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Miyahira AK, Kamran SC, Jamaspishvili T, Marshall CH, Maxwell KN, Parolia A, Zorko NA, Pienta KJ, Soule HR. Disrupting prostate cancer research: Challenge accepted; report from the 2023 Coffey-Holden Prostate Cancer Academy Meeting. Prostate 2024; 84:993-1015. [PMID: 38682886 DOI: 10.1002/pros.24721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024]
Abstract
INTRODUCTION The 2023 Coffey-Holden Prostate Cancer Academy (CHPCA) Meeting, themed "Disrupting Prostate Cancer Research: Challenge Accepted," was convened at the University of California, Los Angeles, Luskin Conference Center, in Los Angeles, CA, from June 22 to 25, 2023. METHODS The 2023 marked the 10th Annual CHPCA Meeting, a discussion-oriented scientific think-tank conference convened annually by the Prostate Cancer Foundation, which centers on innovative and emerging research topics deemed pivotal for advancing critical unmet needs in prostate cancer research and clinical care. The 2023 CHPCA Meeting was attended by 81 academic investigators and included 40 talks across 8 sessions. RESULTS The central topic areas covered at the meeting included: targeting transcription factor neo-enhancesomes in cancer, AR as a pro-differentiation and oncogenic transcription factor, why few are cured with androgen deprivation therapy and how to change dogma to cure metastatic prostate cancer without castration, reducing prostate cancer morbidity and mortality with genetics, opportunities for radiation to enhance therapeutic benefit in oligometastatic prostate cancer, novel immunotherapeutic approaches, and the new era of artificial intelligence-driven precision medicine. DISCUSSION This article provides an overview of the scientific presentations delivered at the 2023 CHPCA Meeting, such that this knowledge can help in facilitating the advancement of prostate cancer research worldwide.
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Affiliation(s)
- Andrea K Miyahira
- Science Department, Prostate Cancer Foundation, Santa Monica, California, USA
| | - Sophia C Kamran
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tamara Jamaspishvili
- Department of Pathology and Laboratory Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Catherine H Marshall
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kara N Maxwell
- Department of Medicine-Hematology/Oncology and Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Medicine Service, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, Pennsylvania, USA
| | - Abhijit Parolia
- Department of Pathology, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Nicholas A Zorko
- Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
- University of Minnesota Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kenneth J Pienta
- The James Buchanan Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Howard R Soule
- Science Department, Prostate Cancer Foundation, Santa Monica, California, USA
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Plym A, Zhang Y, Stopsack KH, Ugalde-Morales E, Seibert TM, Conti DV, Haiman CA, Baras A, Stocks T, Drake I, Penney KL, Giovannucci E, Kibel AS, Wiklund F, Mucci LA. Early Prostate Cancer Deaths Among Men With Higher vs Lower Genetic Risk. JAMA Netw Open 2024; 7:e2420034. [PMID: 38958976 PMCID: PMC11222990 DOI: 10.1001/jamanetworkopen.2024.20034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/23/2024] [Indexed: 07/04/2024] Open
Abstract
Importance Prostate cancer, a leading cause of cancer death among men, urgently requires new prevention strategies, which may involve targeting men with an underlying genetic susceptibility. Objective To explore differences in risk of early prostate cancer death among men with higher vs lower genetic risk to inform prevention efforts. Design, Setting, and Participants This cohort study used a combined analysis of genotyped men without prostate cancer at inclusion and with lifestyle data in 2 prospective cohort studies in Sweden and the US, the Malmö Diet and Cancer Study (MDCS) and the Health Professionals Follow-Up Study (HPFS), followed up from 1991 to 2019. Data were analyzed between April 2023 and April 2024. Exposures Men were categorized according to modifiable lifestyle behaviors and genetic risk. A polygenic risk score above the median or a family history of cancer defined men at higher genetic risk (67% of the study population); the remaining men were categorized as being at lower genetic risk. Main Outcomes and Measures Prostate cancer death analyzed using time-to-event analysis estimating hazard ratios (HR), absolute risks, and preventable deaths by age. Results Among the 19 607 men included for analysis, the median (IQR) age at inclusion was 59.0 (53.0-64.7) years (MDCS) and 65.1 (58.0-71.8) years (HPFS). During follow-up, 107 early (by age 75 years) and 337 late (after age 75 years) prostate cancer deaths were observed. Compared with men at lower genetic risk, men at higher genetic risk had increased rates of both early (HR, 3.26; 95% CI, 1.82-5.84) and late (HR, 2.26; 95% CI, 1.70-3.01) prostate cancer death, and higher lifetime risks of prostate cancer death (3.1% vs 1.3% [MDCS] and 2.3% vs 0.6% [HPFS]). Men at higher genetic risk accounted for 94 of 107 early prostate cancer deaths (88%), of which 36% (95% CI, 12%-60%) were estimated to be preventable through adherence to behaviors associated with a healthy lifestyle (not smoking, healthy weight, high physical activity, and a healthy diet). Conclusions and Relevance In this 20-year follow-up study, men with a genetic predisposition accounted for the vast majority of early prostate cancer deaths, of which one-third were estimated to be preventable. This suggests that men at increased genetic risk should be targeted in prostate cancer prevention strategies.
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Affiliation(s)
- Anna Plym
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
- Department of Urology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yiwen Zhang
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Konrad H. Stopsack
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Emilio Ugalde-Morales
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Tyler M. Seibert
- Department of Radiation Medicine and Applied Sciences, Department of Radiology, and Department of Bioengineering, University of California San Diego, La Jolla
| | - David V. Conti
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles
| | - Christopher A. Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, New York
| | - Tanja Stocks
- Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Isabel Drake
- Department of Clinical Sciences in Malmö, Lund University, Malmö, Sweden
- Skåne University Hospital, Malmö, Sweden
| | - Kathryn L. Penney
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Edward Giovannucci
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Adam S. Kibel
- Department of Urology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Lorelei A. Mucci
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
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Hayes V, Gong T, Jiang J, Bornman R, Gheybi K, Stricker P, Weischenfeldt J, Mutambirwa S. Rare pathogenic structural variants show potential to enhance prostate cancer germline testing for African men. RESEARCH SQUARE 2024:rs.3.rs-4531885. [PMID: 38947031 PMCID: PMC11213160 DOI: 10.21203/rs.3.rs-4531885/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Prostate cancer (PCa) is highly heritable, with men of African ancestry at greatest risk and associated lethality. Lack of representation in genomic data means germline testing guidelines exclude for African men. Established that structural variations (SVs) are major contributors to human disease and prostate tumourigenesis, their role is under-appreciated in familial and therapeutic testing. Utilising a clinico-methodologically matched African (n = 113) versus European (n = 57) deep-sequenced PCa resource, we interrogated 42,966 high-quality germline SVs using a best-fit pathogenicity prediction workflow. We identified 15 potentially pathogenic SVs representing 12.4% African and 7.0% European patients, of which 72% and 86% met germline testing standard-of-care recommendations, respectively. Notable African-specific loss-of-function gene candidates include DNA damage repair MLH1 and BARD1 and tumour suppressors FOXP1, WASF1 and RB1. Representing only a fraction of the vast African diaspora, this study raises considerations with respect to the contribution of kilo-to-mega-base rare variants to PCa pathogenicity and African associated disparity.
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Affiliation(s)
| | | | - Jue Jiang
- Garvan Institute of Medical Research
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Pagadala MS, Lui A, Lynch J, Karunamuni R, Lee KM, Plym A, Rose BS, Carter H, Kibel AS, DuVall SL, Vassy J, Gaziano JM, Panizzon MS, Hauger RL, Seibert TM. Healthy lifestyle and prostate cancer risk in the Million Veteran Program. Cancer 2024. [PMID: 38865417 DOI: 10.1002/cncr.35434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/24/2024] [Accepted: 05/21/2024] [Indexed: 06/14/2024]
Abstract
BACKGROUND This study aims to assess the impact of healthy lifestyle on prostate cancer (PCa) risk in a diverse population. METHODS Data for 281,923 men from the Million Veteran Program (MVP), a nationwide, health system-based cohort study, were analyzed. Self-reported information at enrollment included smoking status, exercise, diet, family history of PCa, and race/ethnicity. Body mass index (BMI) was obtained from clinical records. Genetic risk was assessed via a validated polygenic score. Cox proportional hazards models were used to assess associations with PCa outcomes. RESULTS After accounting for ancestry, family history, and genetic risk, smoking was associated with an increased risk of metastatic PCa (hazard ratio [HR], 1.83; 95% confidence interval [CI], 1.64-2.02; p < 10-16) and fatal PCa (HR, 2.73; 95% CI, 2.36-3.25; p < 10-16). Exercise was associated with a reduced risk of fatal PCa (HR, 0.86; 95% CI, 0.76-0.98; p = .03). Higher BMI was associated with a slightly reduced risk of fatal PCa, and diet score was not independently associated with any end point. Association with exercise was strongest among those who had nonmetastatic PCa at MVP enrollment. Absolute reductions in the risk of fatal PCa via lifestyle factors were greatest among men of African ancestry (1.7% for nonsmokers vs. 6.1% for smokers) or high genetic risk (1.4% for nonsmokers vs. 4.3% for smokers). CONCLUSIONS Healthy lifestyle is minimally related to the overall risk of developing PCa but is associated with a substantially reduced risk of dying from PCa. In multivariable analyses, both exercise and not smoking remain independently associated with reduced metastatic and fatal PCa.
