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Kańduła MM, Aldoshin AD, Singh S, Kolaczyk ED, Kreil D. ViLoN-a multi-layer network approach to data integration demonstrated for patient stratification. Nucleic Acids Res 2022; 51:e6. [PMID: 36395816 PMCID: PMC9841426 DOI: 10.1093/nar/gkac988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 10/11/2022] [Accepted: 11/02/2022] [Indexed: 11/19/2022] Open
Abstract
With more and more data being collected, modern network representations exploit the complementary nature of different data sources as well as similarities across patients. We here introduce the Variation of information fused Layers of Networks algorithm (ViLoN), a novel network-based approach for the integration of multiple molecular profiles. As a key innovation, it directly incorporates prior functional knowledge (KEGG, GO). In the constructed network of patients, patients are represented by networks of pathways, comprising genes that are linked by common functions and joint regulation in the disease. Patient stratification remains a key challenge both in the clinic and for research on disease mechanisms and treatments. We thus validated ViLoN for patient stratification on multiple data type combinations (gene expression, methylation, copy number), showing substantial improvements and consistently competitive performance for all. Notably, the incorporation of prior functional knowledge was critical for good results in the smaller cohorts (rectum adenocarcinoma: 90, esophageal carcinoma: 180), where alternative methods failed.
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Affiliation(s)
- Maciej M Kańduła
- Institute of Molecular Biotechnology, Boku University Vienna, Austria,Janssen Pharmaceutica NV, Beerse, Belgium
| | | | - Swati Singh
- Institute of Molecular Biotechnology, Boku University Vienna, Austria,Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India
| | - Eric D Kolaczyk
- Correspondence may also be addressed to Eric D. Kolaczyk. Tel: +1 514 398 3805;
| | - David P Kreil
- To whom correspondence should be addressed. Tel: +43 1 47654 79009;
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Morra A, Escala-Garcia M, Beesley J, Keeman R, Canisius S, Ahearn TU, Andrulis IL, Anton-Culver H, Arndt V, Auer PL, Augustinsson A, Beane Freeman LE, Becher H, Beckmann MW, Behrens S, Bojesen SE, Bolla MK, Brenner H, Brüning T, Buys SS, Caan B, Campa D, Canzian F, Castelao JE, Chang-Claude J, Chanock SJ, Cheng TYD, Clarke CL, Colonna SV, Couch FJ, Cox A, Cross SS, Czene K, Daly MB, Dennis J, Dörk T, Dossus L, Dunning AM, Dwek M, Eccles DM, Ekici AB, Eliassen AH, Eriksson M, Evans DG, Fasching PA, Flyger H, Fritschi L, Gago-Dominguez M, García-Sáenz JA, Giles GG, Grip M, Guénel P, Gündert M, Hahnen E, Haiman CA, Håkansson N, Hall P, Hamann U, Hart SN, Hartikainen JM, Hartmann A, He W, Hooning MJ, Hoppe R, Hopper JL, Howell A, Hunter DJ, Jager A, Jakubowska A, Janni W, John EM, Jung AY, Kaaks R, Keupers M, Kitahara CM, Koutros S, Kraft P, Kristensen VN, Kurian AW, Lacey JV, Lambrechts D, Le Marchand L, Lindblom A, Linet M, Luben RN, Lubiński J, Lush M, Mannermaa A, Manoochehri M, Margolin S, Martens JWM, Martinez ME, Mavroudis D, Michailidou K, Milne RL, Mulligan AM, Muranen TA, Nevanlinna H, Newman WG, Nielsen SF, Nordestgaard BG, Olshan AF, Olsson H, Orr N, Park-Simon TW, Patel AV, Peissel B, Peterlongo P, Plaseska-Karanfilska D, Prajzendanc K, Prentice R, Presneau N, Rack B, Rennert G, Rennert HS, Rhenius V, Romero A, Roylance R, Ruebner M, Saloustros E, Sawyer EJ, Schmutzler RK, Schneeweiss A, Scott C, Shah M, Smichkoska S, Southey MC, Stone J, Surowy H, Swerdlow AJ, Tamimi RM, Tapper WJ, Teras LR, Terry MB, Tollenaar RAEM, Tomlinson I, Troester MA, Truong T, Vachon CM, Wang Q, Hurson AN, Winqvist R, Wolk A, Ziogas A, Brauch H, García-Closas M, Pharoah PDP, Easton DF, Chenevix-Trench G, Schmidt MK. Association of germline genetic variants with breast cancer-specific survival in patient subgroups defined by clinic-pathological variables related to tumor biology and type of systemic treatment. Breast Cancer Res 2021; 23:86. [PMID: 34407845 PMCID: PMC8371820 DOI: 10.1186/s13058-021-01450-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/28/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Given the high heterogeneity among breast tumors, associations between common germline genetic variants and survival that may exist within specific subgroups could go undetected in an unstratified set of breast cancer patients. METHODS We performed genome-wide association analyses within 15 subgroups of breast cancer patients based on prognostic factors, including hormone receptors, tumor grade, age, and type of systemic treatment. Analyses were based on 91,686 female patients of European ancestry from the Breast Cancer Association Consortium, including 7531 breast cancer-specific deaths over a median follow-up of 8.1 years. Cox regression was used to assess associations of common germline variants with 15-year and 5-year breast cancer-specific survival. We assessed the probability of these associations being true positives via the Bayesian false discovery probability (BFDP < 0.15). RESULTS Evidence of associations with breast cancer-specific survival was observed in three patient subgroups, with variant rs5934618 in patients with grade 3 tumors (15-year-hazard ratio (HR) [95% confidence interval (CI)] 1.32 [1.20, 1.45], P = 1.4E-08, BFDP = 0.01, per G allele); variant rs4679741 in patients with ER-positive tumors treated with endocrine therapy (15-year-HR [95% CI] 1.18 [1.11, 1.26], P = 1.6E-07, BFDP = 0.09, per G allele); variants rs1106333 (15-year-HR [95% CI] 1.68 [1.39,2.03], P = 5.6E-08, BFDP = 0.12, per A allele) and rs78754389 (5-year-HR [95% CI] 1.79 [1.46,2.20], P = 1.7E-08, BFDP = 0.07, per A allele), in patients with ER-negative tumors treated with chemotherapy. CONCLUSIONS We found evidence of four loci associated with breast cancer-specific survival within three patient subgroups. There was limited evidence for the existence of associations in other patient subgroups. However, the power for many subgroups is limited due to the low number of events. Even so, our results suggest that the impact of common germline genetic variants on breast cancer-specific survival might be limited.
