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Wang J, Zhou F, Li C, Yin N, Liu H, Zhuang B, Huang Q, Wen Y. Gene Association Analysis of Quantitative Trait Based on Functional Linear Regression Model with Local Sparse Estimator. Genes (Basel) 2023; 14:genes14040834. [PMID: 37107592 PMCID: PMC10137544 DOI: 10.3390/genes14040834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Functional linear regression models have been widely used in the gene association analysis of complex traits. These models retain all the genetic information in the data and take full advantage of spatial information in genetic variation data, which leads to brilliant detection power. However, the significant association signals identified by the high-power methods are not all the real causal SNPs, because it is easy to regard noise information as significant association signals, leading to a false association. In this paper, a method based on the sparse functional data association test (SFDAT) of gene region association analysis is developed based on a functional linear regression model with local sparse estimation. The evaluation indicators CSR and DL are defined to evaluate the feasibility and performance of the proposed method with other indicators. Simulation studies show that: (1) SFDAT performs well under both linkage equilibrium and linkage disequilibrium simulation; (2) SFDAT performs successfully for gene regions (including common variants, low-frequency variants, rare variants and mix variants); (3) With power and type I error rates comparable to OLS and Smooth, SFDAT has a better ability to handle the zero regions. The Oryza sativa data set is analyzed by SFDAT. It is shown that SFDAT can better perform gene association analysis and eliminate the false positive of gene localization. This study showed that SFDAT can lower the interference caused by noise while maintaining high power. SFDAT provides a new method for the association analysis between gene regions and phenotypic quantitative traits.
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Affiliation(s)
- Jingyu Wang
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Statistics and Application, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Fujie Zhou
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Statistics and Application, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cheng Li
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Statistics and Application, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ning Yin
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Statistics and Application, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huiming Liu
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Statistics and Application, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Binxian Zhuang
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Statistics and Application, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qingyu Huang
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Statistics and Application, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yongxian Wen
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Statistics and Application, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence:
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2
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Prahl JD, Pierce SE, van der Schans EJC, Coetzee GA, Tyson T. The Parkinson's disease variant rs356182 regulates neuronal differentiation independently from alpha-synuclein. Hum Mol Genet 2022; 32:1-14. [PMID: 35866299 PMCID: PMC9837835 DOI: 10.1093/hmg/ddac161] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/16/2022] [Accepted: 07/10/2022] [Indexed: 01/25/2023] Open
Abstract
One of the most significant risk variants for Parkinson's disease (PD), rs356182, is located at the PD-associated locus near the alpha-synuclein (α-syn) encoding gene, SNCA. SNCA-proximal variants, including rs356182, are thought to function in PD risk through enhancers via allele-specific regulatory effects on SNCA expression. However, this interpretation discounts the complex activity of genetic enhancers and possible non-conical functions of α-syn. Here we investigated a novel risk mechanism for rs356182. We use CRISPR-Cas9 in LUHMES cells, a model for dopaminergic midbrain neurons, to generate precise hemizygous lesions at rs356182. The PD-protective (A/-), PD-risk (G/-) and wild-type (A/G) clones were neuronally differentiated and then compared transcriptionally and morphologically. Among the affected genes was SNCA, whose expression was promoted by the PD-protective allele (A) and repressed in its absence. In addition to SNCA, hundreds of genes were differentially expressed and associated with neurogenesis and axonogenesis-an effect not typically ascribed to α-syn. We also found that the transcription factor FOXO3 specifically binds to the rs356182 A-allele in differentiated LUHMES cells. Finally, we compared the results from the rs356182-edited cells to our previously published knockouts of SNCA and found only minimal overlap between the sets of significant differentially expressed genes. Together, the data implicate a risk mechanism for rs356182 in which the risk-allele (G) is associated with abnormal neuron development, independent of SNCA expression. We speculate that these pathological effects manifest as a diminished population of dopaminergic neurons during development leading to the predisposition for PD later in life.
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Affiliation(s)
- Jordan D Prahl
- To whom correspondence should be addressed. Tel: +1 6162345793; Fax: +1 6162345001;
| | - Steven E Pierce
- Department of Neurodegenerative Research, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids MI 49503, USA
| | - Edwin J C van der Schans
- Department of Neurodegenerative Research, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids MI 49503, USA
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Saunders EJ, Kote-Jarai Z, Eeles RA. Identification of Germline Genetic Variants that Increase Prostate Cancer Risk and Influence Development of Aggressive Disease. Cancers (Basel) 2021; 13:760. [PMID: 33673083 PMCID: PMC7917798 DOI: 10.3390/cancers13040760] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/15/2022] Open
Abstract
Prostate cancer (PrCa) is a heterogeneous disease, which presents in individual patients across a diverse phenotypic spectrum ranging from indolent to fatal forms. No robust biomarkers are currently available to enable routine screening for PrCa or to distinguish clinically significant forms, therefore late stage identification of advanced disease and overdiagnosis plus overtreatment of insignificant disease both remain areas of concern in healthcare provision. PrCa has a substantial heritable component, and technological advances since the completion of the Human Genome Project have facilitated improved identification of inherited genetic factors influencing susceptibility to development of the disease within families and populations. These genetic markers hold promise to enable improved understanding of the biological mechanisms underpinning PrCa development, facilitate genetically informed PrCa screening programmes and guide appropriate treatment provision. However, insight remains largely lacking regarding many aspects of their manifestation; especially in relation to genes associated with aggressive phenotypes, risk factors in non-European populations and appropriate approaches to enable accurate stratification of higher and lower risk individuals. This review discusses the methodology used in the elucidation of genetic loci, genes and individual causal variants responsible for modulating PrCa susceptibility; the current state of understanding of the allelic spectrum contributing to PrCa risk; and prospective future translational applications of these discoveries in the developing eras of genomics and personalised medicine.
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Affiliation(s)
- Edward J. Saunders
- The Institute of Cancer Research, London SM2 5NG, UK; (Z.K.-J.); (R.A.E.)
| | - Zsofia Kote-Jarai
- The Institute of Cancer Research, London SM2 5NG, UK; (Z.K.-J.); (R.A.E.)
| | - Rosalind A. Eeles
- The Institute of Cancer Research, London SM2 5NG, UK; (Z.K.-J.); (R.A.E.)
- Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
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4
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Pioneer of prostate cancer: past, present and the future of FOXA1. Protein Cell 2020; 12:29-38. [PMID: 32946061 PMCID: PMC7815845 DOI: 10.1007/s13238-020-00786-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 08/18/2020] [Indexed: 01/27/2023] Open
Abstract
Prostate cancer is the most commonly diagnosed non-cutaneous cancers in North American men. While androgen deprivation has remained as the cornerstone of prostate cancer treatment, resistance ensues leading to lethal disease. Forkhead box A1 (FOXA1) encodes a pioneer factor that induces open chromatin conformation to allow the binding of other transcription factors. Through direct interactions with the Androgen Receptor (AR), FOXA1 helps to shape AR signaling that drives the growth and survival of normal prostate and prostate cancer cells. FOXA1 also possesses an AR-independent role of regulating epithelial-to-mesenchymal transition (EMT). In prostate cancer, mutations converge onto the coding sequence and cis-regulatory elements (CREs) of FOXA1, leading to functional alterations. In addition, FOXA1 activity in prostate cancer can be modulated post-translationally through various mechanisms such as LSD1-mediated protein demethylation. In this review, we describe the latest discoveries related to the function and regulation of FOXA1 in prostate cancer, pointing to their relevance to guide future clinical interventions.
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Tong Y, Tang Y, Li S, Zhao F, Ying J, Qu Y, Niu X, Mu D. Cumulative evidence of relationships between multiple variants in 8q24 region and cancer incidence. Medicine (Baltimore) 2020; 99:e20716. [PMID: 32590746 PMCID: PMC7328976 DOI: 10.1097/md.0000000000020716] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified multiple independent cancer susceptibility loci at chromosome 8q24. We aimed to evaluate the associations between variants in the 8q24 region and cancer susceptibility. A comprehensive research synopsis and meta-analysis was performed to evaluate associations between 28 variants in 8q24 and risk of 7 cancers using data from 103 eligible articles totaling 146,932 cancer cases and 219,724 controls. Results: 20 variants were significantly associated with risk of prostate cancer, colorectal cancer, thyroid cancer, breast cancer, bladder cancer, stomach cancer, and glioma, including 1 variant associated with prostate cancer, colorectal cancer, and thyroid cancer. Cumulative epidemiological evidence of an association was graded as strong for DG8S737 -8 allele, rs10090154, rs7000448 in prostate cancer, rs10808556 in colorectal cancer, rs55705857 in gliomas, rs9642880 in bladder cancer, moderate for rs16901979, rs1447295, rs6983267, rs7017300, rs7837688, rs1016343, rs620861, rs10086908 associated in prostate cancer, rs10505477, rs6983267 in colorectal cancer, rs6983267 in thyroid cancer, rs13281615 in breast cancer, and rs1447295 in stomach cancer, weak for rs6983561, rs13254738, rs7008482, rs4242384 in prostate cancer. Data from ENCODE suggested that these variants with strong evidence and other correlated variants might fall within putative functional regions. Our study provides summary evidence that common variants in the 8q24 are associated with risk of multiple cancers in this large-scale research synopsis and meta-analysis. Further studies are needed to explore the mechanisms underlying variants in the 8q24 involved in various human cancers.
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Affiliation(s)
- Yu Tong
- Department of Pediatrics
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
| | - Ying Tang
- Department of Pediatrics
- Department of Diagnostic Ultrasound
| | - Shiping Li
- Department of Pediatrics
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
| | - Fengyan Zhao
- Department of Pediatrics
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
| | - Junjie Ying
- Department of Pediatrics
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
| | - Yi Qu
- Department of Pediatrics
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
| | - Xiaoyu Niu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Dezhi Mu
- Department of Pediatrics
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
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Farashi S, Kryza T, Clements J, Batra J. Post-GWAS in prostate cancer: from genetic association to biological contribution. Nat Rev Cancer 2019; 19:46-59. [PMID: 30538273 DOI: 10.1038/s41568-018-0087-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genome-wide association studies (GWAS) have been successful in deciphering the genetic component of predisposition to many human complex diseases including prostate cancer. Germline variants identified by GWAS progressively unravelled the substantial knowledge gap concerning prostate cancer heritability. With the beginning of the post-GWAS era, more and more studies reveal that, in addition to their value as risk markers, germline variants can exert active roles in prostate oncogenesis. Consequently, current research efforts focus on exploring the biological mechanisms underlying specific susceptibility loci known as causal variants by applying novel and precise analytical methods to available GWAS data. Results obtained from these post-GWAS analyses have highlighted the potential of exploiting prostate cancer risk-associated germline variants to identify new gene networks and signalling pathways involved in prostate tumorigenesis. In this Review, we describe the molecular basis of several important prostate cancer-causal variants with an emphasis on using post-GWAS analysis to gain insight into cancer aetiology. In addition to discussing the current status of post-GWAS studies, we also summarize the main molecular mechanisms of potential causal variants at prostate cancer risk loci and explore the major challenges in moving from association to functional studies and their implication in clinical translation.
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Affiliation(s)
- Samaneh Farashi
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Thomas Kryza
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Judith Clements
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Jyotsna Batra
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia.
- Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia.
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7
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Matejcic M, Saunders EJ, Dadaev T, Brook MN, Wang K, Sheng X, Olama AAA, Schumacher FR, Ingles SA, Govindasami K, Benlloch S, Berndt SI, Albanes D, Koutros S, Muir K, Stevens VL, Gapstur SM, Tangen CM, Batra J, Clements J, Gronberg H, Pashayan N, Schleutker J, Wolk A, West C, Mucci L, Kraft P, Cancel-Tassin G, Sorensen KD, Maehle L, Grindedal EM, Strom SS, Neal DE, Hamdy FC, Donovan JL, Travis RC, Hamilton RJ, Rosenstein B, Lu YJ, Giles GG, Kibel AS, Vega A, Bensen JT, Kogevinas M, Penney KL, Park JY, Stanford JL, Cybulski C, Nordestgaard BG, Brenner H, Maier C, Kim J, Teixeira MR, Neuhausen SL, De Ruyck K, Razack A, Newcomb LF, Lessel D, Kaneva R, Usmani N, Claessens F, Townsend PA, Gago-Dominguez M, Roobol MJ, Menegaux F, Khaw KT, Cannon-Albright LA, Pandha H, Thibodeau SN, Schaid DJ, Wiklund F, Chanock SJ, Easton DF, Eeles RA, Kote-Jarai Z, Conti DV, Haiman CA. Germline variation at 8q24 and prostate cancer risk in men of European ancestry. Nat Commun 2018; 9:4616. [PMID: 30397198 PMCID: PMC6218483 DOI: 10.1038/s41467-018-06863-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 10/01/2018] [Indexed: 02/07/2023] Open
Abstract
Chromosome 8q24 is a susceptibility locus for multiple cancers, including prostate cancer. Here we combine genetic data across the 8q24 susceptibility region from 71,535 prostate cancer cases and 52,935 controls of European ancestry to define the overall contribution of germline variation at 8q24 to prostate cancer risk. We identify 12 independent risk signals for prostate cancer (p < 4.28 × 10-15), including three risk variants that have yet to be reported. From a polygenic risk score (PRS) model, derived to assess the cumulative effect of risk variants at 8q24, men in the top 1% of the PRS have a 4-fold (95%CI = 3.62-4.40) greater risk compared to the population average. These 12 variants account for ~25% of what can be currently explained of the familial risk of prostate cancer by known genetic risk factors. These findings highlight the overwhelming contribution of germline variation at 8q24 on prostate cancer risk which has implications for population risk stratification.