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Affiliation(s)
- Meghana S Pagadala
- Research Service, Veterans Affairs (VA) San Diego Healthcare System, San Diego, California, USA
- Medical Scientist Training Program, University of California San Diego, La Jolla, California, USA
- Biomedical Science Program, University of California San Diego, La Jolla, California, USA
| | - Asona Lui
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, California, USA
- Cancer Center, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Julie Lynch
- VA Informatics and Computing Infrastructure, VA Salt Lake City Healthcare System, Salt Lake City, Utah, USA
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Roshan Karunamuni
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, California, USA
| | - Kyung Min Lee
- VA Informatics and Computing Infrastructure, VA Salt Lake City Healthcare System, Salt Lake City, Utah, USA
| | - Anna Plym
- Department of Urology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Brent S Rose
- Research Service, Veterans Affairs (VA) San Diego Healthcare System, San Diego, California, USA
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, California, USA
| | - Hannah Carter
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Adam S Kibel
- Department of Urology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Scott L DuVall
- VA Informatics and Computing Infrastructure, VA Salt Lake City Healthcare System, Salt Lake City, Utah, USA
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Jason Vassy
- VA Boston Healthcare System, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - J Michael Gaziano
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Matthew S Panizzon
- Research Service, Veterans Affairs (VA) San Diego Healthcare System, San Diego, California, USA
- Center for Behavioral Genetics of Aging, University of California San Diego, La Jolla, California, USA
| | - Richard L Hauger
- Research Service, Veterans Affairs (VA) San Diego Healthcare System, San Diego, California, USA
- Center for Behavioral Genetics of Aging, University of California San Diego, La Jolla, California, USA
- Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, San Diego, California, USA
| | - Tyler M Seibert
- Research Service, Veterans Affairs (VA) San Diego Healthcare System, San Diego, California, USA
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, California, USA
- Department of Radiology, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
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Kingdom R, Beaumont RN, Wood AR, Weedon MN, Wright CF. Genetic modifiers of rare variants in monogenic developmental disorder loci. Nat Genet 2024; 56:861-868. [PMID: 38637616 PMCID: PMC11096126 DOI: 10.1038/s41588-024-01710-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/06/2024] [Indexed: 04/20/2024]
Abstract
Rare damaging variants in a large number of genes are known to cause monogenic developmental disorders (DDs) and have also been shown to cause milder subclinical phenotypes in population cohorts. Here, we show that carrying multiple (2-5) rare damaging variants across 599 dominant DD genes has an additive adverse effect on numerous cognitive and socioeconomic traits in UK Biobank, which can be partially counterbalanced by a higher educational attainment polygenic score (EA-PGS). Phenotypic deviators from expected EA-PGS could be partly explained by the enrichment or depletion of rare DD variants. Among carriers of rare DD variants, those with a DD-related clinical diagnosis had a substantially lower EA-PGS and more severe phenotype than those without a clinical diagnosis. Our results suggest that the overall burden of both rare and common variants can modify the expressivity of a phenotype, which may then influence whether an individual reaches the threshold for clinical disease.
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Affiliation(s)
- Rebecca Kingdom
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Robin N Beaumont
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Andrew R Wood
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Michael N Weedon
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Caroline F Wright
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK.
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Saunders EJ, Dadaev T, Brook MN, Wakerell S, Govindasami K, Rageevakumar R, Hussain N, Osborne A, Keating D, Lophatananon A, Muir KR, Darst BF, Conti DV, Haiman CA, Antoniou AC, Eeles RA, Kote-Jarai Z. Identification of Genes with Rare Loss of Function Variants Associated with Aggressive Prostate Cancer and Survival. Eur Urol Oncol 2024; 7:248-257. [PMID: 38458890 DOI: 10.1016/j.euo.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/10/2024] [Accepted: 02/09/2024] [Indexed: 03/10/2024]
Abstract
BACKGROUND Prostate cancer (PrCa) is a substantial cause of mortality among men globally. Rare germline mutations in BRCA2 have been validated robustly as increasing risk of aggressive forms with a poorer prognosis; however, evidence remains less definitive for other genes. OBJECTIVE To detect genes associated with PrCa aggressiveness, through a pooled analysis of rare variant sequencing data from six previously reported studies in the UK Genetic Prostate Cancer Study (UKGPCS). DESIGN, SETTING, AND PARTICIPANTS We accumulated a cohort of 6805 PrCa cases, in which a set of ten candidate genes had been sequenced in all samples. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS We examined the association between rare putative loss of function (pLOF) variants in each gene and aggressive classification (defined as any of death from PrCa, metastatic disease, stage T4, or both stage T3 and Gleason score ≥8). Secondary analyses examined staging phenotypes individually. Cox proportional hazards modelling and Kaplan-Meier survival analyses were used to further examine the relationship between mutation status and survival. RESULTS AND LIMITATIONS We observed associations between PrCa aggressiveness and pLOF mutations in ATM, BRCA2, MSH2, and NBN (odds ratio = 2.67-18.9). These four genes and MLH1 were additionally associated with one or more secondary analysis phenotype. Carriers of germline mutations in these genes experienced shorter PrCa-specific survival (hazard ratio = 2.15, 95% confidence interval 1.79-2.59, p = 4 × 10-16) than noncarriers. CONCLUSIONS This study provides further support that rare pLOF variants in specific genes are likely to increase aggressive PrCa risk and may help define the panel of informative genes for screening and treatment considerations. PATIENT SUMMARY By combining data from several previous studies, we have been able to enhance knowledge regarding genes in which inherited mutations would be expected to increase the risk of more aggressive PrCa. This may, in the future, aid in the identification of men at an elevated risk of dying from PrCa.
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Affiliation(s)
- Edward J Saunders
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Tokhir Dadaev
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Mark N Brook
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Sarah Wakerell
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Koveela Govindasami
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Reshma Rageevakumar
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Nafisa Hussain
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Andrea Osborne
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Diana Keating
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | | | - Kenneth R Muir
- Division of Population Health, University of Manchester, Manchester, UK
| | - Burcu F Darst
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA; Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David V Conti
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Christopher A Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Antonis C Antoniou
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK; The Royal Marsden NHS Foundation Trust, London, UK
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.
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7
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He XY, Wu BS, Yang L, Guo Y, Deng YT, Li ZY, Fei CJ, Liu WS, Ge YJ, Kang J, Feng J, Cheng W, Dong Q, Yu JT. Genetic associations of protein-coding variants in venous thromboembolism. Nat Commun 2024; 15:2819. [PMID: 38561338 PMCID: PMC10984941 DOI: 10.1038/s41467-024-47178-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
Previous genetic studies of venous thromboembolism (VTE) have been largely limited to common variants, leaving the genetic determinants relatively incomplete. We performed an exome-wide association study of VTE among 14,723 cases and 334,315 controls. Fourteen known and four novel genes (SRSF6, PHPT1, CGN, and MAP3K2) were identified through protein-coding variants, with broad replication in the FinnGen cohort. Most genes we discovered exhibited the potential to predict future VTE events in longitudinal analysis. Notably, we provide evidence for the additive contribution of rare coding variants to known genome-wide polygenic risk in shaping VTE risk. The identified genes were enriched in pathways affecting coagulation and platelet activation, along with liver-specific expression. The pleiotropic effects of these genes indicated the potential involvement of coagulation factors, blood cell traits, liver function, and immunometabolic processes in VTE pathogenesis. In conclusion, our study unveils the valuable contribution of protein-coding variants in VTE etiology and sheds new light on its risk stratification.
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Affiliation(s)
- Xiao-Yu He
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bang-Sheng Wu
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Liu Yang
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu Guo
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yue-Ting Deng
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ze-Yu Li
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Chen-Jie Fei
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei-Shi Liu
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi-Jun Ge
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jujiao Kang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Jianfeng Feng
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China
- Department of Computer Science, University of Warwick, Coventry, UK
| | - Wei Cheng
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China.
- Department of Computer Science, University of Warwick, Coventry, UK.
| | - Qiang Dong
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Jin-Tai Yu
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.
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Bhérer C, Eveleigh R, Trajanoska K, St-Cyr J, Paccard A, Nadukkalam Ravindran P, Caron E, Bader Asbah N, McClelland P, Wei C, Baumgartner I, Schindewolf M, Döring Y, Perley D, Lefebvre F, Lepage P, Bourgey M, Bourque G, Ragoussis J, Mooser V, Taliun D. A cost-effective sequencing method for genetic studies combining high-depth whole exome and low-depth whole genome. NPJ Genom Med 2024; 9:8. [PMID: 38326393 PMCID: PMC10850497 DOI: 10.1038/s41525-024-00390-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/07/2023] [Indexed: 02/09/2024] Open
Abstract
Whole genome sequencing (WGS) at high-depth (30X) allows the accurate discovery of variants in the coding and non-coding DNA regions and helps elucidate the genetic underpinnings of human health and diseases. Yet, due to the prohibitive cost of high-depth WGS, most large-scale genetic association studies use genotyping arrays or high-depth whole exome sequencing (WES). Here we propose a cost-effective method which we call "Whole Exome Genome Sequencing" (WEGS), that combines low-depth WGS and high-depth WES with up to 8 samples pooled and sequenced simultaneously (multiplexed). We experimentally assess the performance of WEGS with four different depth of coverage and sample multiplexing configurations. We show that the optimal WEGS configurations are 1.7-2.0 times cheaper than standard WES (no-plexing), 1.8-2.1 times cheaper than high-depth WGS, reach similar recall and precision rates in detecting coding variants as WES, and capture more population-specific variants in the rest of the genome that are difficult to recover when using genotype imputation methods. We apply WEGS to 862 patients with peripheral artery disease and show that it directly assesses more known disease-associated variants than a typical genotyping array and thousands of non-imputable variants per disease-associated locus.
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Affiliation(s)
- Claude Bhérer
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, Québec, Canada
| | - Robert Eveleigh
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
| | - Katerina Trajanoska
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, Québec, Canada
| | - Janick St-Cyr
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
| | - Antoine Paccard
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
| | - Praveen Nadukkalam Ravindran
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, Québec, Canada
| | - Elizabeth Caron
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
| | - Nimara Bader Asbah
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
| | - Peyton McClelland
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, Québec, Canada
| | - Clare Wei
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, Québec, Canada
| | - Iris Baumgartner
- Division of Angiology, Swiss Cardiovascular Center, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Marc Schindewolf
- Division of Angiology, Swiss Cardiovascular Center, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Yvonne Döring
- Division of Angiology, Swiss Cardiovascular Center, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians University Munich, Pettenkoferstr 9, 80336, Munich, Germany
| | - Danielle Perley
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
| | - François Lefebvre
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
| | - Pierre Lepage
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
| | | | - Guillaume Bourque
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
| | - Vincent Mooser
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, Québec, Canada
| | - Daniel Taliun
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada.
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada.
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, Québec, Canada.