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Affiliation(s)
- Anna Morra
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, 1066 CX The Netherlands
| | - Maria Escala-Garcia
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, 1066 CX The Netherlands
| | - Jonathan Beesley
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland Australia
| | - Renske Keeman
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, 1066 CX The Netherlands
| | - Sander Canisius
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, 1066 CX The Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Thomas U. Ahearn
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Irene L. Andrulis
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Fred A. Litwin Center for Cancer Genetics, Toronto, ON Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
| | - Hoda Anton-Culver
- Department of Medicine, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA USA
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul L. Auer
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA USA
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI USA
| | - Annelie Augustinsson
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Laura E. Beane Freeman
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Heiko Becher
- Institute of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias W. Beckmann
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg (FAU), Erlangen, Germany
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stig E. Bojesen
- Copenhagen University Hospital, Copenhagen General Population Study, Herlev and Gentofte Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manjeet K. Bolla
- Department of Public Health and Primary Care, University of Cambridge, Centre for Cancer Genetic Epidemiology, Cambridge, UK
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Thomas Brüning
- Institute of the Ruhr University Bochum (IPA), Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Bochum, Germany
| | - Saundra S. Buys
- Department of Medicine, Huntsman Cancer Institute, Salt Lake City, UT USA
| | - Bette Caan
- Division of Research, Kaiser Permanente, Oakland, CA USA
| | - Daniele Campa
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Biology, University of Pisa, Pisa, Italy
| | - Federico Canzian
- German Cancer Research Center (DKFZ), Genomic Epidemiology Group, Heidelberg, Germany
| | - Jose E. Castelao
- Instituto de Investigacion Sanitaria Galicia Sur (IISGS), Xerencia de Xestion Integrada de Vigo-SERGAS, Oncology and Genetics Unit, Vigo, Spain
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephen J. Chanock
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Ting-Yuan David Cheng
- Division of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY USA
| | - Christine L. Clarke
- Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales Australia
| | - Sarah V. Colonna
- Department of Medicine, Huntsman Cancer Institute, Salt Lake City, UT USA
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Angela Cox
- Department of Oncology and Metabolism, University of Sheffield, Sheffield Institute for Nucleic Acids (SInFoNiA), Sheffield, UK
| | - Simon S. Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mary B. Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA USA
| | - Joe Dennis
- Department of Public Health and Primary Care, University of Cambridge, Centre for Cancer Genetic Epidemiology, Cambridge, UK
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Laure Dossus
- Nutrition and Metabolism Section, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Alison M. Dunning
- Department of Oncology, University of Cambridge, Centre for Cancer Genetic Epidemiology, Cambridge, UK
| | - Miriam Dwek
- School of Life Sciences, University of Westminster, London, UK
| | - Diana M. Eccles
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Arif B. Ekici
- Institute of Human Genetics, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg (FAU), Erlangen, Germany
| | - A. Heather Eliassen
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Channing Division of Network Medicine, Boston, MA USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - D. Gareth Evans
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, 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
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg (FAU), Erlangen, Germany
- Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, David Geffen School of Medicine, Los Angeles, CA USA
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Lin Fritschi
- School of Public Health, Curtin University, Perth, Western Australia Australia
| | - Manuela Gago-Dominguez
- Galician Public Foundation of Genomic Medicine (FPGMX), Genomic Medicine Group, International Cancer Genetics and Epidemiology Group, Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
- University of California San Diego, Moores Cancer Center, La Jolla, CA USA
| | - José A. García-Sáenz
- Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro Investigación Biomédica en Red de Cáncer (CIBERONC), Medical Oncology Department, Hospital Clínico San Carlos, Madrid, Spain
| | - Graham G. Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria Australia
| | - Mervi Grip
- Department of Surgery, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Pascal Guénel
- Team Exposome and Heredity, INSERM, University Paris-Saclay, Center for Research in Epidemiology and Population Health (CESP), Villejuif, France
| | - Melanie Gündert
- Molecular Epidemiology Group, C080, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg, University of Heidelberg, Heidelberg, Germany
- German Research Center for Environmental Health, Institute of Diabetes Research, Helmholtz Zentrum München, Neuherberg, Germany
| | - Eric Hahnen
- Faculty of Medicine and University Hospital Cologne, Center for Familial Breast and Ovarian Cancer, University of Cologne, Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, Center for Integrated Oncology (CIO), University of Cologne, Cologne, Germany
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Niclas Håkansson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steven N. Hart
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN USA
| | - Jaana M. Hartikainen
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
| | - Arndt Hartmann
- Institute of Pathology, Comprehensive Cancer Center Erlangen Nuremberg, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Wei He
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Maartje J. Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Reiner Hoppe
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
| | - Anthony Howell
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - David J. Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - kConFab Investigators
- Research Department, Peter MacCallum Cancer Center, Melbourne, Victoria Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria Australia
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
| | - Wolfgang Janni
- Department of Gynaecology and Obstetrics, University Hospital Ulm, Ulm, Germany
| | - Esther M. John
- Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA USA
| | - Audrey Y. Jung
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Machteld Keupers
- Department of Radiation Oncology, University Hospitals Leuven, , University of Leuven, Leuven, Belgium
| | - Cari M. Kitahara
- Division of Cancer Epidemiology and Genetics, Radiation Epidemiology Branch, National Cancer Institute, Bethesda, MD USA
| | - Stella Koutros
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Vessela N. Kristensen
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Allison W. Kurian
- Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA USA
| | - James V. Lacey
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, CA USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA USA
| | - Diether Lambrechts
- VIB Center for Cancer Biology, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI USA
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Martha Linet
- Division of Cancer Epidemiology and Genetics, Radiation Epidemiology Branch, National Cancer Institute, Bethesda, MD USA
| | - Robert N. Luben
- Clinical Gerontology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Michael Lush
- Department of Public Health and Primary Care, University of Cambridge, Centre for Cancer Genetic Epidemiology, Cambridge, UK
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Kuopio University Hospital, Biobank of Eastern Finland, Kuopio, Finland
| | - Mehdi Manoochehri
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sara Margolin
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
- Department of Clinical Science and Education, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden
| | - John W. M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Maria Elena Martinez
- University of California San Diego, Moores Cancer Center, La Jolla, CA USA
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA USA
| | - Dimitrios Mavroudis
- Department of Medical Oncology, University Hospital of Heraklion, Heraklion, Greece
| | - Kyriaki Michailidou
- Department of Public Health and Primary Care, University of Cambridge, Centre for Cancer Genetic Epidemiology, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
- The Cyprus Institute of Neurology & Genetics, Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Roger L. Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria Australia