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Affiliation(s)
- Marco Matejcic
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, 90033, USA
| | | | - Tokhir Dadaev
- The Institute of Cancer Research, London, SW7 3RP, UK
| | - Mark N Brook
- The Institute of Cancer Research, London, SW7 3RP, UK
| | - Kan Wang
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, 90033, USA
| | - Xin Sheng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, 90033, USA
| | - Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106-7219, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, 44106, USA
| | - Sue A Ingles
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, 90033, USA
| | | | - Sara Benlloch
- The Institute of Cancer Research, London, SW7 3RP, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Kenneth Muir
- Institute of Population Health, University of Manchester, Manchester, M13 9PL, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Victoria L Stevens
- Epidemiology Research Program, American Cancer Society, 250 Williams Street, Atlanta, GA, 30303, USA
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, 250 Williams Street, Atlanta, GA, 30303, USA
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Jyotsna Batra
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Brisbane, QLD, 4059, Australia
- Translational Research Institute, Brisbane, QLD, 4102, Australia
| | - Judith Clements
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Brisbane, QLD, 4059, Australia
- Translational Research Institute, Brisbane, QLD, 4102, Australia
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, SE-171 77, Stockholm, Sweden
| | - Nora Pashayan
- Centre for Cancer Genetic Epidemiology, Department of Oncology, Strangeways Research Laboratory, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Applied Health Research, University College London, London, WC1E 7HB, UK
| | - Johanna Schleutker
- Department of Medical Biochemistry and Genetics, Institute of Biomedicine, University of Turku, FI-20014, Turku, Finland
- Tyks Microbiology and Genetics, Department of Medical Genetics, Turku University Hospital, 20521, Turku, Finland
- BioMediTech, University of Tampere, 33520, Tampere, Finland
| | - Alicja Wolk
- Division of Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Catharine West
- Division of Cancer Sciences, Manchester Academic Health Science Centre, Radiotherapy Related Research, Manchester NIHR Biomedical Research Centre, The Christie Hospital NHS Foundation Trust, University of Manchester, Manchester, M13 9PL, UK
| | - Lorelei Mucci
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, 02115, USA
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Géraldine Cancel-Tassin
- GRC N°5 ONCOTYPE-URO, UPMC Univ Paris 06, Tenon Hospital, F-75020, Paris, France
- CeRePP, Tenon Hospital, F-75020, Paris, France
| | - Karina D Sorensen
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, 8200, Aarhus N, Denmark
| | - Lovise Maehle
- Department of Medical Genetics, Oslo University Hospital, 0424, Oslo, Norway
| | - Eli M Grindedal
- Department of Medical Genetics, Oslo University Hospital, 0424, Oslo, Norway
| | - Sara S Strom
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - David E Neal
- Department of Oncology, Addenbrooke's Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX1 2JD, UK
| | - Jenny L Donovan
- School of Social and Community Medicine, University of Bristol, Canynge Hall, 39 Whatley Road, Bristol, BS8 2PS, UK
| | - Ruth C Travis
- Cancer Epidemiology, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Robert J Hamilton
- Department of Surgical Oncology, Princess Margaret Cancer Centre, Toronto, ON, M5G 2M9, Canada
| | - Barry Rosenstein
- Department of Radiation Oncology, 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, 10029-5674, USA
| | - Yong-Jie Lu
- Centre for Molecular Oncology, John Vane Science Centre, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Graham G Giles
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Adam S Kibel
- Division of Urologic Surgery, Brigham and Womens Hospital, Boston, MA, 02115, USA
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica, CIBERER, IDIS, 15706, Santiago de Compostela, Spain
| | - Jeanette T Bensen
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Columbia, SC, 29208, USA
| | - Manolis Kogevinas
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona Institute for Global Health (ISGlobal), 08003, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), 28029, Madrid, Spain
- IMIM (Hospital del Mar Research Institute), 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002, Barcelona, Spain
| | - Kathryn L Penney
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, MA, 02184, USA
| | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, 98195, USA
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-115, Szczecin, Poland
| | - Børge G Nordestgaard
- Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, 2200, Copenhagen, Denmark
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120, Heidelberg, Germany
| | - Christiane Maier
- Institute for Human Genetics, University Hospital Ulm, 89075, Ulm, Germany
| | - Jeri Kim
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute of Porto, 4200-072, Porto, Portugal
- Biomedical Sciences Institute (ICBAS), University of Porto, 4050-313, Porto, Portugal
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA
| | - Kim De Ruyck
- Ghent University, Faculty of Medicine and Health Sciences, Basic Medical Sciences, B-9000, Gent, Belgium
| | - Azad Razack
- Department of Surgery, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Lisa F Newcomb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
- Department of Urology, University of Washington, Seattle, WA, 98195, USA
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, D-20246, Hamburg, Germany
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical University of Sofia, 1431, Sofia, Bulgaria
| | - Nawaid Usmani
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, T6G 1Z2, Canada
- Division of Radiation Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, T6G 1Z2, Canada
| | - Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, BE-3000, Leuven, Belgium
| | - Paul A Townsend
- Manchester Cancer Research Centre, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Research Centre, Health Innovation Manchester, University of Manchester, Manchester, M13 9WL, UK
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, Servicio Galego de Saúde, SERGAS, 15706, Santiago de Compostela, Spain
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92037, USA
| | - Monique J Roobol
- Department of Urology, Erasmus University Medical Center, 3015 CE, Rotterdam, The Netherlands
| | - Florence Menegaux
- Cancer and Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, 94807, Villejuif Cédex, France
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, University of Cambridge, Cambridge, CB2 2QQ, UK
| | - Lisa A Cannon-Albright
- Division of Genetic Epidemiology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, 84148, USA
| | - Hardev Pandha
- The University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Stephen N Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Daniel J Schaid
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, SE-171 77, Stockholm, Sweden
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, Strangeways Research Laboratory, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Rosalind A Eeles
- The Institute of Cancer Research, London, SW7 3RP, UK
- Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | | | - David V Conti
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, 90033, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, 90033, USA.
