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Coggins NB, Stultz J, O'Geen H, Carvajal-Carmona LG, Segal DJ. Methods for Scarless, Selection-Free Generation of Human Cells and Allele-Specific Functional Analysis of Disease-Associated SNPs and Variants of Uncertain Significance. Sci Rep 2017; 7:15044. [PMID: 29118424 PMCID: PMC5678142 DOI: 10.1038/s41598-017-15407-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/24/2017] [Indexed: 11/09/2022] Open
Abstract
With the continued emergence of risk loci from Genome-Wide Association studies and variants of uncertain significance identified from patient sequencing, better methods are required to translate these human genetic findings into improvements in public health. Here we combine CRISPR/Cas9 gene editing with an innovative high-throughput genotyping pipeline utilizing KASP (Kompetitive Allele-Specific PCR) genotyping technology to create scarless isogenic cell models of cancer variants in ~1 month. We successfully modeled two novel variants previously identified by our lab in the PALB2 gene in HEK239 cells, resulting in isogenic cells representing all three genotypes for both variants. We also modeled a known functional risk SNP of colorectal cancer, rs6983267, in HCT-116 cells. Cells with extremely low levels of gene editing could still be identified and isolated using this approach. We also introduce a novel molecular assay, ChIPnQASO (Chromatin Immunoprecipitation and Quantitative Allele-Specific Occupation), which uses the same technology to reveal allele-specific function of these variants at the DNA-protein interaction level. We demonstrated preferential binding of the transcription factor TCF7L2 to the rs6983267 risk allele over the non-risk. Our pipeline provides a platform for functional variant discovery and validation that is accessible and broadly applicable for the progression of efforts towards precision medicine.
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Affiliation(s)
- Nicole B Coggins
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, 95616, USA
| | - Jacob Stultz
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, 95616, USA
| | - Henriette O'Geen
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, 95616, USA
| | - Luis G Carvajal-Carmona
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, 95616, USA.
| | - David J Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, 95616, USA.
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52
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Gallagher MD, Posavi M, Huang P, Unger TL, Berlyand Y, Gruenewald AL, Chesi A, Manduchi E, Wells AD, Grant SFA, Blobel GA, Brown CD, Chen-Plotkin AS. A Dementia-Associated Risk Variant near TMEM106B Alters Chromatin Architecture and Gene Expression. Am J Hum Genet 2017; 101:643-663. [PMID: 29056226 DOI: 10.1016/j.ajhg.2017.09.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 09/08/2017] [Indexed: 12/13/2022] Open
Abstract
Neurodegenerative diseases pose an extraordinary threat to the world's aging population, yet no disease-modifying therapies are available. Although genome-wide association studies (GWASs) have identified hundreds of risk loci for neurodegeneration, the mechanisms by which these loci influence disease risk are largely unknown. Here, we investigated the association between common genetic variants at the 7p21 locus and risk of the neurodegenerative disease frontotemporal lobar degeneration. We showed that variants associated with disease risk correlate with increased expression of the 7p21 gene TMEM106B and no other genes; co-localization analyses implicated a common causal variant underlying both association with disease and association with TMEM106B expression in lymphoblastoid cell lines and human brain. Furthermore, increases in the amount of TMEM106B resulted in increases in abnormal lysosomal phenotypes and cell toxicity in both immortalized cell lines and neurons. We then combined fine-mapping, bioinformatics, and bench-based approaches to functionally characterize all candidate causal variants at this locus. This approach identified a noncoding variant, rs1990620, that differentially recruits CTCF in lymphoblastoid cell lines and human brain to influence CTCF-mediated long-range chromatin-looping interactions between multiple cis-regulatory elements, including the TMEM106B promoter. Our findings thus provide an in-depth analysis of the 7p21 locus linked by GWASs to frontotemporal lobar degeneration, nominating a causal variant and causal mechanism for allele-specific expression and disease association at this locus. Finally, we show that genetic variants associated with risk of neurodegenerative diseases beyond frontotemporal lobar degeneration are enriched in CTCF-binding sites found in brain-relevant tissues, implicating CTCF-mediated gene regulation in risk of neurodegeneration more generally.
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Affiliation(s)
- Michael D Gallagher
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marijan Posavi
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peng Huang
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Travis L Unger
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yosef Berlyand
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Analise L Gruenewald
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elisabetta Manduchi
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Struan F A Grant
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Gerd A Blobel
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Christopher D Brown
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Alice S Chen-Plotkin
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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53
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Sattarifard H, Hashemi M, Hassanzarei S, Narouie B, Bahari G. Association between genetic polymorphisms of long non-coding RNA PRNCR1 and prostate cancer risk in a sample of the Iranian population. Mol Clin Oncol 2017; 7:1152-1158. [PMID: 29285392 DOI: 10.3892/mco.2017.1462] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/18/2017] [Indexed: 12/19/2022] Open
Abstract
The aim of the present study was to determine whether there is an association between the long non-coding RNA (lncRNA) prostate cancer-associated non-coding RNA 1 (PRNCR1) polymorphisms and prostate cancer (PCa) risk in a sample of the Iranian population. This case-control study was performed on 178 patients with PCa and 180 subjects with benign prostatic hyperplasia (BPH). Genotyping assay was performed by polymerase chain reaction-restriction fragment length polymorphism. The findings indicated that the GG genotype of the rs13252298 A>G variant significantly increased the risk of PCa (odds ratio=3.49, 95% confidence interval: 1.79-6.81, P=0.0001) compared with AA+AG. As regards the rs1456315 G>A polymorphism, the AG genotype and G allele significantly increased the risk of PCa. As regards the rs7841060 T>G variant, the findings demonstrated that this TG genotype and the G allele significantly increased the risk of PCa. The rs7007694 T>C variant was not found to be associated with the risk of PCa. Haplotype analysis indicated that GTGA and GTGG significantly increased the risk of PCa compared with rs1456315A/rs7007694T/rs7841060T/rs13252298G (ATTG). The PRNCR1 variants were not found to be significantly associated with the clinicopathological characteristics of PCa patients. In conclusion, our findings support an association between PRNCR1 variants and the risk of PCa in a sample of the Iranian population.
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Affiliation(s)
- Hedieh Sattarifard
- Cellular and Molecular Research Center, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-43181, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-43181, Iran
| | - Mohammad Hashemi
- Cellular and Molecular Research Center, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-43181, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-43181, Iran
| | - Shekoofeh Hassanzarei
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-43181, Iran
| | - Behzad Narouie
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran 198396-3113, Iran
| | - Gholamreza Bahari
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-43181, Iran
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54
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Elkon R, Agami R. Characterization of noncoding regulatory DNA in the human genome. Nat Biotechnol 2017; 35:732-746. [DOI: 10.1038/nbt.3863] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 03/31/2017] [Indexed: 12/22/2022]
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55
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Canver MC, Bauer DE, Orkin SH. Functional interrogation of non-coding DNA through CRISPR genome editing. Methods 2017; 121-122:118-129. [PMID: 28288828 PMCID: PMC5483188 DOI: 10.1016/j.ymeth.2017.03.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/18/2017] [Accepted: 03/03/2017] [Indexed: 12/26/2022] Open
Abstract
Methodologies to interrogate non-coding regions have lagged behind coding regions despite comprising the vast majority of the genome. However, the rapid evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing has provided a multitude of novel techniques for laboratory investigation including significant contributions to the toolbox for studying non-coding DNA. CRISPR-mediated loss-of-function strategies rely on direct disruption of the underlying sequence or repression of transcription without modifying the targeted DNA sequence. CRISPR-mediated gain-of-function approaches similarly benefit from methods to alter the targeted sequence through integration of customized sequence into the genome as well as methods to activate transcription. Here we review CRISPR-based loss- and gain-of-function techniques for the interrogation of non-coding DNA.
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Affiliation(s)
| | - Daniel E Bauer
- Harvard Medical School, Boston, MA 02115, United States; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, United States; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States.
| | - Stuart H Orkin
- Harvard Medical School, Boston, MA 02115, United States; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, United States; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States; Howard Hughes Medical Institute, Boston, MA 02115, United States.
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56
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Lakshminarasimhan R, Andreu-Vieyra C, Lawrenson K, Duymich CE, Gayther SA, Liang G, Jones PA. Down-regulation of ARID1A is sufficient to initiate neoplastic transformation along with epigenetic reprogramming in non-tumorigenic endometriotic cells. Cancer Lett 2017; 401:11-19. [PMID: 28483516 DOI: 10.1016/j.canlet.2017.04.040] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 04/25/2017] [Accepted: 04/26/2017] [Indexed: 12/28/2022]
Abstract
The chromatin remodeler AT-Rich Interactive Domain 1A (ARID1A) is frequently mutated in ovarian clear cell carcinoma (OCCC) and endometriosis precursor lesions. Here, we show that knocking down ARID1A in an immortalized endometriosis cell line is sufficient to induce phenotypic changes indicative of neoplastic transformation as evidenced by higher efficiency of anchorage-independent growth, increased propensity to adhere to collagen, and greater capacity to invade basement membrane extract in vitro. ARID1A knockdown is associated with expression dysregulation of 99 target genes, and many of these expression changes are also observed in primary OCCC tissues. Further, pathway analysis indicates these genes fall within networks highly relevant to tumorigenesis including integrin and paxillin pathways. We demonstrate that the down-regulation of ARID1A does not markedly alter global chromatin accessibility or DNA methylation but unexpectedly, we find strong increases in the active H3K27ac mark in promoter regions and decreases of H3K27ac at potential enhancers. Taken together, these data provide evidence that ARID1A mutation can be an early stage event in the oncogenic transformation of endometriosis cells giving rise to OCCC.
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Affiliation(s)
- Ranjani Lakshminarasimhan
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Claudia Andreu-Vieyra
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Kate Lawrenson
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA; Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA
| | - Christopher E Duymich
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Simon A Gayther
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA; Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Gangning Liang
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
| | - Peter A Jones
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Biochemistry & Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Van Andel Research Institute, Grand Rapids, MI 49503, USA.