| | - Anna Marie Mulligan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
- University Health Network, Laboratory Medicine Program, Toronto, ON Canada
| | - Taru A. Muranen
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - William G. Newman
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, 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
| | - Sune F. Nielsen
- Copenhagen University Hospital, Copenhagen General Population Study, Herlev and Gentofte Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Børge G. Nordestgaard
- Copenhagen University Hospital, Copenhagen General Population Study, Herlev and Gentofte Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrew F. Olshan
- Department of Epidemiology, Gillings School of Global Public Health and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Håkan Olsson
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Nick Orr
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland, UK
| | | | - Alpa V. Patel
- Department of Population Science, American Cancer Society, Atlanta, GA USA
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM - the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Dijana Plaseska-Karanfilska
- MASA, Research Centre for Genetic Engineering and Biotechnology ‘Georgi D. Efremov’, Skopje, Republic of North Macedonia
| | - Karolina Prajzendanc
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Ross Prentice
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Nadege Presneau
- School of Life Sciences, University of Westminster, London, UK
| | - Brigitte Rack
- Department of Gynaecology and Obstetrics, University Hospital Ulm, Ulm, Germany
| | - Gad Rennert
- Carmel Medical Center and Technion Faculty of Medicine, Clalit National Cancer Control Center, Haifa, Israel
| | - Hedy S. Rennert
- Carmel Medical Center and Technion Faculty of Medicine, Clalit National Cancer Control Center, Haifa, Israel
| | - Valerie Rhenius
- Department of Oncology, University of Cambridge, Centre for Cancer Genetic Epidemiology, Cambridge, UK
| | - Atocha Romero
- Medical Oncology Department, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | | | - Matthias Ruebner
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg (FAU), Erlangen, Germany
| | | | - Elinor J. Sawyer
- School of Cancer & Pharmaceutical Sciences, Comprehensive Cancer Centre, Guy’s Campus, King’s College London, London, UK
| | - Rita K. Schmutzler
- Faculty of Medicine and University Hospital Cologne, Center for Familial Breast and Ovarian Cancer, University of Cologne, Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, Center for Integrated Oncology (CIO), University of Cologne, Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Andreas Schneeweiss
- Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg, University of Heidelberg, Heidelberg, Germany
- University Hospital and German Cancer Research Center, National Center for Tumor Diseases, Heidelberg, Germany
| | - Christopher Scott
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN USA
| | - Mitul Shah
- Department of Oncology, University of Cambridge, Centre for Cancer Genetic Epidemiology, Cambridge, UK
| | - Snezhana Smichkoska
- Medical Faculty, University Clinic of Radiotherapy and Oncology, Ss. Cyril and Methodius University in Skopje, Skopje, Republic of North Macedonia
| | - Melissa C. Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria Australia
| | - Jennifer Stone
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
- Genetic Epidemiology Group, School of Population and Global Health, University of Western Australia, Perth, Western Australia Australia
| | - Harald Surowy
- Molecular Epidemiology Group, C080, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Anthony J. Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Rulla M. Tamimi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY USA
| | | | - Lauren R. Teras
- Department of Population Science, American Cancer Society, Atlanta, GA USA
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY USA
| | | | - Ian Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- University of Oxford, Wellcome Trust Centre for Human Genetics and Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Melissa A. Troester
- Department of Epidemiology, Gillings School of Global Public Health and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Thérèse Truong
- Team Exposome and Heredity, INSERM, University Paris-Saclay, Center for Research in Epidemiology and Population Health (CESP), Villejuif, France
| | - Celine M. Vachon
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, MN USA
| | - Qin Wang
- Department of Public Health and Primary Care, University of Cambridge, Centre for Cancer Genetic Epidemiology, Cambridge, UK
| | - Amber N. Hurson
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Argyrios Ziogas
- Department of Medicine, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA USA
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- iFIT-Cluster of Excellence, University of Tübingen, Tübingen, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) Partner Site Tübingen, Tübingen, Germany
| | - Montserrat García-Closas
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Paul D. P. Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Centre for Cancer Genetic Epidemiology, Cambridge, UK
- Department of Oncology, University of Cambridge, Centre for Cancer Genetic Epidemiology, Cambridge, UK
| | - Douglas F. Easton
- Department of Public Health and Primary Care, University of Cambridge, Centre for Cancer Genetic Epidemiology, Cambridge, UK
- Department of Oncology, University of Cambridge, Centre for Cancer Genetic Epidemiology, Cambridge, UK
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland Australia
| | - Marjanka K. Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, 1066 CX The Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
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3
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Muranen TA, Khan S, Fagerholm R, Aittomäki K, Cunningham JM, Dennis J, Leslie G, McGuffog L, Parsons MT, Simard J, Slager S, Soucy P, Easton DF, Tischkowitz M, Spurdle AB, Schmutzler RK, Wappenschmidt B, Hahnen E, Hooning MJ, Singer CF, Wagner G, Thomassen M, Pedersen IS, Domchek SM, Nathanson KL, Lazaro C, Rossing CM, Andrulis IL, Teixeira MR, James P, Garber J, Weitzel JN, Jakubowska A, Yannoukakos D, John EM, Southey MC, Schmidt MK, Antoniou AC, Chenevix-Trench G, Blomqvist C, Nevanlinna H. Association of germline variation with the survival of women with BRCA1/2 pathogenic variants and breast cancer. NPJ Breast Cancer 2020; 6:44. [PMID: 32964118 PMCID: PMC7483417 DOI: 10.1038/s41523-020-00185-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/11/2020] [Indexed: 02/02/2023] Open
Abstract
Germline genetic variation has been suggested to influence the survival of breast cancer patients independently of tumor pathology. We have studied survival associations of genetic variants in two etiologically unique groups of breast cancer patients, the carriers of germline pathogenic variants in BRCA1 or BRCA2 genes. We found that rs57025206 was significantly associated with the overall survival, predicting higher mortality of BRCA1 carrier patients with estrogen receptor-negative breast cancer, with a hazard ratio 4.37 (95% confidence interval 3.03-6.30, P = 3.1 × 10-9). Multivariable analysis adjusted for tumor characteristics suggested that rs57025206 was an independent survival marker. In addition, our exploratory analyses suggest that the associations between genetic variants and breast cancer patient survival may depend on tumor biological subgroup and clinical patient characteristics.
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Affiliation(s)
- Taru A. Muranen
- University of Helsinki, Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | - Sofia Khan
- University of Helsinki, Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
- University of Turku and Åbo Akademi University, Turku Bioscience Centre, Turku, Finland
| | - Rainer Fagerholm
- University of Helsinki, Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | - Kristiina Aittomäki
- University of Helsinki, Department of Clinical Genetics, Helsinki University Hospital, Helsinki, Finland
| | - Julie M. Cunningham
- Mayo Clinic, Department of Laboratory Medicine and Pathology, Rochester, MN USA
| | - Joe Dennis
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Goska Leslie
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Lesley McGuffog
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Michael T. Parsons
- QIMR Berghofer Medical Research Institute, Department of Genetics and Computational Biology, Brisbane, QLD Australia
| | - Jacques Simard
- CHU de Quebec Research Center, Genomics Center, Québec City, QC Canada
| | - Susan Slager
- Mayo Clinic, Department of Health Sciences Research, Rochester, MN USA
| | - Penny Soucy
- CHU de Quebec Research Center, Genomics Center, Québec City, QC Canada
| | - 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
| | - Marc Tischkowitz
- McGill University, Program in Cancer Genetics, Departments of Human Genetics and Oncology, Montréal, QC Canada
- University of Cambridge, Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK
| | - Amanda B. Spurdle
- QIMR Berghofer Medical Research Institute, Department of Genetics and Computational Biology, Brisbane, QLD Australia