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9
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Hughley RW, Matejcic M, Song Z, Sheng X, Wan P, Xia L, Hart SN, Hu C, Yadav S, Lubmawa A, Kiddu V, Asiimwe F, Amanya C, Mutema G, Job K, Ssebakumba MK, Ingles SA, Hamilton AS, Couch FJ, Watya S, Conti DV, Darst BF, Haiman CA. Polygenic Risk Score Modifies Prostate Cancer Risk of Pathogenic Variants in Men of African Ancestry. CANCER RESEARCH COMMUNICATIONS 2023; 3:2544-2550. [PMID: 38014910 PMCID: PMC10720390 DOI: 10.1158/2767-9764.crc-23-0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/17/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023]
Abstract
Prostate cancer risk is influenced by rare and common germline variants. We examined the aggregate association of rare germline pathogenic/likely pathogenic/deleterious (P/LP/D) variants in ATM, BRCA2, PALB2, and NBN with a polygenic risk score (PRS) on prostate cancer risk among 1,796 prostate cancer cases (222 metastatic) and 1,424 controls of African ancestry. Relative to P/LP/D non-carriers at average genetic risk (33%-66% of PRS), men with low (0%-33%) and high (66%-100%) PRS had Odds Ratios (ORs) for overall prostate cancer of 2.08 [95% confidence interval (CI) = 0.58-7.49] and 18.06 (95% CI = 4.24-76.84) among P/LP/D carriers and 0.57 (95% CI = 0.46-0.71) and 3.02 (95% CI = 2.53-3.60) among non-carriers, respectively. The OR for metastatic prostate cancer was 2.73 (95% CI = 0.24-30.54) and 28.99 (95% CI = 4.39-191.43) among P/LP/D carriers and 0.54 (95% CI = 0.31-0.95) and 3.22 (95% CI = 2.20-4.73) among non-carriers, for men with low and high PRS, respectively. Lifetime absolute risks of overall prostate cancer increased with PRS (low to high) from 9.8% to 51.5% in P/LP/D carriers and 5.5% to 23.9% in non-carriers. Lifetime absolute risks of metastatic prostate cancer increased with PRS from 1.9% to 18.1% in P/LP/D carriers and 0.3% to 2.2% in non-carriers These findings suggest that assessment of prostate cancer risk for rare variant carriers should include PRS status. SIGNIFICANCE These findings highlight the importance of considering rare and common variants to comprehensively assess prostate cancer risk in men of African ancestry.
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Affiliation(s)
- Raymond W. Hughley
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Marco Matejcic
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ziwei Song
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Xin Sheng
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Peggy Wan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Lucy Xia
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Steven N. Hart
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Chunling Hu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | | | | | | | - Colline Amanya
- Makerere University College of Health Sciences, Kampala, Uganda
| | | | | | | | - Sue A. Ingles
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ann S. Hamilton
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Fergus J. Couch
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Stephen Watya
- Uro Care, Kampala, Uganda
- Makerere University College of Health Sciences, Kampala, Uganda
| | - David V. Conti
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Burcu F. Darst
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
- Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Christopher A. Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
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10
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Hurwitz LM, Beane Freeman LE, Andreotti G, Hofmann JN, Parks CG, Sandler DP, Lubin JH, Liu J, Jones K, Berndt SI, Koutros S. Joint associations between established genetic susceptibility loci, pesticide exposures, and risk of prostate cancer. ENVIRONMENTAL RESEARCH 2023; 237:117063. [PMID: 37659638 PMCID: PMC10591852 DOI: 10.1016/j.envres.2023.117063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/20/2023] [Accepted: 08/31/2023] [Indexed: 09/04/2023]
Abstract
More than 200 genetic variants have been independently associated with prostate cancer risk. Studies among farmers have also observed increased prostate cancer risk associated with exposure to specific organophosphate (fonofos, terbufos, malathion, dimethoate) and organochlorine (aldrin, chlordane) insecticides. We examined the joint associations between these pesticides, established prostate cancer loci, and prostate cancer risk among 1,162 cases (588 aggressive) and 2,206 frequency-matched controls nested in the Agricultural Health Study cohort. History of lifetime pesticide use was combined with a polygenic risk score (PRS) generated using 256 established prostate cancer risk variants. Logistic regression models estimated the joint associations of the pesticides, the PRS, and the 256 individual genetic variants with risk of total and aggressive prostate cancer. Likelihood ratio tests assessed multiplicative interaction. We observed interaction between ever use of fonofos and the PRS in relation to total and aggressive prostate cancer risk. Compared to the reference group (never use, PRS < median), men with ever use of fonofos and PRS > median had elevated risks of total (OR 1.35 [1.06-1.73], p-interaction = 0.03) and aggressive (OR 1.49 [1.09-2.04], p-interaction = 0.19) prostate cancer. There was also suggestion of interaction between pesticides and individual genetic variants occurring in regions associated with DNA damage response (CDH3, EMSY genes) and with variants related to altered androgen receptor-driven transcriptional programs critical for prostate cancer. Our study provides evidence that men with greater genetic susceptibility to prostate cancer may be at higher risk if they are also exposed to pesticides and suggests potential mechanisms by which pesticides may increase prostate cancer risk.
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Affiliation(s)
- Lauren M Hurwitz
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD, USA.
| | - Laura E Beane Freeman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD, USA
| | - Gabriella Andreotti
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD, USA
| | - Jonathan N Hofmann
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD, USA
| | - Christine G Parks
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Jay H Lubin
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD, USA
| | - Jia Liu
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD, USA; Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD, USA; Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sonja I Berndt
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD, USA
| | - Stella Koutros
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD, USA
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11
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Hanson H, Astiazaran-Symonds E, Amendola LM, Balmaña J, Foulkes WD, James P, Klugman S, Ngeow J, Schmutzler R, Voian N, Wick MJ, Pal T, Tischkowitz M, Stewart DR. Management of individuals with germline pathogenic/likely pathogenic variants in CHEK2: A clinical practice resource of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100870. [PMID: 37490054 PMCID: PMC10623578 DOI: 10.1016/j.gim.2023.100870] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 07/26/2023] Open
Abstract
PURPOSE Although the role of CHEK2 germline pathogenic variants in cancer predisposition is well known, resources for managing CHEK2 heterozygotes in clinical practice are limited. METHODS An international workgroup developed guidance on clinical management of CHEK2 heterozygotes informed by peer-reviewed publications from PubMed. RESULTS Although CHEK2 is considered a moderate penetrance gene, cancer risks may be considered as a continuous variable, which are influenced by family history and other modifiers. Consequently, early cancer detection and prevention for CHEK2 heterozygotes should be guided by personalized risk estimates. Such estimates may result in both downgrading lifetime breast cancer risks to those similar to the general population or upgrading lifetime risk to a level at which CHEK2 heterozygotes are offered high-risk breast surveillance according to country-specific guidelines. Risk-reducing mastectomy should be guided by personalized risk estimates and shared decision making. Colorectal and prostate cancer surveillance should be considered based on assessment of family history. For CHEK2 heterozygotes who develop cancer, no specific targeted medical treatment is recommended at this time. CONCLUSION Systematic prospective data collection is needed to establish the spectrum of CHEK2-associated cancer risks and to determine yet-unanswered questions, such as the outcomes of surveillance, response to cancer treatment, and survival after cancer diagnosis.
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Affiliation(s)
- Helen Hanson
- Southwest Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Esteban Astiazaran-Symonds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD; Department of Medicine, College of Medicine-Tucson, University of Arizona, Tucson, AZ
| | | | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain; Medical Oncology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Hospital Campus, Barcelona, Spain
| | - William D Foulkes
- Departments of Human Genetics, Oncology and Medicine, McGill University, Montréal, QC, Canada
| | - Paul James
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia; Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Susan Klugman
- Division of Reproductive & Medical Genetics, Department of Obstetrics & Gynecology and Women's Health, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Joanne Ngeow
- Genomic Medicine, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Rita Schmutzler
- Center of Integrated Oncology (CIO), University of Cologne, Cologne, Germany; Center for Hereditary Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
| | - Nicoleta Voian
- Providence Genetic Risk Clinic, Providence Cancer Institute, Portland, OR
| | - Myra J Wick
- Departments of Obstetrics and Gynecology and Clinical Genomics, Mayo Clinic, Rochester, MN
| | - Tuya Pal
- Department of Medicine, Vanderbilt University Medical Center/Vanderbilt-Ingram Cancer Center, Nashville, TN
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
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12
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Blinka S, Mishra R, Hsieh AC. ELAC2 is a functional prostate cancer risk allele. Trends Mol Med 2023; 29:586-588. [PMID: 37353407 PMCID: PMC10527048 DOI: 10.1016/j.molmed.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 06/25/2023]
Abstract
Stentenbach and colleagues have unveiled a functional role of a human germline mutation found in the ribonuclease (RNase) Z enzyme, ELAC2, in prostate cancer. Here, we discuss the importance of these findings in enhancing our understanding of how risk variants enable prostate cancer progression and the post-transcriptional mechanisms underlying oncogenesis.
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Affiliation(s)
- Steven Blinka
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Mishra
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Andrew C Hsieh
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; School of Medicine, University of Washington, Seattle, WA 98195, USA.
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13
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Ruan X, Huang D, Huang J, Tsu JHL, Na R. Genetic risk assessment of lethal prostate cancer using polygenic risk score and hereditary cancer susceptibility genes. J Transl Med 2023; 21:446. [PMID: 37415201 PMCID: PMC10327136 DOI: 10.1186/s12967-023-04316-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND The genetic risk of aggressive prostate cancer (PCa) is hard to be assessed due to the lack of aggressiveness-related single-nucleotide polymorphisms (SNPs). Prostate volume (PV) is a potential well-established risk factor for aggressive PCa, we hypothesize that polygenic risk score (PRS) based on benign prostate hyperplasia (BPH) or PV-related SNPs may also predict the risk of aggressive PCa or PCa death. METHODS We evaluated a PRS using 21 BPH/PV-associated SNPs, two established PCa risk-related PRS and 10 guideline-recommended hereditary cancer risk genes in the population-based UK Biobank cohort (N = 209,502). RESULTS The BPH/PV PRS was significantly inversely associated with the incidence of lethal PCa as well as the natural progress in PCa patients (hazard ratio, HR = 0.92, 95% confidence interval [CI]: 0.87-0.98, P = 0.02; HR = 0.92, 95% CI 0.86-0.98, P = 0.01). Compared with men at the top 25th PRS, PCa patients with bottom 25th PRS would have a 1.41-fold (HR, 95% CI 1.16-1.69, P = 0.001) increased PCa fatal risk and shorter survival time at 0.37 yr (95% CI 0.14-0.61, P = 0.002). In addition, patients with BRCA2 or PALB2 pathogenic mutations would also have a high risk of PCa death (HR = 3.90, 95% CI 2.34-6.51, P = 1.79 × 10-7; HR = 4.29, 95% CI 1.36-13.50, P = 0.01, respectively). However, no interactive but independent effects were detected between this PRS and pathogenic mutations. CONCLUSIONS Our findings provide a new measurement of PCa patients' natural disease outcomes via genetic risk ways.