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57
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Phelan CM, Kuchenbaecker KB, Tyrer JP, Kar SP, Lawrenson K, Winham SJ, Dennis J, Pirie A, Riggan M, Chornokur G, Earp MA, Lyra PC, Lee JM, Coetzee S, Beesley J, McGuffog L, Soucy P, Dicks E, Lee A, Barrowdale D, Lecarpentier J, Leslie G, Aalfs CM, Aben KK, Adams M, Adlard J, Andrulis IL, Anton-Culver H, Antonenkova N, Aravantinos G, Arnold N, Arun BK, Arver B, Azzollini J, Balmaña J, Banerjee SN, Barjhoux L, Barkardottir RB, Bean Y, Beckmann MW, Beeghly-Fadiel A, Benitez J, Bermisheva M, Bernardini MQ, Birrer MJ, Bjorge L, Black A, Blankstein K, Blok MJ, Bodelon C, Bogdanova N, Bojesen A, Bonanni B, Borg Å, Bradbury AR, Brenton JD, Brewer C, Brinton L, Broberg P, Brooks-Wilson A, Bruinsma F, Brunet J, Buecher B, Butzow R, Buys SS, Caldes T, Caligo MA, Campbell I, Cannioto R, Carney ME, Cescon T, Chan SB, Chang-Claude J, Chanock S, Chen XQ, Chiew YE, Chiquette J, Chung WK, Claes KB, Conner T, Cook LS, Cook J, Cramer DW, Cunningham JM, D’Aloisio AA, Daly MB, Damiola F, Damirovna SD, Dansonka-Mieszkowska A, Dao F, Davidson R, DeFazio A, Delnatte C, Doheny KF, Diez O, Ding YC, Doherty JA, Domchek SM, Dorfling CM, Dörk T, Dossus L, Duran M, Dürst M, Dworniczak B, Eccles D, Edwards T, Eeles R, Eilber U, Ejlertsen B, Ekici AB, Ellis S, Elvira M, Eng KH, Engel C, Evans DG, Fasching PA, Ferguson S, Ferrer SF, Flanagan JM, Fogarty ZC, Fortner RT, Fostira F, Foulkes WD, Fountzilas G, Fridley BL, Friebel TM, Friedman E, Frost D, Ganz PA, Garber J, García MJ, Garcia-Barberan V, Gehrig A, Gentry-Maharaj A, Gerdes AM, Giles GG, Glasspool R, Glendon G, Godwin AK, Goldgar DE, Goranova T, Gore M, Greene MH, Gronwald J, Gruber S, Hahnen E, Haiman CA, Håkansson N, Hamann U, Hansen TV, Harrington PA, Harris HR, Hauke J, Hein A, Henderson A, Hildebrandt MA, Hillemanns P, Hodgson S, Høgdall CK, Høgdall E, Hogervorst FB, Holland H, Hooning MJ, Hosking K, Huang RY, Hulick PJ, Hung J, Hunter DJ, Huntsman DG, Huzarski T, Imyanitov EN, Isaacs C, Iversen ES, Izatt L, Izquierdo A, Jakubowska A, James P, Janavicius R, Jernetz M, Jensen A, Jensen UB, John EM, Johnatty S, Jones ME, Kannisto P, Karlan BY, Karnezis A, Kast K, Kennedy CJ, Khusnutdinova E, Kiemeney LA, Kiiski JI, Kim SW, Kjaer SK, Köbel M, Kopperud RK, Kruse TA, Kupryjanczyk J, Kwong A, Laitman Y, Lambrechts D, Larrañaga N, Larson MC, Lazaro C, Le ND, Le Marchand L, Lee JW, Lele SB, Leminen A, Leroux D, Lester J, Lesueur F, Levine DA, Liang D, Liebrich C, Lilyquist J, Lipworth L, Lissowska J, Lu KH, Lubiński J, Luccarini C, Lundvall L, Mai PL, Mendoza-Fandiño G, Manoukian S, Massuger LF, May T, Mazoyer S, McAlpine JN, McGuire V, McLaughlin JR, McNeish I, Meijers-Heijboer H, Meindl A, Menon U, Mensenkamp AR, Merritt MA, Milne RL, Mitchell G, Modugno F, Moes-Sosnowska J, Moffitt M, Montagna M, Moysich KB, Mulligan AM, Musinsky J, Nathanson KL, Nedergaard L, Ness RB, Neuhausen SL, Nevanlinna H, Niederacher D, Nussbaum RL, Odunsi K, Olah E, Olopade OI, Olsson H, Olswold C, O’Malley DM, Ong KR, Onland-Moret NC, Orr N, Orsulic S, Osorio A, Palli D, Papi L, Park-Simon TW, Paul J, Pearce CL, Pedersen IS, Peeters PH, Peissel B, Peixoto A, Pejovic T, Pelttari LM, Permuth JB, Peterlongo P, Pezzani L, Pfeiler G, Phillips KA, Piedmonte M, Pike MC, Piskorz AM, Poblete SR, Pocza T, Poole EM, Poppe B, Porteous ME, Prieur F, Prokofyeva D, Pugh E, Pujana MA, Pujol P, Radice P, Rantala J, Rappaport-Fuerhauser C, Rennert G, Rhiem K, Rice P, Richardson A, Robson M, Rodriguez GC, Rodríguez-Antona C, Romm J, Rookus MA, Rossing MA, Rothstein JH, Rudolph A, Runnebaum IB, Salvesen HB, Sandler DP, Schoemaker MJ, Senter L, Setiawan VW, Severi G, Sharma P, Shelford T, Siddiqui N, Side LE, Sieh W, Singer CF, Sobol H, Song H, Southey MC, Spurdle AB, Stadler Z, Steinemann D, Stoppa-Lyonnet D, Sucheston-Campbell LE, Sukiennicki G, Sutphen R, Sutter C, Swerdlow AJ, Szabo CI, Szafron L, Tan YY, Taylor JA, Tea MK, Teixeira MR, Teo SH, Terry KL, Thompson PJ, Thomsen LCV, Thull DL, Tihomirova L, Tinker AV, Tischkowitz M, Tognazzo S, Toland AE, Tone A, Trabert B, Travis RC, Trichopoulou A, Tung N, Tworoger SS, van Altena AM, Van Den Berg D, van der Hout AH, van der Luijt RB, Van Heetvelde M, Van Nieuwenhuysen E, van Rensburg EJ, Vanderstichele A, Varon-Mateeva R, Ana V, Edwards DV, Vergote I, Vierkant RA, Vijai J, Vratimos A, Walker L, Walsh C, Wand D, Wang-Gohrke S, Wappenschmidt B, Webb PM, Weinberg CR, Weitzel JN, Wentzensen N, Whittemore AS, Wijnen JT, Wilkens LR, Wolk A, Woo M, Wu X, Wu AH, Yang H, Yannoukakos D, Ziogas A, Zorn KK, Narod SA, Easton DF, Amos CI, Schildkraut JM, Ramus SJ, Ottini L, Goodman MT, Park SK, Kelemen LE, Risch HA, Thomassen M, Offit K, Simard J, Schmutzler RK, Hazelett D, Monteiro AN, Couch FJ, Berchuck A, Chenevix-Trench G, Goode EL, Sellers TA, Gayther SA, Antoniou AC, Pharoah PD. Identification of 12 new susceptibility loci for different histotypes of epithelial ovarian cancer. Nat Genet 2017; 49:680-691. [PMID: 28346442 PMCID: PMC5612337 DOI: 10.1038/ng.3826] [Citation(s) in RCA: 304] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 03/03/2017] [Indexed: 12/14/2022]
Abstract
To identify common alleles associated with different histotypes of epithelial ovarian cancer (EOC), we pooled data from multiple genome-wide genotyping projects totaling 25,509 EOC cases and 40,941 controls. We identified nine new susceptibility loci for different EOC histotypes: six for serous EOC histotypes (3q28, 4q32.3, 8q21.11, 10q24.33, 18q11.2 and 22q12.1), two for mucinous EOC (3q22.3 and 9q31.1) and one for endometrioid EOC (5q12.3). We then performed meta-analysis on the results for high-grade serous ovarian cancer with the results from analysis of 31,448 BRCA1 and BRCA2 mutation carriers, including 3,887 mutation carriers with EOC. This identified three additional susceptibility loci at 2q13, 8q24.1 and 12q24.31. Integrated analyses of genes and regulatory biofeatures at each locus predicted candidate susceptibility genes, including OBFC1, a new candidate susceptibility gene for low-grade and borderline serous EOC.
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Affiliation(s)
- Catherine M. Phelan
- Departments of Cancer Epidemiology and Gynecologic Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Karoline B. Kuchenbaecker
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, UK
| | - Jonathan P. Tyrer
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Siddhartha P. Kar
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Kate Lawrenson
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA
| | - Stacey J. Winham
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Joe Dennis
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Ailith Pirie
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Marjorie Riggan
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Ganna Chornokur
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Madalene A. Earp
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Paulo C. Lyra
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Janet M. Lee
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Simon Coetzee
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jonathan Beesley
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Penny Soucy
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center and Laval University, 2705 Laurier Boulevard, Quebec City (Quebec), Canada
| | - Ed Dicks
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Andrew Lee
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Daniel Barrowdale
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Julie Lecarpentier
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Goska Leslie
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Cora M. Aalfs
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Katja K.H. Aben
- Radboud university medical center, Radboud Institute for Health Sciences, Department for Health Evidence, Nijmegen, The Netherlands
- Netherlands Comprehensive Cancer Organisation, Utrecht, The Netherlands
| | - Marcia Adams
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224
| | - Julian Adlard
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, UK
| | - Irene L. Andrulis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Departments of Molecular Genetics and Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, Director of Genetic Epidemiology Research Institute, UCI Center for Cancer Genetics Research & Prevention, School of Medicine, University of California Irvine, Irvine, California, USA
| | | | - AOCS study group
- A list of members and affiliations appears in the Supplementary note
| | | | - Norbert Arnold
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Germany
| | - Banu K. Arun
- Department of Breast Medical Oncology and Clinical Cancer Genetics Program, University Of Texas MD Andersson Cancer Center, 1515 Pressler Street, CBP 5, Houston, TX, USA
| | - Brita Arver
- Department of Oncology and Pathology, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Jacopo Azzollini
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale Tumori (INT), Via Giacomo Venezian 1, 20133 Milan, Italy
| | - Judith Balmaña
- Department of Medical Oncology, University Hospital, Vall d’Hebron, Barcelona, Spain
| | | | - Laure Barjhoux
- Bâtiment Cheney D, Centre Léon Bérard, 28 rue Laënnec, Lyon, France
| | - Rosa B. Barkardottir
- Laboratory of Cell Biology, Department of Pathology, hus 9, Landspitali-LSH v/Hringbraut, 101 Reykjavik, Iceland
- BMC (Biomedical Centre), Faculty of Medicine, University of Iceland, Vatnsmyrarvegi 16, 101 Reykjavik, Iceland
| | - Yukie Bean
- Department of Gynecologic Oncology, Oregon Health & Science University, Portland, OR, USA; Knight Cancer Institute, Portland, OR, USA
| | - Matthias W. Beckmann
- Universtiy Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen Nuremberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
| | - Alicia Beeghly-Fadiel
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Institute for Medicine and Public Health, Vanderbilt University Medical Center, Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Javier Benitez
- Human Genetics Group, Spanish National Cancer Centre (CNIO), and Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics, Ufa Science Center, Russian Academy of Sciences, Ufa, Bashkortostan, Russia
| | - Marcus Q. Bernardini
- Division of Gynecologic Oncology, Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada
| | | | - Line Bjorge
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Amanda Black
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Kenneth Blankstein
- Clinical Cancer Genetics, for the City of Hope Clinical Cancer Genetics Community Research Network, Duarte, CA, USA
| | - Marinus J. Blok
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Clara Bodelon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Natalia Bogdanova
- Radiation Oncology Research Unit, Hannover Medical School, Hannover, Germany
| | - Anders Bojesen
- Department of Clinical Genetics, Vejle Hospital, Vejle, Denmark
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia (IEO), via Ripamonti 435, 20141 Milan, Italy
| | - Åke Borg
- Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
| | - Angela R. Bradbury
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA, USA
| | - James D. Brenton
- Cancer Research UK (CRUK) Cambridge Institute, University of Cambridge
| | - Carole Brewer
- Department of Clinical Genetics, Royal Devon and Exeter Hospital, Exeter, UK
| | - Louise Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Per Broberg
- Department of Cancer Epidemiology, University Hospital, Lund, Lund University, Lund, Sweden
| | - Angela Brooks-Wilson
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - Fiona Bruinsma
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Joan Brunet
- Genetic Counseling Unit, Hereditary Cancer Program, IDIBGI (Institut d’Investigació Biomèdica de Girona), Catalan Institute of Oncology. Av. França s/n. 1707 Girona, Spain
| | - Bruno Buecher
- Service de Génétique Oncologique, Institut Curie, 26, rue d’Ulm, Paris Cedex 05, France
| | - Ralf Butzow
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Saundra S. Buys
- Department of Medicine, Huntsman Cancer Institute, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
| | - Trinidad Caldes
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Martin Lagos s/n, Madrid, Spain
| | - Maria A. Caligo
- Section of Genetic Oncology, Dept. of Laboratory Medicine, University and University Hospital of Pisa, Pisa Italy
| | - Ian Campbell
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Department of Pathology, University of Melbourne, Parkville, VIC, Australia
| | - Rikki Cannioto
- Cancer Pathology & Prevention, Division of Cancer Prevention and Population Sciences, Roswell Park Cancer Institute, Buffalo, NY
| | - Michael E. Carney
- Department of Obstetrics and Gynecology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA
| | - Terence Cescon
- Clinical Cancer Genetics, for the City of Hope Clinical Cancer Genetics Community Research Network, Duarte, CA, USA
| | - Salina B. Chan
- University of California, San Francisco, 1600 Divisadero Street, C415, San Francisco, CA 94143 - 1714, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Xiao Qing Chen
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Yoke-Eng Chiew
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
| | - Jocelyne Chiquette
- Unité de Recherche en Santé des Populations, Centre des Maladies du Sein Deschênes-Fabia, Centre de Recherche FRSQ du Centre Hospitalier Affilié Universitaire de Québec, Québec, QC, Canada
| | - Wendy K. Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | | | - Thomas Conner
- Department of Medicine, Huntsman Cancer Institute, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
| | - Linda S. Cook
- Division of Epidemiology, Biostatistics and Preventative Medicine, Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, USA
| | - Jackie Cook
- Sheffield Clinical Genetics Service, Sheffield Children’s Hospital, Sheffield, UK
| | - Daniel W. Cramer
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Julie M. Cunningham
- Department of Laboratory Medicine and Pathology,Division of Experimental Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Mary B. Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | | | | | - Agnieszka Dansonka-Mieszkowska
- Department of Pathology and Laboratory Diagnostics, the Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Fanny Dao
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rosemarie Davidson
- Department of Clinical Genetics, South Glasgow University Hospitals, Glasgow, UK
| | - Anna DeFazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
| | - Capucine Delnatte
- Unité d’oncogénétique, ICO-Centre René Gauducheau, Boulevard Jacques Monod, 44805 Nantes Saint Herblain Cedex, France
| | - Kimberly F. Doheny
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224
| | - Orland Diez
- Oncogenetics Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Clinical and Molecular Genetics Area, Vall d’Hebron University Hospital. Barcelona, Spain
| | - Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jennifer Anne Doherty
- Department of Epidemiology, The Geisel School of Medicine - at Dartmouth, Hanover, New Hampshire, USA
| | - Susan M. Domchek
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA, USA
| | - Cecilia M. Dorfling
- Cancer Genetics Laboratory, Department of Genetics, University of Pretoria,Pretoria, South Africa
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Laure Dossus
- Nutrition and Metabolism Section, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Mercedes Duran
- Institute of Biology and Molecular Genetics, Universidad de Valladolid (IBGM-UVA), Valladolid, Spain
| | - Matthias Dürst
- Department of Gynecology, Jena University Hospital - Friedrich Schiller University, Jena, Germany
| | | | - Diana Eccles
- University of Southampton Faculty of Medicine, Southampton University Hospitals NHS Trust, Southampton, UK
| | - Todd Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Institute for Medicine and Public Health, Vanderbilt University Medical Center, Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Ros Eeles
- Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Ursula Eilber
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bent Ejlertsen
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Arif B. Ekici
- Institute of Human Genetics, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Steve Ellis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Mingajeva Elvira