| | - kConFab Investigators
- University of Helsinki, Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
- University of Turku and Åbo Akademi University, Turku Bioscience Centre, Turku, Finland
- University of Helsinki, Department of Clinical Genetics, Helsinki University Hospital, Helsinki, Finland
- Mayo Clinic, Department of Laboratory Medicine and Pathology, Rochester, MN USA
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
- QIMR Berghofer Medical Research Institute, Department of Genetics and Computational Biology, Brisbane, QLD Australia
- CHU de Quebec Research Center, Genomics Center, Québec City, QC Canada
- Mayo Clinic, Department of Health Sciences Research, Rochester, MN USA
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge, UK
- McGill University, Program in Cancer Genetics, Departments of Human Genetics and Oncology, Montréal, QC Canada
- University of Cambridge, Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Hereditary Breast and Ovarian Cancer, Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
- Erasmus MC Cancer Institute, Department of Medical Oncology, Family Cancer Clinic, Rotterdam, The Netherlands
- Medical University of Vienna, Dept of OB/GYN and Comprehensive Cancer Center, Vienna, Austria
- Odense University Hospital, Department of Clinical Genetics, Odence C, Denmark
- Aalborg University Hospital, Molecular Diagnostics, Aalborg, Denmark
- Aalborg University, Dept of Clinical Medicine, Aalborg, Denmark
- Perelman School of Medicine at the University of Pennsylvania, Department of Medicine, Abramson Cancer Center, Philadelphia, PA USA
- ICO-IDIBELL (Bellvitge Biomedical Research Institute, Catalan Institute of Oncology), CIBERONC, Molecular Diagnostic Unit, Hereditary Cancer Program, Barcelona, Spain
- Rigshospitalet, Copenhagen University Hospital, Center for Genomic Medicine, Copenhagen, Denmark
- 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
- Portuguese Oncology Institute, Department of Genetics, Porto, Portugal
- University of Porto, Biomedical Sciences Institute (ICBAS), Porto, Portugal
- Peter MacCallum Cancer Center, Parkville Familial Cancer Centre, Melbourne, VIC Australia
- The University of Melbourne, Sir Peter MacCallum Department of Oncology, Melbourne, VIC Australia
- Dana-Farber Cancer Institute, Cancer Risk and Prevention Clinic, Boston, MA USA
- City of Hope, Clinical Cancer Genomics, Duarte, CA USA
- Pomeranian Medical University, Department of Genetics and Pathology, Szczecin, Poland
- Pomeranian Medical University, Independent Laboratory of Molecular Biology and Genetic Diagnostics, Szczecin, Poland
- National Centre for Scientific Research ‘Demokritos’, Molecular Diagnostics Laboratory, INRASTES, Athens, Greece
- Stanford Cancer Institute, Stanford University School of Medicine, Department of Medicine, Division of Oncology, Stanford, CA USA
- Monash University, Precision Medicine, School of Clinical Sciences at Monash Health, Clayton, VIC Australia
- The University of Melbourne, Department of Clinical Pathology, Melbourne, VIC Australia
- The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Division of Molecular Pathology, Amsterdam, The Netherlands
- The Netherlands Cancer Institute-Antoni van Leeuwenhoek hospital, Division of Psychosocial Research and Epidemiology, Amsterdam, The Netherlands
- University of Helsinki, Department of Oncology, Helsinki University Hospital, Helsinki, Finland
- Örebro University Hospital, Department of Oncology, Örebro, Sweden
| | - Rita K. Schmutzler
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Hereditary Breast and Ovarian Cancer, Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Barbara Wappenschmidt
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Hereditary Breast and Ovarian Cancer, Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Eric Hahnen
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Hereditary Breast and Ovarian Cancer, Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Maartje J. Hooning
- Erasmus MC Cancer Institute, Department of Medical Oncology, Family Cancer Clinic, Rotterdam, The Netherlands
| | - HEBON Investigators
- University of Helsinki, Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
- University of Turku and Åbo Akademi University, Turku Bioscience Centre, Turku, Finland
- University of Helsinki, Department of Clinical Genetics, Helsinki University Hospital, Helsinki, Finland
- Mayo Clinic, Department of Laboratory Medicine and Pathology, Rochester, MN USA
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
- QIMR Berghofer Medical Research Institute, Department of Genetics and Computational Biology, Brisbane, QLD Australia
- CHU de Quebec Research Center, Genomics Center, Québec City, QC Canada
- Mayo Clinic, Department of Health Sciences Research, Rochester, MN USA
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge, UK
- McGill University, Program in Cancer Genetics, Departments of Human Genetics and Oncology, Montréal, QC Canada
- University of Cambridge, Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Hereditary Breast and Ovarian Cancer, Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
- Erasmus MC Cancer Institute, Department of Medical Oncology, Family Cancer Clinic, Rotterdam, The Netherlands
- Medical University of Vienna, Dept of OB/GYN and Comprehensive Cancer Center, Vienna, Austria
- Odense University Hospital, Department of Clinical Genetics, Odence C, Denmark
- Aalborg University Hospital, Molecular Diagnostics, Aalborg, Denmark
- Aalborg University, Dept of Clinical Medicine, Aalborg, Denmark
- Perelman School of Medicine at the University of Pennsylvania, Department of Medicine, Abramson Cancer Center, Philadelphia, PA USA
- ICO-IDIBELL (Bellvitge Biomedical Research Institute, Catalan Institute of Oncology), CIBERONC, Molecular Diagnostic Unit, Hereditary Cancer Program, Barcelona, Spain
- Rigshospitalet, Copenhagen University Hospital, Center for Genomic Medicine, Copenhagen, Denmark
- 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
- Portuguese Oncology Institute, Department of Genetics, Porto, Portugal
- University of Porto, Biomedical Sciences Institute (ICBAS), Porto, Portugal
- Peter MacCallum Cancer Center, Parkville Familial Cancer Centre, Melbourne, VIC Australia
- The University of Melbourne, Sir Peter MacCallum Department of Oncology, Melbourne, VIC Australia
- Dana-Farber Cancer Institute, Cancer Risk and Prevention Clinic, Boston, MA USA
- City of Hope, Clinical Cancer Genomics, Duarte, CA USA
- Pomeranian Medical University, Department of Genetics and Pathology, Szczecin, Poland
- Pomeranian Medical University, Independent Laboratory of Molecular Biology and Genetic Diagnostics, Szczecin, Poland
- National Centre for Scientific Research ‘Demokritos’, Molecular Diagnostics Laboratory, INRASTES, Athens, Greece
- Stanford Cancer Institute, Stanford University School of Medicine, Department of Medicine, Division of Oncology, Stanford, CA USA
- Monash University, Precision Medicine, School of Clinical Sciences at Monash Health, Clayton, VIC Australia
- The University of Melbourne, Department of Clinical Pathology, Melbourne, VIC Australia
- The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Division of Molecular Pathology, Amsterdam, The Netherlands
- The Netherlands Cancer Institute-Antoni van Leeuwenhoek hospital, Division of Psychosocial Research and Epidemiology, Amsterdam, The Netherlands
- University of Helsinki, Department of Oncology, Helsinki University Hospital, Helsinki, Finland
- Örebro University Hospital, Department of Oncology, Örebro, Sweden
| | - Christian F. Singer
- Medical University of Vienna, Dept of OB/GYN and Comprehensive Cancer Center, Vienna, Austria
| | - Gabriel Wagner
- Medical University of Vienna, Dept of OB/GYN and Comprehensive Cancer Center, Vienna, Austria
| | - Mads Thomassen
- Odense University Hospital, Department of Clinical Genetics, Odence C, Denmark
| | - Inge Sokilde Pedersen
- Aalborg University Hospital, Molecular Diagnostics, Aalborg, Denmark
- Aalborg University, Dept of Clinical Medicine, Aalborg, Denmark
| | - Susan M. Domchek
- Perelman School of Medicine at the University of Pennsylvania, Department of Medicine, Abramson Cancer Center, Philadelphia, PA USA
| | - Katherine L. Nathanson
- Perelman School of Medicine at the University of Pennsylvania, Department of Medicine, Abramson Cancer Center, Philadelphia, PA USA
| | - Conxi Lazaro
- ICO-IDIBELL (Bellvitge Biomedical Research Institute, Catalan Institute of Oncology), CIBERONC, Molecular Diagnostic Unit, Hereditary Cancer Program, Barcelona, Spain
| | - Caroline Maria Rossing
- Rigshospitalet, Copenhagen University Hospital, Center for Genomic Medicine, Copenhagen, Denmark
| | - 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
| | - Manuel R. Teixeira
- Portuguese Oncology Institute, Department of Genetics, Porto, Portugal
- University of Porto, Biomedical Sciences Institute (ICBAS), Porto, Portugal
| | - Paul James
- Peter MacCallum Cancer Center, Parkville Familial Cancer Centre, Melbourne, VIC Australia
- The University of Melbourne, Sir Peter MacCallum Department of Oncology, Melbourne, VIC Australia
| | - Judy Garber
- Dana-Farber Cancer Institute, Cancer Risk and Prevention Clinic, Boston, MA USA
| | | | - SWE-BRCA Investigators
- University of Helsinki, Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