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Affiliation(s)
- Xiaohao Ruan
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Da Huang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jingyi Huang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - James Hok-Leung Tsu
- Division of Urology, Department of Surgery, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - Rong Na
- Division of Urology, Department of Surgery, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China.
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14
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Lui AJ, Pagadala MS, Zhong AY, Lynch J, Karunamuni R, Lee KM, Plym A, Rose BS, Carter H, Kibel AS, DuVall SL, Gaziano JM, Panizzon MS, Hauger RL, Seibert TM. Agent Orange exposure and prostate cancer risk in the Million Veteran Program. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.14.23291413. [PMID: 37398205 PMCID: PMC10312838 DOI: 10.1101/2023.06.14.23291413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Purpose Exposure to Agent Orange, a known carcinogen, might increase risk of prostate cancer (PCa). We sought to investigate the association of Agent Orange exposure and PCa risk when accounting for race/ethnicity, family history, and genetic risk in a diverse population of US Vietnam War veterans. Methods & Materials This study utilized the Million Veteran Program (MVP), a national, population-based cohort study of United States military veterans conducted 2011-2021 with 590,750 male participants available for analysis. Agent Orange exposure was obtained using records from the Department of Veterans Affairs (VA) using the US government definition of Agent Orange exposure: active service in Vietnam while Agent Orange was in use. Only veterans who were on active duty (anywhere in the world) during the Vietnam War were included in this analysis (211,180 participants). Genetic risk was assessed via a previously validated polygenic hazard score calculated from genotype data. Age at diagnosis of any PCa, diagnosis of metastatic PCa, and death from PCa were assessed via Cox proportional hazards models. Results Exposure to Agent Orange was associated with increased PCa diagnosis (HR 1.04, 95% CI 1.01-1.06, p=0.003), primarily among Non-Hispanic White men (HR 1.09, 95% CI 1.06- 1.12, p<0.001). When accounting for race/ethnicity and family history, Agent Orange exposure remained an independent risk factor for PCa diagnosis (HR 1.06, 95% CI 1.04-1.09, p<0.05). Univariable associations of Agent Orange exposure with PCa metastasis (HR 1.08, 95% CI 0.99-1.17) and PCa death (HR 1.02, 95% CI 0.84-1.22) did not reach significance on multivariable analysis. Similar results were found when accounting for polygenic hazard score. Conclusions Among US Vietnam War veterans, Agent Orange exposure is an independent risk factor for PCa diagnosis, though associations with PCa metastasis or death are unclear when accounting for race/ethnicity, family history, and/or polygenic risk.
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15
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Herberts C, Wyatt AW, Nguyen PL, Cheng HH. Genetic and Genomic Testing for Prostate Cancer: Beyond DNA Repair. Am Soc Clin Oncol Educ Book 2023; 43:e390384. [PMID: 37207301 DOI: 10.1200/edbk_390384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Significant progress has been made in genetic and genomic testing for prostate cancer across the disease spectrum. Molecular profiling is increasingly relevant for routine clinical management, fueled in part by advancements in testing technology and integration of biomarkers into clinical trials. In metastatic prostate cancer, defects in DNA damage response genes are now established predictors of benefit to US Food and Drug Administration-approved poly (ADP-ribose) polymerase inhibitors and immune checkpoint inhibitors, and trials are actively investigating these and other targeted treatment strategies in earlier disease states. Excitingly, opportunities for molecularly informed management beyond DNA damage response genes are also maturing. Germline genetic variants (eg, BRCA2 or MSH2/6) and polygenic germline risk scores are being investigated to inform cancer screening and active surveillance in at-risk carriers. RNA expression tests have recently gained traction in localized prostate cancer, enabling patient risk stratification and tailored treatment intensification via radiotherapy and/or androgen deprivation therapy for localized or salvage treatment. Finally, emerging minimally invasive circulating tumor DNA technology promises to enhance biomarker testing in advanced disease pending additional methodological and clinical validation. Collectively, genetic and genomic tests are rapidly becoming indispensable tools for informing the optimal clinical management of prostate cancer.
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Affiliation(s)
- Cameron Herberts
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Paul L Nguyen
- Harvard Medical School, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA
| | - Heather H Cheng
- University of Washington, Fred Hutchinson Cancer Center, Seattle, WA
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16
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Wei J, Beebe-Dimmer J, Shi Z, Sample C, Yan G, Rifkin AS, Sadeghpour A, Gielzak M, Choi S, Moon D, Zheng SL, Helfand BT, Walsh PC, Xu J, Cooney KA, Isaacs WB. Association of rare, recurrent nonsynonymous variants in the germline of prostate cancer patients of African ancestry. Prostate 2023; 83:454-461. [PMID: 36567534 DOI: 10.1002/pros.24477] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/28/2022] [Accepted: 12/02/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND Although men of African ancestry (AA) have the highest mortality rate from prostate cancer (PCa), relatively little is known about the germline variants that are associated with PCa risk in AA men. The goal of this study is to systematically evaluate rare, recurrent nonsynonymous variants across the exome for their association with PCa in AA men. METHODS Whole exome sequencing (WES) of germline DNA in two AA PCa patient cohorts of Johns Hopkins Hospital (N = 960) and Wayne State University (N = 747) was performed. All nonsynonymous variants present in both case cohorts, with a carrier rate between 0.5% and 1%, were identified. Their carrier rates were compared with rates from 8128 African/African American (AFR) control subjects from The Genome Aggregation Database (gnomAD) using Fisher's exact test. Significant variants, defined as false discovery rate (FDR) adjusted p-value ≤ 0.05, were further evaluated in AA PCa cases (N = 132) and controls (N = 1184) from the UK Biobank (UKB). RESULTS Two variants reached a pre-specified statistical significance level. The first was p.R14Q in GPRC5C (found in 0.47% of PCa cases and 0.01% of population controls); odds ratio (OR) for PCa was 37.46 (95% confidence interval CI 4.68-299.72), pexact = 7.01E-06, FDR-adjusted p-value = 0.05. The second was p.R511Q in IGF1R (found in 0.53% of PCa cases and 0.01% of population controls); OR for PCa was 21.54 (95%CI 4.65-99.76), pexact = 5.51E-06, FDR-adjusted p-value = 0.05. The mean percentage of African ancestry was similar between variant carriers and noncarriers of each variant, p > 0.05. In the UKB AA men, GPRC5C R14Q was 0.76% and 0.08% in cases and controls, respectively, OR for PCa was 9.00 (95%CI 0.56-145.23), pexact = 0.19. However, IGF1R R511Q was not found in cases or controls. CONCLUSIONS This WES study identified two rare, recurrent nonsynonymous PCa risk-associated variants in AA. Confirmation in additional large populations of AA PCa cases and controls is required.
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Affiliation(s)
- Jun Wei
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Jennifer Beebe-Dimmer
- Barabara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Zhuqing Shi
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Christopher Sample
- Department of Medicine, Duke University School of Medicine and Duke Cancer Institute, Durham, North Carolina, USA
| | - Guifang Yan
- Department of Urology, The Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Andrew S Rifkin
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Azita Sadeghpour
- Department of Medicine, Duke University School of Medicine and Duke Cancer Institute, Durham, North Carolina, USA
| | - Marta Gielzak
- Department of Urology, The Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Sodam Choi
- Department of Urology, The Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - David Moon
- Department of Medicine, Duke University School of Medicine and Duke Cancer Institute, Durham, North Carolina, USA
| | - S Lilly Zheng
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Brian T Helfand
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
- Department of Surgery, University of Chicago Pritzker School of Medicine, Chicago, Illinois, USA
| | - Patrick C Walsh
- Department of Urology, The Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Kathleen A Cooney
- Department of Medicine, Duke University School of Medicine and Duke Cancer Institute, Durham, North Carolina, USA
| | - William B Isaacs
- Department of Urology, The Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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17
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Schaffer KR, Shi M, Shelley JP, Tosoian JJ, Kachuri L, Witte JS, Mosley JD. A Polygenic Risk Score for Prostate Cancer Risk Prediction. JAMA Intern Med 2023; 183:386-388. [PMID: 36877498 PMCID: PMC9989952 DOI: 10.1001/jamainternmed.2022.6795] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/12/2022] [Indexed: 03/07/2023]
Abstract
This retrospective cohort study compares 2 risk calculator systems that compute the probabilities of finding high-grade or any cancer on biopsy results in men undergoing a first prostate biopsy.
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Affiliation(s)
- Kerry R. Schaffer
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt–Ingram Cancer Center, Nashville, Tennessee
| | - Mingjian Shi
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - John P. Shelley
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jeffrey J. Tosoian
- Vanderbilt–Ingram Cancer Center, Nashville, Tennessee
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University, Stanford, California
| | - John S. Witte
- Department of Epidemiology and Population Health, Stanford University, Stanford, California
- Department of Biomedical Data Science and Genetics (by courtesy), Stanford University, Stanford, California
| | - Jonathan D. Mosley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
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18
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Genetic Risk Prediction for Prostate Cancer: Implications for Early Detection and Prevention. Eur Urol 2023; 83:241-248. [PMID: 36609003 DOI: 10.1016/j.eururo.2022.12.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/15/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023]
Abstract
CONTEXT Prostate cancer (PCa) is a leading cause of death and partially heritable. Genetic risk prediction might be useful for strategies to reduce PCa mortality through early detection and prevention. OBJECTIVE To review evidence for genetic risk prediction for PCa. EVIDENCE ACQUISITION A collaborative literature review was conducted using PubMed and Google Scholar. Search terms included genetic, risk, prediction, and "prostate cancer". Articles addressing screening, early detection, or prevention were prioritized, as were studies involving diverse populations. EVIDENCE SYNTHESIS Rare pathogenic mutations (RPMs), especially in DNA damage repair genes, increase PCa risk. RPMs in BRCA2 are most clearly deleterious, conferring 2-8.6 times higher risk of PCa and a higher risk of aggressive disease. Common genetic variants can be combined into genetic risk scores (GRSs). A high GRS (top 20-25% of the population) confers two to three times higher risk of PCa than average; a very high GRS (top 1-5%) confers six to eight times higher risk. GRSs are not specific for aggressive PCa, possibly due to methodological limitations and/or a field effect of an elevated risk for both low- and high-grade PCa. It is challenging to disentangle genetics from structural racism and social determinants of health to understand PCa racial disparities. GRSs are independently associated with a lethal PCa risk after accounting for family history and race/ancestry. Healthy lifestyle might partially mitigate the risk of lethal PCa. CONCLUSIONS Genetic risk assessment is becoming more common; implementation studies are needed to understand the implications and to avoid exacerbating healthcare disparities. Men with a high genetic risk of PCa can reasonably be encouraged to adhere to a healthy lifestyle. PATIENT SUMMARY Prostate cancer risk is inherited through rare mutations and through the combination of hundreds of common genetic markers. Some men with a high genetic risk (especially BRCA2 mutations) likely benefit from early screening for prostate cancer. The risk of lethal prostate cancer can be reduced through a healthy lifestyle.