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Study EMBRACE
- A list of members and affiliations appears in the Supplementary note
| | - Kevin H. Eng
- Department of Biostatistics & Bioinformatics, Roswell park Institute, Buffalo, NY, USA
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - D. Gareth Evans
- Genomic Medicine, Manchester Academic Health Sciences Centre, University of Manchester, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Peter A. Fasching
- Universtiy Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen Nuremberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
- University of California at Los Angeles, David Geffen School of Medicine, Department of Medicine, Division of Hematology and Oncology, Los Angeles, CA, USA
| | - Sarah Ferguson
- Division of Gynecologic Oncology, Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada
| | - Sandra Fert Ferrer
- Laboratoire de Génétique Chromosomique, Hôtel Dieu Centre Hospitalier, Chambéry, France
| | - James M. Flanagan
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Zachary C. Fogarty
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Renée T. Fortner
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, Athens, Greece
| | - William D. Foulkes
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montreal, Quebec, Canada
| | - George Fountzilas
- Department of Medical Oncology, Papageorgiou, Hospital, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Brooke L. Fridley
- Biostatistics and Informatics Shared Resource, University of Kansas Medical Center, Kansas City, KS, USA
| | - Tara M. Friebel
- Harvard TH Chan School of Public Health and Dana Farber Cancer Institute, 1101 Dana Building, 450 Brookline Ave, Boston, MA 02215, USA
| | - Eitan Friedman
- The Susanne Levy Gertner Oncogenetics Unit, Institute of Human Genetics, Chaim Sheba Medical Center, Ramat Gan 52621, and Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Debra Frost
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Patricia A. Ganz
- UCLA Schools of Medicine and Public Health, Division of Cancer Prevention and Control Research, Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Judy Garber
- Cancer Risk and Prevention Clinic, Dana Farber Cancer Institute, Boston, MA, USA
| | - María J. García
- Human Genetics Group, Spanish National Cancer Centre (CNIO), and Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Vanesa Garcia-Barberan
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Martin Lagos s/n, Madrid, Spain
| | - Andrea Gehrig
- Centre of Familial Breast and Ovarian Cancer, Department of Medical Genetics, Institute of Human Genetics, University Würzburg, Germany
| | | | | | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Graham G. Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | | | - Gord Glendon
- Ontario Cancer Genetics Network: Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - David E. Goldgar
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Teodora Goranova
- Cancer Research UK (CRUK) Cambridge Institute, University of Cambridge
| | - Martin Gore
- Department of Medicine, Royal Marsden Hospital, London, UK
| | - Mark H. Greene
- Clinical Genetics Branch,DCEG, NCI, NIH, 9609 Medical Center Drive, Room 6E-454, Bethesda, MD, USA
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Stephen Gruber
- Keck School of Medicine, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO) and Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, Cologne, Germany
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Niclas Håkansson
- Karolinska Institutet, Department of Environmental Medicine, Division of Nutritional Epidemiology, SE-171 77 STOCKHOLM, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Thomas V.O. Hansen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Patricia A. Harrington
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Holly R Harris
- Karolinska Institutet, Department of Environmental Medicine, Division of Nutritional Epidemiology, SE-171 77 STOCKHOLM, Sweden
| | - Jan Hauke
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO) and Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, Cologne, Germany
| | - HEBON Study
- A list of members and affiliations appears in the Supplementary note
| | - Alexander Hein
- Universtiy Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen Nuremberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
| | - Alex Henderson
- Institute of Genetic Medicine, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, UK
| | | | - Peter Hillemanns
- Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Shirley Hodgson
- Medical Genetics Unit, St George’s, University of London, UK
| | - Claus K. Høgdall
- Department of Gynecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Estrid Høgdall
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
- Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | | | - Helene Holland
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Maartje J. Hooning
- Department of Medical Oncology, Family Cancer Clinic, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Karen Hosking
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Ruea-Yea Huang
- Center For Immunotherapy, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Peter J. Hulick
- Center for Medical Genetics, NorthShore University HealthSystem, University of Chicago Pritzker School of Medicine, 1000 Central Street, Suite 620,Evanston, IL 60201,US
| | - Jillian Hung
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
| | - David J. Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, The Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - David G. Huntsman
- British Columbia’s Ovarian Cancer Research (OVCARE) Program, Vancouver General Hospital, BC Cancer Agency and University of British Columbia; Departments of Pathology and Laboratory Medicine, Obstetrics and Gynaecology and Molecular Oncology, Vancouver, British Columbia, CANADA
| | - Tomasz Huzarski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | | | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, 3800 Reservoir Road NW, Washington, DC, USA
| | - Edwin S. Iversen
- Department of Statistical Science, Duke University, Durham, North Carolina, USA
| | - Louise Izatt
- Clinical Genetics, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Angel Izquierdo
- Genetic Counseling Unit, Hereditary Cancer Program, IDIBGI (Institut d’Investigació Biomèdica de Girona), Catalan Institute of Oncology. Av. França s/n. 1707 Girona, Spain
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Paul James
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Locked Bag 1, A’Beckett Street, Melbourne, VIC 8006 AUSTRALIA; Sir Peter MacCallum Dept of Oncology, University of Melbourne, VIC 3010
| | - Ramunas Janavicius
- Vilnius University Hospital Santariskiu Clinics, Hematology, Oncology and Transfusion Medicine Center, Department of Molecular and Regenerative Medicine, Vilnius, Lithuania
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Mats Jernetz
- Department of Obstetrics and Gynecology Lund University Hospital, Lund Sweden
| | - Allan Jensen
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Uffe Birk Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Brendstrupgaardsvej 21C, Aarhus N, Denmark
| | - Esther M. John
- Department of Epidemiology, Cancer Prevention Institute of California, Fremont, California, USA
| | - Sharon Johnatty
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Michael E. Jones
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Päivi Kannisto
- Department of Obstetrics and Gynecology Lund University Hospital, Lund Sweden
| | - Beth Y. Karlan
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA
| | - Anthony Karnezis
- British Columbia’s Ovarian Cancer Research (OVCARE) Program, Vancouver General Hospital, BC Cancer Agency and University of British Columbia; Departments of Pathology and Laboratory Medicine, Obstetrics and Gynaecology and Molecular Oncology, Vancouver, British Columbia, CANADA
| | - Karin Kast
- Department of Gynaecology and Obstetrics, University Hospital Carl Gustav Carus, Technical University Dresden, Germany
| | | | - Catherine J. Kennedy
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Science Center, Russian Academy of Sciences, Ufa, Bashkortostan, Russia
| | - Lambertus A. Kiemeney
- Radboud university medical center, Radboud Institute for Health Sciences, Department for Health Evidence, Nijmegen, The Netherlands
| | - Johanna I. Kiiski
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, HUS, Finland
| | - Sung-Won Kim
- Department of Surgery, Breast Care Center, Daerim St. Mary’s Hospital, 657 Siheung-daero, Yeongdeungpo-gu, Seoul, 150-822, Korea
| | - Susanne K. Kjaer
- Department of Gynecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Martin Köbel
- Department of Pathology, University of Calgary, Calgary, Alberta, Canada
| | - Reidun K. Kopperud
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Torben A. Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
| | - Jolanta Kupryjanczyk
- Department of Pathology and Laboratory Diagnostics, the Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Ava Kwong
- The Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong
- Department of Surgery, The University of Hong Kong, Hong Kong
- Cancer Genetics Center and Department of Surgery, Hong Kong Sanatorium and Hospital, Hong Kong
| | - Yael Laitman
- The Susanne Levy Gertner Oncogenetics Unit, Institute of Human Genetics, Chaim Sheba Medical Center, Ramat Gan 52621, and Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Diether Lambrechts
- Vesalius Research Center, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, KULeuven, Belgium
| | - Nerea Larrañaga
- Public Health Division of Gipuzkoa, Regional Government of the Basque Country, Spain
- CIBER of Epidemiology and Public Health (CIBERESP), Spain
| | - Melissa C. Larson
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Conxi Lazaro
- Molecular Diagnostic Unit, Hereditary Cancer Program, IDIBELL-Catalan Institute of Oncology, Barcelona, Spain
| | - Nhu D. Le
- Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Loic Le Marchand
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Hawaii, USA
| | - Jong Won Lee
- Department of Surgery, Ulsan College of Medicine and Asan Medical Center, Seoul, Korea
| | - Shashikant B. Lele
- Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Arto Leminen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, HUS, Finland
| | - Dominique Leroux
- Département de Génétique, Centre Hospitalier Universitaire de Grenoble, BP 217, Grenoble Cedex 9, France
| | - Jenny Lester
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA
| | - Fabienne Lesueur
- Institut Curie, PSL Research Unviersity and Inserm, U900, Paris, France; Mines Paris Tech, Fontainebleau, France
| | - Douglas A. Levine
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dong Liang
- College of Pharmacy and Health Sciences, Texas Southern University, Houston, Texas, USA
| | - Clemens Liebrich
- Cancer Center Wolfsburg, Clinics of Gynaecology, Wolfsburg, Germany
| | - Jenna Lilyquist
- Department of Health Sciences Research, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Loren Lipworth
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Karen H. Lu
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Craig Luccarini
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Lene Lundvall
- The Juliane Marie Centre, Department of Gynecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Phuong L. Mai
- Clinical Genetics Branch,DCEG, NCI, NIH, 9609 Medical Center Drive, Room 6E-454, Bethesda, MD, USA
| | | | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale Tumori (INT), Via Giacomo Venezian 1, 20133 Milan, Italy
| | - Leon F.A.G. Massuger
- Radboud university medical center, Radboud Institute for Health Sciences, Department for Health Evidence, Nijmegen, The Netherlands
| | - Taymaa May
- Division of Gynecologic Oncology, Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada
| | - Sylvie Mazoyer
- INSERM U1052, CNRS UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Centre Léon Bérard, Lyon, France
| | - Jessica N. McAlpine
- Ovarian Cancer Research (OVCARE) Program - Gynecologic Tissue Bank, Vancouver General Hospital and BC Cancer Agency, Vancouver, British Columbia CANADA
| | - Valerie McGuire
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Iain McNeish
- Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Beatson Institute for Cancer Research, Glasgow, UK
| | - Hanne Meijers-Heijboer
- Department of Clinical Genetics, VU University Medical Centre, P.O. Box 7057, 1007 MB Amsterdam, the Netherlands
| | - Alfons Meindl
- Department of Gynaecology and Obstetrics, Division of Tumor Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Usha Menon
- Women’s Cancer, Institute for Women’s Health, University College London, London, United Kingdom
| | - Arjen R. Mensenkamp
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Melissa A. Merritt
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - Roger L. Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Australia
| | - Gillian Mitchell
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Locked Bag 1, A’Beckett Street, Melbourne, VIC 8006 AUSTRALIA; Sir Peter MacCallum Dept of Oncology, University of Melbourne, VIC 3010
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Francesmary Modugno
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
- Ovarian Cancer Center of Excellence, Womens Cancer Research Program, Magee-Womens Research Institute and University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
| | - Joanna Moes-Sosnowska
- Department of Pathology and Laboratory Diagnostics, the Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Melissa Moffitt
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Via Gattamelata 64, Padua, Italy
| | - Kirsten B. Moysich
- Cancer Pathology & Prevention, Division of Cancer Prevention and Population Sciences, Roswell Park Cancer Institute, Buffalo, NY
| | - Anna Marie Mulligan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine, and the Keenan Research Centre of the Li Ka Shing Knowledge Institute, St Michael’s Hospital, Toronto, ON, Canada
| | - Jacob Musinsky
- Clinical Genetics Research Laboratory, Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10044, USA
| | - Katherine L. Nathanson
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA, USA
| | - Lotte Nedergaard
- Department of Pathology, Rigshospitalet, University of Copenhagen, Denmark
| | - Roberta B. Ness
- The University of Texas School of Public Health, Houston, TX, USA
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, HUS, Finland
| | - Dieter Niederacher
- Department of Gynaecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Germany
| | - Robert L. Nussbaum
- Invitae Corporation and University of Southern California, San Francisco, 513 Parnassus Ave., HSE 901E, San Francisco, CA. 94143 – 0794
| | - Kunle Odunsi
- Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Olufunmilayo I. Olopade
- Center for Clinical Cancer Genetics and Global Health, University of Chicago Medical Center, 5841 South Maryland Avenue, MC 2115 Chicago, IL, USA
| | - Håkan Olsson
- Department of Cancer Epidemiology, University Hospital, Lund, Lund University, Lund, Sweden
- Department of Oncology, Lund University Hospital, Lund, Sweden
| | - Curtis Olswold
- Department of Health Sciences Research, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - David M. O’Malley
- The Ohio State University and the James Cancer Center, Columbus, Ohio, USA
| | - Kai-ren Ong
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital Healthcare NHS Trust, Edgbaston, Birmingham, UK
| | | | - OPAL study group
- A list of members and affiliations appears in the Supplementary note
| | - Nicholas Orr
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Sandra Orsulic
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA
| | - Ana Osorio
- Human Genetics Group, Spanish National Cancer Centre (CNIO), and Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Domenico Palli
- Molecular and Nutritional Epidemiology Unit, Cancer Research and Prevention Institute ISPO, Florence, Italy
| | - Laura Papi
- Unit of Medical Genetics, Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | | | - James Paul
- Cancer Research UK Clinical Trials Unit, Institute of Cancer Sciences, University of Glasgow, UK
| | - Celeste L. Pearce
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Inge Søkilde Pedersen
- Section of Molecular Diagnostics, Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark
| | - Petra H.M. Peeters
