101
|
Gnanapragasam VJ, Hori S, Johnston T, Smith D, Muir K, Alonzi R, Winkler M, Warren A, Staffurth J, Khoo V, Tree A, Macneill A, McMenemin R, Mason M, Cathcart P, de Souza N, Sooriakumaran P, Weston R, Wylie J, Hall E, Lane A, Cross W, Syndikus I, Koupparis A. Clinical management and research priorities for high-risk prostate cancer in the UK: Meeting report of a multidisciplinary panel in conjunction with the NCRI Prostate Cancer Clinical Studies Localised Subgroup. JOURNAL OF CLINICAL UROLOGY 2016. [DOI: 10.1177/2051415816651362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The management of high-risk prostate cancer has become increasingly sophisticated, with refinements in radical therapy and the inclusion of adjuvant local and systemic therapies. Despite this, high-risk prostate cancer continues to have significant treatment failure rates, with progression to metastasis, castrate resistance and ultimately disease-specific death. In an effort to discuss the challenges in this field, the UK National Clinical Research Institute’s Prostate Cancer Clinical Studies localised subgroup convened a multidisciplinary national meeting in the autumn of 2014. The remit of the meeting was to debate and reach a consensus on the key clinical and research challenges in high-risk prostate cancer and to identify themes that the UK would be best placed to pursue to help improve outcomes. This report presents the outcome of those discussions and the key recommendations for future research in this highly heterogeneous disease entity.
Collapse
|
102
|
Ghoussaini M, French JD, Michailidou K, Nord S, Beesley J, Canisus S, Hillman KM, Kaufmann S, Sivakumaran H, Moradi Marjaneh M, Lee JS, Dennis J, Bolla MK, Wang Q, Dicks E, Milne RL, Hopper JL, Southey MC, Schmidt MK, Broeks A, Muir K, Lophatananon A, Fasching PA, Beckmann MW, Fletcher O, Johnson N, Sawyer EJ, Tomlinson I, Burwinkel B, Marme F, Guénel P, Truong T, Bojesen SE, Flyger H, Benitez J, González-Neira A, Alonso MR, Pita G, Neuhausen SL, Anton-Culver H, Brenner H, Arndt V, Meindl A, Schmutzler RK, Brauch H, Hamann U, Tessier DC, Vincent D, Nevanlinna H, Khan S, Matsuo K, Ito H, Dörk T, Bogdanova NV, Lindblom A, Margolin S, Mannermaa A, Kosma VM, Wu AH, Van Den Berg D, Lambrechts D, Floris G, Chang-Claude J, Rudolph A, Radice P, Barile M, Couch FJ, Hallberg E, Giles GG, Haiman CA, Le Marchand L, Goldberg MS, Teo SH, Yip CH, Borresen-Dale AL, Zheng W, Cai Q, Winqvist R, Pylkäs K, Andrulis IL, Devilee P, Tollenaar RAEM, García-Closas M, Figueroa J, Hall P, Czene K, Brand JS, Darabi H, Eriksson M, Hooning MJ, Koppert LB, Li J, Shu XO, Zheng Y, Cox A, Cross SS, Shah M, Rhenius V, Choi JY, Kang D, Hartman M, Chia KS, Kabisch M, Torres D, Luccarini C, Conroy DM, Jakubowska A, Lubinski J, Sangrajrang S, Brennan P, Olswold C, Slager S, Shen CY, Hou MF, Swerdlow A, Schoemaker MJ, Simard J, Pharoah PDP, Kristensen V, Chenevix-Trench G, Easton DF, Dunning AM, Edwards SL. Evidence that the 5p12 Variant rs10941679 Confers Susceptibility to Estrogen-Receptor-Positive Breast Cancer through FGF10 and MRPS30 Regulation. Am J Hum Genet 2016; 99:903-911. [PMID: 27640304 PMCID: PMC5065698 DOI: 10.1016/j.ajhg.2016.07.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 07/16/2016] [Indexed: 11/24/2022] Open
Abstract
Genome-wide association studies (GWASs) have revealed increased breast cancer risk associated with multiple genetic variants at 5p12. Here, we report the fine mapping of this locus using data from 104,660 subjects from 50 case-control studies in the Breast Cancer Association Consortium (BCAC). With data for 3,365 genotyped and imputed SNPs across a 1 Mb region (positions 44,394,495-45,364,167; NCBI build 37), we found evidence for at least three independent signals: the strongest signal, consisting of a single SNP rs10941679, was associated with risk of estrogen-receptor-positive (ER+) breast cancer (per-g allele OR ER+ = 1.15; 95% CI 1.13-1.18; p = 8.35 × 10-30). After adjustment for rs10941679, we detected signal 2, consisting of 38 SNPs more strongly associated with ER-negative (ER-) breast cancer (lead SNP rs6864776: per-a allele OR ER- = 1.10; 95% CI 1.05-1.14; p conditional = 1.44 × 10-12), and a single signal 3 SNP (rs200229088: per-t allele OR ER+ = 1.12; 95% CI 1.09-1.15; p conditional = 1.12 × 10-05). Expression quantitative trait locus analysis in normal breast tissues and breast tumors showed that the g (risk) allele of rs10941679 was associated with increased expression of FGF10 and MRPS30. Functional assays demonstrated that SNP rs10941679 maps to an enhancer element that physically interacts with the FGF10 and MRPS30 promoter regions in breast cancer cell lines. FGF10 is an oncogene that binds to FGFR2 and is overexpressed in ∼10% of human breast cancers, whereas MRPS30 plays a key role in apoptosis. These data suggest that the strongest signal of association at 5p12 is mediated through coordinated activation of FGF10 and MRPS30, two candidate genes for breast cancer pathogenesis.