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19
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Mroczek M, Liu J, Sypniewski M, Pieńkowski T, Itrych B, Stojak J, Pronobis-Szczylik B, Stępień M, Kaja E, Dąbrowski M, Suchocki T, Wojtaszewska M, Zawadzki P, Mach A, Sztromwasser P, Król ZJ, Szyda J, Dobosz P. The cancer-risk variant frequency among Polish population reported by the first national whole-genome sequencing study. Front Oncol 2023; 13:1045817. [PMID: 36845707 PMCID: PMC9950741 DOI: 10.3389/fonc.2023.1045817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 01/20/2023] [Indexed: 02/12/2023] Open
Abstract
Introduction Population-based cancer screening has raised many controversies in recent years, not only regarding the costs but also regarding the ethical nature and issues related to variant interpretation. Nowadays, genetic cancer screening standards are different in every country and usually encompass only individuals with a personal or family history of relevant cancer. Methods Here we performed a broad genetic screening for cancer-related rare germline variants on population data from the Thousand Polish Genomes database based on 1076 Polish unrelated individuals that underwent whole genome sequencing (WGS). Results We identified 19 551 rare variants in 806 genes related to oncological diseases, among them 89% have been located in non-coding regions. The combined BRCA1/BRCA2 pathogenic/likely pathogenic according to ClinVar allele frequency in the unselected population of 1076 Poles was 0.42%, corresponding to nine carriers. Discussion Altogether, on the population level, we found especially problematic the assessment of the pathogenicity of variants and the relation of ACMG guidelines to the population frequency. Some of the variants may be overinterpreted as disease-causing due to their rarity or lack of annotation in the databases. On the other hand, some relevant variants may have been overseen given that there is little pooled population whole genome data on oncology. Before population WGS screening will become a standard, further studies are needed to assess the frequency of the variants suspected to be pathogenic on the population level and with reporting of likely benign variants.
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Affiliation(s)
- Magdalena Mroczek
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland,*Correspondence: Magdalena Mroczek,
| | - Jakub Liu
- Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Mateusz Sypniewski
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
| | - Tadeusz Pieńkowski
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland,Postgraduate Medical Education Center, Warsaw, Poland
| | - Bartosz Itrych
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
| | - Joanna Stojak
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland,Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology, Polish Academy of Science, Jastrzębiec, Poland
| | | | - Maria Stępień
- Department of Sports Medicine, Doctoral School, Medical University of Lublin, Lublin, Poland
| | - Elżbieta Kaja
- Department of Medical Chemistry and Laboratory Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Tomasz Suchocki
- Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland,National Research Institute of Animal Production, Balice, Poland
| | - Marzena Wojtaszewska
- Department of Haematology, Institute of Medical Sciences, College of Medical Sciences, University of Rzeszów, Rzeszów, Poland,Department of Haematology, Frederic Chopin Provincial Specialist Hospital, Rzeszów, Poland
| | | | - Anna Mach
- Department of Psychiatry, Medical University of Warsaw, Warsaw, Poland
| | | | - Zbigniew J. Król
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
| | - Joanna Szyda
- Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland,National Research Institute of Animal Production, Balice, Poland
| | - Paula Dobosz
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
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20
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Nyberg T, Brook MN, Ficorella L, Lee A, Dennis J, Yang X, Wilcox N, Dadaev T, Govindasami K, Lush M, Leslie G, Lophatananon A, Muir K, Bancroft E, Easton DF, Tischkowitz M, Kote-Jarai Z, Eeles R, Antoniou AC. CanRisk-Prostate: A Comprehensive, Externally Validated Risk Model for the Prediction of Future Prostate Cancer. J Clin Oncol 2023; 41:1092-1104. [PMID: 36493335 PMCID: PMC9928632 DOI: 10.1200/jco.22.01453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/26/2022] [Accepted: 10/07/2022] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Prostate cancer (PCa) is highly heritable. No validated PCa risk model currently exists. We therefore sought to develop a genetic risk model that can provide personalized predicted PCa risks on the basis of known moderate- to high-risk pathogenic variants, low-risk common genetic variants, and explicit cancer family history, and to externally validate the model in an independent prospective cohort. MATERIALS AND METHODS We developed a risk model using a kin-cohort comprising individuals from 16,633 PCa families ascertained in the United Kingdom from 1993 to 2017 from the UK Genetic Prostate Cancer Study, and complex segregation analysis adjusting for ascertainment. The model was externally validated in 170,850 unaffected men (7,624 incident PCas) recruited from 2006 to 2010 to the independent UK Biobank prospective cohort study. RESULTS The most parsimonious model included the effects of pathogenic variants in BRCA2, HOXB13, and BRCA1, and a polygenic score on the basis of 268 common low-risk variants. Residual familial risk was modeled by a hypothetical recessively inherited variant and a polygenic component whose standard deviation decreased log-linearly with age. The model predicted familial risks that were consistent with those reported in previous observational studies. In the validation cohort, the model discriminated well between unaffected men and men with incident PCas within 5 years (C-index, 0.790; 95% CI, 0.783 to 0.797) and 10 years (C-index, 0.772; 95% CI, 0.768 to 0.777). The 50% of men with highest predicted risks captured 86.3% of PCa cases within 10 years. CONCLUSION To our knowledge, this is the first validated risk model offering personalized PCa risks. The model will assist in counseling men concerned about their risk and can facilitate future risk-stratified population screening approaches.
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Affiliation(s)
- Tommy Nyberg
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
- MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom
| | - Mark N. Brook
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Lorenzo Ficorella
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Andrew Lee
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Xin Yang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Naomi Wilcox
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Tokhir Dadaev
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Koveela Govindasami
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Michael Lush
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Goska Leslie
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Artitaya Lophatananon
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Kenneth Muir
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Elizabeth Bancroft
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
- Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Marc Tischkowitz
- Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Zsofia Kote-Jarai
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Rosalind Eeles
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
- Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
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21
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Wang A, Xu Y, Yu Y, Nead KT, Kim T, Xu K, Dadaev T, Saunders E, Sheng X, Wan P, Pooler L, Xia LY, Chanock S, Berndt SI, Gapstur SM, Stevens V, Albanes D, Weinstein SJ, Gnanapragasam V, Giles GG, Nguyen-Dumont T, Milne RL, Pomerantz MM, Schmidt JA, Stopsack KH, Mucci LA, Catalona WJ, Hetrick KN, Doheny KF, MacInnis RJ, Southey MC, Eeles RA, Wiklund F, Kote-Jarai Z, de Smith AJ, Conti DV, Huff C, Haiman CA, Darst BF. Clonal hematopoiesis and risk of prostate cancer in large samples of European ancestry men. Hum Mol Genet 2023; 32:489-495. [PMID: 36018819 PMCID: PMC9851740 DOI: 10.1093/hmg/ddac214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 07/31/2022] [Accepted: 08/22/2022] [Indexed: 01/24/2023] Open
Abstract
Little is known regarding the potential relationship between clonal hematopoiesis (CH) of indeterminate potential (CHIP), which is the expansion of hematopoietic stem cells with somatic mutations, and risk of prostate cancer, the fifth leading cause of cancer death of men worldwide. We evaluated the association of age-related CHIP with overall and aggressive prostate cancer risk in two large whole-exome sequencing studies of 75 047 European ancestry men, including 7663 prostate cancer cases, 2770 of which had aggressive disease, and 3266 men carrying CHIP variants. We found that CHIP, defined by over 50 CHIP genes individually and in aggregate, was not significantly associated with overall (aggregate HR = 0.93, 95% CI = 0.76-1.13, P = 0.46) or aggressive (aggregate OR = 1.14, 95% CI = 0.92-1.41, P = 0.22) prostate cancer risk. CHIP was weakly associated with genetic risk of overall prostate cancer, measured using a polygenic risk score (OR = 1.05 per unit increase, 95% CI = 1.01-1.10, P = 0.01). CHIP was not significantly associated with carrying pathogenic/likely pathogenic/deleterious variants in DNA repair genes, which have previously been found to be associated with aggressive prostate cancer. While findings from this study suggest that CHIP is likely not a risk factor for prostate cancer, it will be important to investigate other types of CH in association with prostate cancer risk.