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht, the Netherlands
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale Tumori (INT), Via Giacomo Venezian 1, 20133 Milan, Italy
| | - Ana Peixoto
- Department of Genetics, Portuguese Oncology Institute, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Tanja Pejovic
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Liisa M. Pelttari
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, HUS, Finland
| | | | - Paolo Peterlongo
- IFOM, The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, c/o IFOM-IEO campus, via Adamello 16 , 20139 Milan, Italy
| | - Lidia Pezzani
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale Tumori (INT), Via Giacomo Venezian 1, 20133 Milan, Italy
| | - Georg Pfeiler
- Dept of OB/GYN, Medical University of Vienna and Comprehensive Cancer Center, Vienna, Austria, Waehringer Guertel 18-20, A 1090 Vienna, Austria
| | - Kelly-Anne Phillips
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Division of Cancer Medicine, Peter MacCallum Cancer Centre, Locked Bag 1, A’Beckett St, East Melbourne, Victoria 8006, Australia
| | - Marion Piedmonte
- NRG Oncology, Statistics and Data Management Center, Roswell Park Cancer Institute, Elm St & Carlton St, Buffalo, NY 14263, USA
| | - Malcolm C. Pike
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna M. Piskorz
- Cancer Research UK (CRUK) Cambridge Institute, University of Cambridge
| | - Samantha R. Poblete
- Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Timea Pocza
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Elizabeth M. Poole
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Bruce Poppe
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Mary E. Porteous
- South East of Scotland Regional Genetics Service, Western General Hospital, Edinburgh, UK
| | - Fabienne Prieur
- Service de Génétique Clinique Chromosomique et Moléculaire, Centre Hospitalier Universitaire de St Etienne, St Etienne, France
| | - Darya Prokofyeva
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Elizabeth Pugh
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224
| | - Miquel Angel Pujana
- Translational Research Laboratory, IDIBELL (Bellvitge Biomedical Research Institute),Catalan Institute of Oncology, Barcelona, Spain
| | - Pascal Pujol
- Unité d’Oncogénétique, CHU Arnaud de Villeneuve, Montpellier, France
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy
| | - Johanna Rantala
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Christine Rappaport-Fuerhauser
- Dept of OB/GYN, Medical University of Vienna and Comprehensive Cancer Center, Vienna, Austria, Waehringer Guertel 18-20, A 1090 Vienna, Austria
| | - Gad Rennert
- Clalit National Israeli Cancer Control Center and Department of Community Medicine and Epidemiology, Carmel Medical Center and B. Rappaport Faculty of Medicine, Haifa, Israel
| | - Kerstin Rhiem
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO) and Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, Cologne, Germany
| | - Patricia Rice
- Clinical Cancer Genetics, for the City of Hope Clinical Cancer Genetics Community Research Network, Duarte, CA, USA
| | - Andrea Richardson
- Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Boston, MA USA
| | - Mark Robson
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gustavo C. Rodriguez
- Division of Gynecologic Oncology, NorthShore University HealthSystem, University of Chicago, Evanston, IL, USA
| | - Cristina Rodríguez-Antona
- Hereditary Endocrine Cancer group, Spanish National Cancer Research Center (CNIO), and Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Jane Romm
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224
| | - Matti A. Rookus
- Department of Epidemiology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mary Anne Rossing
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Joseph H. Rothstein
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ingo B. Runnebaum
- Department of Gynecology, Jena University Hospital - Friedrich Schiller University, Jena, Germany
| | - Helga B. Salvesen
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Dale P. Sandler
- Epidemiology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | | | - Leigha Senter
- Clinical Cancer Genetics Program, Division of Human Genetics, Department of Internal Medicine, The Comprehensive Cancer Center, The Ohio State University, Columbus, USA
| | - V. Wendy Setiawan
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Gianluca Severi
- Université Paris-Saclay, Université Paris-Sud, UVSQ, CESP, INSERM, Villejuif, France
- Gustave Roussy, F-94805, Villejuif, France
- Human Genetics Foundation (HuGeF), Torino, Italy
- Cancer Council Victoria and University of Melbourne, Australia
| | - Priyanka Sharma
- Department of Hematology and Oncology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Tameka Shelford
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224
| | - Nadeem Siddiqui
- Department of Gynaecological Oncology, Glasgow Royal Infirmary, Glasgow, UK
| | - Lucy E. Side
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Trust, London, UK
| | - Weiva Sieh
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Christian F. Singer
- Dept of OB/GYN, Medical University of Vienna and Comprehensive Cancer Center, Vienna, Austria, Waehringer Guertel 18-20, A 1090 Vienna, Austria
| | - Hagay Sobol
- Département Oncologie Génétique, Prévention et Dépistage, INSERM CIC-P9502, Institut Paoli-Calmettes/Université d’Aix-Marseille II, Marseille, France
| | - Honglin Song
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Melissa C. Southey
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, VIC, Australia
| | - Amanda B. Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Zsofia Stadler
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Doris Steinemann
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | | | | | - Grzegorz Sukiennicki
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Rebecca Sutphen
- Epidemiology Center, College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Christian Sutter
- Institute of Human Genetics, Department of Human Genetics, University Hospital Heidelberg, Germany
| | - Anthony J. Swerdlow
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Csilla I. Szabo
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lukasz Szafron
- Department of Pathology and Laboratory Diagnostics, the Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Yen Y. Tan
- Dept of OB/GYN, Medical University of Vienna and Comprehensive Cancer Center, Vienna, Austria, Waehringer Guertel 18-20, A 1090 Vienna, Austria
| | - Jack A. Taylor
- Epidemiology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Muy-Kheng Tea
- Dept of OB/GYN, Medical University of Vienna and Comprehensive Cancer Center, Vienna, Austria, Waehringer Guertel 18-20, A 1090 Vienna, Austria
| | - Manuel R. Teixeira
- Department of Genetics, Portuguese Oncology Institute, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal and Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Soo-Hwang Teo
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, Subang Jaya, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya Medical Centre, University Malaya, Kuala Lumpur, Malaysia
| | - Kathryn L. Terry
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T. Chan School of Public Health, Boston, MA, USA
| | - Pamela J. Thompson
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Liv Cecilie Vestrheim Thomsen
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Darcy L. Thull
- Magee-Womens Hospital of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Laima Tihomirova
- Latvian Biomedical Research and Study Centre. Ratsupites str 1, Riga, Latvia
| | - Anna V. Tinker
- Ovarian Cancer Research (OVCARE) Program - Cheryl Brown Ovarian Cancer Outcomes Unit (CBOCOU), BC Cancer Agency, Vancouver, British Columbia CANADA
| | - Marc Tischkowitz
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montreal, Quebec, Canada
- Department of Medical Genetics, Box 134, Level 6 Addenbrooke’s Treatment Centre, Addenbrooke’s Hosptital, Hills Road, Cambridge CB2 0QQ, UK
| | - Silvia Tognazzo
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Via Gattamelata 64, Padua, Italy
| | - Amanda Ewart Toland
- Divison of Human Cancer Genetics, Departments of Internal Medicine and Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Alicia Tone
- Division of Gynecologic Oncology, Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada
| | - Britton Trabert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Ruth C. Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Antonia Trichopoulou
- Hellenic Health Foundation, Athens, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Dept. of Hygiene, Epidemiology and Medical Statistics, University of Athens Medical School, Greece
| | - Nadine Tung
- Department of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Shelley S. Tworoger
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T. Chan School of Public Health, Boston, MA, USA
| | - Anne M. van Altena
- Division of Gynecologic Oncology, Department of Obstetrics and Gynaecology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - David Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | | | - Rob B. van der Luijt
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Els Van Nieuwenhuysen
- Division of Gynecologic Oncology , Department of Obstetrics and Gynaecology and Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | | | - Adriaan Vanderstichele
- Division of Gynecologic Oncology , Department of Obstetrics and Gynaecology and Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | | | - Vega Ana
- Fundación Pública Galega de Medicina Xenómica, Servizo Galego de Saúde (SERGAS), Instituto de Investigaciones Sanitarias (IDIS), Santiago de Compostela, Spain
- Grupo de Medicina Xenómica, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Digna Velez Edwards
- Vanderbilt Epidemiology Center, Vanderbilt Genetics Institute, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ignace Vergote
- Division of Gynecologic Oncology , Department of Obstetrics and Gynaecology and Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Robert A. Vierkant
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Joseph Vijai
- Clinical Genetics Research Laboratory, Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10044, USA
| | - Athanassios Vratimos
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, Athens, Greece
| | - Lisa Walker
- Oxford Regional Genetics Service, Churchill Hospital, Oxford, UK
| | - Christine Walsh
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA
| | - Dorothea Wand
- Institute of Human Genetics, University Hospital, Leipzig, Germany
| | - Shan Wang-Gohrke
- Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
| | - Barbara Wappenschmidt
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO) and Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, Cologne, Germany
| | - Penelope M. Webb
- Population Health Department, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia
| | - Clarice R. Weinberg
- Biostatistics and Computational Biology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | | | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Alice S. Whittemore
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Data Management Science- Stanford University School of Medicine, Stanford, CA, USA
| | - Juul T. Wijnen
- Department of Human Genetics and Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Lynne R. Wilkens
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Hawaii, USA
| | - Alicja Wolk
- Karolinska Institutet, Department of Environmental Medicine, Division of Nutritional Epidemiology, SE-171 77 STOCKHOLM, Sweden
| | - Michelle Woo
- British Columbia’s Ovarian Cancer Research (OVCARE) Program, Vancouver General Hospital, BC Cancer Agency and University of British Columbia; Departments of Pathology and Laboratory Medicine, Obstetrics and Gynaecology and Molecular Oncology, Vancouver, British Columbia, CANADA
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anna H. Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Hannah Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, Athens, Greece
| | - Argyrios Ziogas
- Department of Epidemiology, University of California Irvine, Irvine, CA, USA
| | - Kristin K. Zorn
- Magee-Womens Hospital of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Steven A. Narod
- Women’s College Research Institute, University of Toronto, Toronto, ON, Canada
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Christopher I. Amos
- Center for Genomic Medicine, Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Williamson Translational Research Building, Room HB 7261, Lebanon, NH 03756, USA
| | - Joellen M. Schildkraut
- Department of Public Health Sciences, The University of Virginia, Charlottesville, VA, USA
| | - Susan J. Ramus
- School of Women’s and Children’s Health, Lowy Cancer Research Centre, The University of New South Wales UNSW Sydney NSW 2052 AUSTRALIA
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst NSW 2010, Australia
| | - Laura Ottini
- Department of Molecular Medicine, University La Sapienza, c/oPoliclinico Umberto I, viale Regina Elena 324, 00161 Rome, Italy
| | - Marc T. Goodman
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Community and Population Health Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Sue K. Park
- Department of Preventive Medicine, College of Medicine, Seoul National University, 103 Daehak-ro, Jongno-gu, Seoul 110-799, Korea
- Seoul National University Cancer Research Institute, 103 Daehak-ro, Jongno-gu, Seoul 110-799, Korea
- Department of Biomedical Science, Graduate School, Seoul National University, 103 Daehak-ro, Jongno-gu, Seoul 110-799, Korea
| | - Linda E. Kelemen
- Department of Public Health Sciences, College of Medicine, Medical University of South Carolina,Charleston, SC 29425
| | - Harvey A. Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
| | - Kenneth Offit
- Clinical Genetics Research Laboratory, Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10044, USA
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center and Laval University, 2705 Laurier Boulevard, Quebec City (Quebec), Canada
| | - Rita Katharina Schmutzler
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO) and Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, Cologne, Germany
| | - Dennis Hazelett
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Alvaro N. Monteiro
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology,Division of Experimental Pathology, Mayo Clinic, Rochester, MN, USA
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Ellen L. Goode
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Thomas A. Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Simon A. Gayther
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Paul D.P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
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Lu Q, Livi GP, Modha S, Yusa K, Macarrón R, Dow DJ. Applications of CRISPR genome editing technology in drug target identification and validation. Expert Opin Drug Discov 2017; 12:541-552. [DOI: 10.1080/17460441.2017.1317244] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Savio AJ, Bapat B. Modulation of transcription factor binding and epigenetic regulation of the MLH1 CpG island and shore by polymorphism rs1800734 in colorectal cancer. Epigenetics 2017; 12:441-448. [PMID: 28304185 DOI: 10.1080/15592294.2017.1305527] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The MLH1 promoter polymorphism rs1800734 is associated with MLH1 CpG island hypermethylation and expression loss in colorectal cancer (CRC). Conversely, variant rs1800734 is associated with MLH1 shore, but not island, hypomethylation in peripheral blood mononuclear cell DNA. To explore these distinct patterns, MLH1 CpG island and shore methylation was assessed in CRC cell lines stratified by rs1800734 genotype. Cell lines containing the variant A allele demonstrated MLH1 shore hypomethylation compared to wild type (GG). There was significant enrichment of transcription factor AP4 at the MLH1 promoter in GG and GA cell lines, but not the AA cell line, by chromatin immunoprecipitation studies. Preferential binding to the G allele was confirmed by sequencing in the GA cell line. The enhancer-associated histone modification H3K4me1 was enriched at the MLH1 shore; however, H3K27ac was not, indicating the shore is an inactive enhancer. These results demonstrate the role of variant rs1800734 in altering transcription factor binding as well as epigenetics at regions beyond the MLH1 CpG island in which it is located.