- University of Turku and Åbo Akademi University, Turku Bioscience Centre, Turku, Finland
- University of Helsinki, Department of Clinical Genetics, Helsinki University Hospital, Helsinki, Finland
- Mayo Clinic, Department of Laboratory Medicine and Pathology, Rochester, MN USA
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
- QIMR Berghofer Medical Research Institute, Department of Genetics and Computational Biology, Brisbane, QLD Australia
- CHU de Quebec Research Center, Genomics Center, Québec City, QC Canada
- Mayo Clinic, Department of Health Sciences Research, Rochester, MN USA
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge, UK
- McGill University, Program in Cancer Genetics, Departments of Human Genetics and Oncology, Montréal, QC Canada
- University of Cambridge, Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Hereditary Breast and Ovarian Cancer, Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
- Erasmus MC Cancer Institute, Department of Medical Oncology, Family Cancer Clinic, Rotterdam, The Netherlands
- Medical University of Vienna, Dept of OB/GYN and Comprehensive Cancer Center, Vienna, Austria
- Odense University Hospital, Department of Clinical Genetics, Odence C, Denmark
- Aalborg University Hospital, Molecular Diagnostics, Aalborg, Denmark
- Aalborg University, Dept of Clinical Medicine, Aalborg, Denmark
- Perelman School of Medicine at the University of Pennsylvania, Department of Medicine, Abramson Cancer Center, Philadelphia, PA USA
- ICO-IDIBELL (Bellvitge Biomedical Research Institute, Catalan Institute of Oncology), CIBERONC, Molecular Diagnostic Unit, Hereditary Cancer Program, Barcelona, Spain
- Rigshospitalet, Copenhagen University Hospital, Center for Genomic Medicine, Copenhagen, Denmark
- 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
- Portuguese Oncology Institute, Department of Genetics, Porto, Portugal
- University of Porto, Biomedical Sciences Institute (ICBAS), Porto, Portugal
- Peter MacCallum Cancer Center, Parkville Familial Cancer Centre, Melbourne, VIC Australia
- The University of Melbourne, Sir Peter MacCallum Department of Oncology, Melbourne, VIC Australia
- Dana-Farber Cancer Institute, Cancer Risk and Prevention Clinic, Boston, MA USA
- City of Hope, Clinical Cancer Genomics, Duarte, CA USA
- Pomeranian Medical University, Department of Genetics and Pathology, Szczecin, Poland
- Pomeranian Medical University, Independent Laboratory of Molecular Biology and Genetic Diagnostics, Szczecin, Poland
- National Centre for Scientific Research ‘Demokritos’, Molecular Diagnostics Laboratory, INRASTES, Athens, Greece
- Stanford Cancer Institute, Stanford University School of Medicine, Department of Medicine, Division of Oncology, Stanford, CA USA
- Monash University, Precision Medicine, School of Clinical Sciences at Monash Health, Clayton, VIC Australia
- The University of Melbourne, Department of Clinical Pathology, Melbourne, VIC Australia
- The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Division of Molecular Pathology, Amsterdam, The Netherlands
- The Netherlands Cancer Institute-Antoni van Leeuwenhoek hospital, Division of Psychosocial Research and Epidemiology, Amsterdam, The Netherlands
- University of Helsinki, Department of Oncology, Helsinki University Hospital, Helsinki, Finland
- Örebro University Hospital, Department of Oncology, Örebro, Sweden
| | - Anna Jakubowska
- Pomeranian Medical University, Department of Genetics and Pathology, Szczecin, Poland
- Pomeranian Medical University, Independent Laboratory of Molecular Biology and Genetic Diagnostics, Szczecin, Poland
| | - Drakoulis Yannoukakos
- National Centre for Scientific Research ‘Demokritos’, Molecular Diagnostics Laboratory, INRASTES, Athens, Greece
| | - Esther M. John
- Stanford Cancer Institute, Stanford University School of Medicine, Department of Medicine, Division of Oncology, Stanford, CA USA
| | - Melissa C. Southey
- Monash University, Precision Medicine, School of Clinical Sciences at Monash Health, Clayton, VIC Australia
- The University of Melbourne, Department of Clinical Pathology, Melbourne, VIC Australia
| | - Marjanka K. Schmidt
- The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Division of Molecular Pathology, Amsterdam, The Netherlands
- The Netherlands Cancer Institute-Antoni van Leeuwenhoek hospital, Division of Psychosocial Research and Epidemiology, Amsterdam, The Netherlands
| | - Antonis C. Antoniou
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Georgia Chenevix-Trench
- QIMR Berghofer Medical Research Institute, Department of Genetics and Computational Biology, Brisbane, QLD Australia
| | - Carl Blomqvist
- University of Helsinki, Department of Oncology, Helsinki University Hospital, Helsinki, Finland
- Örebro University Hospital, Department of Oncology, Örebro, Sweden
| | - Heli Nevanlinna
- University of Helsinki, Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
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4
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Li X, Li X, Yin Z, Jiang M, Tian W, Tang M, Zhou B. Polymorphisms of rs4787050 and rs8045980 are associated with lung cancer risk in northeast Chinese female nonsmokers. Biomark Med 2019; 13:1119-1128. [PMID: 31512508 DOI: 10.2217/bmm-2018-0482] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Aim: We studied the association between two single-nucleotide polymorphisms (SNPs: rs4787050 and rs8045980) in RBFOX1 and lung cancer risk, and explored the interaction between the two SNPs and exposure to cooking oil fume on lung cancer risk in northeast Chinese female nonsmokers. Methods: Northeast Chinese female nonsmokers were enrolled into the study (people with lung cancer, 647; people without lung cancer, 675). All statistical analyses were performed using SPSS software. Results: The SNPs rs4787050 and rs8045980 showed a significant association with susceptibility to lung cancer. Moreover, cooking oil fume exposure was found to increase the risk of lung cancer. However, no gene-environment interactions were discovered. Conclusion: The present study revealed that rs4787050 and rs8045980 in RBFOX1 may be meaningful as a novel biomarker for lung cancer susceptibility.
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Affiliation(s)
- Xiaoying Li
- Department of Clinical Epidemiology, First Affiliated Hospital of China Medical University, Shenyang 110001, PR China.,Department of Epidemiology, School of Public Health, China Medical University, Shenyang, 110122, PR China
| | - Xuelian Li
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, 110122, PR China
| | - Zhihua Yin
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, 110122, PR China
| | - Min Jiang
- Department of Clinical Epidemiology, First Affiliated Hospital of China Medical University, Shenyang 110001, PR China.,Department of Epidemiology, School of Public Health, China Medical University, Shenyang, 110122, PR China
| | - Wen Tian
- Department of Clinical Epidemiology, First Affiliated Hospital of China Medical University, Shenyang 110001, PR China.,Department of Epidemiology, School of Public Health, China Medical University, Shenyang, 110122, PR China
| | - Man Tang
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, PR China
| | - Baosen Zhou
- Department of Clinical Epidemiology, First Affiliated Hospital of China Medical University, Shenyang 110001, PR China.,Department of Epidemiology, School of Public Health, China Medical University, Shenyang, 110122, PR China
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5
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Paganetti H, Blakely E, Carabe-Fernandez A, Carlson DJ, Das IJ, Dong L, Grosshans D, Held KD, Mohan R, Moiseenko V, Niemierko A, Stewart RD, Willers H. Report of the AAPM TG-256 on the relative biological effectiveness of proton beams in radiation therapy. Med Phys 2019; 46:e53-e78. [PMID: 30661238 DOI: 10.1002/mp.13390] [Citation(s) in RCA: 182] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/21/2018] [Accepted: 01/13/2019] [Indexed: 12/14/2022] Open
Abstract
The biological effectiveness of proton beams relative to photon beams in radiation therapy has been taken to be 1.1 throughout the history of proton therapy. While potentially appropriate as an average value, actual relative biological effectiveness (RBE) values may differ. This Task Group report outlines the basic concepts of RBE as well as the biophysical interpretation and mathematical concepts. The current knowledge on RBE variations is reviewed and discussed in the context of the current clinical use of RBE and the clinical relevance of RBE variations (with respect to physical as well as biological parameters). The following task group aims were designed to guide the current clinical practice: Assess whether the current clinical practice of using a constant RBE for protons should be revised or maintained. Identifying sites and treatment strategies where variable RBE might be utilized for a clinical benefit. Assess the potential clinical consequences of delivering biologically weighted proton doses based on variable RBE and/or LET models implemented in treatment planning systems. Recommend experiments needed to improve our current understanding of the relationships among in vitro, in vivo, and clinical RBE, and the research required to develop models. Develop recommendations to minimize the effects of uncertainties associated with proton RBE for well-defined tumor types and critical structures.