Collapse
|
103
|
Bonilla C, Lewis SJ, Rowlands MA, Gaunt TR, Davey Smith G, Gunnell D, Palmer T, Donovan JL, Hamdy FC, Neal DE, Eeles R, Easton D, Kote-Jarai Z, Al Olama AA, Benlloch S, Muir K, Giles GG, Wiklund F, Grönberg H, Haiman CA, Schleutker J, Nordestgaard BG, Travis RC, Pashayan N, Khaw KT, Stanford JL, Blot WJ, Thibodeau S, Maier C, Kibel AS, Cybulski C, Cannon-Albright L, Brenner H, Park J, Kaneva R, Batra J, Teixeira MR, Pandha H, Lathrop M, Martin RM, Holly JMP. Assessing the role of insulin-like growth factors and binding proteins in prostate cancer using Mendelian randomization: Genetic variants as instruments for circulating levels. Int J Cancer 2016; 139:1520-33. [PMID: 27225428 PMCID: PMC4957617 DOI: 10.1002/ijc.30206] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 04/04/2016] [Accepted: 04/07/2016] [Indexed: 02/02/2023]
Abstract
Circulating insulin-like growth factors (IGFs) and their binding proteins (IGFBPs) are associated with prostate cancer. Using genetic variants as instruments for IGF peptides, we investigated whether these associations are likely to be causal. We identified from the literature 56 single nucleotide polymorphisms (SNPs) in the IGF axis previously associated with biomarker levels (8 from a genome-wide association study [GWAS] and 48 in reported candidate genes). In ∼700 men without prostate cancer and two replication cohorts (N ∼ 900 and ∼9,000), we examined the properties of these SNPS as instrumental variables (IVs) for IGF-I, IGF-II, IGFBP-2 and IGFBP-3. Those confirmed as strong IVs were tested for association with prostate cancer risk, low (< 7) vs. high (≥ 7) Gleason grade, localised vs. advanced stage, and mortality, in 22,936 controls and 22,992 cases. IV analysis was used in an attempt to estimate the causal effect of circulating IGF peptides on prostate cancer. Published SNPs in the IGFBP1/IGFBP3 gene region, particularly rs11977526, were strong instruments for IGF-II and IGFBP-3, less so for IGF-I. Rs11977526 was associated with high (vs. low) Gleason grade (OR per IGF-II/IGFBP-3 level-raising allele 1.05; 95% CI: 1.00, 1.10). Using rs11977526 as an IV we estimated the causal effect of a one SD increase in IGF-II (∼265 ng/mL) on risk of high vs. low grade disease as 1.14 (95% CI: 1.00, 1.31). Because of the potential for pleiotropy of the genetic instruments, these findings can only causally implicate the IGF pathway in general, not any one specific biomarker.
Collapse
|
104
|
Castaño-Betancourt MC, Evans DS, Ramos YFM, Boer CG, Metrustry S, Liu Y, den Hollander W, van Rooij J, Kraus VB, Yau MS, Mitchell BD, Muir K, Hofman A, Doherty M, Doherty S, Zhang W, Kraaij R, Rivadeneira F, Barrett-Connor E, Maciewicz RA, Arden N, Nelissen RGHH, Kloppenburg M, Jordan JM, Nevitt MC, Slagboom EP, Hart DJ, Lafeber F, Styrkarsdottir U, Zeggini E, Evangelou E, Spector TD, Uitterlinden AG, Lane NE, Meulenbelt I, Valdes AM, van Meurs JBJ. Novel Genetic Variants for Cartilage Thickness and Hip Osteoarthritis. PLoS Genet 2016; 12:e1006260. [PMID: 27701424 PMCID: PMC5049763 DOI: 10.1371/journal.pgen.1006260] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 07/26/2016] [Indexed: 12/31/2022] Open
Abstract
Osteoarthritis is one of the most frequent and disabling diseases of the elderly. Only few genetic variants have been identified for osteoarthritis, which is partly due to large phenotype heterogeneity. To reduce heterogeneity, we here examined cartilage thickness, one of the structural components of joint health. We conducted a genome-wide association study of minimal joint space width (mJSW), a proxy for cartilage thickness, in a discovery set of 13,013 participants from five different cohorts and replication in 8,227 individuals from seven independent cohorts. We identified five genome-wide significant (GWS, P≤5·0×10-8) SNPs annotated to four distinct loci. In addition, we found two additional loci that were significantly replicated, but results of combined meta-analysis fell just below the genome wide significance threshold. The four novel associated genetic loci were located in/near TGFA (rs2862851), PIK3R1 (rs10471753), SLBP/FGFR3 (rs2236995), and TREH/DDX6 (rs496547), while the other two (DOT1L and SUPT3H/RUNX2) were previously identified. A systematic prioritization for underlying causal genes was performed using diverse lines of evidence. Exome sequencing data (n = 2,050 individuals) indicated that there were no rare exonic variants that could explain the identified associations. In addition, TGFA, FGFR3 and PIK3R1 were differentially expressed in OA cartilage lesions versus non-lesioned cartilage in the same individuals. In conclusion, we identified four novel loci (TGFA, PIK3R1, FGFR3 and TREH) and confirmed two loci known to be associated with cartilage thickness.The identified associations were not caused by rare exonic variants. This is the first report linking TGFA to human OA, which may serve as a new target for future therapies.