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Affiliation(s)
- Andrea J Savio
- a Lunenfeld-Tanenbaum Research Institute, Sinai Health System , Toronto , Ontario , Canada.,b Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario , Canada
| | - Bharati Bapat
- a Lunenfeld-Tanenbaum Research Institute, Sinai Health System , Toronto , Ontario , Canada.,b Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario , Canada.,c Department of Pathology , University Health Network , Toronto , Ontario , Canada
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Hashemi M, Danesh H, Bizhani F, Narouie B, Sotoudeh M, Nouralizadeh A, Sharifiaghdas F, Bahari G, Taheri M. Pri-miR-34b/c rs4938723 polymorphism increased the risk of prostate cancer. Cancer Biomark 2017; 18:155-159. [DOI: 10.3233/cbm-160058] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Mohammad Hashemi
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Hiva Danesh
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Fatemeh Bizhani
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Behzad Narouie
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Sotoudeh
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Akbar Nouralizadeh
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzaneh Sharifiaghdas
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Gholamreza Bahari
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mohsen Taheri
- Genetics of Non Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
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Guo H, Ahmed M, Hua J, Soares F, He HH. Crucial role of noncoding RNA in driving prostate cancer development and progression. Epigenomics 2017; 9:1-3. [DOI: 10.2217/epi-2016-0134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Haiyang Guo
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Musaddeque Ahmed
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Junjie Hua
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Fraser Soares
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Housheng Hansen He
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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Amos CI, Dennis J, Wang Z, Byun J, Schumacher FR, Gayther SA, Casey G, Hunter DJ, Sellers TA, Gruber SB, Dunning AM, Michailidou K, Fachal L, Doheny K, Spurdle AB, Li Y, Xiao X, Romm J, Pugh E, Coetzee GA, Hazelett DJ, Bojesen SE, Caga-Anan C, Haiman CA, Kamal A, Luccarini C, Tessier D, Vincent D, Bacot F, Van Den Berg DJ, Nelson S, Demetriades S, Goldgar DE, Couch FJ, Forman JL, Giles GG, Conti DV, Bickeböller H, Risch A, Waldenberger M, Brüske-Hohlfeld I, Hicks BD, Ling H, McGuffog L, Lee A, Kuchenbaecker K, Soucy P, Manz J, Cunningham JM, Butterbach K, Kote-Jarai Z, Kraft P, FitzGerald L, Lindström S, Adams M, McKay JD, Phelan CM, Benlloch S, Kelemen LE, Brennan P, Riggan M, O'Mara TA, Shen H, Shi Y, Thompson DJ, Goodman MT, Nielsen SF, Berchuck A, Laboissiere S, Schmit SL, Shelford T, Edlund CK, Taylor JA, Field JK, Park SK, Offit K, Thomassen M, Schmutzler R, Ottini L, Hung RJ, Marchini J, Amin Al Olama A, Peters U, Eeles RA, Seldin MF, Gillanders E, Seminara D, Antoniou AC, Pharoah PDP, Chenevix-Trench G, Chanock SJ, Simard J, Easton DF. The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers. Cancer Epidemiol Biomarkers Prev 2017; 26:126-135. [PMID: 27697780 PMCID: PMC5224974 DOI: 10.1158/1055-9965.epi-16-0106] [Citation(s) in RCA: 240] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 06/30/2016] [Accepted: 07/29/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Common cancers develop through a multistep process often including inherited susceptibility. Collaboration among multiple institutions, and funding from multiple sources, has allowed the development of an inexpensive genotyping microarray, the OncoArray. The array includes a genome-wide backbone, comprising 230,000 SNPs tagging most common genetic variants, together with dense mapping of known susceptibility regions, rare variants from sequencing experiments, pharmacogenetic markers, and cancer-related traits. METHODS The OncoArray can be genotyped using a novel technology developed by Illumina to facilitate efficient genotyping. The consortium developed standard approaches for selecting SNPs for study, for quality control of markers, and for ancestry analysis. The array was genotyped at selected sites and with prespecified replicate samples to permit evaluation of genotyping accuracy among centers and by ethnic background. RESULTS The OncoArray consortium genotyped 447,705 samples. A total of 494,763 SNPs passed quality control steps with a sample success rate of 97% of the samples. Participating sites performed ancestry analysis using a common set of markers and a scoring algorithm based on principal components analysis. CONCLUSIONS Results from these analyses will enable researchers to identify new susceptibility loci, perform fine-mapping of new or known loci associated with either single or multiple cancers, assess the degree of overlap in cancer causation and pleiotropic effects of loci that have been identified for disease-specific risk, and jointly model genetic, environmental, and lifestyle-related exposures. IMPACT Ongoing analyses will shed light on etiology and risk assessment for many types of cancer. Cancer Epidemiol Biomarkers Prev; 26(1); 126-35. ©2016 AACR.
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Affiliation(s)
- Christopher I Amos
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire.
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jinyoung Byun
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Fredrick R Schumacher
- Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Simon A Gayther
- The Center for Bioinformatics and Functional Genomics at Cedars Sinai Medical Center, Greater Los Angeles Area, Los Angeles, California
| | - Graham Casey
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - David J Hunter
- Department of Epidemiology, Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Thomas A Sellers
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Stephen B Gruber
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Laura Fachal
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Kimberly Doheny
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Amanda B Spurdle
- Molecular Cancer Epidemiology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Yafang Li
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Xiangjun Xiao
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Jane Romm
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Elizabeth Pugh
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | | | | | - Stig E Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Charlisse Caga-Anan
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Christopher A Haiman
- The Center for Bioinformatics and Functional Genomics at Cedars Sinai Medical Center, Greater Los Angeles Area, Los Angeles, California
| | - Ahsan Kamal
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Daniel Tessier
- Génome Québec Innovation Centre, Montreal, Canada and McGill University, Montreal, Canada
| | - Daniel Vincent
- Génome Québec Innovation Centre, Montreal, Canada and McGill University, Montreal, Canada
| | - François Bacot
- Génome Québec Innovation Centre, Montreal, Canada and McGill University, Montreal, Canada
| | - David J Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Stefanie Nelson
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Stephen Demetriades
- University Health Network- The Princess Margaret Cancer Centre, Toronto, California
| | | | | | - Judith L Forman
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Cancer, Genetics and Immunology, Menzies Institute for Medical Research, Hobart, Australia
| | - David V Conti
- Division of Biostatistics, Department of Preventive Medicine, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Angela Risch
- University of Salzburg and Cancer Cluster Salzburg, Salzburg, Austria
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg, Germany
- Translational Lung Research Center Heidelberg, Member of the German Center for Lung Research, Heidelberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Irene Brüske-Hohlfeld
- Helmholtz Zentrum München, Institut für Epidemiologie I, Neuherberg, Oberschleissheim, Germany
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Hua Ling
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Lesley McGuffog
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Cancer, Genetics and Immunology, Menzies Institute for Medical Research, Hobart, Australia
| | - Andrew Lee
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Karoline Kuchenbaecker
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Penny Soucy
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec and Laval University, Québec City, Canada
| | - Judith Manz
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Katja Butterbach
- Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | | | - Peter Kraft
- Department of Epidemiology, Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Liesel FitzGerald
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Cancer, Genetics and Immunology, Menzies Institute for Medical Research, Hobart, Australia
| | - Sara Lindström
- Department of Epidemiology, Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Marcia Adams
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - James D McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Catherine M Phelan
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Sara Benlloch
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Linda E Kelemen
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
| | - Paul Brennan
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Marjorie Riggan
- Department of Gynecology, Duke University Medical Center, Durham, North Carolina
| | - Tracy A O'Mara
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, P.R. China
| | - Yongyong Shi
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | | | - Sune F Nielsen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Andrew Berchuck
- Department of Gynecology, Duke University Medical Center, Durham, North Carolina
| | - Sylvie Laboissiere
- Génome Québec Innovation Centre, Montreal, Canada and McGill University, Montreal, Canada
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center, Tampa, Florida
| | - Tameka Shelford
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Christopher K Edlund
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Jack A Taylor
- Molecular and Genetic Epidemiology Group, National Institute for Environmental Health Sciences, Research Triangle Park, North Carolina
| | - John K Field
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Sue K Park
- College of Medicine, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Kenneth Offit
- Clinical Genetics Service, Memorial Hospital, New York, New York
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Rita Schmutzler
- Zentrum Familiärer Brust- und Eierstockkrebs, Universitätsklinikum Köln, Köln, Germany
| | - Laura Ottini
- Department of Molecular Medicine, Sapienza, University of Rome, Rome, Italy
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | | | - Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Michael F Seldin
- Department of Biochemistry and Molecular Medicine, University of California at Davis, Davis, California
- Department of Internal Medicine, University of California at Davis, Davis, California
| | - Elizabeth Gillanders
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Daniela Seminara
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | | | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Jacques Simard
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec and Laval University, Québec City, Canada
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
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Cesaratto L, Grisard E, Coan M, Zandonà L, De Mattia E, Poletto E, Cecchin E, Puglisi F, Canzonieri V, Mucignat MT, Zucchetto A, Stocco G, Colombatti A, Nicoloso MS, Spizzo R. BNC2 is a putative tumor suppressor gene in high-grade serous ovarian carcinoma and impacts cell survival after oxidative stress. Cell Death Dis 2016; 7:e2374. [PMID: 27899818 PMCID: PMC5059877 DOI: 10.1038/cddis.2016.278] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 07/04/2016] [Accepted: 07/29/2016] [Indexed: 12/21/2022]
Abstract
Rs3814113 is the single-nucleotide polymorphism (SNP) showing the strongest association with high-grade serous ovarian carcinoma (HGSOC) incidence and is located in an intergenic region about 44 kb downstream of basonuclin 2 (BNC2) gene. Lifetime number of ovulations is associated with increased risk to develop HGSOC, probably because of cell damage of extrauterine Müllerian epithelium by ovulation-induced oxidative stress. However, the impact of low-penetrance HGSOC risk alleles (e.g. rs3814113) on the damage induced by oxidative stress remains unclear. Therefore, the purpose of this study was to investigate whether rs3814113 genetic interval regulates BNC2 expression and whether BNC2 expression levels impact on cell survival after oxidative stress. To do this, we analyzed gene expression levels of BNC2 first in HGSOC data sets and then in an isogenic cell line that we engineered to carry a 5 kb deletion around rs3814113. Finally, we silenced BNC2 and measured surviving cells after hydrogen peroxide (H2O2) treatment to simulate oxidative stress after ovulation. In this paper, we describe that BNC2 expression levels are reduced in HGSOC samples compared with control samples, and that BNC2 expression levels decrease following oxidative stress and ovulation in vitro and in vivo, respectively. Moreover, deletion of 5 kb surrounding rs3814113 decreases BNC2 expression levels in an isogenic cell line, and silencing of BNC2 expression levels increases cell survival after H2O2 treatment. Altogether, our findings suggest that the intergenic region located around rs3814113 regulates BNC2 expression, which in turn affects cell survival after oxidative stress response. Indeed, HGSOC samples present lower BNC2 expression levels that probably, in the initial phases of oncogenic transformation, conferred resistance to oxidative stress and ultimately reduced the clearance of cells with oxidative-induced damages.