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Affiliation(s)
- Harald Paganetti
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eleanor Blakely
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - David J Carlson
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
| | - Indra J Das
- New York University Langone Medical Center & Laura and Isaac Perlmutter Cancer Center, New York, NY, USA
| | - Lei Dong
- Department of Radiation Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - David Grosshans
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kathryn D Held
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Radhe Mohan
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vitali Moiseenko
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, USA
| | - Andrzej Niemierko
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Robert D Stewart
- Department of Radiation Oncology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Henning Willers
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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6
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Association between breast cancer risk factors and molecular type in postmenopausal patients with hormone receptor-positive early breast cancer. Breast Cancer Res Treat 2019; 174:453-461. [PMID: 30603996 DOI: 10.1007/s10549-018-05115-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/20/2018] [Indexed: 12/17/2022]
Abstract
PURPOSE Evidence shows that genetic and non-genetic risk factors for breast cancer (BC) differ relative to the molecular subtype. This analysis aimed to investigate associations between epidemiological risk factors and immunohistochemical subtypes in a cohort of postmenopausal, hormone receptor-positive BC patients. METHODS The prospective, single-arm, multicenter phase IV PreFace study (Evaluation of Predictive Factors Regarding the Effectivity of Aromatase Inhibitor Therapy) included 3529 postmenopausal patients with hormone receptor-positive early BC. Data on their epidemiological risk factors were obtained from patients' diaries and their medical histories. Data on estrogen receptor, progesterone receptor, and HER2 receptor status were obtained from pathology reports. Patients with incomplete information were excluded. Data were analyzed using conditional inference regression analysis, analysis of variance, and the chi-squared test. RESULTS In a cohort of 3392 patients, the strongest association with the molecular subtypes of BC was found for hormone replacement therapy (HRT) before diagnosis of early BC. The analysis showed that patients who took HRT at diagnosis had luminal A-like BC more often (83.7%) than those who had never taken HRT or had stopped taking it (75.5%). Luminal B-like BC and HER2-positive BC were diagnosed more often in women who had never taken HRT or had stopped taking it (13.3% and 11.2%, respectively) than in women who were taking HRT at diagnosis of BC (8.3% and 8.0%, respectively). CONCLUSIONS This analysis shows an association between HRT and the distribution of molecular subtypes of BC. However, no associations between other factors (e.g., age at diagnosis, body mass index, smoking status, age at menopause, number of deliveries, age at first delivery, breastfeeding history, or family history) were noted.
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7
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McGeehan RE, Cockram LA, Littlewood DTJ, Keatley K, Eccles DM, An Q. Deep sequencing reveals the mitochondrial DNA variation landscapes of breast-to-brain metastasis blood samples. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 29:703-713. [PMID: 28712340 DOI: 10.1080/24701394.2017.1350950] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/02/2017] [Indexed: 12/11/2022]
Abstract
Breast-to-brain metastasis (BBM) often represents a terminal event, due to the inability of many systemic treatments to cross the blood-brain barrier (BBB), rendering the brain a sanctuary site for tumour cells. Identifying genetic variations that can predict the patients who will develop BBM would allow targeting of adjuvant treatments to reduce risk while disease bulk is minimal. Germ-line genetic variations may contribute to whether a BBM forms by influencing the primary tumour subtype that presents, or by influencing the host response to the tumour or treatment regimen, or by facilitating transition of tumour cells across the BBB and establish a viable brain metastasis. The role of mitochondrial DNA (mtDNA) variants specifically in BBM is underexplored. Consequently, using a sensitive deep sequencing approach, we characterized the mtDNA variation landscapes of blood samples derived from 13 females who were diagnosed with early-onset breast cancer and later went on to develop BBM. We also predicted the potential pathogenic significance of variations identified in all mtDNA-encoded oxidative phosphorylation (OXPHOS) proteins using 3D protein structural mapping and analysis, to identify variations worthy of follow-up. From the 70 variations found in protein coding regions, we reveal novel links between three specific mtDNA variations and altered OXPHOS structure and function in 23% of the BBM samples. Further studies are required to confirm the origin of mtDNA variations, and whether they correlate with (1) the predicted alterations in mitochondrial function and (2) increased risk of developing breast-to-brain metastasis using a much larger cohort of samples.
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Affiliation(s)
- Rhiannon E McGeehan
- a Brain Tumour Research Centre, Institute of Biological and Biomedical Sciences , University of Portsmouth , Portsmouth , UK
| | - Lewis A Cockram
- a Brain Tumour Research Centre, Institute of Biological and Biomedical Sciences , University of Portsmouth , Portsmouth , UK
- b School of Pharmacy and Biomedical Sciences, Institute of Biological and Biomedical Sciences , University of Portsmouth , Portsmouth , UK
| | | | - Kathleen Keatley
- a Brain Tumour Research Centre, Institute of Biological and Biomedical Sciences , University of Portsmouth , Portsmouth , UK
- d School of Biological Sciences, Institute of Biological and Biomedical Sciences , University of Portsmouth , Portsmouth , UK
| | - Diana M Eccles
- e Cancer Sciences Academic Unit, Faculty of Medicine , University of Southampton , Southampton , UK
| | - Qian An
- b School of Pharmacy and Biomedical Sciences, Institute of Biological and Biomedical Sciences , University of Portsmouth , Portsmouth , UK
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8
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Wunderle M, Olmes G, Nabieva N, Häberle L, Jud SM, Hein A, Rauh C, Hack CC, Erber R, Ekici AB, Hoyer J, Vasileiou G, Kraus C, Reis A, Hartmann A, Schulz-Wendtland R, Lux MP, Beckmann MW, Fasching PA. Risk, Prediction and Prevention of Hereditary Breast Cancer - Large-Scale Genomic Studies in Times of Big and Smart Data. Geburtshilfe Frauenheilkd 2018; 78:481-492. [PMID: 29880983 PMCID: PMC5986564 DOI: 10.1055/a-0603-4350] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 04/09/2018] [Accepted: 04/09/2018] [Indexed: 12/24/2022] Open
Abstract
Over the last two decades genetic testing for mutations in
BRCA1
and
BRCA2
has become standard of care for women and men who are at familial risk for breast or ovarian cancer. Currently, genetic testing more often also includes so-called panel genes, which are assumed to be moderate-risk genes for breast cancer. Recently, new large-scale studies provided more information about the risk estimation of those genes. The utilization of information on panel genes with regard to their association with the individual breast cancer risk might become part of future clinical practice. Furthermore, large efforts have been made to understand the influence of common genetic variants with a low impact on breast cancer risk. For this purpose, almost 450 000 individuals have been genotyped for almost 500 000 genetic variants in the OncoArray project. Based on first results it can be assumed that – together with previously identified common variants – more than 170 breast cancer risk single nucleotide polymorphisms can explain up to 18% of familial breast cancer risk. The knowledge about genetic and non-genetic risk factors and its implementation in clinical practice could especially be of use for individualized prevention. This includes an individualized risk prediction as well as the individualized selection of screening methods regarding imaging and possible lifestyle interventions. The aim of this review is to summarize the most recent developments in this area and to provide an overview on breast cancer risk genes, risk prediction models and their utilization for the individual patient.
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Affiliation(s)
- Marius Wunderle
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Gregor Olmes
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Naiba Nabieva
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Lothar Häberle
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany.,Biostatistics Unit, Department of Gynecology and Obstetrics, Erlangen University Hospital, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Sebastian M Jud
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Alexander Hein
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Claudia Rauh
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Carolin C Hack
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Ramona Erber
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Juliane Hoyer
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Georgia Vasileiou
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Cornelia Kraus
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Rüdiger Schulz-Wendtland
- Institute of Diagnostic Radiology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Michael P Lux
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
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9
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Koster R, Panagiotou OA, Wheeler WA, Karlins E, Gastier-Foster JM, de Toledo SRC, Petrilli AS, Flanagan AM, Tirabosco R, Andrulis IL, Wunder JS, Gokgoz N, Patiño-Garcia A, Lecanda F, Serra M, Hattinger C, Picci P, Scotlandi K, Thomas DM, Ballinger ML, Gorlick R, Barkauskas DA, Spector LG, Tucker M, Hicks BD, Yeager M, Hoover RN, Wacholder S, Chanock SJ, Savage SA, Mirabello L. Genome-wide association study identifies the GLDC/IL33 locus associated with survival of osteosarcoma patients. Int J Cancer 2018; 142:1594-1601. [PMID: 29210060 PMCID: PMC5814322 DOI: 10.1002/ijc.31195] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 11/13/2017] [Indexed: 12/31/2022]
Abstract
Survival rates for osteosarcoma, the most common primary bone cancer, have changed little over the past three decades and are particularly low for patients with metastatic disease. We conducted a multi-institutional genome-wide association study (GWAS) to identify germline genetic variants associated with overall survival in 632 patients with osteosarcoma, including 523 patients of European ancestry and 109 from Brazil. We conducted a time-to-event analysis and estimated hazard ratios (HR) and 95% confidence intervals (CI) using Cox proportional hazards models, with and without adjustment for metastatic disease. The results were combined across the European and Brazilian case sets using a random-effects meta-analysis. The strongest association after meta-analysis was for rs3765555 at 9p24.1, which was inversely associated with overall survival (HR = 1.76; 95% CI 1.41-2.18, p = 4.84 × 10-7 ). After imputation across this region, the combined analysis identified two SNPs that reached genome-wide significance. The strongest single association was with rs55933544 (HR = 1.9; 95% CI 1.5-2.4; p = 1.3 × 10-8 ), which localizes to the GLDC gene, adjacent to the IL33 gene and was consistent across both the European and Brazilian case sets. Using publicly available data, the risk allele was associated with lower expression of IL33 and low expression of IL33 was associated with poor survival in an independent set of patients with osteosarcoma. In conclusion, we have identified the GLDC/IL33 locus on chromosome 9p24.1 as associated with overall survival in patients with osteosarcoma. Further studies are needed to confirm this association and shed light on the biological underpinnings of this susceptibility locus.