Collapse
|
105
|
Shi J, Zhang Y, Zheng W, Michailidou K, Ghoussaini M, Bolla MK, Wang Q, Dennis J, Lush M, Milne RL, Shu XO, Beesley J, Kar S, Andrulis IL, Anton-Culver H, Arndt V, Beckmann MW, Zhao Z, Guo X, Benitez J, Beeghly-Fadiel A, Blot W, Bogdanova NV, Bojesen SE, Brauch H, Brenner H, Brinton L, Broeks A, Brüning T, Burwinkel B, Cai H, Canisius S, Chang-Claude J, Choi JY, Couch FJ, Cox A, Cross SS, Czene K, Darabi H, Devilee P, Droit A, Dork T, Fasching PA, Fletcher O, Flyger H, Fostira F, Gaborieau V, García-Closas M, Giles GG, Guenel P, Haiman CA, Hamann U, Hartman M, Miao H, Hollestelle A, Hopper JL, Hsiung CN, Ito H, Jakubowska A, Johnson N, Torres D, Kabisch M, Kang D, Khan S, Knight JA, Kosma VM, Lambrechts D, Li J, Lindblom A, Lophatananon A, Lubinski J, Mannermaa A, Manoukian S, Le Marchand L, Margolin S, Marme F, Matsuo K, McLean C, Meindl A, Muir K, Neuhausen SL, Nevanlinna H, Nord S, Børresen-Dale AL, Olson JE, Orr N, van den Ouweland AM, Peterlongo P, Putti TC, Rudolph A, Sangrajrang S, Sawyer EJ, Schmidt MK, Schmutzler RK, Shen CY, Hou MF, Shrubsole MJ, Southey MC, Swerdlow A, Teo SH, Thienpont B, Toland AE, Tollenaar RA, Tomlinson I, Truong T, Tseng CC, Wen W, Winqvist R, Wu AH, Yip CH, Zamora PM, Zheng Y, Floris G, Cheng CY, Hooning MJ, Martens JW, Seynaeve C, Kristensen VN, Hall P, Pharoah PD, Simard J, Chenevix-Trench G, Dunning AM, Antoniou AC, Easton DF, Cai Q, Long J. Fine-scale mapping of 8q24 locus identifies multiple independent risk variants for breast cancer. Int J Cancer 2016; 139:1303-1317. [PMID: 27087578 PMCID: PMC5110427 DOI: 10.1002/ijc.30150] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 01/11/2016] [Accepted: 01/19/2016] [Indexed: 02/03/2023]
Abstract
Previous genome-wide association studies among women of European ancestry identified two independent breast cancer susceptibility loci represented by single nucleotide polymorphisms (SNPs) rs13281615 and rs11780156 at 8q24. A fine-mapping study across 2.06 Mb (chr8:127,561,724-129,624,067, hg19) in 55,540 breast cancer cases and 51,168 controls within the Breast Cancer Association Consortium was conducted. Three additional independent association signals in women of European ancestry, represented by rs35961416 (OR = 0.95, 95% CI = 0.93-0.97, conditional p = 5.8 × 10(-6) ), rs7815245 (OR = 0.94, 95% CI = 0.91-0.96, conditional p = 1.1 × 10(-6) ) and rs2033101 (OR = 1.05, 95% CI = 1.02-1.07, conditional p = 1.1 × 10(-4) ) were found. Integrative analysis using functional genomic data from the Roadmap Epigenomics, the Encyclopedia of DNA Elements project, the Cancer Genome Atlas and other public resources implied that SNPs rs7815245 in Signal 3, and rs1121948 in Signal 5 (in linkage disequilibrium with rs11780156, r(2) = 0.77), were putatively functional variants for two of the five independent association signals. The results highlighted multiple 8q24 variants associated with breast cancer susceptibility in women of European ancestry.
Collapse
|
106
|
Darabi H, Beesley J, Droit A, Kar S, Nord S, Moradi Marjaneh M, Soucy P, Michailidou K, Ghoussaini M, Fues Wahl H, Bolla MK, Wang Q, Dennis J, Alonso MR, Andrulis IL, Anton-Culver H, Arndt V, Beckmann MW, Benitez J, Bogdanova NV, Bojesen SE, Brauch H, Brenner H, Broeks A, Brüning T, Burwinkel B, Chang-Claude J, Choi JY, Conroy DM, Couch FJ, Cox A, Cross SS, Czene K, Devilee P, Dörk T, Easton DF, Fasching PA, Figueroa J, Fletcher O, Flyger H, Galle E, García-Closas M, Giles GG, Goldberg MS, González-Neira A, Guénel P, Haiman CA, Hallberg E, Hamann U, Hartman M, Hollestelle A, Hopper JL, Ito H, Jakubowska A, Johnson N, Kang D, Khan S, Kosma VM, Kriege M, Kristensen V, Lambrechts D, Le Marchand L, Lee SC, Lindblom A, Lophatananon A, Lubinski J, Mannermaa A, Manoukian S, Margolin S, Matsuo K, Mayes R, McKay J, Meindl A, Milne RL, Muir K, Neuhausen SL, Nevanlinna H, Olswold C, Orr N, Peterlongo P, Pita G, Pylkäs K, Rudolph A, Sangrajrang S, Sawyer EJ, Schmidt MK, Schmutzler RK, Seynaeve C, Shah M, Shen CY, Shu XO, Southey MC, Stram DO, Surowy H, Swerdlow A, Teo SH, Tessier DC, Tomlinson I, Torres D, Truong T, Vachon CM, Vincent D, Winqvist R, Wu AH, Wu PE, Yip CH, Zheng W, Pharoah PDP, Hall P, Edwards SL, Simard J, French JD, Chenevix-Trench G, Dunning AM. Fine scale mapping of the 17q22 breast cancer locus using dense SNPs, genotyped within the Collaborative Oncological Gene-Environment Study (COGs). Sci Rep 2016; 6:32512. [PMID: 27600471 PMCID: PMC5013272 DOI: 10.1038/srep32512] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 08/03/2016] [Indexed: 02/02/2023] Open
Abstract
Genome-wide association studies have found SNPs at 17q22 to be associated with breast cancer risk. To identify potential causal variants related to breast cancer risk, we performed a high resolution fine-mapping analysis that involved genotyping 517 SNPs using a custom Illumina iSelect array (iCOGS) followed by imputation of genotypes for 3,134 SNPs in more than 89,000 participants of European ancestry from the Breast Cancer Association Consortium (BCAC). We identified 28 highly correlated common variants, in a 53 Kb region spanning two introns of the STXBP4 gene, that are strong candidates for driving breast cancer risk (lead SNP rs2787486 (OR = 0.92; CI 0.90-0.94; P = 8.96 × 10(-15))) and are correlated with two previously reported risk-associated variants at this locus, SNPs rs6504950 (OR = 0.94, P = 2.04 × 10(-09), r(2) = 0.73 with lead SNP) and rs1156287 (OR = 0.93, P = 3.41 × 10(-11), r(2) = 0.83 with lead SNP). Analyses indicate only one causal SNP in the region and several enhancer elements targeting STXBP4 are located within the 53 kb association signal. Expression studies in breast tumor tissues found SNP rs2787486 to be associated with increased STXBP4 expression, suggesting this may be a target gene of this locus.