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Affiliation(s)
- Laura Cesaratto
- Division of Experimental Oncology2, Department of Translational Research, Centro di Riferimento Oncologico (CRO Aviano), National Cancer Institute, Aviano, Italy
| | - Eleonora Grisard
- Division of Experimental Oncology2, Department of Translational Research, Centro di Riferimento Oncologico (CRO Aviano), National Cancer Institute, Aviano, Italy
| | - Michela Coan
- Division of Experimental Oncology2, Department of Translational Research, Centro di Riferimento Oncologico (CRO Aviano), National Cancer Institute, Aviano, Italy
- Department of Life and Reproduction Sciences, University of Verona, Verona, Italy
| | - Luigi Zandonà
- Division of Experimental Oncology2, Department of Translational Research, Centro di Riferimento Oncologico (CRO Aviano), National Cancer Institute, Aviano, Italy
| | - Elena De Mattia
- Division of Experimental and Clinical Pharmacology, Department of Translational Research Centro di Riferimento Oncologico (CRO Aviano), National Cancer Institute, Aviano, Italy
| | - Elena Poletto
- Department of Oncology, University Hospital of Udine, Udine, Italy
| | - Erika Cecchin
- Division of Experimental and Clinical Pharmacology, Department of Translational Research Centro di Riferimento Oncologico (CRO Aviano), National Cancer Institute, Aviano, Italy
| | - Fabio Puglisi
- Department of Oncology, University Hospital of Udine, Udine, Italy
- Department of Medical and Biological Sciences, University of Udine, Udine, Italy
| | - Vincenzo Canzonieri
- Division of Pathology, Department of Translational Research, CRO Aviano National Cancer Institute, Aviano, Italy
| | - Maria Teresa Mucignat
- Division of Experimental Oncology2, Department of Translational Research, Centro di Riferimento Oncologico (CRO Aviano), National Cancer Institute, Aviano, Italy
| | - Antonella Zucchetto
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico (CRO Aviano), National Cancer Institute, Aviano, Italy
| | - Gabriele Stocco
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Alfonso Colombatti
- Division of Experimental Oncology2, Department of Translational Research, Centro di Riferimento Oncologico (CRO Aviano), National Cancer Institute, Aviano, Italy
| | - Milena S Nicoloso
- Division of Experimental Oncology2, Department of Translational Research, Centro di Riferimento Oncologico (CRO Aviano), National Cancer Institute, Aviano, Italy
| | - Riccardo Spizzo
- Division of Experimental Oncology2, Department of Translational Research, Centro di Riferimento Oncologico (CRO Aviano), National Cancer Institute, Aviano, Italy
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Lawrenson K, Kar S, McCue K, Kuchenbaeker K, Michailidou K, Tyrer J, Beesley J, Ramus SJ, Li Q, Delgado MK, Lee JM, Aittomäki K, Andrulis IL, Anton-Culver H, Arndt V, Arun BK, Arver B, Bandera EV, Barile M, Barkardottir RB, Barrowdale D, Beckmann MW, Benitez J, Berchuck A, Bisogna M, Bjorge L, Blomqvist C, Blot W, Bogdanova N, Bojesen A, Bojesen SE, Bolla MK, Bonanni B, Børresen-Dale AL, Brauch H, Brennan P, Brenner H, Bruinsma F, Brunet J, Buhari SA, Burwinkel B, Butzow R, Buys SS, Cai Q, Caldes T, Campbell I, Canniotto R, Chang-Claude J, Chiquette J, Choi JY, Claes KBM, Cook LS, Cox A, Cramer DW, Cross SS, Cybulski C, Czene K, Daly MB, Damiola F, Dansonka-Mieszkowska A, Darabi H, Dennis J, Devilee P, Diez O, Doherty JA, Domchek SM, Dorfling CM, Dörk T, Dumont M, Ehrencrona H, Ejlertsen B, Ellis S, Engel C, Lee E, Evans DG, Fasching PA, Feliubadalo L, Figueroa J, Flesch-Janys D, Fletcher O, Flyger H, Foretova L, Fostira F, Foulkes WD, Fridley BL, Friedman E, Frost D, Gambino G, Ganz PA, Garber J, García-Closas M, Gentry-Maharaj A, Ghoussaini M, Giles GG, Glasspool R, Godwin AK, Goldberg MS, Goldgar DE, González-Neira A, Goode EL, Goodman MT, Greene MH, Gronwald J, Guénel P, Haiman CA, Hall P, Hallberg E, Hamann U, Hansen TVO, Harrington PA, Hartman M, Hassan N, Healey S, Heitz F, Herzog J, Høgdall E, Høgdall CK, Hogervorst FBL, Hollestelle A, Hopper JL, Hulick PJ, Huzarski T, Imyanitov EN, Isaacs C, Ito H, Jakubowska A, Janavicius R, Jensen A, John EM, Johnson N, Kabisch M, Kang D, Kapuscinski M, Karlan BY, Khan S, Kiemeney LA, Kjaer SK, Knight JA, Konstantopoulou I, Kosma VM, Kristensen V, Kupryjanczyk J, Kwong A, de la Hoya M, Laitman Y, Lambrechts D, Le N, De Leeneer K, Lester J, Levine DA, Li J, Lindblom A, Long J, Lophatananon A, Loud JT, Lu K, Lubinski J, Mannermaa A, Manoukian S, Le Marchand L, Margolin S, Marme F, Massuger LFAG, Matsuo K, Mazoyer S, McGuffog L, McLean C, McNeish I, Meindl A, Menon U, Mensenkamp AR, Milne RL, Montagna M, Moysich KB, Muir K, Mulligan AM, Nathanson KL, Ness RB, Neuhausen SL, Nevanlinna H, Nord S, Nussbaum RL, Odunsi K, Offit K, Olah E, Olopade OI, Olson JE, Olswold C, O'Malley D, Orlow I, Orr N, Osorio A, Park SK, Pearce CL, Pejovic T, Peterlongo P, Pfeiler G, Phelan CM, Poole EM, Pylkäs K, Radice P, Rantala J, Rashid MU, Rennert G, Rhenius V, Rhiem K, Risch HA, Rodriguez G, Rossing MA, Rudolph A, Salvesen HB, Sangrajrang S, Sawyer EJ, Schildkraut JM, Schmidt MK, Schmutzler RK, Sellers TA, Seynaeve C, Shah M, Shen CY, Shu XO, Sieh W, Singer CF, Sinilnikova OM, Slager S, Song H, Soucy P, Southey MC, Stenmark-Askmalm M, Stoppa-Lyonnet D, Sutter C, Swerdlow A, Tchatchou S, Teixeira MR, Teo SH, Terry KL, Terry MB, Thomassen M, Tibiletti MG, Tihomirova L, Tognazzo S, Toland AE, Tomlinson I, Torres D, Truong T, Tseng CC, Tung N, Tworoger SS, Vachon C, van den Ouweland AMW, van Doorn HC, van Rensburg EJ, Van't Veer LJ, Vanderstichele A, Vergote I, Vijai J, Wang Q, Wang-Gohrke S, Weitzel JN, Wentzensen N, Whittemore AS, Wildiers H, Winqvist R, Wu AH, Yannoukakos D, Yoon SY, Yu JC, Zheng W, Zheng Y, Khanna KK, Simard J, Monteiro AN, French JD, Couch FJ, Freedman ML, Easton DF, Dunning AM, Pharoah PD, Edwards SL, Chenevix-Trench G, Antoniou AC, Gayther SA. Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus. Nat Commun 2016; 7:12675. [PMID: 27601076 PMCID: PMC5023955 DOI: 10.1038/ncomms12675] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 07/20/2016] [Indexed: 02/02/2023] Open
Abstract
A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (P=9.2 × 10(-20)), ER-negative BC (P=1.1 × 10(-13)), BRCA1-associated BC (P=7.7 × 10(-16)) and triple negative BC (P-diff=2 × 10(-5)). Genotype-gene expression associations are identified for candidate target genes ANKLE1 (P=2 × 10(-3)) and ABHD8 (P<2 × 10(-3)). Chromosome conformation capture identifies interactions between four candidate SNPs and ABHD8, and luciferase assays indicate six risk alleles increased transactivation of the ADHD8 promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces ANKLE1 downregulation; and mRNA stability assays indicate functional effects for an ANKLE1 3'-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate ABHD8 and perhaps ANKLE1 expression, and indicate common mechanisms underlying breast and ovarian cancer risk.
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Affiliation(s)
- Kate Lawrenson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Siddhartha Kar
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Karen McCue
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Karoline Kuchenbaeker
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Kyriaki Michailidou
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Jonathan Tyrer
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Jonathan Beesley
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Susan J. Ramus
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Qiyuan Li
- Medical College, Xiamen University, Xiamen 361102, China
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Melissa K. Delgado
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Janet M. Lee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Hospital, University of Helsinki, Helsinki 00029 HUS, Finland
| | - Irene L. Andrulis
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, Genetic Epidemiology Research Institute, School of Medicine, University of California Irvine, Irvine, California 92697, USA
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Banu K. Arun
- University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Brita Arver
- Department of Oncology, Karolinska University Hospital, Stockholm 171 77, Sweden
| | - Elisa V. Bandera
- Cancer Prevention and Control, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Monica Barile
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, Milan 20141, Italy
| | - Rosa B. Barkardottir
- Department of Pathology, Landspitali University Hospital and BMC (Biomedical Centre), Faculty of Medicine, University of Iceland, Reykjavik 600169-2039, Iceland
| | - Daniel Barrowdale
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Matthias W. Beckmann
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen 91054, Germany
| | - Javier Benitez
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid E-28029, Spain
- Centro de Investigación en Red de Enfermedades Raras, Valencia 28029, Spain
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Maria Bisogna
- Gynecology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York 10065, USA
| | - Line Bjorge
- Department of Gynecology and Obstetrics, Haukeland University Hospital, 5021 Bergen, Norway
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, N-5020 Bergen, Norway
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital, University of Helsinki, Helsinki FIN-00029, Finland
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
- International Epidemiology Institute, Rockville, Maryland 20850, USA
| | - Natalia Bogdanova
- Gynaecology Research Unit, Hannover Medical School, Hannover D-30625, Germany
| | - Anders Bojesen
- Department of Clinical Genetics, Vejle Hospital, Vejle 7100, Denmark
| | - Stig E. Bojesen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev 2730, Denmark
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, Herlev 2730, Denmark
| | - Manjeet K. Bolla
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, Milan 20141, Italy
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo N-0310, Norway
- K.G. Jebsen Center for Breast Cancer Research, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo N-0310, Norway
| | - Hiltrud Brauch
- Dr Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart D-70376, Germany
- University of Tübingen, Tübingen 72074, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon 69008, France
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ), Heidelberg 69121, Germany
| | - Fiona Bruinsma
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
| | - Joan Brunet
- Genetic Counseling Unit, Hereditary Cancer Program, IDIBGI (Institut d'Investigació Biomèdica de Girona), Catalan Institute of Oncology, Girona 08908, Spain
| | - Shaik Ahmad Buhari
- Department of Surgery, National University Health System, Singapore 119077, Singapore
| | - Barbara Burwinkel
- Molecular Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg 69120, Germany
| | - Ralf Butzow
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki 00029 HUS, Finland
- Department of Pathology, Helsinki University Central Hospital, Helsinki 00029, Finland
| | - Saundra S. Buys
- Department of Medicine, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
| | - Trinidad Caldes
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC (El Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid 28040, Spain
| | - Ian Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria 3002, Australia
| | - Rikki Canniotto
- Cancer Pathology & Prevention, Division of Cancer Prevention and Population Sciences, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo 14263, New York, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg 69121, Germany
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Jocelyne Chiquette
- Unité de recherche en santé des populations, Centre des maladies du sein Deschênes-Fabia, Centre de recherche FRSQ du Centre hospitalier affilié universitaire de Québec, Québec City, Québec G1J 1Z4, Canada
| | - Ji-Yeob Choi
- Cancer Research Institute, Seoul National University, Seoul 08826, Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
| | | | - Linda S. Cook
- Division of Epidemiology and Biostatistics, Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Angela Cox
- Sheffield Cancer Research, Department of Oncology, University of Sheffield, Sheffield S10 2TN, UK
| | - Daniel W. Cramer
- Harvard HT Chan School of Public Health, Boston, Massachusetts 02115, USA
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Simon S. Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield S10 2TN, UK
| | - Cezary Cybulski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 70-115, Poland
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Mary B. Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
| | - Francesca Damiola
- INSERM U1052, CNRS UMR5286, Université Lyon, Centre de Recherche en Cancérologie de Lyon, Lyon 69373, France
| | - Agnieszka Dansonka-Mieszkowska
- Department of Pathology and Laboratory Diagnostics the Maria Sklodowska Curie Memorial Cancer Center and Institute of Oncology, Warsaw 44-101, Poland
| | - Hatef Darabi
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Joe Dennis
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden 2333, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333, The Netherlands
| | - Orland Diez
- Oncogenetics Group, University Hospital Vall d'Hebron, Vall d'Hebron Institute of Oncology (VHIO) and Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Jennifer A. Doherty
- Department of Community and Family Medicine, Section of Biostatistics & Epidemiology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03755, USA
| | - Susan M. Domchek
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | | | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover D-30625, Germany
| | - Martine Dumont
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec City, Québec G1V 4G2, Canada
| | - Hans Ehrencrona
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 751 05, Sweden
- Department of Clinical Genetics, Lund University Hospital, Lund 221 00, Sweden
| | - Bent Ejlertsen
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, 2100 Copenhagen, Denmark
| | - Steve Ellis
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, 04107 Leipzig, Germany
| | - Eunjung Lee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - D. Gareth Evans
- Genomic Medicine, Manchester Academic Health Sciences Centre, Institute of Human Development, Manchester University, Central Manchester University Hospitals NHS Foundation Trust, Manchester M13 9PL, UK
| | - Peter A. Fasching
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen 91054, Germany
- University of California at Los Angeles, David Geffen School of Medicine, Department of Medicine, Division of Hematology and Oncology, Los Angeles California 90095, USA
| | - Lidia Feliubadalo
- Molecular Diagnostic Unit, Hereditary Cancer Program, IDIBELL (Bellvitge Biomedical Research Institute),Catalan Institute of Oncology, Barcelona 08908, Spain
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland 20892, USA
| | - Dieter Flesch-Janys
- Institute for Medical Biometrics and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
- Department of Cancer Epidemiology, Clinical Cancer Registry, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Olivia Fletcher
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London SW7 3RP, UK
| | - Henrik Flyger
- Department of Breast Surgery, Herlev Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark
| | - Lenka Foretova
- Masaryk Memorial Cancer Institute and Medical Faculty MU, 625 00 Brno, Czech Republic
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, (INRASTES) Institute of Nuclear and Radiological Sciences and Technology, National Centre for Scientific Research ‘Demokritos', Aghia Paraskevi Attikis, Athens 153 10, Greece
| | - William D. Foulkes
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montreal, Montreal, Quebec H2W 1S6, Canada
| | - Brooke L. Fridley
- Biostatistics and Informatics Shared Resource, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Eitan Friedman
- Susanne Levy Gertner Oncogenetics Unit, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Debra Frost
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Gaetana Gambino
- Section of Genetic Oncology, Department of Laboratory Medicine, University and University Hospital of Pisa, Pisa 56126, Italy
| | - Patricia A. Ganz
- UCLA Schools of Medicine and Public Health, Division of Cancer Prevention & Control Research, Jonsson Comprehensive Cancer Center, Los Angeles, California 90024, USA
| | - Judy Garber
- Cancer Risk and Prevention Clinic, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland 20892, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | | | - Maya Ghoussaini
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Graham G. Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Rosalind Glasspool
- Cancer Research UK Clinical Trials Unit, The Beatson West of Scotland Cancer Centre, Glasgow G12 0YN, UK
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Mark S. Goldberg
- Division of Clinical Epidemiology, Royal Victoria Hospital, McGill University, Montreal, Québec H3A 1A1, Canada
- Department of Medicine, McGill University, Montreal, Québec H3A 1A1, Canada
| | - David E. Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA
| | - Anna González-Neira
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid E-28029, Spain
| | - Ellen L. Goode
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55902, USA
| | - Marc T. Goodman
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
- Community and Population Health Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Mark H. Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland 20892, USA
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, 70-204 Szczecin, Poland
| | - Pascal Guénel
- Environmental Epidemiology of Cancer, Center for Research in Epidemiology and Population Health, INSERM, 94805 Villejuif, France
- University Paris-Sud, 91405 Villejuif, France
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Emily Hallberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55902, USA
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Thomas V. O. Hansen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, 2100 Copenhagen, Denmark
| | - Patricia A. Harrington
- Department of Oncology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Mikael Hartman
- Department of Surgery, National University Health System, Singapore 119077, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore Singapore 119077, Singapore
| | - Norhashimah Hassan
- Breast Cancer Research Unit, Cancer Research Institute, University Malaya Medical Centre, 50603 Kuala Lumpur, Malaysia
- Cancer Research Initiatives Foundation, Subang Jaya, 47500 Selangor, Malaysia
| | - Sue Healey
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, 45136 Essen, Germany
