Additional SNPs improve risk stratification of a polygenic hazard score for prostate cancer.


Journal

Prostate cancer and prostatic diseases
ISSN: 1476-5608
Titre abrégé: Prostate Cancer Prostatic Dis
Pays: England
ID NLM: 9815755

Informations de publication

Date de publication:
06 2021
Historique:
received: 15 09 2020
accepted: 04 12 2020
revised: 10 11 2020
pubmed: 10 1 2021
medline: 19 1 2022
entrez: 9 1 2021
Statut: ppublish

Résumé

Polygenic hazard scores (PHS) can identify individuals with increased risk of prostate cancer. We estimated the benefit of additional SNPs on performance of a previously validated PHS (PHS46). 180 SNPs, shown to be previously associated with prostate cancer, were used to develop a PHS model in men with European ancestry. A machine-learning approach, LASSO-regularized Cox regression, was used to select SNPs and to estimate their coefficients in the training set (75,596 men). Performance of the resulting model was evaluated in the testing/validation set (6,411 men) with two metrics: (1) hazard ratios (HRs) and (2) positive predictive value (PPV) of prostate-specific antigen (PSA) testing. HRs were estimated between individuals with PHS in the top 5% to those in the middle 40% (HR95/50), top 20% to bottom 20% (HR80/20), and bottom 20% to middle 40% (HR20/50). PPV was calculated for the top 20% (PPV80) and top 5% (PPV95) of PHS as the fraction of individuals with elevated PSA that were diagnosed with clinically significant prostate cancer on biopsy. 166 SNPs had non-zero coefficients in the Cox model (PHS166). All HR metrics showed significant improvements for PHS166 compared to PHS46: HR95/50 increased from 3.72 to 5.09, HR80/20 increased from 6.12 to 9.45, and HR20/50 decreased from 0.41 to 0.34. By contrast, no significant differences were observed in PPV of PSA testing for clinically significant prostate cancer. Incorporating 120 additional SNPs (PHS166 vs PHS46) significantly improved HRs for prostate cancer, while PPV of PSA testing remained the same.

Sections du résumé

BACKGROUND
Polygenic hazard scores (PHS) can identify individuals with increased risk of prostate cancer. We estimated the benefit of additional SNPs on performance of a previously validated PHS (PHS46).
MATERIALS AND METHOD
180 SNPs, shown to be previously associated with prostate cancer, were used to develop a PHS model in men with European ancestry. A machine-learning approach, LASSO-regularized Cox regression, was used to select SNPs and to estimate their coefficients in the training set (75,596 men). Performance of the resulting model was evaluated in the testing/validation set (6,411 men) with two metrics: (1) hazard ratios (HRs) and (2) positive predictive value (PPV) of prostate-specific antigen (PSA) testing. HRs were estimated between individuals with PHS in the top 5% to those in the middle 40% (HR95/50), top 20% to bottom 20% (HR80/20), and bottom 20% to middle 40% (HR20/50). PPV was calculated for the top 20% (PPV80) and top 5% (PPV95) of PHS as the fraction of individuals with elevated PSA that were diagnosed with clinically significant prostate cancer on biopsy.
RESULTS
166 SNPs had non-zero coefficients in the Cox model (PHS166). All HR metrics showed significant improvements for PHS166 compared to PHS46: HR95/50 increased from 3.72 to 5.09, HR80/20 increased from 6.12 to 9.45, and HR20/50 decreased from 0.41 to 0.34. By contrast, no significant differences were observed in PPV of PSA testing for clinically significant prostate cancer.
CONCLUSIONS
Incorporating 120 additional SNPs (PHS166 vs PHS46) significantly improved HRs for prostate cancer, while PPV of PSA testing remained the same.

Identifiants

pubmed: 33420416
doi: 10.1038/s41391-020-00311-2
pii: 10.1038/s41391-020-00311-2
pmc: PMC8157993
mid: NIHMS1700848
doi:

Substances chimiques

Biomarkers, Tumor 0

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

532-541

Subventions

Organisme : NCI NIH HHS
ID : U10 CA037429
Pays : United States
Organisme : NCI NIH HHS
ID : U01 CA182883
Pays : United States
Organisme : NCI NIH HHS
ID : UG1 CA189974
Pays : United States
Organisme : NIBIB NIH HHS
ID : K08 EB026503
Pays : United States

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Auteurs

Roshan A Karunamuni (RA)

Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, USA. rakarunamuni@health.ucsd.edu.