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8
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Teerlink CC, Leongamornlert D, Dadaev T, Thomas A, Farnham J, Stephenson RA, Riska S, McDonnell SK, Schaid DJ, Catalona WJ, Zheng SL, Cooney KA, Ray AM, Zuhlke KA, Lange EM, Giles GG, Southey MC, Fitzgerald LM, Rinckleb A, Luedeke M, Maier C, Stanford JL, Ostrander EA, Kaikkonen EM, Sipeky C, Tammela T, Schleutker J, Wiley KE, Isaacs SD, Walsh PC, Isaacs WB, Xu J, Cancel-Tassin G, Cussenot O, Mandal D, Laurie C, Laurie C, Thibodeau SN, Eeles RA, Kote-Jarai Z, Cannon-Albright L. Genome-wide association of familial prostate cancer cases identifies evidence for a rare segregating haplotype at 8q24.21. Hum Genet 2016; 135:923-38. [PMID: 27262462 PMCID: PMC5020907 DOI: 10.1007/s00439-016-1690-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/26/2016] [Indexed: 10/21/2022]
Abstract
Previous genome-wide association studies (GWAS) of prostate cancer risk focused on cases unselected for family history and have reported over 100 significant associations. The International Consortium for Prostate Cancer Genetics (ICPCG) has now performed a GWAS of 2511 (unrelated) familial prostate cancer cases and 1382 unaffected controls from 12 member sites. All samples were genotyped on the Illumina 5M+exome single nucleotide polymorphism (SNP) platform. The GWAS identified a significant evidence for association for SNPs in six regions previously associated with prostate cancer in population-based cohorts, including 3q26.2, 6q25.3, 8q24.21, 10q11.23, 11q13.3, and 17q12. Of note, SNP rs138042437 (p = 1.7e(-8)) at 8q24.21 achieved a large estimated effect size in this cohort (odds ratio = 13.3). 116 previously sampled affected relatives of 62 risk-allele carriers from the GWAS cohort were genotyped for this SNP, identifying 78 additional affected carriers in 62 pedigrees. A test for an excess number of affected carriers among relatives exhibited strong evidence for co-segregation of the variant with disease (p = 8.5e(-11)). The majority (92 %) of risk-allele carriers at rs138042437 had a consistent estimated haplotype spanning approximately 100 kb of 8q24.21 that contained the minor alleles of three rare SNPs (dosage minor allele frequencies <1.7 %), rs183373024 (PRNCR1), previously associated SNP rs188140481, and rs138042437 (CASC19). Strong evidence for co-segregation of a SNP on the haplotype further characterizes the haplotype as a prostate cancer predisposition locus.
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Affiliation(s)
- Craig C Teerlink
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA.
| | - Daniel Leongamornlert
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK
| | - Tokhir Dadaev
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK
| | - Alun Thomas
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA
| | - James Farnham
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA
| | - Robert A Stephenson
- Department of Urology, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA
| | - Shaun Riska
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Shannon K McDonnell
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Daniel J Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - William J Catalona
- Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - S Lilly Zheng
- Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Kathleen A Cooney
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Anna M Ray
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Kimberly A Zuhlke
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Ethan M Lange
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, 3010, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - Melissa C Southey
- Department of Pathology, University of Melbourne, Melbourne, 3010, Australia
| | - Liesel M Fitzgerald
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, 3004, Australia
| | - Antje Rinckleb
- Department of Urology, University Hospital Ulm, 53179, Ulm, Germany
| | - Manuel Luedeke
- Department of Urology, University Hospital Ulm, 53179, Ulm, Germany
| | - Christiane Maier
- Institute for Human Genetics, University of Ulm, 89081, Ulm, Germany
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, WA, 98109, USA
| | - Elaine A Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Elina M Kaikkonen
- Department of Medical Biochemistry and Genetics, University of Turku, 20520, Turku, Finland
| | - Csilla Sipeky
- Department of Medical Biochemistry and Genetics, University of Turku, 20520, Turku, Finland
| | - Teuvo Tammela
- Department of Urology, University of Tampere and Tampere University Hospital, 33520, Tampere, Finland
| | - Johanna Schleutker
- Tyks Microbiology and Genetics, Department of Medical Genetics, Turku University Hospital, 20520, Turku, Finland
| | - Kathleen E Wiley
- Brady Urological Institute, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Sarah D Isaacs
- Brady Urological Institute, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Patrick C Walsh
- Brady Urological Institute, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - William B Isaacs
- Brady Urological Institute, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, IL, 60201, USA
| | | | - Olivier Cussenot
- CeRePP, Hopital Tenon, Assistance Publique-Hopitaux de Paris, 75020, Paris, France
| | - Diptasri Mandal
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Cecelia Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Cathy Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Stephen N Thibodeau
- Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK
| | - Lisa Cannon-Albright
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, 84148, USA
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9
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Wu X, Gu J. Heritability of prostate cancer: a tale of rare variants and common single nucleotide polymorphisms. ANNALS OF TRANSLATIONAL MEDICINE 2016; 4:206. [PMID: 27294245 DOI: 10.21037/atm.2016.05.31] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jian Gu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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10
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Gusev A, Shi H, Kichaev G, Pomerantz M, Li F, Long HW, Ingles SA, Kittles RA, Strom SS, Rybicki BA, Nemesure B, Isaacs WB, Zheng W, Pettaway CA, Yeboah ED, Tettey Y, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Chokkalingam AP, John EM, Murphy AB, Signorello LB, Carpten J, Leske MC, Wu SY, Hennis AJM, Neslund-Dudas C, Hsing AW, Chu L, Goodman PJ, Klein EA, Witte JS, Casey G, Kaggwa S, Cook MB, Stram DO, Blot WJ, Eeles RA, Easton D, Kote-Jarai ZS, Al Olama AA, Benlloch S, Muir K, Giles GG, Southey MC, Fitzgerald LM, Gronberg H, Wiklund F, Aly M, Henderson BE, Schleutker J, Wahlfors T, Tammela TLJ, Nordestgaard BG, Key TJ, Travis RC, Neal DE, Donovan JL, Hamdy FC, Pharoah P, Pashayan N, Khaw KT, Stanford JL, Thibodeau SN, McDonnell SK, Schaid DJ, Maier C, Vogel W, Luedeke M, Herkommer K, Kibel AS, Cybulski C, Wokolorczyk D, Kluzniak W, Cannon-Albright L, Teerlink C, Brenner H, Dieffenbach AK, Arndt V, Park JY, Sellers TA, Lin HY, Slavov C, Kaneva R, Mitev V, Batra J, Spurdle A, Clements JA, Teixeira MR, Pandha H, Michael A, Paulo P, Maia S, Kierzek A, Conti DV, Albanes D, Berg C, Berndt SI, Campa D, Crawford ED, Diver WR, Gapstur SM, Gaziano JM, Giovannucci E, Hoover R, Hunter DJ, Johansson M, Kraft P, Le Marchand L, Lindström S, Navarro C, Overvad K, Riboli E, Siddiq A, Stevens VL, Trichopoulos D, Vineis P, Yeager M, Trynka G, Raychaudhuri S, Schumacher FR, Price AL, Freedman ML, Haiman CA, Pasaniuc B. Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation. Nat Commun 2016; 7:10979. [PMID: 27052111 PMCID: PMC4829663 DOI: 10.1038/ncomms10979] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 02/03/2016] [Indexed: 12/22/2022] Open
Abstract
Although genome-wide association studies have identified over 100 risk loci that explain ∼33% of familial risk for prostate cancer (PrCa), their functional effects on risk remain largely unknown. Here we use genotype data from 59,089 men of European and African American ancestries combined with cell-type-specific epigenetic data to build a genomic atlas of single-nucleotide polymorphism (SNP) heritability in PrCa. We find significant differences in heritability between variants in prostate-relevant epigenetic marks defined in normal versus tumour tissue as well as between tissue and cell lines. The majority of SNP heritability lies in regions marked by H3k27 acetylation in prostate adenoc7arcinoma cell line (LNCaP) or by DNaseI hypersensitive sites in cancer cell lines. We find a high degree of similarity between European and African American ancestries suggesting a similar genetic architecture from common variation underlying PrCa risk. Our findings showcase the power of integrating functional annotation with genetic data to understand the genetic basis of PrCa.
