amplification status, TP53 mutation status, and loss of heterozygosity patterns. With the PGM, all conventional detected mutations were confirmed, and an additional variant of unknown significance in ATM was detected in one of the tumors. The multifocal NSCLC of this patient represents two unrelated primary tumors. Our results suggest that multifocal NSCLC should be considered as potentially multiple primary tumors. As the presence of activating EGFR mutations has important therapeutic consequences, EGFR testing should be performed on all tumor foci present. In the present case, targeted next generation sequencing using the PGM appeared to be accurate and comparable with conventional molecular determinations. However, the application of the PGM in routine pathology molecular diagnostics needs validation in larger series of cases.
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Affiliation(s)
- Willemina R R Geurts-Giele
- Department of Pathology, Josephine Nefkens Institute, Erasmus MC, University Medical Center, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.
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12
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Leenen CHM, Geurts-Giele WRR, Dubbink HJ, Reddingius R, van den Ouweland AM, Tops CMJ, van de Klift HM, Kuipers EJ, van Leerdam ME, Dinjens WNM, Wagner A. Pitfalls in molecular analysis for mismatch repair deficiency in a family with biallelic pms2 germline mutations. Clin Genet 2011; 80:558-65. [DOI: 10.1111/j.1399-0004.2010.01608.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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