Minh-Phuong Huynh-Le (MP)

Radiation Oncology, George Washington University, Washington, DC, USA.

Chun C Fan (CC)

Center for Human Development, University of California San Diego, La Jolla, CA, USA.

Wesley Thompson (W)

Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, CA, USA.

Rosalind A Eeles (RA)

The Institute of Cancer Research, London, SM2 5NG, UK.
Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK.

Zsofia Kote-Jarai (Z)

The Institute of Cancer Research, London, SM2 5NG, UK.

Kenneth Muir (K)

Division of Population Health, Health Services Research and Primary Care, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK.

Artitaya Lophatananon (A)

Division of Population Health, Health Services Research and Primary Care, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.

Johanna Schleutker (J)

Institute of Biomedicine, University of Turku, Turku, Finland.
Department of Medical Genetics, Genomics, Laboratory Division, Turku University Hospital, PO Box 52, 20521, Turku, Finland.

Nora Pashayan (N)

Department of Applied Health Research, University College London, London, WC1E 7HB, UK.
Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge, CB1 8RN, UK.

Jyotsna Batra (J)

Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, 4059, Australia.
Translational Research Institute, Brisbane, QLD, 4102, Australia.

Henrik Grönberg (H)

Department of Medical Epidemiology and Biostatistics, Karolinska Institute, SE-171 77, Stockholm, Sweden.

Eleanor I Walsh (EI)

Bristol Medical School, Department of Population Health Sciences, University of Bristol, Bristol, UK.

Emma L Turner (EL)

Bristol Medical School, Department of Population Health Sciences, University of Bristol, Bristol, UK.

Athene Lane (A)

Bristol Medical School, Department of Population Health Sciences, University of Bristol, Bristol, UK.
MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.

Richard M Martin (RM)

Bristol Medical School, Department of Population Health Sciences, University of Bristol, Bristol, UK.
MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol NHS Foundation Trust and the University of Bristol, Bristol, UK.

David E Neal (DE)

Nuffield Department of Surgical Sciences, University of Oxford, Room 6603, Level 6, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK.
Department of Oncology, University of Cambridge, Box 279, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK.
Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.

Jenny L Donovan (JL)

School of Social and Community Medicine, University of Bristol, Bristol, UK.

Freddie C Hamdy (FC)

Nuffield Department of Surgical Sciences, University of Oxford, Room 6603, Level 6, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK.
Faculty of Medical Science, University of Oxford, John Radcliffe Hospital, Oxford, UK.

Børge G Nordestgaard (BG)

Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark.
Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, 2200, Copenhagen, Denmark.

Catherine M Tangen (CM)

SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

Robert J MacInnis (RJ)

Cancer Epidemiology Division, Cancer Council Victoria, 615 St Kilda Road, Melbourne, VIC, 3004, Australia.
Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Grattan Street, Parkville, VIC, 3010, Australia.

Alicja Wolk (A)

Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, SE-171 77, Stockholm, Sweden.
Department of Surgical Sciences, Uppsala University, 75185, Uppsala, Sweden.

Demetrius Albanes (D)

Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.

Christopher A Haiman (CA)

Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, 90015, USA.

Ruth C Travis (RC)

Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK.

Janet L Stanford (JL)

Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA.
Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, 98195, USA.

Lorelei A Mucci (LA)

Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA.

Catharine M L West (CML)

Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Radiotherapy Related Research, The Christie Hospital NHS Foundation Trust, Manchester, M13 9PL, UK.

Sune F Nielsen (SF)

Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark.
Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, 2200, Copenhagen, Denmark.

Adam S Kibel (AS)

Division of Urologic Surgery, Brigham and Womens Hospital, 75 Francis Street, Boston, MA, 02115, USA.

Fredrik Wiklund (F)

Department of Medical Epidemiology and Biostatistics, Karolinska Institute, SE-171 77, Stockholm, Sweden.

Olivier Cussenot (O)

Sorbonne Universite, GRC n°5, AP-HP, Tenon Hospital, 4 rue de la Chine, F-75020, Paris, France.
CeRePP, Tenon Hospital, F-75020, Paris, France.

Sonja I Berndt (SI)

Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.

Stella Koutros (S)

Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.