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Affiliation(s)
- Alexander Gusev
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Huwenbo Shi
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Gleb Kichaev
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Mark Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Fugen Li
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Henry W. Long
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts 02115, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Sue A. Ingles
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Rick A. Kittles
- University of Arizona College of Medicine and University of Arizona Cancer Center, Tucson, Arizona 85721, USA
| | - Sara S. Strom
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Benjamin A. Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, Michigan 48202, USA
| | - Barbara Nemesure
- Department of Preventive Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - William B. Isaacs
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, Maryland 21205, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Curtis A. Pettaway
- Department of Urology, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Edward D. Yeboah
- Korle Bu Teaching Hospital, Accra, Ghana
- University of Ghana Medical School, Accra, Ghana
| | - Yao Tettey
- Korle Bu Teaching Hospital, Accra, Ghana
- University of Ghana Medical School, Accra, Ghana
| | - Richard B. Biritwum
- Korle Bu Teaching Hospital, Accra, Ghana
- University of Ghana Medical School, Accra, Ghana
| | - Andrew A. Adjei
- Korle Bu Teaching Hospital, Accra, Ghana
- University of Ghana Medical School, Accra, Ghana
| | - Evelyn Tay
- Korle Bu Teaching Hospital, Accra, Ghana
- University of Ghana Medical School, Accra, Ghana
| | | | | | | | - Esther M. John
- Cancer Prevention Institute of California, Fremont, California 94538, USA
- Stanford University School of Medicine and Stanford Cancer Institute, Palo Alto, California 94305, USA
| | - Adam B. Murphy
- Department of Urology, Northwestern University, Chicago, Illinois 60611, USA
| | - Lisa B. Signorello
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- International Epidemiology Institute, Rockville, Maryland 20850, USA
| | - John Carpten
- The Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - M. Cristina Leske
- Department of Preventive Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Suh-Yuh Wu
- Department of Preventive Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Anslem J. M. Hennis
- Department of Preventive Medicine, Stony Brook University, Stony Brook, New York 11794, USA
- Chronic Disease Research Centre and Faculty of Medical Sciences, University of the West Indies, Bridgetown, Barbados
| | | | - Ann W. Hsing
- Cancer Prevention Institute of California, Fremont, California 94538, USA
- Stanford University School of Medicine and Stanford Cancer Institute, Palo Alto, California 94305, USA
| | - Lisa Chu
- Cancer Prevention Institute of California, Fremont, California 94538, USA
- Stanford University School of Medicine and Stanford Cancer Institute, Palo Alto, California 94305, USA
| | - Phyllis J. Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Eric A. Klein
- Glickman Urological & Kidney Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - John S. Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California 94118, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California 94118, USA
| | - Graham Casey
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Sam Kaggwa
- Department of Surgery, Makerere University College of Health Sciences, Kampala 94118, Uganda
| | - Michael B. Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Daniel O. Stram
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - William J. Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
- International Epidemiology Institute, Rockville, Maryland 20850, USA
| | - Rosalind A. Eeles
- The Institute of Cancer Research, Sutton SM2 5NG, UK
- Royal Marsden National Health Service (NHS) Foundation Trust, London and Sutton, UK
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | | | - Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - Sara Benlloch
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - Kenneth Muir
- Institute of Population Health, University of Manchester, Manchester M13 9PL, UK
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Graham G. Giles
- Cancer Epidemiology Centre, The Cancer Council Victoria, 615 St Kilda Road, Melbourne, Victoria 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria 3004, Australia
| | - Melissa C. Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Grattan Street, Parkville, Victoria 3010, Australia
| | - Liesel M. Fitzgerald
- Cancer Epidemiology Centre, The Cancer Council Victoria, 615 St Kilda Road, Melbourne, Victoria 3004, Australia
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm 171 77, Sweden
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm 171 77, Sweden
| | - Markus Aly
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm 171 77, Sweden
- Department of Clinical Sciences at Danderyds Hospital, Stockholm 171 77, Sweden
| | - Brian E. Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California 90007, USA
| | - Johanna Schleutker
- Department of Medical Biochemistry and Genetics Institute of Biomedicine Kiinamyllynkatu 10, University of Turku, Turku FI-20014, Finland
- BioMediTech, University of Tampere and FimLab Laboratories, Tampere 33200, Finland
| | - Tiina Wahlfors
- BioMediTech, University of Tampere and FimLab Laboratories, Tampere 33200, Finland
| | - Teuvo L. J. Tammela
- Department of Urology, Tampere University Hospital and Medical School, University of Tampere, Tampere 33200, Finland
| | - Børge G. Nordestgaard
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev Ringvej 75, Herlev DK-2730, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1165, Densmark
| | - Tim J. Key
- Cancer Epidemiology, Nuffield Department of Population Health; University of Oxford, Oxford OX3 7LF, UK
| | - Ruth C. Travis
- Cancer Epidemiology, Nuffield Department of Population Health; University of Oxford, Oxford OX3 7LF, UK
| | - David E. Neal
- University of Cambridge, Department of Oncology, Addenbrooke's Hospital, Box 279, Hills Road, Cambridge CB2 0QQ
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Jenny L. Donovan
- School of Social and Community Medicine, University of Bristol, Canynge Hall, 39 Whatley Road, Bristol BS8 2PS, UK
| | - Freddie C. Hamdy
- Department of Public Health, Section for Epidemiology, Aarhus University, Aarhus OX1 3PN, Denmark
- Faculty of Medical Science, University of Oxford, John Radcliffe Hospital, Oxford OX1 3PN, UK
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
| | - Nora Pashayan
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Laboratory, Worts Causeway, Cambridge CB1 8RN, UK
- University College London, Department of Applied Health Research, 1-19 Torrington Place, London WC1E 7HB, UK
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, University of Cambridge, Cambridge CB1 8RN, UK
| | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington 98109, USA
| | | | | | | | - Christiane Maier
- Institute of Human Genetics, University Hospital Ulm, 89081 Ulm, Germany
| | - Walther Vogel
- Institute of Human Genetics, University Hospital Ulm, 89081 Ulm, Germany
| | - Manuel Luedeke
- Department of Urology, University Hospital Ulm, 89081 Ulm, Germany
| | - Kathleen Herkommer
- Department of Urology, Klinikum rechts der Isar der Technischen Universitaet Muenchen, 81675 Munich, Germany
| | - Adam S. Kibel
- Division of Urologic Surgery, Brigham and Womens Hospital, Dana-Farber Cancer Institute, 75 Francis Street, Boston, Massachusetts 02115, USA
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Dominika Wokolorczyk
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Wojciech Kluzniak
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Lisa Cannon-Albright
- Division of Genetic Epidemiology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah 84132, USA
| | - Craig Teerlink
- Division of Genetic Epidemiology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah 84132, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
| | - Aida K. Dieffenbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Jong Y. Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, Florida 33612, USA
| | - Thomas A. Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, Florida 33612, USA
| | - Hui-Yi Lin
- Biostatistics Program, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, Florida 33612, USA
| | - Chavdar Slavov
- Department of Urology and Alexandrovska University Hospital, Medical University, Sofia 1431, Bulgaria
| | - Radka Kaneva
- Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Medical University, Sofia, 2 Zdrave Str., Sofia 1431, Bulgaria
| | - Vanio Mitev
- Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Medical University, Sofia, 2 Zdrave Str., Sofia 1431, Bulgaria
| | - Jyotsna Batra
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Amanda Spurdle
- Molecular Cancer Epidemiology Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland 4000, Australia
| | - Judith A. Clements
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Manuel R. Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto 4200, Portugal
- Biomedical Sciences Institute (ICBAS), University of Porto, Porto 4200, Portugal
| | - Hardev Pandha
- The University of Surrey, Guildford, Surrey GU2 7XH, UK
| | | | - Paula Paulo
- Department of Genetics, Portuguese Oncology Institute, Porto 4200, Portugal
| | - Sofia Maia
- Department of Genetics, Portuguese Oncology Institute, Porto 4200, Portugal
| | | | - David V. Conti
- Department of Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California 90033, USA
| | - Demetrius Albanes
- Nutritional Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institute of Health, Bethesda, Maryland 20892, USA
| | - Christine Berg
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins Medicine, Baltimore, Maryland 21287, USA
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Daniele Campa
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - E. David Crawford
- Urologic Oncology, University of Colorado at Denver Health Sciences Center, Denver, Colorado 80230, USA
| | - W. Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia 30303, USA
| | - Susan M. Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia 30303, USA
| | - J. Michael Gaziano
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
- Division of Aging, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Edward Giovannucci
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Robert Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - David J. Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Mattias Johansson
- International Agency for Research on Cancer, Lyon 69008, France
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå 907 36, Sweden
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii 96813, USA
| | - Sara Lindström
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Carmen Navarro
- Department of Epidemiology, Regional Health Authority, Murcia 30009, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 28029, Spain
| | - Kim Overvad
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins Medicine, Baltimore, Maryland 21287, USA
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - Afshan Siddiq
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - Victoria L. Stevens
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia 30303, USA
| | - Dimitrios Trichopoulos
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Bureau of Epidemiologic Research, Academy of Athens, Athens 106 79, Greece
- Hellenic Health Foundation, Athens 106 79, Greece
| | - Paolo Vineis
- HuGeF Foundation, Torino 10126, Italy
- School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Gosia Trynka
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Soumya Raychaudhuri
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Institute of Inflammation and Repair, University of Manchester, Manchester M13 9PT, UK
| | - Frederick R. Schumacher
- Department of Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California 90033, USA
| | - Alkes L. Price
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Matthew L. Freedman
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts 02115, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Christopher A. Haiman
- Department of Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California 90033, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, California 90095, USA
- Departments of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, USA
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California 90095, USA
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11
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Whitington T, Gao P, Song W, Ross-Adams H, Lamb AD, Yang Y, Svezia I, Klevebring D, Mills IG, Karlsson R, Halim S, Dunning MJ, Egevad L, Warren AY, Neal DE, Grönberg H, Lindberg J, Wei GH, Wiklund F. Gene regulatory mechanisms underpinning prostate cancer susceptibility. Nat Genet 2016; 48:387-97. [PMID: 26950096 DOI: 10.1038/ng.3523] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 02/08/2016] [Indexed: 12/29/2022]
Abstract
Molecular characterization of genome-wide association study (GWAS) loci can uncover key genes and biological mechanisms underpinning complex traits and diseases. Here we present deep, high-throughput characterization of gene regulatory mechanisms underlying prostate cancer risk loci. Our methodology integrates data from 295 prostate cancer chromatin immunoprecipitation and sequencing experiments with genotype and gene expression data from 602 prostate tumor samples. The analysis identifies new gene regulatory mechanisms affected by risk locus SNPs, including widespread disruption of ternary androgen receptor (AR)-FOXA1 and AR-HOXB13 complexes and competitive binding mechanisms. We identify 57 expression quantitative trait loci at 35 risk loci, which we validate through analysis of allele-specific expression. We further validate predicted regulatory SNPs and target genes in prostate cancer cell line models. Finally, our integrated analysis can be accessed through an interactive visualization tool. This analysis elucidates how genome sequence variation affects disease predisposition via gene regulatory mechanisms and identifies relevant genes for downstream biomarker and drug development.
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Affiliation(s)
- Thomas Whitington
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ping Gao
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Wei Song
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Helen Ross-Adams
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Alastair D Lamb
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.,Department of Urology, Addenbrooke's Hospital, Cambridge, UK
| | - Yuehong Yang
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Ilaria Svezia
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Daniel Klevebring
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ian G Mills
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.,Department of Molecular Oncology, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway.,Prostate Cancer UK/Movember Centre of Excellence for Prostate Cancer Research, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Silvia Halim
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.,Cancer Research UK Beatson Institute, Glasgow, UK
| | - Mark J Dunning
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Lars Egevad
- Department of Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden.,Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Anne Y Warren
- Department of Pathology, Addenbrooke's Hospital, Cambridge, UK
| | - David E Neal
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Gong-Hong Wei
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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12
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Zhang G, Zhao Y, Liu Y, Kao LP, Wang X, Skerry B, Li Z. FOXA1 defines cancer cell specificity. SCIENCE ADVANCES 2016; 2:e1501473. [PMID: 27034986 PMCID: PMC4803482 DOI: 10.1126/sciadv.1501473] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/27/2016] [Indexed: 06/05/2023]
Abstract
A transcription factor functions differentially and/or identically in multiple cell types. However, the mechanism for cell-specific regulation of a transcription factor remains to be elucidated. We address how a single transcription factor, forkhead box protein A1 (FOXA1), forms cell-specific genomic signatures and differentially regulates gene expression in four human cancer cell lines (HepG2, LNCaP, MCF7, and T47D). FOXA1 is a pioneer transcription factor in organogenesis and cancer progression. Genomewide mapping of FOXA1 by chromatin immunoprecipitation sequencing annotates that target genes associated with FOXA1 binding are mostly common to these cancer cells. However, most of the functional FOXA1 target genes are specific to each cancer cell type. Further investigations using CRISPR-Cas9 genome editing technology indicate that cell-specific FOXA1 regulation is attributable to unique FOXA1 binding, genetic variations, and/or potential epigenetic regulation. Thus, FOXA1 controls the specificity of cancer cell types. We raise a "flower-blooming" hypothesis for cell-specific transcriptional regulation based on these observations.