Collapse
|
107
|
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.
Collapse
|
108
|
Kar SP, Beesley J, Amin Al Olama A, Michailidou K, Tyrer J, Kote-Jarai ZS, Lawrenson K, Lindstrom S, Ramus SJ, Thompson DJ, Kibel AS, Dansonka-Mieszkowska A, Michael A, Dieffenbach AK, Gentry-Maharaj A, Whittemore AS, Wolk A, Monteiro A, Peixoto A, Kierzek A, Cox A, Rudolph A, Gonzalez-Neira A, Wu AH, Lindblom A, Swerdlow A, Ziogas A, Ekici AB, Burwinkel B, Karlan BY, Nordestgaard BG, Blomqvist C, Phelan C, McLean C, Pearce CL, Vachon C, Cybulski C, Slavov C, Stegmaier C, Maier C, Ambrosone CB, Høgdall CK, Teerlink CC, Kang D, Tessier DC, Schaid DJ, Stram DO, Cramer DW, Neal DE, Eccles D, Flesch-Janys D, Edwards DRV, Wokozorczyk D, Levine DA, Yannoukakos D, Sawyer EJ, Bandera EV, Poole EM, Goode EL, Khusnutdinova E, Høgdall E, Song F, Bruinsma F, Heitz F, Modugno F, Hamdy FC, Wiklund F, Giles GG, Olsson H, Wildiers H, Ulmer HU, Pandha H, Risch HA, Darabi H, Salvesen HB, Nevanlinna H, Gronberg H, Brenner H, Brauch H, Anton-Culver H, Song H, Lim HY, McNeish I, Campbell I, Vergote I, Gronwald J, Lubiński J, Stanford JL, Benítez J, Doherty JA, Permuth JB, Chang-Claude J, Donovan JL, Dennis J, Schildkraut JM, Schleutker J, Hopper JL, Kupryjanczyk J, Park JY, Figueroa J, Clements JA, Knight JA, Peto J, Cunningham JM, Pow-Sang J, Batra J, Czene K, Lu KH, Herkommer K, Khaw KT, Matsuo K, Muir K, Offitt K, Chen K, Moysich KB, Aittomäki K, Odunsi K, Kiemeney LA, Massuger LFAG, Fitzgerald LM, Cook LS, Cannon-Albright L, Hooning MJ, Pike MC, Bolla MK, Luedeke M, Teixeira MR, Goodman MT, Schmidt MK, Riggan M, Aly M, Rossing MA, Beckmann MW, Moisse M, Sanderson M, Southey MC, Jones M, Lush M, Hildebrandt MAT, Hou MF, Schoemaker MJ, Garcia-Closas M, Bogdanova N, Rahman N, Le ND, Orr N, Wentzensen N, Pashayan N, Peterlongo P, Guénel P, Brennan P, Paulo P, Webb PM, Broberg P, Fasching PA, Devilee P, Wang Q, Cai Q, Li Q, Kaneva R, Butzow R, Kopperud RK, Schmutzler RK, Stephenson RA, MacInnis RJ, Hoover RN, Winqvist R, Ness R, Milne RL, Travis RC, Benlloch S, Olson SH, McDonnell SK, Tworoger SS, Maia S, Berndt S, Lee SC, Teo SH, Thibodeau SN, Bojesen SE, Gapstur SM, Kjær SK, Pejovic T, Tammela TLJ, Dörk T, Brüning T, Wahlfors T, Key TJ, Edwards TL, Menon U, Hamann U, Mitev V, Kosma VM, Setiawan VW, Kristensen V, Arndt V, Vogel W, Zheng W, Sieh W, Blot WJ, Kluzniak W, Shu XO, Gao YT, Schumacher F, Freedman ML, Berchuck A, Dunning AM, Simard J, Haiman CA, Spurdle A, Sellers TA, Hunter DJ, Henderson BE, Kraft P, Chanock SJ, Couch FJ, Hall P, Gayther SA, Easton DF, Chenevix-Trench G, Eeles R, Pharoah PDP, Lambrechts D. Genome-Wide Meta-Analyses of Breast, Ovarian, and Prostate Cancer Association Studies Identify Multiple New Susceptibility Loci Shared by at Least Two Cancer Types. Cancer Discov 2016; 6:1052-67. [PMID: 27432226 PMCID: PMC5010513 DOI: 10.1158/2159-8290.cd-15-1227] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 06/07/2016] [Indexed: 02/02/2023]
Abstract
UNLABELLED Breast, ovarian, and prostate cancers are hormone-related and may have a shared genetic basis, but this has not been investigated systematically by genome-wide association (GWA) studies. Meta-analyses combining the largest GWA meta-analysis data sets for these cancers totaling 112,349 cases and 116,421 controls of European ancestry, all together and in pairs, identified at P < 10(-8) seven new cross-cancer loci: three associated with susceptibility to all three cancers (rs17041869/2q13/BCL2L11; rs7937840/11q12/INCENP; rs1469713/19p13/GATAD2A), two breast and ovarian cancer risk loci (rs200182588/9q31/SMC2; rs8037137/15q26/RCCD1), and two breast and prostate cancer risk loci (rs5013329/1p34/NSUN4; rs9375701/6q23/L3MBTL3). Index variants in five additional regions previously associated with only one cancer also showed clear association with a second cancer type. Cell-type-specific expression quantitative trait locus and enhancer-gene interaction annotations suggested target genes with potential cross-cancer roles at the new loci. Pathway analysis revealed significant enrichment of death receptor signaling genes near loci with P < 10(-5) in the three-cancer meta-analysis. SIGNIFICANCE We demonstrate that combining large-scale GWA meta-analysis findings across cancer types can identify completely new risk loci common to breast, ovarian, and prostate cancers. We show that the identification of such cross-cancer risk loci has the potential to shed new light on the shared biology underlying these hormone-related cancers. Cancer Discov; 6(9); 1052-67. ©2016 AACR.This article is highlighted in the In This Issue feature, p. 932.