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Affiliation(s)
- Anqi Wang
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Yili Xu
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Yao Yu
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77230, USA
| | - Kevin T Nead
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77230, USA
| | - TaeBeom Kim
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77230, USA
| | - Keren Xu
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Tokhir Dadaev
- The Institute of Cancer Research, London, SM2 5NG, UK
| | - Ed Saunders
- The Institute of Cancer Research, London, SM2 5NG, UK
| | - Xin Sheng
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Peggy Wan
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Loreall Pooler
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Lucy Y Xia
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Stephen Chanock
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sonja I Berndt
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | - Demetrius Albanes
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Vincent Gnanapragasam
- Division of Urology, Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria 3168, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Victoria 3010, Australia
| | - Tu Nguyen-Dumont
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria 3168, Australia
- Department of Clinical Pathology, The University of Melbourne, Victoria 3010, Australia
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria 3168, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Victoria 3010, Australia
| | | | - Julie A Schmidt
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
- Department of Clinical Epidemiology, Department of Clinical Medicine, Aarhus University Hospital and Aarhus University, Aarhus N, DK-8200, Denmark
| | | | - Lorelei A Mucci
- Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - William J Catalona
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kurt N Hetrick
- Department of Genetic Medicine, Center for Inherited Disease Research, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Kimberly F Doheny
- Department of Genetic Medicine, Center for Inherited Disease Research, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Robert J MacInnis
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Victoria 3010, Australia
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria 3168, Australia
- Department of Clinical Pathology, The University of Melbourne, Victoria 3010, Australia
| | - Rosalind A Eeles
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | | | | | - Adam J de Smith
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - David V Conti
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Chad Huff
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77230, USA
| | - Christopher A Haiman
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Burcu F Darst
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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22
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Stalbow LA, Preuss MH, Smit RAJ, Chami N, Bjørkhaug L, Aukrust I, Gloyn AL, Loos RJF. The contribution of functional HNF1A variants and polygenic susceptibility to risk of type 2 diabetes in ancestrally diverse populations. Diabetologia 2023; 66:116-126. [PMID: 36216889 PMCID: PMC9729131 DOI: 10.1007/s00125-022-05806-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/08/2022] [Indexed: 01/26/2023]
Abstract
AIMS/HYPOTHESIS We examined the contribution of rare HNF1A variants to type 2 diabetes risk and age of diagnosis, and the extent to which their impact is affected by overall genetic susceptibility, across three ancestry groups. METHODS Using exome sequencing data of 160,615 individuals of the UK Biobank and 18,797 individuals of the BioMe Biobank, we identified 746 carriers of rare functional HNF1A variants (minor allele frequency ≤1%), of which 507 carry variants in the functional domains. We calculated polygenic risk scores (PRSs) based on genome-wide association study summary statistics for type 2 diabetes, and examined the association of HNF1A variants and PRS with risk of type 2 diabetes and age of diagnosis. We also tested whether the PRS affects the association between HNF1A variants and type 2 diabetes risk by including an interaction term. RESULTS Rare HNF1A variants that are predicted to impair protein function are associated with increased risk of type 2 diabetes in individuals of European ancestry (OR 1.46, p=0.049), particularly when the variants are located in the functional domains (OR 1.89, p=0.002). No association was observed for individuals of African ancestry (OR 1.10, p=0.60) or Hispanic-Latino ancestry (OR 1.00, p=1.00). Rare functional HNF1A variants were associated with an earlier age at diagnosis in the Hispanic-Latino population (β=-5.0 years, p=0.03), and this association was marginally more pronounced for variants in the functional domains (β=-5.59 years, p=0.03). No associations were observed for other ancestries (African ancestry β=-2.7 years, p=0.13; European ancestry β=-3.5 years, p=0.20). A higher PRS was associated with increased odds of type 2 diabetes in all ancestries (OR 1.61-2.11, p<10-5) and an earlier age at diagnosis in individuals of African ancestry (β=-1.4 years, p=3.7 × 10-6) and Hispanic-Latino ancestry (β=-2.4 years, p<2 × 10-16). Furthermore, a higher PRS exacerbated the effect of the functional HNF1A variants on type 2 diabetes in the European ancestry population (pinteraction=0.037). CONCLUSIONS/INTERPRETATION We show that rare functional HNF1A variants, in particular those located in the functional domains, increase the risk of type 2 diabetes, at least among individuals of European ancestry. Their effect is even more pronounced in individuals with a high polygenic susceptibility. Our analyses highlight the importance of the location of functional variants within a gene and an individual's overall polygenic susceptibility, and emphasise the need for more genetic data in non-European populations.
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Affiliation(s)
- Lauren A Stalbow
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roelof A J Smit
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lise Bjørkhaug
- Department of Safety, Chemistry and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | - Ingvild Aukrust
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Anna L Gloyn
- Department of Pediatrics, Division of Endocrinology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medicine, University of Copenhagen, Copenhagen, Denmark.
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23
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Wang TM, He YQ, Xue WQ, Zhang JB, Xia YF, Deng CM, Zhang WL, Xiao RW, Liao Y, Yang DW, Zhou T, Li DH, Luo LT, Tong XT, Wu YX, Chen XY, Li XZ, Zhang PF, Zheng XH, Zhang SD, Hu YZ, Wang F, Wu ZY, Zheng MQ, Huang JW, Jia YJ, Yuan LL, You R, Zhou GQ, Lu LX, Liu YY, Chen MY, Feng L, Dai W, Ren ZF, Mai HQ, Sun Y, Ma J, Zheng W, Lung ML, Jia WH. Whole-Exome Sequencing Study of Familial Nasopharyngeal Carcinoma and Its Implication for Identifying High-Risk Individuals. J Natl Cancer Inst 2022; 114:1689-1697. [PMID: 36066420 DOI: 10.1093/jnci/djac177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/28/2022] [Accepted: 08/31/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC) is closely associated with genetic factors and Epstein-Barr virus infection, showing strong familial aggregation. Individuals with a family history suffer elevated NPC risk, requiring effective genetic counseling for risk stratification and individualized prevention. METHODS We performed whole-exome sequencing on 502 familial NPC patients and 404 unaffected relatives and controls. We systematically evaluated the established cancer predisposition genes and investigated novel NPC susceptibility genes, making comparisons with 21 other familial cancers in the UK biobank (N = 5218). RESULTS Rare pathogenic mutations in the established cancer predisposition genes were observed in familial NPC patients, including ERCC2 (1.39%), TP63 (1.00%), MUTYH (0.80%), and BRCA1 (0.80%). Additionally, 6 novel susceptibility genes were identified. RAD54L, involved in the DNA repair pathway together with ERCC2, MUTYH, and BRCA1, showed the highest frequency (4.18%) in familial NPC. Enrichment analysis found mutations in TP63 were enriched in familial NPC, and RAD54L and EML2 were enriched in both NPC and other Epstein-Barr virus-associated cancers. Besides rare variants, common variants reported in the studies of sporadic NPC were also associated with familial NPC risk. Individuals in the top quantile of common variant-derived genetic risk score while carrying rare variants exhibited increased NPC risk (odds ratio = 13.47, 95% confidence interval = 6.33 to 28.68, P = 1.48 × 10-11); men in this risk group showed a cumulative lifetime risk of 24.19%, much higher than those in the bottom common variant-derived genetic risk score quantile and without rare variants (2.04%). CONCLUSIONS This study expands the catalog of NPC susceptibility genes and provides the potential for risk stratification of individuals with an NPC family history.
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Affiliation(s)
- Tong-Min Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Yong-Qiao He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Wen-Qiong Xue
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Jiang-Bo Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Yun-Fei Xia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Chang-Mi Deng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Wen-Li Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Ruo-Wen Xiao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Ying Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Da-Wei Yang
- School of Public Health, Sun Yat-sen University, Guangzhou, P. R. China
| | - Ting Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Dan-Hua Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Lu-Ting Luo
- School of Public Health, Sun Yat-sen University, Guangzhou, P. R. China
| | - Xia-Ting Tong
- School of Public Health, Sun Yat-sen University, Guangzhou, P. R. China
| | - Yan-Xia Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Xue-Yin Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Xi-Zhao Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Pei-Fen Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Xiao-Hui Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Shao-Dan Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Ye-Zhu Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Fang Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Zi-Yi Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Mei-Qi Zheng
- School of Public Health, Sun Yat-sen University, Guangzhou, P. R. China
| | - Jing-Wen Huang
- School of Public Health, Sun Yat-sen University, Guangzhou, P. R. China
| | - Yi-Jing Jia
- School of Public Health, Sun Yat-sen University, Guangzhou, P. R. China
| | - Lei-Lei Yuan
- School of Public Health, Sun Yat-sen University, Guangzhou, P. R. China
| | - Rui You
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Guan-Qun Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Li-Xia Lu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Yu-Ying Liu
- Department of Cancer Prevention, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Ming-Yuan Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Lin Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Wei Dai
- Department of Clinical Oncology, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China
| | - Ze-Fang Ren
- School of Public Health, Sun Yat-sen University, Guangzhou, P. R. China
| | - Hai-Qiang Mai
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Ying Sun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Jun Ma
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Maria Li Lung
- Department of Clinical Oncology, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
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24
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Plym A, Zhang Y, Stopsack KH, Jee YH, Wiklund F, Kibel AS, Kraft P, Giovannucci E, Penney KL, Mucci LA. Family History of Prostate and Breast Cancer Integrated with a Polygenic Risk Score Identifies Men at Highest Risk of Dying from Prostate Cancer before Age 75 Years. Clin Cancer Res 2022; 28:4926-4933. [PMID: 36103261 PMCID: PMC9660541 DOI: 10.1158/1078-0432.ccr-22-1723] [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: 05/31/2022] [Revised: 08/04/2022] [Accepted: 09/12/2022] [Indexed: 01/24/2023]
Abstract
PURPOSE Family history of prostate cancer is one of the few universally accepted risk factors for prostate cancer. How much an assessment of inherited polygenic risk for prostate cancer adds to lifetime risk stratification beyond family history is unknown. EXPERIMENTAL DESIGN We followed 10,120 men in the Health Professionals Follow-up Study with existing genotype data for risk of prostate cancer and prostate cancer-specific death. We assessed to what extent family history of prostate or breast cancer, combined with a validated polygenic risk score (PRS) including 269 prostate cancer risk variants, identifies men at risk of prostate cancer and prostate cancer death across the age span. RESULTS During 20 years of follow-up, 1,915 prostate cancer and 166 fatal prostate cancer events were observed. Men in the top PRS quartile with a family history of prostate or breast cancer had the highest rate of both prostate cancer and prostate cancer-specific death. Compared with men at lowest genetic risk (bottom PRS quartile and no family history), the HR was 6.95 [95% confidence interval (CI), 5.57-8.66] for prostate cancer and 4.84 (95% CI, 2.59-9.03) for prostate cancer death. Men in the two upper PRS quartiles (50%-100%) or with a family history of prostate or breast cancer (61.8% of the population) accounted for 97.5% of prostate cancer deaths by age 75 years. CONCLUSIONS Our study shows that prostate cancer risk stratification on the basis of family history and inherited polygenic risk can identify men at highest risk of dying from prostate cancer before age 75 years.