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13
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Rand KA, Rohland N, Tandon A, Stram A, Sheng X, Do R, Pasaniuc B, Allen A, Quinque D, Mallick S, Le Marchand L, Kaggwa S, Lubwama A, Stram DO, Watya S, Henderson BE, Conti DV, Reich D, Haiman CA. Whole-exome sequencing of over 4100 men of African ancestry and prostate cancer risk. Hum Mol Genet 2016; 25:371-81. [PMID: 26604137 PMCID: PMC4865031 DOI: 10.1093/hmg/ddv462] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 09/14/2015] [Accepted: 11/06/2015] [Indexed: 12/31/2022] Open
Abstract
Prostate cancer is the most common non-skin cancer in males, with a ∼1.5-2-fold higher incidence in African American men when compared with whites. Epidemiologic evidence supports a large heritable contribution to prostate cancer, with over 100 susceptibility loci identified to date that can explain ∼33% of the familial risk. To explore the contribution of both rare and common variation in coding regions to prostate cancer risk, we sequenced the exomes of 2165 prostate cancer cases and 2034 controls of African ancestry at a mean coverage of 10.1×. We identified 395 220 coding variants down to 0.05% frequency [57% non-synonymous (NS), 42% synonymous and 1% gain or loss of stop codon or splice site variant] in 16 751 genes with the strongest associations observed in SPARCL1 on 4q22.1 (rs13051, Ala49Asp, OR = 0.78, P = 1.8 × 10(-6)) and PTPRR on 12q15 (rs73341069, Val239Ile, OR = 1.62, P = 2.5 × 10(-5)). In gene-level testing, the two most significant genes were C1orf100 (P = 2.2 × 10(-4)) and GORAB (P = 2.3 × 10(-4)). We did not observe exome-wide significant associations (after correcting for multiple hypothesis testing) in single variant or gene-level testing in the overall case-control or case-case analyses of disease aggressiveness. In this first whole-exome sequencing study of prostate cancer, our findings do not provide strong support for the hypothesis that NS coding variants down to 0.5-1.0% frequency have large effects on prostate cancer risk in men of African ancestry. Higher-coverage sequencing efforts in larger samples will be needed to study rarer variants with smaller effect sizes associated with prostate cancer risk.
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Affiliation(s)
- Kristin A Rand
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Arti Tandon
- Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alex Stram
- Department of Preventive Medicine, Keck School of Medicine
| | - Xin Sheng
- Department of Preventive Medicine, Keck School of Medicine
| | - Ron Do
- Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, Department of Human Genetics, David Geffen School of Medicine, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alex Allen
- Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dominique Quinque
- Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Loic Le Marchand
- Epidemiology Program, Cancer Research Center, University of Hawaii, Honolulu, HI 96813, USA
| | | | - Alex Lubwama
- School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda and
| | - Daniel O Stram
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Stephen Watya
- School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda and Uro Care, Kampala, Uganda
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - David V Conti
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA,
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14
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Mancuso N, Rohland N, Rand KA, Tandon A, Allen A, Quinque D, Mallick S, Li H, Stram A, Sheng X, Kote-Jarai Z, Easton DF, Eeles RA, Le Marchand L, Lubwama A, Stram D, Watya S, Conti DV, Henderson B, Haiman CA, Pasaniuc B, Reich D. The contribution of rare variation to prostate cancer heritability. Nat Genet 2016; 48:30-5. [PMID: 26569126 PMCID: PMC7534691 DOI: 10.1038/ng.3446] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/20/2015] [Indexed: 12/13/2022]
Abstract
We report targeted sequencing of 63 known prostate cancer risk regions in a multi-ancestry study of 9,237 men and use the data to explore the contribution of low-frequency variation to disease risk. We show that SNPs with minor allele frequencies (MAFs) of 0.1-1% explain a substantial fraction of prostate cancer risk in men of African ancestry. We estimate that these SNPs account for 0.12 (standard error (s.e.) = 0.05) of variance in risk (∼42% of the variance contributed by SNPs with MAF of 0.1-50%). This contribution is much larger than the fraction of neutral variation due to SNPs in this class, implying that natural selection has driven down the frequency of many prostate cancer risk alleles; we estimate the coupling between selection and allelic effects at 0.48 (95% confidence interval [0.19, 0.78]) under the Eyre-Walker model. Our results indicate that rare variants make a disproportionate contribution to genetic risk for prostate cancer and suggest the possibility that rare variants may also have an outsize effect on other common traits.
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Affiliation(s)
- Nicholas Mancuso
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
| | - Kristin A Rand
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Arti Tandon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
| | - Alexander Allen
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
| | - Dominique Quinque
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
| | - Heng Li
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
| | - Alex Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Xin Sheng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | | | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Rosalind A Eeles
- The Institute of Cancer Research, London, UK
- Royal Marsden National Health Service (NHS) Foundation Trust, London and Sutton, UK
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Alex Lubwama
- School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
| | - Daniel Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Stephen Watya
- School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
| | - David V Conti
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Brian Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
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15
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Ren XQ, Zhang JG, Xin SY, Cheng T, Li L, Ren WH. Variants on 8q24 and prostate cancer risk in Chinese population: a meta-analysis. Int J Clin Exp Med 2015; 8:8561-8570. [PMID: 26309507 PMCID: PMC4538115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 05/26/2015] [Indexed: 06/04/2023]
Abstract
Previous studies have identified 8q24 as an important region to prostate cancer (PCa) susceptibility. The aim of this study was to investigate the role of six genetic variants on 8q24 (rs1447295, A; rs6983267, G; rs6983561, C; rs7837688, T; rs10090154, T and rs16901979, A) on PCa risk in Chinese population. Online electronic databases were searched to retrieve related articles concerning the association between 8q24 variants and PCa risk in men of Chinese population published between 2000 and 2014. Odds ratio (ORs) with its 95% correspondence interval (CI) were employed to assess the strength of association. Total eleven case-control studies were screened out, including 2624 PCa patients and 2438 healthy controls. Our results showed that three risk alleles of rs1447295 A (OR=1.35, 95% CI=1.19-1.53, P<0.00001), rs6983561 C (C vs. A: OR=1.41, 95% CI=1.21-1.63, P<0.00001) and rs10090154 T (T vs. C: OR=1.48, 95% CI=1.22-1.80, P<0.00001) on8q24 were significantly associated with PCa risk in Chinese population. Furthermore, genotypes of rs1447295, AA+AC; rs6983561, CC+AC and CC; rs10090154, TT+TC; and rs16901979, AA were associated with PCa as well (P<0.01). No association was found between rs6983267, rs7837688 and PCa risk. In conclusions, variants including rs1447295, rs6983561, rs10090154 and rs16901979 on 8q24 might be associated with PCa risk in Chinese population, indicating these four variations may contribute risk to this disease. This meta-analysis was the first study to assess the role of 8q24 variants on PCa risk in Chinese population.