Collapse
|
109
|
Fehringer G, Kraft P, Pharoah PD, Eeles RA, Chatterjee N, Schumacher FR, Schildkraut JM, Lindström S, Brennan P, Bickeböller H, Houlston RS, Landi MT, Caporaso N, Risch A, Amin Al Olama A, Berndt SI, Giovannucci EL, Grönberg H, Kote-Jarai Z, Ma J, Muir K, Stampfer MJ, Stevens VL, Wiklund F, Willett WC, Goode EL, Permuth JB, Risch HA, Reid BM, Bezieau S, Brenner H, Chan AT, Chang-Claude J, Hudson TJ, Kocarnik JK, Newcomb PA, Schoen RE, Slattery ML, White E, Adank MA, Ahsan H, Aittomäki K, Baglietto L, Blomquist C, Canzian F, Czene K, Dos-Santos-Silva I, Eliassen AH, Figueroa JD, Flesch-Janys D, Fletcher O, Garcia-Closas M, Gaudet MM, Johnson N, Hall P, Hazra A, Hein R, Hofman A, Hopper JL, Irwanto A, Johansson M, Kaaks R, Kibriya MG, Lichtner P, Liu J, Lund E, Makalic E, Meindl A, Müller-Myhsok B, Muranen TA, Nevanlinna H, Peeters PH, Peto J, Prentice RL, Rahman N, Sanchez MJ, Schmidt DF, Schmutzler RK, Southey MC, Tamimi R, Travis RC, Turnbull C, Uitterlinden AG, Wang Z, Whittemore AS, Yang XR, Zheng W, Buchanan DD, Casey G, Conti DV, Edlund CK, Gallinger S, Haile RW, Jenkins M, Le Marchand L, Li L, Lindor NM, Schmit SL, Thibodeau SN, Woods MO, Rafnar T, Gudmundsson J, Stacey SN, Stefansson K, Sulem P, Chen YA, Tyrer JP, Christiani DC, Wei Y, Shen H, Hu Z, Shu XO, Shiraishi K, Takahashi A, Bossé Y, Obeidat M, Nickle D, Timens W, Freedman ML, Li Q, Seminara D, Chanock SJ, Gong J, Peters U, Gruber SB, Amos CI, Sellers TA, Easton DF, Hunter DJ, Haiman CA, Henderson BE, Hung RJ. Cross-Cancer Genome-Wide Analysis of Lung, Ovary, Breast, Prostate, and Colorectal Cancer Reveals Novel Pleiotropic Associations. Cancer Res 2016; 76:5103-14. [PMID: 27197191 PMCID: PMC5010493 DOI: 10.1158/0008-5472.can-15-2980] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 04/05/2016] [Indexed: 01/26/2023]
Abstract
Identifying genetic variants with pleiotropic associations can uncover common pathways influencing multiple cancers. We took a two-stage approach to conduct genome-wide association studies for lung, ovary, breast, prostate, and colorectal cancer from the GAME-ON/GECCO Network (61,851 cases, 61,820 controls) to identify pleiotropic loci. Findings were replicated in independent association studies (55,789 cases, 330,490 controls). We identified a novel pleiotropic association at 1q22 involving breast and lung squamous cell carcinoma, with eQTL analysis showing an association with ADAM15/THBS3 gene expression in lung. We also identified a known breast cancer locus CASP8/ALS2CR12 associated with prostate cancer, a known cancer locus at CDKN2B-AS1 with different variants associated with lung adenocarcinoma and prostate cancer, and confirmed the associations of a breast BRCA2 locus with lung and serous ovarian cancer. This is the largest study to date examining pleiotropy across multiple cancer-associated loci, identifying common mechanisms of cancer development and progression. Cancer Res; 76(17); 5103-14. ©2016 AACR.
Collapse
|
110
|
Wyszynski A, Hong CC, Lam K, Michailidou K, Lytle C, Yao S, Zhang Y, Bolla MK, Wang Q, Dennis J, Hopper JL, Southey MC, Schmidt MK, Broeks A, Muir K, Lophatananon A, Fasching PA, Beckmann MW, Peto J, Dos-Santos-Silva I, Sawyer EJ, Tomlinson I, Burwinkel B, Marme F, Guénel P, Truong T, Bojesen SE, Nordestgaard BG, González-Neira A, Benitez J, Neuhausen SL, Brenner H, Dieffenbach AK, Meindl A, Schmutzler RK, Brauch H, Nevanlinna H, Khan S, Matsuo K, Ito H, Dörk T, Bogdanova NV, Lindblom A, Margolin S, Mannermaa A, Kosma VM, Wu AH, Van Den Berg D, Lambrechts D, Wildiers H, Chang-Claude J, Rudolph A, Radice P, Peterlongo P, Couch FJ, Olson JE, Giles GG, Milne RL, Haiman CA, Henderson BE, Dumont M, Teo SH, Wong TY, Kristensen V, Zheng W, Long J, Winqvist R, Pylkäs K, Andrulis IL, Knight JA, Devilee P, Seynaeve C, García-Closas M, Figueroa J, Klevebring D, Czene K, Hooning MJ, van den Ouweland AMW, Darabi H, Shu XO, Gao YT, Cox A, Blot W, Signorello LB, Shah M, Kang D, Choi JY, Hartman M, Miao H, Hamann U, Jakubowska A, Lubinski J, Sangrajrang S, McKay J, Toland AE, Yannoukakos D, Shen CY, Wu PE, Swerdlow A, Orr N, Simard J, Pharoah PDP, Dunning AM, Chenevix-Trench G, Hall P, Bandera E, Amos C, Ambrosone C, Easton DF, Cole MD. An intergenic risk locus containing an enhancer deletion in 2q35 modulates breast cancer risk by deregulating IGFBP5 expression. Hum Mol Genet 2016; 25:3863-3876. [PMID: 27402876 PMCID: PMC5216618 DOI: 10.1093/hmg/ddw223] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 06/11/2016] [Accepted: 07/04/2016] [Indexed: 12/20/2022] Open
Abstract