- Department of Gynecology and Gynecologic Oncology, Dr Horst Schmidt Kliniken Wiesbaden, 65199 Wiesbaden, Germany
| | - Josef Herzog
- Clinical Cancer Genetics, for the City of Hope Clinical Cancer Genetics Community Research Network, Duarte California 91010, USA
| | - Estrid Høgdall
- Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, 2730 Copenhagen, Denmark
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
| | - Claus K. Høgdall
- Department of Gynecology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Antoinette Hollestelle
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, 3015 Rotterdam, The Netherlands
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Peter J. Hulick
- Center for Medical Genetics, NorthShore University Health System, Evanston, Illinois, 60201, USA
| | - Tomasz Huzarski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 70-115, Poland
| | | | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington District of Columbia 20057, USA
| | - Hidemi Ito
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Aichi 464-8681, Japan
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 70-115, Poland
| | - Ramunas Janavicius
- State Research Institute Centre for Innovative Medicine, LT-01102 Vilnius, Lithuania
| | - Allan Jensen
- Department of Gynecology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Esther M. John
- Department of Epidemiology, Cancer Prevention Institute of California, Fremont, California 94538, USA
| | - Nichola Johnson
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London SW7 3RP, UK
| | - Maria Kabisch
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Daehee Kang
- Cancer Research Institute, Seoul National University, Seoul 08826, Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul 08826, Korea
| | - Miroslav Kapuscinski
- Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Beth Y. Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Sofia Khan
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki 00029 HUS, Finland
| | - Lambertus A. Kiemeney
- Radboud University Medical Centre, Radboud Institute for Health Sciences, 6500 Nijmegen, The Netherlands
| | - Susanne Kruger Kjaer
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
- Department of Gynecology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Julia A. Knight
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario M5T 3M7, Canada
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, (INRASTES) Institute of Nuclear and Radiological Sciences and Technology, National Centre for Scientific Research ‘Demokritos', Aghia Paraskevi Attikis, Athens 153 10, Greece
| | - Veli-Matti Kosma
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, 70210 Kuopio, Finland
- Cancer Center, Kuopio University Hospital, 70210 Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, 70210 Kuopio, Finland
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo N-0310, Norway
- K.G. Jebsen Center for Breast Cancer Research, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo N-0310, Norway
- Department of Clinical Molecular Biology, Oslo University Hospital, University of Oslo, 1478 Oslo, Norway
| | - Jolanta Kupryjanczyk
- Department of Pathology and Laboratory Diagnostics the Maria Sklodowska Curie Memorial Cancer Center and Institute of Oncology, Warsaw 44-101, Poland
| | - Ava Kwong
- The Hong Kong Hereditary Breast Cancer Family Registry, Cancer Genetics Center, Hong Kong Sanatorium and Hospital, Hong Kong, China
- Department of Surgery, The University of Hong Kong, Hong Kong, China
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC (El Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid 28040, Spain
| | - Yael Laitman
- Susanne Levy Gertner Oncogenetics Unit, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Diether Lambrechts
- Vesalius Research Center, VIB, 3000 Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, 3000 Leuven, Belgium
| | - Nhu Le
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University, Ghent 9000, Belgium
| | - Jenny Lester
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Douglas A. Levine
- Gynecology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York 10065, USA
| | - Jingmei Li
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
| | - Artitaya Lophatananon
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry CV4 7AL, UK
| | - Jennifer T. Loud
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland 20892, USA
| | - Karen Lu
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 70-115, Poland
| | - Arto Mannermaa
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, 70210 Kuopio, Finland
- Cancer Center, Kuopio University Hospital, 70210 Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, 70210 Kuopio, Finland
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale Tumori (INT), 20133 Milan, Italy
| | | | - Sara Margolin
- Department of Oncology - Pathology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Frederik Marme
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg 69120, Germany
- National Center for Tumour Diseases, University of Heidelberg, 69117 Heidelberg, Germany
| | - Leon F. A. G. Massuger
- Department of Gynaecology, Radboud University Medical Centre, 6500 Nijmegen, The Netherlands
| | - Keitaro Matsuo
- Department of Preventive Medicine, Kyushu University Faculty of Medical Sciences, Fukuoka 812-8582, Japan
| | - Sylvie Mazoyer
- INSERM U1052, CNRS UMR5286, Université Lyon, Centre de Recherche en Cancérologie de Lyon, Lyon 69373, France
| | - Lesley McGuffog
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Catriona McLean
- Anatomical Pathology, The Alfred Hospital, Melbourne, Victoria 3004, Australia
| | - Iain McNeish
- Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Beatson Institute for Cancer Research, Glasgow G61 1BD, UK
| | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Technische Universität München, 81675 Munich, Germany
| | - Usha Menon
- Women's Cancer, UCL EGA Institute for Women's Health, London WC1E 6AU, UK
| | - Arjen R. Mensenkamp
- Department of Human Genetics, Radboud University Medical Centre, 6500 Nijmegen, The Netherlands
| | - Roger L. Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Instituto Oncologico Veneto IOV, IRCCS, 35128 Padua, Italy
| | - Kirsten B. Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | - Kenneth Muir
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry CV4 7AL, UK
- Institute of Population Health, University of Manchester, Manchester M13 9PL, UK
| | - Anna Marie Mulligan
- Laboratory Medicine Program, University Health Network, Toronto, Ontario M5G 1L7, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Katherine L. Nathanson
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Roberta B. Ness
- The University of Texas School of Public Health, Houston, Texas 77030, USA
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki 00029 HUS, Finland
| | - Silje Nord
- K.G. Jebsen Center for Breast Cancer Research, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo N-0310, Norway
| | - Robert L. Nussbaum
- Department of Medicine and Genetics, University of California, San Francisco, California 94143, USA
| | - Kunle Odunsi
- Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York 10065, USA
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, 1122 Budapest, Hungary
| | - Olufunmilayo I. Olopade
- Center for Clinical Cancer Genetics and Global Health, University of Chicago Medical Center, Chicago, Illinois 60637, USA
| | - Janet E. Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55902, USA
| | - Curtis Olswold
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55902, USA
| | - David O'Malley
- The Ohio State University and the James Cancer Center, Columbus, Ohio 43210, USA
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York 10017, USA
| | - Nick Orr
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Ana Osorio
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Centre (CNIO), 28019 Madrid, Spain
- Biomedical Network on Rare Diseases (CIBERER), 28029 Madrid, Spain
| | - Sue Kyung Park
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul 08826, Korea
- Department of Surgery, Seoul National University College of Medicine, Seoul, 03080 Korea
| | - Celeste L. Pearce
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Tanja Pejovic
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, Oregon 97239, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Paolo Peterlongo
- IFOM, The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, 16 20139 Milan, Italy
| | - Georg Pfeiler
- Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Catherine M. Phelan
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida 33606, USA
| | - Elizabeth M. Poole
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumour Biology, Northern Finland Laboratory Centre NordLab, FI-90014 Oulu, Finland
- Laboratory of Cancer Genetics and Tumour Biology, Department of Clinical Chemistry and Biocenter Oulu, University of Oulu, FI-90014 Oulu, Finland
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT), 20133 Milan, Italy
| | - Johanna Rantala
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Muhammad Usman Rashid
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- Department of Basic Sciences, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC), Lahore 54000, Pakistan
| | - Gad Rennert
- Clalit National Israeli Cancer Control Center and Department of Community Medicine and Epidemiology, Carmel Medical Center and B. Rappaport Faculty of Medicine, Haifa 34362, Israel
| | - Valerie Rhenius
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Kerstin Rhiem
- Centre of Familial Breast and Ovarian Cancer, Department of Gynaecology and Obstetrics and Centre for Integrated Oncology (CIO), Center for Molecular Medicine Cologne (CMMC), University Hospital of Cologne, 50931 Cologne, Germany
| | - Harvey A. Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut 06510, USA
| | - Gus Rodriguez
- Division of Gynecologic Oncology, NorthShore University HealthSystem, Evanston, Illinois 60201, USA
| | - Mary Anne Rossing
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
- Department of Epidemiology, University of Washington, Seattle, Washington 98109, USA
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg 69121, Germany
| | - Helga B. Salvesen
- Department of Gynecology and Obstetrics, Haukeland University Hospital, 5021 Bergen, Norway
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, N-5020 Bergen, Norway
| | | | - Elinor J. Sawyer
- Research Oncology, Guy's Hospital, King's College London, London SE1 9RT, UK
| | - Joellen M. Schildkraut
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
- Cancer Control and Population Sciences, Duke Cancer Institute, Durham, North Carolina 27710, USA
| | - Marjanka K. Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, The Netherlands
| | - Rita K. Schmutzler
- Division of Molecular Gyneco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, 50676 Cologne, Germany
- Center for Integrated Oncology, University Hospital of Cologne, 50676 Cologne, Germany
- Center for Molecular Medicine, University Hospital of Cologne, 50676 Cologne, Germany
- Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, 50676 Cologne, Germany
| | - Thomas A. Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida 33606, USA
| | - Caroline Seynaeve
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, 3015 Rotterdam, The Netherlands
| | - Mitul Shah
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Chen-Yang Shen
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- School of Public Health, China Medical University, Taichung 404, Taiwan
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
| | - Weiva Sieh
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford California 94305, USA
| | - Christian F. Singer
- Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Olga M. Sinilnikova
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon – Centre Léon Bérard, Lyon 69008, France
- INSERM U1052, CNRS UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon 69003, France
| | - Susan Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55902, USA
| | - Honglin Song
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Penny Soucy
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec City, Québec G1V 4G2, Canada
| | - Melissa C. Southey
- Department of Pathology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Marie Stenmark-Askmalm
- Department of Clinical Genetics, Lund University Hospital, Lund 221 00, Sweden
- Division of Clinical Genetics, Department of Clinical and Experimental Medicine, Linköping University, 581 83 Linköping, Sweden
| | - Dominique Stoppa-Lyonnet
- Institut Curie, Department of Tumour Biology, Paris, France; Institut Curie, INSERM U830, 75248 Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, 75270 Paris, France
| | - Christian Sutter
- Institute of Human Genetics, Department of Human Genetics, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Anthony Swerdlow
- Division of Breast Cancer Research, The Institute of Cancer Research, London SW7 3RP, UK
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Sandrine Tchatchou
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Manuel R. Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto 4200-072, Portugal
- Biomedical Sciences Institute (ICBAS), Porto University, Porto 4099-002, Portugal
| | - Soo H. Teo
- Breast Cancer Research Unit, Cancer Research Institute, University Malaya Medical Centre, 50603 Kuala Lumpur, Malaysia
- Cancer Research Initiatives Foundation, Subang Jaya, 47500 Selangor, Malaysia
| | - Kathryn L. Terry
- Harvard HT Chan School of Public Health, Boston, Massachusetts 02115, USA
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York 10027, USA
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense C, Denmark
| | - Maria Grazia Tibiletti
- UO Anatomia Patologica, Ospedale di Circolo-Università dell'Insubria, 21100 Varese, Italy
| | - Laima Tihomirova
- Latvian Biomedical Research and Study Centre, Riga LV-1067, Latvia
| | - Silvia Tognazzo
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV - IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico), 64 - 35128 Padua, Italy
| | - Amanda Ewart Toland
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics and Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 7BN, UK
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- Institute of Human Genetics, Pontificia Universidad Javeriana, Cra. 7 #40-62 Bogota, Colombia
| | - Thérèse Truong
- Environmental Epidemiology of Cancer, Center for Research in Epidemiology and Population Health, INSERM, 94805 Villejuif, France
- University Paris-Sud, 91405 Villejuif, France
| | - Chiu-chen Tseng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Nadine Tung
- Department of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - Shelley S. Tworoger
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Celine Vachon
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55902, USA
| | | | - Helena C. van Doorn
- Department of Gynecology, Family Cancer Clinic, Erasmus MC Cancer Institute, 3015 CE Rotterdam, The Netherlands
| | | | - Laura J. Van't Veer
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, The Netherlands
| | - Adriaan Vanderstichele
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, B-3000 Leuven, Belgium
| | - Ignace Vergote
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, B-3000 Leuven, Belgium
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York 10065, USA
| | - Qin Wang
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | | | - Jeffrey N. Weitzel
- Clinical Cancer Genetics, for the City of Hope Clinical Cancer Genetics Community Research Network, Duarte California 91010, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda Maryland 20892, USA
| | - Alice S. Whittemore
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford California 94305, USA
| | - Hans Wildiers
- Multidisciplinary Breast Center, Department of General Medical Oncology, University Hospitals Leuven, B-3000 Leuven, Belgium
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumour Biology, Northern Finland Laboratory Centre NordLab, FI-90014 Oulu, Finland
- Laboratory of Cancer Genetics and Tumour Biology, Department of Clinical Chemistry and Biocenter Oulu, University of Oulu, FI-90014 Oulu, Finland
| | - Anna H. Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research ‘Demokritos', Athens 153 10, Greece
| | - Sook-Yee Yoon
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, 47500 Subang Jaya, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya Medical Centre, University Malaya, 59100 Kuala Lumpur, Malaysia
| | - Jyh-Cherng Yu
- Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, 114 Taiwan
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
| | - Ying Zheng
- Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec City, Québec G1V 4G2, Canada
| | - Alvaro N. Monteiro
- Cancer Epidemiology Program, Division of Population Sciences, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, USA
| | - Juliet D. French
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Fergus J. Couch
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55902, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Matthew L. Freedman
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Douglas F. Easton
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Alison M. Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Paul D. Pharoah
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Stacey L. Edwards
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | | | - Antonis C. Antoniou
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Simon A. Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California 90033, USA
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Coppola CJ, C Ramaker R, Mendenhall EM. Identification and function of enhancers in the human genome. Hum Mol Genet 2016; 25:R190-R197. [PMID: 27402881 DOI: 10.1093/hmg/ddw216] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 06/30/2016] [Indexed: 12/31/2022] Open
Abstract
The study of gene regulation has rapidly advanced by leveraging next-generation sequencing to identify and characterize the cis and trans elements that are critical for defining cell identity. These advances have paralleled a movement towards whole genome sequencing in clinics. These two tracks have increasingly synergized to underscore the importance of cis-regulatory elements in development as well produce countless studies implicating these elements in human disease. Other studies have emphasized the clinical phenotypes associated with variation or mutations in trans factors, including non-coding RNAs and chromatin regulators. These studies highlight the importance of obtaining a comprehensive understanding of mammalian gene regulation for predicting the impact of genetic variation on patient phenotypes. Currently lagging behind the generation of vast datasets and annotations is our ability to examine these putative elements in the dynamic context of a developing organism.