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Affiliation(s)
- Xiao-Qiang Ren
- Department of Urology, The First Affiliated Hospital of Henan University of Science and TechnoloyLuoyang 471003, He’nan, China
| | - Jian-Guo Zhang
- Department of Urology, The First Affiliated Hospital of Henan University of Science and TechnoloyLuoyang 471003, He’nan, China
| | - Shi-Yong Xin
- Department of Urology, The First Affiliated Hospital of Henan University of Science and TechnoloyLuoyang 471003, He’nan, China
| | - Tao Cheng
- Department of Urology, The First Affiliated Hospital of Henan University of Science and TechnoloyLuoyang 471003, He’nan, China
| | - Liang Li
- Department of Urology, The First Affiliated Hospital of Henan University of Science and TechnoloyLuoyang 471003, He’nan, China
| | - Wei-Hua Ren
- Central Laboratory, Luoyang Central Hospital Affiliated to Zhengzhou UniversityLuoyang 471009, He’nan, China
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16
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Abstract
FOXA1 (also known as hepatocyte nuclear factor 3α, or HNF-3α) is a protein of the FKHD family transcription factors. FOXA1 has been termed as a pioneer transcription factor due to its unique ability of chromatin remodeling in which the chromatin can be de-compacted to allow genomic access by nuclear hormone receptors, including androgen receptor (AR) and estrogen receptor (ER). In this review, we discuss our current understanding of FOXA1 regulation of prostatic and non-prostatic AR-chromatin targeting. We present an updated model wherein FOXA1:AR equilibrium in the nuclei defines prostatic AR binding profile, which is perturbed in prostate cancer with FOXA1 and/or AR de-regulation. Finally, we discuss recent efforts in exploring new horizons of AR-independent functions of FOXA1 in prostate cancer and interesting directions to pursue in future studies.
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Affiliation(s)
- Yeqing Angela Yang
- Division of Hematology/Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jindan Yu
- Division of Hematology/Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA ; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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17
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Hazelett DJ, Rhie SK, Gaddis M, Yan C, Lakeland DL, Coetzee SG, Henderson BE, Noushmehr H, Cozen W, Kote-Jarai Z, Eeles RA, Easton DF, Haiman CA, Lu W, Farnham PJ, Coetzee GA. Comprehensive functional annotation of 77 prostate cancer risk loci. PLoS Genet 2014; 10:e1004102. [PMID: 24497837 PMCID: PMC3907334 DOI: 10.1371/journal.pgen.1004102] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 11/14/2013] [Indexed: 11/19/2022] Open
Abstract
Genome-wide association studies (GWAS) have revolutionized the field of cancer genetics, but the causal links between increased genetic risk and onset/progression of disease processes remain to be identified. Here we report the first step in such an endeavor for prostate cancer. We provide a comprehensive annotation of the 77 known risk loci, based upon highly correlated variants in biologically relevant chromatin annotations--we identified 727 such potentially functional SNPs. We also provide a detailed account of possible protein disruption, microRNA target sequence disruption and regulatory response element disruption of all correlated SNPs at r(2) ≥ 0.88%. 88% of the 727 SNPs fall within putative enhancers, and many alter critical residues in the response elements of transcription factors known to be involved in prostate biology. We define as risk enhancers those regions with enhancer chromatin biofeatures in prostate-derived cell lines with prostate-cancer correlated SNPs. To aid the identification of these enhancers, we performed genomewide ChIP-seq for H3K27-acetylation, a mark of actively engaged enhancers, as well as the transcription factor TCF7L2. We analyzed in depth three variants in risk enhancers, two of which show significantly altered androgen sensitivity in LNCaP cells. This includes rs4907792, that is in linkage disequilibrium (r(2) = 0.91) with an eQTL for NUDT11 (on the X chromosome) in prostate tissue, and rs10486567, the index SNP in intron 3 of the JAZF1 gene on chromosome 7. Rs4907792 is within a critical residue of a strong consensus androgen response element that is interrupted in the protective allele, resulting in a 56% decrease in its androgen sensitivity, whereas rs10486567 affects both NKX3-1 and FOXA-AR motifs where the risk allele results in a 39% increase in basal activity and a 28% fold-increase in androgen stimulated enhancer activity. Identification of such enhancer variants and their potential target genes represents a preliminary step in connecting risk to disease process.
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Affiliation(s)
- Dennis J. Hazelett
- Departments of Urology and Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Suhn Kyong Rhie
- Departments of Urology and Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Malaina Gaddis
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Chunli Yan
- Departments of Urology and Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Daniel L. Lakeland
- Sonny Astani Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, California, United States of America
| | - Simon G. Coetzee
- Department of Genetics, University of São Paulo, Ribeirão Preto, Brazil
| | - Ellipse/GAME-ON consortium
- Department of Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | | | - Brian E. Henderson
- Department of Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Houtan Noushmehr
- Department of Genetics, University of São Paulo, Ribeirão Preto, Brazil
| | - Wendy Cozen
- USC Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | | | - Rosalind A. Eeles
- The Institute of Cancer Research, Sutton, United Kingdom
- Royal Marsden National Health Service (NHS) Foundation Trust, London and Sutton, United Kingdom
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Christopher A. Haiman
- Department of Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Wange Lu
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Peggy J. Farnham
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Gerhard A. Coetzee
- Departments of Urology and Preventive Medicine, Norris Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
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Patnala R, Clements J, Batra J. Candidate gene association studies: a comprehensive guide to useful in silico tools. BMC Genet 2013; 14:39. [PMID: 23656885 PMCID: PMC3655892 DOI: 10.1186/1471-2156-14-39] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 04/15/2013] [Indexed: 01/01/2023] Open
Abstract
The candidate gene approach has been a pioneer in the field of genetic epidemiology, identifying risk alleles and their association with clinical traits. With the advent of rapidly changing technology, there has been an explosion of in silico tools available to researchers, giving them fast, efficient resources and reliable strategies important to find casual gene variants for candidate or genome wide association studies (GWAS). In this review, following a description of candidate gene prioritisation, we summarise the approaches to single nucleotide polymorphism (SNP) prioritisation and discuss the tools available to assess functional relevance of the risk variant with consideration to its genomic location. The strategy and the tools discussed are applicable to any study investigating genetic risk factors associated with a particular disease. Some of the tools are also applicable for the functional validation of variants relevant to the era of GWAS and next generation sequencing (NGS).
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Affiliation(s)
- Radhika Patnala
- Australian Prostate Cancer Research Centre - Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia
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