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Affiliation(s)
- Anna Plym
- Urology Division, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Corresponding Author: Anna Plym, Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, Stockholm SE-171 77, Sweden. Phone: 468-5248-0000; Fax: 468-314-975; E-mail:
| | - Yiwen Zhang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Konrad H. Stopsack
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yon Ho Jee
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Adam S. Kibel
- Urology Division, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Edward Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Kathryn L. Penney
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Lorelei A. Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
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25
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Reliability of Ancestry-specific Prostate Cancer Genetic Risk Score in Four Racial and Ethnic Populations. EUR UROL SUPPL 2022; 45:23-30. [DOI: 10.1016/j.euros.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2022] [Indexed: 11/22/2022] Open
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26
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Inherited risk assessment and its clinical utility for predicting prostate cancer from diagnostic prostate biopsies. Prostate Cancer Prostatic Dis 2022; 25:422-430. [PMID: 35347252 DOI: 10.1038/s41391-021-00458-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/25/2021] [Accepted: 09/10/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Many studies on prostate cancer (PCa) germline variants have been published in the last 15 years. This review critically assesses their clinical validity and explores their utility in prediction of PCa detection rates from prostate biopsy. METHODS An integrative review was performed to (1) critically synthesize findings on PCa germline studies from published papers since 2016, including risk-associated single nucleotide polymorphisms (SNPs), polygenic risk score methods such as genetic risk score (GRS), and rare pathogenic mutations (RPMs); (2) exemplify the findings in a large population-based cohort from the UK Biobank (UKB); (3) identify gaps for implementing inherited risk assessment in clinic based on experience from a healthcare system; (4) evaluate available GRS data on their clinical utility in predicting PCa detection rates from prostate biopsies; and (5) describe a prospective germline-based biopsy trial to address existing gaps. RESULTS SNP-based GRS and RPMs in four genes (HOXB13, BRCA2, ATM, and CHEK2) were significantly and consistently associated with PCa risk in large well-designed studies. In the UKB, positive family history, RPMs in the four implicated genes, and a high GRS (>1.5) identified 8.12%, 1.61%, and 17.38% of men to be at elevated PCa risk, respectively, with hazard ratios of 1.84, 2.74, and 2.39, respectively. Additionally, the performance of GRS for predicting PCa detection rate on prostate biopsy was consistently supported in several retrospective analyses of transrectal ultrasound (TRUS)-biopsy cohorts. Prospective studies evaluating the performance of all three inherited measures in predicting PCa detection rate from contemporary multiparametric MRI (mpMRI)-based biopsy are lacking. A multicenter germline-based biopsy trial to address these gaps is warranted. CONCLUSIONS The complementary performance of three inherited risk measures in PCa risk stratification is consistently supported. Their clinical utility in predicting PCa detection rate, if confirmed in prospective clinical trials, may improve current decision-making for prostate biopsy.
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27
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Abstract
BACKGROUND An important fraction (>/~10%) of men with high-risk, localized prostate cancer and metastatic prostate cancer carry germline (heritable) pathogenic and likely pathogenic variants (also known as mutations) in DNA repair genes. These can represent known or suspected autosomal dominant cancer predisposition syndromes. Growing evidence suggests that pathogenic variants in key genes involved in homologous recombination and mismatch DNA repair are important in prostate cancer initiation and/or the development of metastases. AIMS Here we provide a comprehensive review regarding individual genes and available literature regarding risks for developing prostate cancer, and discuss current national guidelines for germline genetic testing in the prostate cancer population and treatment implications. RESULTS The association with prostate cancer risk and treatment implications is best understood for those with germline mutations of BRCA2, with emerging data supporting associations with ATM, CHEK2, BRCA1, HOXB13, MSH2, MSH6, PALB2, TP53 and NBN. Treatment implications in the metastatic castration resistant prostate cancer setting include rucaparib and olaparib, and pembrolizumab with potential clinical trial opportunities in earlier disease settings. DISCUSSION The data summarized in this review has led to the expansion of national guidelines for germline genetic testing in prostate cancer. We review these guidelines, and discuss the importance of cascade genetic testing of relatives, diverse populations with attention to inclusion, as well as prostate cancer screening updates and clinical trial opportunities for men who carry genetic risk factors for prostate cancer.
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Affiliation(s)
- Hiba Khan
- Department of Medicine, Division of Oncology, University of Washington, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Heather H. Cheng
- Department of Medicine, Division of Oncology, University of Washington, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
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28
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Song X, Ru M, Steinsnyder Z, Tkachuk K, Kopp RP, Sullivan J, Gümüş ZH, Offit K, Joseph V, Klein RJ. SNPs at SMG7 Associated with Time from Biochemical Recurrence to Prostate Cancer Death. Cancer Epidemiol Biomarkers Prev 2022; 31:1466-1472. [PMID: 35511739 PMCID: PMC9250608 DOI: 10.1158/1055-9965.epi-22-0053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/25/2022] [Accepted: 05/02/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND A previous genome-wide association study identified several loci with genetic variants associated with prostate cancer survival time in two cohorts from Sweden. Whether these variants have an effect in other populations or if their effect is homogenous across the course of disease is unknown. METHODS These variants were genotyped in a cohort of 1,298 patients. Samples were linked with age, PSA level, Gleason score, cancer stage at surgery, and times from surgery to biochemical recurrence to death from prostate cancer. SNPs rs2702185 and rs73055188 were tested for association with prostate cancer-specific survival time using a multivariate Cox proportional hazard model. SNP rs2702185 was further tested for association with time to biochemical recurrence and time from biochemical recurrence to death with a multi-state model. RESULTS SNP rs2702185 at SMG7 was associated with prostate cancer-specific survival time, specifically the time from biochemical recurrence to prostate cancer death (HR, 2.5; 95% confidence interval, 1.4-4.5; P = 0.0014). Nine variants were in linkage disequilibrium (LD) with rs2702185; one, rs10737246, was found to be most likely to be functional based on LD patterns and overlap with open chromatin. Patterns of open chromatin and correlation with gene expression suggest that this SNP may affect expression of SMG7 in T cells. CONCLUSIONS The SNP rs2702185 at the SMG7 locus is associated with time from biochemical recurrence to prostate cancer death, and its LD partner rs10737246 is predicted to be functional. IMPACT These results suggest that future association studies of prostate cancer survival should consider various intervals over the course of disease.
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Affiliation(s)
- Xiaoyu Song
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
| | - Meng Ru
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
| | - Zoe Steinsnyder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Kaitlyn Tkachuk
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Ryan P. Kopp
- Department of Urology, Oregon Health and Science University, Portland, OR, 97239 USA
| | - John Sullivan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Zeynep H. Gümüş
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Vijai Joseph
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Robert J. Klein
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
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Clark R, Klotz L. Focal therapy: definition and rationale. Curr Opin Urol 2022; 32:218-223. [PMID: 35220365 DOI: 10.1097/mou.0000000000000975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW The role of focal therapy for the treatment of prostate cancer is expanding in clinical practice. The aim of this review is to introduce readers to controversies in the use of focal therapy and its rationale. RECENT FINDINGS There is a growing body of literature regarding the short-term and medium-term cancer control parameters and quality of life outcomes. These are mostly observational studies without a comparative arm. There is a need for high-quality randomize control trials comparing these treatments to definitive standard of care interventions (e.g. surgery or radiotherapy) in appropriate patient populations. SUMMARY Focal therapy for prostate cancer has become an established therapeutic strategy. Evidence continues to accrue regarding its effectiveness. It is a useful treatment option for the appropriately selected patient, with the appeal of improved quality of life compared with standard therapies.
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Affiliation(s)
| | - Laurence Klotz
- Sunnybrook Research Institute, University of Toronto, Toronto, Ontario, Canada
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30
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de la Calle CM, Bhanji Y, Pavlovich CP, Isaacs WB. The role of genetic testing in prostate cancer screening, diagnosis, and treatment. Curr Opin Oncol 2022; 34:212-218. [PMID: 35238838 DOI: 10.1097/cco.0000000000000823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW This review provides an overview of the current role of genetic testing in prostate cancer screening, diagnosis, and treatment. RECENT FINDINGS Recent studies have uncovered few but highly penetrant rare pathogenic mutations (RPMs), in genes, such as BRCA2, with strong prostate cancer risk and outcomes associations. Over 260 single nucleotide polymorphisms (SNPs) have also been identified, each associated with small incremental prostate cancer risk and when combined in a polygenic risk score (PRS), they provide strong prostate cancer risk prediction but do not seem to predict outcomes. Tumor tissue sequencing can also help identify actionable somatic mutations in many patients with advanced prostate cancer and inform on their risk of harboring a germline pathogenic mutation. SUMMARY RPM testing, PRS testing, and tumor sequencing all have current and/or potential future roles in personalized prostate cancer care.
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Affiliation(s)
- Claire M de la Calle
- The James Buchanan Brady Urological Institute, Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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31
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Papachristodoulou A, Abate-Shen C. Precision intervention for prostate cancer: Re-evaluating who is at risk. Cancer Lett 2022; 538:215709. [DOI: 10.1016/j.canlet.2022.215709] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/30/2022] [Accepted: 04/25/2022] [Indexed: 02/08/2023]
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32
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Klein RJ. Polygenic risk scores and prostate cancer screening: a recipe for more overdiagnosis? BJU Int 2022; 129:271. [PMID: 35297162 DOI: 10.1111/bju.15583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/10/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Wang X, Glubb DM, O'Mara TA. 10 Years of GWAS discovery in endometrial cancer: Aetiology, function and translation. EBioMedicine 2022; 77:103895. [PMID: 35219087 PMCID: PMC8881374 DOI: 10.1016/j.ebiom.2022.103895] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/24/2022] Open
Abstract
Endometrial cancer is a common gynaecological cancer with increasing incidence and mortality. In the last decade, endometrial cancer genome-wide association studies (GWAS) have provided a resource to explore aetiology and for functional interpretation of heritable risk variation, informing endometrial cancer biology. Indeed, GWAS data have been used to assess relationships with other traits through correlation and Mendelian randomisation analyses, establishing genetic relationships and potential risk factors. Cross-trait GWAS analyses have increased statistical power and identified novel endometrial cancer risk variation related to other traits. Functional analysis of risk loci has helped prioritise candidate susceptibility genes, revealing molecular mechanisms and networks. Lastly, risk scores generated using endometrial cancer GWAS data may allow for clinical translation through identification of patients at high risk of disease. In the next decade, this knowledge base should enable substantial progress in our understanding of endometrial cancer and, potentially, new approaches for its screening and treatment.