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Affiliation(s)
- Roelof Koster
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Orestis A. Panagiotou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Julie M. Gastier-Foster
- Nationwide Children’s Hospital, and The Ohio State University Department of Pathology and Pediatrics, Columbus, OH, USA
| | | | - Antonio S. Petrilli
- Laboratorio de Genética, Pediatric Oncology Institute, GRAACC/UNIFESP, São Paulo, Brazil
| | - Adrienne M. Flanagan
- UCL Cancer Institute, Huntley Street, London, UK
- Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, UK
| | - Roberto Tirabosco
- Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, UK
| | - Irene L. Andrulis
- Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Jay S. Wunder
- Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Nalan Gokgoz
- Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Ana Patiño-Garcia
- Department of Pediatrics, University Clinic of Navarra, Universidad de Navarra, Pamplona, Spain
| | - Fernando Lecanda
- Department of Pediatrics, University Clinic of Navarra, Universidad de Navarra, Pamplona, Spain
| | - Massimo Serra
- Laboratory of Experimental Oncology, Orthopaedic Rizzoli Institute, Bologna, Italy
| | - Claudia Hattinger
- Laboratory of Experimental Oncology, Orthopaedic Rizzoli Institute, Bologna, Italy
| | - Piero Picci
- Laboratory of Experimental Oncology, Orthopaedic Rizzoli Institute, Bologna, Italy
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, Orthopaedic Rizzoli Institute, Bologna, Italy
| | - David M. Thomas
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Mandy L. Ballinger
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Richard Gorlick
- Albert Einstein College of Medicine, The Children’s Hospital at Montefiore, New York, NY, USA
| | - Donald A. Barkauskas
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Logan G. Spector
- Department of Pediatrics, University of Minnesota Minneapolis, MN, 55455, USA
| | - Margaret Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Belynda D. Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Robert N. Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sholom Wacholder
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sharon A. Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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10
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Taran FA, Schneeweiss A, Lux MP, Janni W, Hartkopf AD, Nabieva N, Overkamp F, Kolberg HC, Hadji P, Tesch H, Wöckel A, Ettl J, Lüftner D, Wallwiener M, Müller V, Beckmann MW, Belleville E, Wallwiener D, Brucker SY, Fasching PA, Fehm TN, Schütz F. Update Breast Cancer 2018 (Part 1) - Primary Breast Cancer and Biomarkers. Geburtshilfe Frauenheilkd 2018; 78:237-245. [PMID: 29576629 PMCID: PMC5862549 DOI: 10.1055/s-0044-101613] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 01/24/2018] [Accepted: 01/24/2018] [Indexed: 12/16/2022] Open
Abstract
This summary provides an overview of how new therapies or new aspects of established therapies relate to the latest findings. Neoadjuvant therapy, local therapy, new aspects of systemic therapy, and prognostic and predictive factors are presented. In the neoadjuvant setting, the association between pathological complete response (pCR) and prognosis is still of interest as is the identification of new molecular predictors for new therapies such as CDK4/6 inhibitors. As regards surgical treatment, the target is still to reduce the aggressiveness of surgery. To achieve this, a better understanding particularly of ductal carcinoma in situ is required. With regard to systemic therapy, more data on the best combinations and therapy sequences for existing therapies is available. Finally, the use of prognostic and predictive factors may help to avoid overtreatment and ensure that patients only receive therapies which have been shown to be effective for their specific condition and have fewer side effects.
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Affiliation(s)
- Florin-Andrei Taran
- Department of Obstetrics and Gynecology, University of Tübingen, Tübingen, Germany
| | - Andreas Schneeweiss
- National Center for Tumor Diseases, Division Gynecologic Oncology, University Hospital Heidelberg, Heidelberg, Germany.,Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Michael P Lux
- Erlangen University Hospital, Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Wolfgang Janni
- Department of Gynecology and Obstetrics, Ulm University Hospital, Ulm, Germany
| | - Andreas D Hartkopf
- Department of Obstetrics and Gynecology, University of Tübingen, Tübingen, Germany
| | - Naiba Nabieva
- Erlangen University Hospital, Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | | | | | - Peyman Hadji
- Department of Bone Oncology, Nordwest Hospital, Frankfurt, Germany
| | - Hans Tesch
- Oncology Practice at Bethanien Hospital Frankfurt, Frankfurt, Germany
| | - Achim Wöckel
- Department of Gynecology and Obstetrics, University Hospital Würzburg, Würzburg, Germany
| | - Johannes Ettl
- Department of Obstetrics and Gynecology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Diana Lüftner
- Charité University Hospital, Berlin, Campus Benjamin Franklin, Department of Hematology, Oncology and Tumour Immunology, Berlin, Germany
| | - Markus Wallwiener
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Volkmar Müller
- Department of Gynecology, Hamburg-Eppendorf University Medical Center, Hamburg, Germany
| | - Matthias W Beckmann
- Erlangen University Hospital, Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | | | - Diethelm Wallwiener
- Department of Obstetrics and Gynecology, University of Tübingen, Tübingen, Germany
| | - Sara Y Brucker
- Department of Obstetrics and Gynecology, University of Tübingen, Tübingen, Germany
| | - Peter A Fasching
- Erlangen University Hospital, Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Tanja N Fehm
- Department of Gynecology and Obstetrics, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Florian Schütz
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
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11
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Khan S, Fagerholm R, Kadalayil L, Tapper W, Aittomäki K, Liu J, Blomqvist C, Eccles D, Nevanlinna H. Meta-analysis of three genome-wide association studies identifies two loci that predict survival and treatment outcome in breast cancer. Oncotarget 2018; 9:4249-4257. [PMID: 29423119 PMCID: PMC5790536 DOI: 10.18632/oncotarget.22747] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 11/09/2017] [Indexed: 11/25/2022] Open
Abstract
The majority of breast cancers are driven by the female hormone oestrogen via oestrogen receptor (ER) alpha. ER-positive patients are commonly treated with adjuvant endocrine therapy, however, resistance is a common occurrence and aside from ER-status, no unequivocal predictive biomarkers are currently in clinical use. In this study, we aimed to identify constitutional genetic variants influencing breast cancer survival among ER-positive patients and specifically, among endocrine-treated patients. We conducted a meta-analysis of three genome-wide association studies comprising in total 3,136 patients with ER-positive breast cancer of which 2,751 had received adjuvant endocrine therapy. We identified a novel locus (rs992531 at 8p21.2) associated with reduced survival among the patients with ER-positive breast cancer (P = 3.77 × 10-8). Another locus (rs7701292 at 5q21.3) was associated with reduced survival among the endocrine-treated patients (P = 2.13 × 10-8). Interaction analysis indicated that the survival association of rs7701292 is treatment-specific and independent of conventional prognostic markers. In silico functional studies suggest plausible biological mechanisms for the observed survival associations and a functional link between the putative target genes of the rs992531 and rs7701292 (RHOBTB2 and RAB9P1, respectively). We further explored the genetic interaction between rs992531 and rs7701292 and found a significant, treatment-specific interactive effect on survival among ER-positive, endocrine-treated patients (hazard ratio = 6.97; 95% confidence interval, 1.79-27.08, Pinteraction= 0.036). This is the first study to identify a genetic interaction that specifically predicts treatment outcome. These findings may provide predictive biomarkers based on germ line genotype informing more personalized treatment selection.