Karina Dalsgaard Sørensen (KD)

Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensen Boulevard 99, 8200, Aarhus, Denmark.
Department of Clinical Medicine, Aarhus University, DK-8200, Aarhus, Denmark.

Cezary Cybulski (C)

International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-115, Szczecin, Poland.

Eli Marie Grindedal (EM)

Department of Medical Genetics, Oslo University Hospital, 0424, Oslo, Norway.

Jong Y Park (JY)

Department of Cancer Epidemiology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA.

Sue A Ingles (SA)

Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, 90015, USA.

Christiane Maier (C)

Humangenetik Tuebingen, Paul-Ehrlich-Str 23, D-72076, Tuebingen, Germany.

Robert J Hamilton (RJ)

Dept. of Surgical Oncology, Princess Margaret Cancer Centre, Toronto, ON, M5G 2M9, Canada.
Dept. of Surgery (Urology), University of Toronto, Toronto, ON, Canada.

Barry S Rosenstein (BS)

Department of Radiation Oncology and Department of Genetics and Genomic Sciences, Box 1236, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-5674, USA.

Ana Vega (A)

Fundación Pública Galega Medicina Xenómica, Santiago de Compostela, 15706, Spain.
Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago De Compostela, 15706, Spain.
Centro de Investigación en Red de Enfermedades Raras (CIBERER), Santiago De Compostela, Spain.

Manolis Kogevinas (M)

ISGlobal, Barcelona, Spain.
IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain.
Universitat Pompeu Fabra (UPF), Barcelona, Spain.
CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.

Kathryn L Penney (KL)

Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, MA, 02184, USA.

Manuel R Teixeira (MR)

Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), 4200-072, Porto, Portugal.
Biomedical Sciences Institute (ICBAS), University of Porto, 4050-313, Porto, Portugal.
Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), 4200-072, Porto, Portugal.

Hermann Brenner (H)

Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany.
German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany.
Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany.

Esther M John (EM)

Departments of Epidemiology & Population Health and of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94304, USA.

Radka Kaneva (R)

Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia, 2 Zdrave Str., 1431, Sofia, Bulgaria.

Christopher J Logothetis (CJ)

The University of Texas M. D. Anderson Cancer Center, Department of Genitourinary Medical Oncology, 1515 Holcombe Blvd., Houston, TX, 77030, USA.

Susan L Neuhausen (SL)

Department of Population Sciences, Beckman Research Institute of the City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA.

Azad Razack (A)

Department of Surgery, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.

Lisa F Newcomb (LF)

Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA.
Department of Urology, University of Washington, 1959 NE Pacific Street, Box 356510, Seattle, WA, 98195, USA.

Marija Gamulin (M)

Division of Medical Oncology, Urogenital Unit, Department of Oncology, University Hospital Centre Zagreb, University of Zagreb, School of Medicine, 10000, Zagreb, Croatia.

Nawaid Usmani (N)

Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, AB, T6G 1Z2, Canada.
Division of Radiation Oncology, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB, T6G 1Z2, Canada.

Frank Claessens (F)

Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU, Leuven, BE-3000, Belgium.

Manuela Gago-Dominguez (M)

Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, Servicio Galego de Saúde, SERGAS, 15706, Santiago de Compostela, Spain.
University of California San Diego, Moores Cancer Center, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, 92093-0012, USA.

Paul A Townsend (PA)

Division of Cancer Sciences, Manchester Cancer Research Centre, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Research Centre, Health Innovation Manchester, Univeristy of Manchester, M13 9WL, Manchester, UK.

Monique J Roobol (MJ)

Department of Urology, Erasmus University Medical Center, 3015 CE, Rotterdam, The Netherlands.

Wei Zheng (W)

Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 800, Nashville, TN, 37232, USA.

Ian G Mills (IG)

Center for Cancer Research and Cell Biology, Queen's University of Belfast, Belfast, UK.

Ole A Andreassen (OA)

NORMENT, KG Jebsen Centre, Oslo University Hospital and University of Oslo, Oslo, Norway.

Anders M Dale (AM)

Department of Radiology, University of California San Diego, La Jolla, CA, USA.

Tyler M Seibert (TM)

Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, USA. tseibert@ucsd.edu.
Department of Radiology, University of California San Diego, La Jolla, CA, USA. tseibert@ucsd.edu.
Department of Bioengineering, University of California San Diego, La Jolla, CA, USA. tseibert@ucsd.edu.

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