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Affiliation(s)
| | - Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA University of Alabama at Birmingham, Birmingham, AL, USA
| | - Eric M Mendenhall
- University of Alabama in Huntsville, Huntsville, AL, USA HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
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Partridge EC, Watkins TA, Mendenhall EM. Every transcription factor deserves its map: Scaling up epitope tagging of proteins to bypass antibody problems. Bioessays 2016; 38:801-11. [PMID: 27311628 DOI: 10.1002/bies.201600028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Genome-wide identification of transcription factor binding sites with the ChIP-seq method is an extremely important scientific endeavor - one that should ideally be performed for every transcription factor in as many cell types as possible. A major hurdle on the way to this goal is the necessity for a specific, ChIP-grade antibody for each transcription factor of interest, which is often not available. Here, we describe CETCh-seq, a recently published method utilizing genome engineering with the CRISPR/Cas9 system to circumvent the need for a specific antibody. Using the CETCh-seq method, targeted genomic editing results in an epitope-tagged transcription factor, which is recognized by a well-characterized, standard antibody, efficacious for ChIP-seq. We have used CETCh-seq in human cancer cell lines as well as mouse embryonic stem cells. We find that roughly 60% of transcription factors tagged using CETCh-seq produce a high quality ChIP-seq map, a significant improvement over traditional antibody-based methods.
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Affiliation(s)
| | | | - Eric M Mendenhall
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.,University of Alabama in Huntsville, AL, USA
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Engel KL, Mackiewicz M, Hardigan AA, Myers RM, Savic D. Decoding transcriptional enhancers: Evolving from annotation to functional interpretation. Semin Cell Dev Biol 2016; 57:40-50. [PMID: 27224938 DOI: 10.1016/j.semcdb.2016.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/06/2016] [Accepted: 05/18/2016] [Indexed: 12/18/2022]
Abstract
Deciphering the intricate molecular processes that orchestrate the spatial and temporal regulation of genes has become an increasingly major focus of biological research. The differential expression of genes by diverse cell types with a common genome is a hallmark of complex cellular functions, as well as the basis for multicellular life. Importantly, a more coherent understanding of gene regulation is critical for defining developmental processes, evolutionary principles and disease etiologies. Here we present our current understanding of gene regulation by focusing on the role of enhancer elements in these complex processes. Although functional genomic methods have provided considerable advances to our understanding of gene regulation, these assays, which are usually performed on a genome-wide scale, typically provide correlative observations that lack functional interpretation. Recent innovations in genome editing technologies have placed gene regulatory studies at an exciting crossroads, as systematic, functional evaluation of enhancers and other transcriptional regulatory elements can now be performed in a coordinated, high-throughput manner across the entire genome. This review provides insights on transcriptional enhancer function, their role in development and disease, and catalogues experimental tools commonly used to study these elements. Additionally, we discuss the crucial role of novel techniques in deciphering the complex gene regulatory landscape and how these studies will shape future research.
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Affiliation(s)
- Krysta L Engel
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States; Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Daniel Savic
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States.
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Jones PD, Kaiser MA, Ghaderi Najafabadi M, McVey DG, Beveridge AJ, Schofield CL, Samani NJ, Webb TR. The Coronary Artery Disease-associated Coding Variant in Zinc Finger C3HC-type Containing 1 (ZC3HC1) Affects Cell Cycle Regulation. J Biol Chem 2016; 291:16318-27. [PMID: 27226629 PMCID: PMC4965579 DOI: 10.1074/jbc.m116.734020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Indexed: 11/29/2022] Open
Abstract
Genome-wide association studies have to date identified multiple coronary artery disease (CAD)-associated loci; however, for most of these loci the mechanism by which they affect CAD risk is unclear. The CAD-associated locus 7q32.2 is unusual in that the lead variant, rs11556924, is not in strong linkage disequilibrium with any other variant and introduces a coding change in ZC3HC1, which encodes NIPA. In this study, we show that rs11556924 polymorphism is associated with lower regulatory phosphorylation of NIPA in the risk variant, resulting in NIPA with higher activity. Using a genome-editing approach we show that this causes an effective decrease in cyclin-B1 stability in the nucleus, thereby slowing its nuclear accumulation. By perturbing the rate of nuclear cyclin-B1 accumulation, rs11556924 alters the regulation of mitotic progression resulting in an extended mitosis. This study shows that the CAD-associated coding polymorphism in ZC3HC1 alters the dynamics of cell-cycle regulation by NIPA.
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Affiliation(s)
- Peter D Jones
- From the Department of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, University of Leicester, Leicester, LE3 9QP and
| | - Michael A Kaiser
- From the Department of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, University of Leicester, Leicester, LE3 9QP and
| | - Maryam Ghaderi Najafabadi
- From the Department of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, University of Leicester, Leicester, LE3 9QP and
| | - David G McVey
- From the Department of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, University of Leicester, Leicester, LE3 9QP and
| | - Allan J Beveridge
- From the Department of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, University of Leicester, Leicester, LE3 9QP and
| | - Christine L Schofield
- Horizon Discovery Limited, 7100 Cambridge Research Park, Waterbeach, Cambridge CB25 9TL, United Kingdom
| | - Nilesh J Samani
- From the Department of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, University of Leicester, Leicester, LE3 9QP and
| | - Tom R Webb
- From the Department of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, University of Leicester, Leicester, LE3 9QP and
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Hashemi M, Moradi N, Ziaee SAM, Narouie B, Soltani MH, Rezaei M, Shahkar G, Taheri M. Association between single nucleotide polymorphism in miR-499, miR-196a2, miR-146a and miR-149 and prostate cancer risk in a sample of Iranian population. J Adv Res 2016; 7:491-8. [PMID: 27222754 DOI: 10.1016/j.jare.2016.03.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/23/2016] [Accepted: 03/24/2016] [Indexed: 01/29/2023] Open
Abstract
MicroRNAs (miRNAs) play an important role in regulating gene expression at the post-transcriptional level and are involved in numerous physiological processes. Accumulating evidence suggests that single-nucleotide polymorphisms (SNPs) in human miRNA genes may affect miRNA biogenesis pathway and influence the susceptibility to several diseases such as cancer. The present study aimed to evaluate the impact of miR-499 rs3746444, miR-196a2 rs11614913, miR-149 rs2292832, and miR-146a rs2910164 polymorphisms on prostate cancer (PCa) risk in a sample of Iranian population. This case-control study was done on 169 patients with pathologically confirmed PCa and 182 benign prostatic hyperplasia (BPH). The genotyping assays were done using T-ARMS-PCR or PCR-RFLP methods. The findings indicated that CC genotype of miR-499 rs3746444 polymorphism increased the risk of PCa (OR = 1.76, 95% CI = 1.12-2.79, P = 0.019) compared to TT genotype. No statistically significant association was found between miR-196a2 rs11614913, miR-149 rs2292832, and miR-146a rs2910164 polymorphisms and PCa risk. In summary, the findings indicated that miR-499 rs3746444 polymorphism increased the risk of PCa in an Iranian population. Further studies with larger sample sizes and different ethnicities are necessary to verify the findings of the present study.
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Affiliation(s)
- Mohammad Hashemi
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran; Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Nazanin Moradi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Seyed Amir Mohsen Ziaee
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Behzad Narouie
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Hosein Soltani
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Rezaei
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Ghazaleh Shahkar
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mohsen Taheri
- Genetics of Non Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
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Bray MS, Loos RJF, McCaffery JM, Ling C, Franks PW, Weinstock GM, Snyder MP, Vassy JL, Agurs-Collins T. NIH working group report-using genomic information to guide weight management: From universal to precision treatment. Obesity (Silver Spring) 2016; 24:14-22. [PMID: 26692578 PMCID: PMC4689320 DOI: 10.1002/oby.21381] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 10/16/2015] [Accepted: 10/17/2015] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Precision medicine utilizes genomic and other data to optimize and personalize treatment. Although more than 2,500 genetic tests are currently available, largely for extreme and/or rare phenotypes, the question remains whether this approach can be used for the treatment of common, complex conditions like obesity, inflammation, and insulin resistance, which underlie a host of metabolic diseases. METHODS This review, developed from a Trans-NIH Conference titled "Genes, Behaviors, and Response to Weight Loss Interventions," provides an overview of the state of genetic and genomic research in the area of weight change and identifies key areas for future research. RESULTS Although many loci have been identified that are associated with cross-sectional measures of obesity/body size, relatively little is known regarding the genes/loci that influence dynamic measures of weight change over time. Although successful short-term weight loss has been achieved using many different strategies, sustainable weight loss has proven elusive for many, and there are important gaps in our understanding of energy balance regulation. CONCLUSIONS Elucidating the molecular basis of variability in weight change has the potential to improve treatment outcomes and inform innovative approaches that can simultaneously take into account information from genomic and other sources in devising individualized treatment plans.
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Affiliation(s)
- Molly S Bray
- Department of Nutritional Sciences, The University of Texas at AustinAustin, Texas, USA
| | - Ruth JF Loos
- Department of Preventive Medicine, The Charles Bronfman Institute for Personalized Medicine, The Mindich Child Health and Development Institute, The Icahn School of Medicine at Mount SinaiNew York City, New York, USA
| | - Jeanne M McCaffery
- Department of Psychiatry and Human Behavior, Weight Control and Diabetes Research Center, The Alpert Medical School of Brown University/The Miriam HospitalProvidence, Rhode Island, USA
| | - Charlotte Ling
- Department of Clinical Sciences, Skåne University HospitalMalmö, Sweden
| | - Paul W Franks
- Department of Clinical Sciences, Skåne University HospitalMalmö, Sweden
| | | | - Michael P Snyder
- Department of Genetics, Stanford University School of MedicineStanford, California, USA
| | - Jason L Vassy
- Division of General Medicine, Brigham and Women's Hospital and Harvard Medical SchoolBoston, Massachusetts, USA
| | - Tanya Agurs-Collins
- Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of HealthBethesda, Maryland, USA.
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