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Affiliation(s)
- Sofia Khan
- Department of Obstetrics and Gynaecology, University of Helsinki and Helsinki University Hospital, Biomedicum, Helsinki, Finland
| | - Rainer Fagerholm
- Department of Obstetrics and Gynaecology, University of Helsinki and Helsinki University Hospital, Biomedicum, Helsinki, Finland
| | - Latha Kadalayil
- Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK
- Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, UK
| | - William Tapper
- Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Hospital and Genome Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Jianjun Liu
- Human Genetics, Genome Institute of Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital, Helsinki, Finland
- Department of Oncology, University of Örebro, Örebro, Sweden
| | - Diana Eccles
- Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK
| | - Heli Nevanlinna
- Department of Obstetrics and Gynaecology, University of Helsinki and Helsinki University Hospital, Biomedicum, Helsinki, Finland
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12
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Musolf AM, Simpson CL, de Andrade M, Mandal D, Gaba C, Yang P, Li Y, You M, Kupert EY, Anderson MW, Schwartz AG, Pinney SM, Amos CI, Bailey-Wilson JE. Parametric Linkage Analysis Identifies Five Novel Genome-Wide Significant Loci for Familial Lung Cancer. Hum Hered 2017; 82:64-74. [PMID: 28817824 DOI: 10.1159/000479028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 06/28/2017] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVE One of four American cancer patients dies of lung cancer. Environmental factors such as tobacco smoking are known to affect lung cancer risk. However, there is a genetic factor to lung cancer risk as well. Here, we perform parametric linkage analysis on family-based genotype data in an effort to find genetic loci linked to the disease. METHODS 197 individuals from families with a high-risk history of lung cancer were recruited and genotyped using an Illumina array. Parametric linkage analyses were performed using an affected-only phenotype model with an autosomal dominant inheritance using a disease allele frequency of 0.01. Three types of analyses were performed: single variant two-point, collapsed haplotype pattern variant two-point, and multipoint analysis. RESULTS Five novel genome-wide significant loci were identified at 18p11.23, 2p22.2, 14q13.1, 16p13, and 20q13.11. The families most informative for linkage were also determined. CONCLUSIONS The 5 novel signals are good candidate regions, containing genes that have been implicated as having somatic changes in lung cancer or other cancers (though not in germ line cells). Targeted sequencing on the significant loci is planned to determine the causal variants at these loci.
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Affiliation(s)
- Anthony M Musolf
- National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA
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13
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Detecting Susceptibility to Breast Cancer with SNP-SNP Interaction Using BPSOHS and Emotional Neural Networks. BIOMED RESEARCH INTERNATIONAL 2017; 2016:5164347. [PMID: 27294121 PMCID: PMC4879248 DOI: 10.1155/2016/5164347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/18/2016] [Accepted: 04/20/2016] [Indexed: 02/08/2023]
Abstract
Studies for the association between diseases and informative single nucleotide polymorphisms (SNPs) have received great attention. However, most of them just use the whole set of useful SNPs and fail to consider the SNP-SNP interactions, while these interactions have already been proven in biology experiments. In this paper, we use a binary particle swarm optimization with hierarchical structure (BPSOHS) algorithm to improve the effective of PSO for the identification of the SNP-SNP interactions. Furthermore, in order to use these SNP interactions in the susceptibility analysis, we propose an emotional neural network (ENN) to treat SNP interactions as emotional tendency. Different from the normal architecture, just as the emotional brain, this architecture provides a specific path to treat the emotional value, by which the SNP interactions can be considered more quickly and directly. The ENN helps us use the prior knowledge about the SNP interactions and other influence factors together. Finally, the experimental results prove that the proposed BPSOHS_ENN algorithm can detect the informative SNP-SNP interaction and predict the breast cancer risk with a much higher accuracy than existing methods.
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14
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Wu L, Yao L, Zhang H, Ouyang T, Li J, Wang T, Fan Z, Fan T, Lin B, Yin CC, Xie Y. A genome-wide association study identifies WT1 variant with better response to 5-fluorouracil, pirarubicin and cyclophosphamide neoadjuvant chemotherapy in breast cancer patients. Oncotarget 2016; 7:5042-52. [PMID: 26573232 PMCID: PMC4826264 DOI: 10.18632/oncotarget.5837] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/30/2015] [Indexed: 01/10/2023] Open
Abstract
Breast cancer is believed to result from the interplay of genetic and non-genetic risk factors, and individual genetic variation may influence the efficacy of chemotherapy. Here we conducted a genome-wide association study to identify single nucleotide polymorphisms (SNPs) associated with response to anthracycline- and taxane-based neoadjuvant chemotherapy in breast cancer patients. In the discovery stage, we divided 92 patients who received anthracycline-based neoadjuvant chemotherapy into 2 groups according to pathologic response and performed a genome-wide study using Affymetrix SNP6.0 genechip. Of 389,795 SNPs associated with pathologic complete response (pCR), we identified 2 SNPs, rs6044100 and rs1799937, that were significantly associated with pCR after neoadjuvant chemotherapy. In the validation stage, genotype analysis of samples from an independent cohort of 401 patients who received anthracycline-based neoadjuvant regimens and 467 patients who received taxane-based regimens was performed using sequencing analysis. We found that only SNP rs1799937, located in the WT1 gene, was associated with pCR after anthracycline-based neoadjuvant therapy (AA vs GG; odds ratio [OR], 2.81; 95% confidence interval [CI], 1.13-6.98; P < 0.05) but not after taxane-based neoadjuvant therapy (AA vs GG; OR, 0.85; 95% CI, 0.36-2.04; P = 0.72). These results suggest that WT1 may be a potential target of anthracycline-based neoadjuvant therapy for breast cancer.
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Affiliation(s)
- Lina Wu
- Central Laboratory, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Beijing Cancer Hospital & Institute, Peking University Cancer Hospital, Beijing, P. R. China
| | - Lu Yao
- Breast Center, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Beijing Cancer Hospital & Institute, Peking University Cancer Hospital, Beijing, P. R. China
| | - Hong Zhang
- Central Laboratory, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Beijing Cancer Hospital & Institute, Peking University Cancer Hospital, Beijing, P. R. China
| | - Tao Ouyang
- Breast Center, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Beijing Cancer Hospital & Institute, Peking University Cancer Hospital, Beijing, P. R. China
| | - Jinfeng Li
- Breast Center, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Beijing Cancer Hospital & Institute, Peking University Cancer Hospital, Beijing, P. R. China
| | - Tianfeng Wang
- Breast Center, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Beijing Cancer Hospital & Institute, Peking University Cancer Hospital, Beijing, P. R. China
| | - Zhaoqing Fan
- Breast Center, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Beijing Cancer Hospital & Institute, Peking University Cancer Hospital, Beijing, P. R. China
| | - Tie Fan
- Breast Center, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Beijing Cancer Hospital & Institute, Peking University Cancer Hospital, Beijing, P. R. China
| | - Benyao Lin
- Breast Center, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Beijing Cancer Hospital & Institute, Peking University Cancer Hospital, Beijing, P. R. China
| | - C Cameron Yin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuntao Xie
- Breast Center, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Beijing Cancer Hospital & Institute, Peking University Cancer Hospital, Beijing, P. R. China
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