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Wang Z, Choi SW, Chami N, Boerwinkle E, Fornage M, Redline S, Bis JC, Brody JA, Psaty BM, Kim W, McDonald MLN, Regan EA, Silverman EK, Liu CT, Vasan RS, Kalyani RR, Mathias RA, Yanek LR, Arnett DK, Justice AE, North KE, Kaplan R, Heckbert S, de Andrade M, Guo X, Lange LA, Rich S, Rotter JI, Ellinor PT, Lubitz SA, Blangero J, Shoemaker MB, Darbar D, Gladwin MT, Albert CM, Chasman DI, Jackson RD, Kooperberg C, Reiner AP, O’Reilly PF, Loos RJF. The Value of Rare Genetic Variation in the Prediction of Common Obesity in European Ancestry Populations. Front Endocrinol (Lausanne) 2022; 13:863893. [PMID: 35592775 PMCID: PMC9110787 DOI: 10.3389/fendo.2022.863893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/11/2022] [Indexed: 01/05/2023] Open
Abstract
Polygenic risk scores (PRSs) aggregate the effects of genetic variants across the genome and are used to predict risk of complex diseases, such as obesity. Current PRSs only include common variants (minor allele frequency (MAF) ≥1%), whereas the contribution of rare variants in PRSs to predict disease remains unknown. Here, we examine whether augmenting the standard common variant PRS (PRScommon) with a rare variant PRS (PRSrare) improves prediction of obesity. We used genome-wide genotyped and imputed data on 451,145 European-ancestry participants of the UK Biobank, as well as whole exome sequencing (WES) data on 184,385 participants. We performed single variant analyses (for both common and rare variants) and gene-based analyses (for rare variants) for association with BMI (kg/m2), obesity (BMI ≥ 30 kg/m2), and extreme obesity (BMI ≥ 40 kg/m2). We built PRSscommon and PRSsrare using a range of methods (Clumping+Thresholding [C+T], PRS-CS, lassosum, gene-burden test). We selected the best-performing PRSs and assessed their performance in 36,757 European-ancestry unrelated participants with whole genome sequencing (WGS) data from the Trans-Omics for Precision Medicine (TOPMed) program. The best-performing PRScommon explained 10.1% of variation in BMI, and 18.3% and 22.5% of the susceptibility to obesity and extreme obesity, respectively, whereas the best-performing PRSrare explained 1.49%, and 2.97% and 3.68%, respectively. The PRSrare was associated with an increased risk of obesity and extreme obesity (ORobesity = 1.37 per SDPRS, Pobesity = 1.7x10-85; ORextremeobesity = 1.55 per SDPRS, Pextremeobesity = 3.8x10-40), which was attenuated, after adjusting for PRScommon (ORobesity = 1.08 per SDPRS, Pobesity = 9.8x10-6; ORextremeobesity= 1.09 per SDPRS, Pextremeobesity = 0.02). When PRSrare and PRScommon are combined, the increase in explained variance attributed to PRSrare was small (incremental Nagelkerke R2 = 0.24% for obesity and 0.51% for extreme obesity). Consistently, combining PRSrare to PRScommon provided little improvement to the prediction of obesity (PRSrare AUC = 0.591; PRScommon AUC = 0.708; PRScombined AUC = 0.710). In summary, while rare variants show convincing association with BMI, obesity and extreme obesity, the PRSrare provides limited improvement over PRScommon in the prediction of obesity risk, based on these large populations.
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Affiliation(s)
- Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Shing Wan Choi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, New York, NY, United States
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Susan Redline
- Division of Sleep Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Wonji Kim
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Merry-Lynn N. McDonald
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Elizabeth A. Regan
- Division of Rheumatology, Department of Medicine, National Jewish Health, Denver, CO, United States
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States
| | - Ramachandran S. Vasan
- National Heart, Lung and Blood Institute’s and Boston University’s Framingham Heart Study, Framingham, MA, United States
- Section of Preventive Medicine and Epidemiology, Evans Department of Medicine, Boston University School of Medicine, Boston, MA, United States
- Whitaker Cardiovascular Institute and Cardiology Section, Evans Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Rita R. Kalyani
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Rasika A. Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Lisa R. Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Donna K. Arnett
- College of Public Health, University of Kentucky, Lexington, KY, United States
| | - Anne E. Justice
- Department of Population Health Services, Geisinger Health, Danville, PA, United States
| | - Kari E. North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Susan R. Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA, United States
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, United States
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Leslie A. Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anchutz Medical Camus, Aurora, CA, United States
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Patrick T. Ellinor
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, United States
| | - Steven A. Lubitz
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, United States
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, United States
| | - M. Benjamin Shoemaker
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Dawood Darbar
- Division of Cardiology, University of Illinois at Chicago, Chicago, IL, United States
| | - Mark T. Gladwin
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Christine M. Albert
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Daniel I. Chasman
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Rebecca D. Jackson
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, The Ohio State University, Columbus, OH, United States
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Alexander P. Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, United States
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Paul F. O’Reilly
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, New York, NY, United States
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Ruth J. F. Loos,
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Tian P, Zhong M, Wei GH. Mechanistic insights into genetic susceptibility to prostate cancer. Cancer Lett 2021; 522:155-163. [PMID: 34560228 DOI: 10.1016/j.canlet.2021.09.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022]
Abstract
Prostate cancer (PCa) is the second most common cancer in men and is a highly heritable disease that affects millions of individuals worldwide. Genome-wide association studies have to date discovered nearly 270 genetic loci harboring hundreds of single nucleotide polymorphisms (SNPs) that are associated with PCa susceptibility. In contrast, the functional characterization of the mechanisms underlying PCa risk association is still growing. Given that PCa risk-associated SNPs are highly enriched in noncoding cis-regulatory genomic regions, accumulating evidence suggests a widespread modulation of transcription factor chromatin binding and allelic enhancer activity by these noncoding SNPs, thereby dysregulating gene expression. Emerging studies have shown that a proportion of noncoding variants can modulate the formation of transcription factor complexes at enhancers and CTCF-mediated 3D genome architecture. Interestingly, DNA methylation-regulated CTCF binding could orchestrate a long-range chromatin interaction between PCa risk enhancer and causative genes. Additionally, one-causal-variant-two-risk genes or multiple-risk-variant-multiple-genes are prevalent in some PCa risk-associated loci. In this review, we will discuss the current understanding of the general principles of SNP-mediated gene regulation, experimental advances, and functional evidence supporting the mechanistic roles of several PCa genetic loci with potential clinical impact on disease prevention and treatment.
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Affiliation(s)
- Pan Tian
- Fudan University Shanghai Cancer Center; Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Mengjie Zhong
- Fudan University Shanghai Cancer Center; Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Gong-Hong Wei
- Fudan University Shanghai Cancer Center; Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
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Wei J, Yang W, Shi Z, Lu L, Wang Q, Resurreccion WK, Engelmann V, Zheng SL, Hulick PJ, Cooney KA, Isaacs WB, Helfand BT, Lu J, Xu J. Observed evidence for guideline-recommended genes in predicting prostate cancer risk from a large population-based cohort. Prostate 2021; 81:1002-1008. [PMID: 34254341 DOI: 10.1002/pros.24195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/02/2021] [Accepted: 06/29/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Germline testing for prostate cancer (PCa) is now recommended by the National Comprehensive Cancer Network. While multi-gene testing has been proposed, evidence for their association with PCa risk is not well established. METHODS We tested associations of pathogenic/likely pathogenic mutations in 10 guideline-recommended genes (ATM, BRCA1, BRCA2, CHEK2, PALB2, MLH1, MSH2, MSH6, PMS2, and HOXB13) with PCa risk in the UK Biobank, a population-based cohort. Mutations were annotated based on prostate-specific transcripts using the American College of Medical Genetics and Genomics standards. Associations were tested in 4399 PCa cases and 85,403 unaffected male controls using logistic regression adjusting for age and genetic background. p < .005 was considered significant based on Bonferroni correction. RESULTS Among the 10 tested genes, significantly higher mutation carrier rates in PCa cases versus controls were found for four genes at p < .005; HOXB13, BRCA2, ATM, and CHEK2, with odds ratios (95% confidence interval) estimated at 4.96 (3.62-6.69), 3.23 (2.23-4.56), 2.95 (2.01-4.22), 1.94 (1.43-2.58), respectively. No significant association was found between mutation carrier status and age at PCa diagnosis or family history of PCa. Despite the large sample size of this study, statistical power remains limited, especially for genes where pathogenic mutation carrier rates are extremely rare (<0.03%). CONCLUSION Observed evidence for PCa risk was found for four of the 10 guideline-recommended genes in this large population-based study. Mutations in these four genes can be interpreted with confidence in genetic counseling for PCa risk assessment. Evidence for the remaining six genes needs to be further evaluated in larger studies.
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Affiliation(s)
- Jun Wei
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois, USA
- Department of Surgery, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Wancai Yang
- Department of Research and Development, GoPath Laboratories LLC, Buffalo Grove, Illinois, USA
| | - Zhuqing Shi
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois, USA
- Department of Surgery, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Lucy Lu
- Department of Research and Development, GoPath Laboratories LLC, Buffalo Grove, Illinois, USA
| | - Qiang Wang
- Department of Research and Development, GoPath Laboratories LLC, Buffalo Grove, Illinois, USA
| | - W Kyle Resurreccion
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois, USA
- Department of Surgery, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Valentina Engelmann
- Department of Research and Development, GoPath Laboratories LLC, Buffalo Grove, Illinois, USA
| | - S Lilly Zheng
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois, USA
- Department of Surgery, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Peter J Hulick
- Department of Medicine, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Kathleen A Cooney
- School of Medicine, Duke Cancer Institute, Duke University, Durham, North Carolina, USA
| | - William B Isaacs
- The Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Brian T Helfand
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois, USA
- Department of Surgery, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Jim Lu
- Department of Research and Development, GoPath Laboratories LLC, Buffalo Grove, Illinois, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois, USA
- Department of Surgery, NorthShore University HealthSystem, Evanston, Illinois, USA
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37
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Incorporation of Polygenic Risk Score into Guidelines for Inherited Risk Assessment for Prostate Cancer. Eur Urol 2021; 80:139-141. [PMID: 34024654 DOI: 10.1016/j.eururo.2021.04.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 04/30/2021] [Indexed: 11/23/2022]
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