Breast cancer is the most diagnosed malignancy and the second leading cause of cancer mortality in females. Previous association studies have identified variants on 2q35 associated with the risk of breast cancer. To identify functional susceptibility loci for breast cancer, we interrogated the 2q35 gene desert for chromatin architecture and functional variation correlated with gene expression. We report a novel intergenic breast cancer risk locus containing an enhancer copy number variation (enCNV; deletion) located approximately 400Kb upstream to IGFBP5, which overlaps an intergenic ERα-bound enhancer that loops to the IGFBP5 promoter. The enCNV is correlated with modified ERα binding and monoallelic-repression of IGFBP5 following oestrogen treatment. We investigated the association of enCNV genotype with breast cancer in 1,182 cases and 1,362 controls, and replicate our findings in an independent set of 62,533 cases and 60,966 controls from 41 case control studies and 11 GWAS. We report a dose-dependent inverse association of 2q35 enCNV genotype (percopy OR = 0.68 95%CI 0.55-0.83, P = 0.0002; replication OR = 0.77 95% CI 0.73-0.82, P = 2.1 × 10-19) and identify 13 additional linked variants (r2 > 0.8) in the 20Kb linkage block containing the enCNV (P = 3.2 × 10-15 - 5.6 × 10-17). These associations were independent of previously reported 2q35 variants, rs13387042/rs4442975 and rs16857609, and were stronger for ER-positive than ER-negative disease. Together, these results suggest that 2q35 breast cancer risk loci may be mediating their effect through IGFBP5.
Collapse
|
111
|
Horne HN, Chung CC, Zhang H, Yu K, Prokunina-Olsson L, Michailidou K, Bolla MK, Wang Q, Dennis J, Hopper JL, Southey MC, Schmidt MK, Broeks A, Muir K, Lophatananon A, Fasching PA, Beckmann MW, Fletcher O, Johnson N, Sawyer EJ, Tomlinson I, Burwinkel B, Marme F, Guénel P, Truong T, Bojesen SE, Flyger H, Benitez J, González-Neira A, Anton-Culver H, Neuhausen SL, Brenner H, Arndt V, Meindl A, Schmutzler RK, Brauch H, Hamann U, Nevanlinna H, Khan S, Matsuo K, Iwata H, Dörk T, Bogdanova NV, Lindblom A, Margolin S, Mannermaa A, Kosma VM, Chenevix-Trench G, Wu AH, ven den Berg D, Smeets A, Zhao H, Chang-Claude J, Rudolph A, Radice P, Barile M, Couch FJ, Vachon C, Giles GG, Milne RL, Haiman CA, Marchand LL, Goldberg MS, Teo SH, Taib NAM, Kristensen V, Borresen-Dale AL, Zheng W, Shrubsole M, Winqvist R, Jukkola-Vuorinen A, Andrulis IL, Knight JA, Devilee P, Seynaeve C, García-Closas M, Czene K, Darabi H, Hollestelle A, Martens JWM, Li J, Lu W, Shu XO, Cox A, Cross SS, Blot W, Cai Q, Shah M, Luccarini C, Baynes C, Harrington P, Kang D, Choi JY, Hartman M, Chia KS, Kabisch M, Torres D, Jakubowska A, Lubinski J, Sangrajrang S, Brennan P, Slager S, Yannoukakos D, Shen CY, Hou MF, Swerdlow A, Orr N, Simard J, Hall P, Pharoah PDP, Easton DF, Chanock SJ, Dunning AM, Figueroa JD. Fine-Mapping of the 1p11.2 Breast Cancer Susceptibility Locus. PLoS One 2016; 11:e0160316. [PMID: 27556229 PMCID: PMC4996485 DOI: 10.1371/journal.pone.0160316] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 07/18/2016] [Indexed: 02/02/2023] Open
Abstract
The Cancer Genetic Markers of Susceptibility genome-wide association study (GWAS) originally identified a single nucleotide polymorphism (SNP) rs11249433 at 1p11.2 associated with breast cancer risk. To fine-map this locus, we genotyped 92 SNPs in a 900kb region (120,505,799-121,481,132) flanking rs11249433 in 45,276 breast cancer cases and 48,998 controls of European, Asian and African ancestry from 50 studies in the Breast Cancer Association Consortium. Genotyping was done using iCOGS, a custom-built array. Due to the complicated nature of the region on chr1p11.2: 120,300,000-120,505,798, that lies near the centromere and contains seven duplicated genomic segments, we restricted analyses to 429 SNPs excluding the duplicated regions (42 genotyped and 387 imputed). Per-allelic associations with breast cancer risk were estimated using logistic regression models adjusting for study and ancestry-specific principal components. The strongest association observed was with the original identified index SNP rs11249433 (minor allele frequency (MAF) 0.402; per-allele odds ratio (OR) = 1.10, 95% confidence interval (CI) 1.08-1.13, P = 1.49 x 10-21). The association for rs11249433 was limited to ER-positive breast cancers (test for heterogeneity P≤8.41 x 10-5). Additional analyses by other tumor characteristics showed stronger associations with moderately/well differentiated tumors and tumors of lobular histology. Although no significant eQTL associations were observed, in silico analyses showed that rs11249433 was located in a region that is likely a weak enhancer/promoter. Fine-mapping analysis of the 1p11.2 breast cancer susceptibility locus confirms this region to be limited to risk to cancers that are ER-positive.
Collapse
|
112
|
Khankari NK, Murff HJ, Zeng C, Wen W, Eeles RA, Easton DF, Kote-Jarai Z, Al Olama AA, Benlloch S, Muir K, Giles GG, Wiklund F, Gronberg H, Haiman CA, Schleutker J, Nordestgaard BG, Travis RC, Donovan JL, Pashayan N, Khaw KT, Stanford JL, Blot WJ, Thibodeau SN, Maier C, Kibel AS, Cybulski C, Cannon-Albright L, Brenner H, Park J, Kaneva R, Batra J, Teixeira MR, Pandha H, Zheng W. Polyunsaturated fatty acids and prostate cancer risk: a Mendelian randomisation analysis from the PRACTICAL consortium. Br J Cancer 2016; 115:624-31. [PMID: 27490808 PMCID: PMC4997551 DOI: 10.1038/bjc.2016.228] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/30/2016] [Accepted: 07/06/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Prostate cancer is a common cancer worldwide with no established modifiable lifestyle factors to guide prevention. The associations between polyunsaturated fatty acids (PUFAs) and prostate cancer risk have been inconsistent. Using Mendelian randomisation, we evaluated associations between PUFAs and prostate cancer risk. METHODS We used individual-level data from a consortium of 22 721 cases and 23 034 controls of European ancestry. Externally-weighted PUFA-specific polygenic risk scores (wPRSs), with explanatory variation ranging from 0.65 to 33.07%, were constructed and used to evaluate associations with prostate cancer risk per one standard deviation (s.d.) increase in genetically-predicted plasma PUFA levels using multivariable-adjusted unconditional logistic regression. RESULTS No overall association was observed between the genetically-predicted PUFAs evaluated in this study and prostate cancer risk. However, risk reductions were observed for short-chain PUFAs, linoleic (ORLA=0.95, 95%CI=0.92, 0.98) and α-linolenic acids (ORALA=0.96, 95%CI=0.93, 0.98), among men <62 years; whereas increased risk was found among men ⩾62 years for LA (ORLA=1.04, 95%CI=1.01, 1.07). For long-chain PUFAs (i.e., arachidonic, eicosapentaenoic, and docosapentaenoic acids), increased risks were observed among men <62 years (ORAA=1.05, 95%CI=1.02, 1.08; OREPA=1.04, 95%CI=1.01, 1.06; ORDPA=1.05, 95%CI=1.02, 1.08). CONCLUSION Results from this study suggest that circulating ω-3 and ω-6 PUFAs may have a different role in the aetiology of early- and late-onset prostate cancer.
Collapse
|
113
|
Muir K. The development of social sensitivity. INTERNATIONAL JOURNAL OF BEHAVIORAL DEVELOPMENT 2016. [DOI: 10.1177/016502548000300411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
114
|
Murray S, Bashir K, Lees KR, Muir K, MacAlpine C, Roberts M, Langhorne P. Epidemiological Aspects of Referral to TIA Clinics in Glasgow. Scott Med J 2016; 52:4-8. [PMID: 17373416 DOI: 10.1258/rsmsmj.52.1.4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A retrospective cohort study was carried out of new referrals to transient ischaemic attack (TIA) clinics in Glasgow. The aims of the study were to describe the profile of referrals and to assess the odds ratios for TIA, minor stroke or amaurosis fugax of both cardiovascular risk factors and clinical features. In total, data were collected for 813 new referrals in a period of six months. Thirteen point eight percent of referrals were from other Health Boards. The overall referral rate among residents of Greater Glasgow NHS Board was 165.6 per 100,000 per year. About 20% of referrals were made by clinicians in secondary care. The specialties from which referrals were most commonly made were accident and emergency, general medicine, ophthalmology and geriatric assessment. The most common risk factors in patients referred were hypertension (52.9%), smoking (31.7%), ischaemic heart disease (22.7%) and former smokers (22.4%). The most common clinical features were hemiparesis (13.3%), weakness of an upper limb (8.7%), vertigo (7.9%) and dysphasia (7.3%). In 48.7% of cases, a non-cerebrovascular diagnosis was made. Separate multivariate models were established for risk factors and clinical features. In the model for risk factors, five factors were significant for risk of TIA, stroke or amaurosis fugax. These were hyperlipidaemia, age over 64 years, hypertension, smoking and ex-smoking. In the model for clinical features, five factors were also significant. These were visual field defect, speech defact, facial weakness and hemiparesis.
Collapse
|
115
|
Zeng C, Guo X, Long J, Kuchenbaecker KB, Droit A, Michailidou K, Ghoussaini M, Kar S, Freeman A, Hopper JL, Milne RL, Bolla MK, Wang Q, Dennis J, Agata S, Ahmed S, Aittomäki K, Andrulis IL, Anton-Culver H, Antonenkova NN, Arason A, Arndt V, Arun BK, Arver B, Bacot F, Barrowdale D, Baynes C, Beeghly-Fadiel A, Benitez J, Bermisheva M, Blomqvist C, Blot WJ, Bogdanova NV, Bojesen SE, Bonanni B, Borresen-Dale AL, Brand JS, Brauch H, Brennan P, Brenner H, Broeks A, Brüning T, Burwinkel B, Buys SS, Cai Q, Caldes T, Campbell I, Carpenter J, Chang-Claude J, Choi JY, Claes KBM, Clarke C, Cox A, Cross SS, Czene K, Daly MB, de la Hoya M, De Leeneer K, Devilee P, Diez O, Domchek SM, Doody M, Dorfling CM, Dörk T, Dos-Santos-Silva I, Dumont M, Dwek M, Dworniczak B, Egan K, Eilber U, Einbeigi Z, Ejlertsen B, Ellis S, Frost D, Lalloo F, Fasching PA, Figueroa J, Flyger H, Friedlander M, Friedman E, Gambino G, Gao YT, Garber J, García-Closas M, Gehrig A, Damiola F, Lesueur F, Mazoyer S, Stoppa-Lyonnet D, Giles GG, Godwin AK, Goldgar DE, González-Neira A, Greene MH, Guénel P, Haeberle L, Haiman CA, Hallberg E, Hamann U, Hansen TVO, Hart S, Hartikainen JM, Hartman M, Hassan N, Healey S, Hogervorst FBL, Verhoef S, Hendricks CB, Hillemanns P, Hollestelle A, Hulick PJ, Hunter DJ, Imyanitov EN, Isaacs C, Ito H, Jakubowska A, Janavicius R, Jaworska-Bieniek K, Jensen UB, John EM, Joly Beauparlant C, Jones M, Kabisch M, Kang D, Karlan BY, Kauppila S, Kerin MJ, Khan S, Khusnutdinova E, Knight JA, Konstantopoulou I, Kraft P, Kwong A, Laitman Y, Lambrechts D, Lazaro C, Le Marchand L, Lee CN, Lee MH, Lester J, Li J, Liljegren A, Lindblom A, Lophatananon A, Lubinski J, Mai PL, Mannermaa A, Manoukian S, Margolin S, Marme F, Matsuo K, McGuffog L, Meindl A, Menegaux F, Montagna M, Muir K, Mulligan AM, Nathanson KL, Neuhausen SL, Nevanlinna H, Newcomb PA, Nord S, Nussbaum RL, Offit K, Olah E, Olopade OI, Olswold C, Osorio A, Papi L, Park-Simon TW, Paulsson-Karlsson Y, Peeters S, Peissel B, Peterlongo P, Peto J, Pfeiler G, Phelan CM, Presneau N, Radice P, Rahman N, Ramus SJ, Rashid MU, Rennert G, Rhiem K, Rudolph A, Salani R, Sangrajrang S, Sawyer EJ, Schmidt MK, Schmutzler RK, Schoemaker MJ, Schürmann P, Seynaeve C, Shen CY, Shrubsole MJ, Shu XO, Sigurdson A, Singer CF, Slager S, Soucy P, Southey M, Steinemann D, Swerdlow A, Szabo CI, Tchatchou S, Teixeira MR, Teo SH, Terry MB, Tessier DC, Teulé A, Thomassen M, Tihomirova L, Tischkowitz M, Toland AE, Tung N, Turnbull C, van den Ouweland AMW, van Rensburg EJ, Ven den Berg D, Vijai J, Wang-Gohrke S, Weitzel JN, Whittemore AS, Winqvist R, Wong TY, Wu AH, Yannoukakos D, Yu JC, Pharoah PDP, Hall P, Chenevix-Trench G, Dunning AM, Simard J, Couch FJ, Antoniou AC, Easton DF, Zheng W. Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus. Breast Cancer Res 2016; 18:64. [PMID: 27459855 PMCID: PMC4962376 DOI: 10.1186/s13058-016-0718-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 05/18/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Multiple recent genome-wide association studies (GWAS) have identified a single nucleotide polymorphism (SNP), rs10771399, at 12p11 that is associated with breast cancer risk. METHOD We performed a fine-scale mapping study of a 700 kb region including 441 genotyped and more than 1300 imputed genetic variants in 48,155 cases and 43,612 controls of European descent, 6269 cases and 6624 controls of East Asian descent and 1116 cases and 932 controls of African descent in the Breast Cancer Association Consortium (BCAC; http://bcac.ccge.medschl.cam.ac.uk/ ), and in 15,252 BRCA1 mutation carriers in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Stepwise regression analyses were performed to identify independent association signals. Data from the Encyclopedia of DNA Elements project (ENCODE) and the Cancer Genome Atlas (TCGA) were used for functional annotation. RESULTS Analysis of data from European descendants found evidence for four independent association signals at 12p11, represented by rs7297051 (odds ratio (OR) = 1.09, 95 % confidence interval (CI) = 1.06-1.12; P = 3 × 10(-9)), rs805510 (OR = 1.08, 95 % CI = 1.04-1.12, P = 2 × 10(-5)), and rs1871152 (OR = 1.04, 95 % CI = 1.02-1.06; P = 2 × 10(-4)) identified in the general populations, and rs113824616 (P = 7 × 10(-5)) identified in the meta-analysis of BCAC ER-negative cases and BRCA1 mutation carriers. SNPs rs7297051, rs805510 and rs113824616 were also associated with breast cancer risk at P < 0.05 in East Asians, but none of the associations were statistically significant in African descendants. Multiple candidate functional variants are located in putative enhancer sequences. Chromatin interaction data suggested that PTHLH was the likely target gene of these enhancers. Of the six variants with the strongest evidence of potential functionality, rs11049453 was statistically significantly associated with the expression of PTHLH and its nearby gene CCDC91 at P < 0.05. CONCLUSION This study identified four independent association signals at 12p11 and revealed potentially functional variants, providing additional insights into the underlying biological mechanism(s) for the association observed between variants at 12p11 and breast cancer risk.
Collapse
Grants
- U10 CA180868 NCI NIH HHS
- R01 CA140323 NCI NIH HHS
- R01 CA176785 NCI NIH HHS
- R37 CA070867 NCI NIH HHS
- U10 CA027469 NCI NIH HHS
- U01 CA116167 NCI NIH HHS
- 16561 Cancer Research UK
- R03 CA173531 NCI NIH HHS
- G0700491 Medical Research Council
- N02CP11019 NCI NIH HHS
- 10124 Cancer Research UK
- UG1 CA189867 NCI NIH HHS
- RC4 CA153828 NCI NIH HHS
- U10 CA101165 NCI NIH HHS
- R01 CA142996 NCI NIH HHS
- P50 CA125183 NCI NIH HHS
- P01 CA087969 NCI NIH HHS
- UM1 CA164920 NCI NIH HHS
- P30 CA168524 NCI NIH HHS
- U01 CA161032 NCI NIH HHS
- R01 CA092447 NCI NIH HHS
- R01 CA058860 NCI NIH HHS
- 20861 Cancer Research UK
- K07 CA092044 NCI NIH HHS
- UL1 TR000124 NCATS NIH HHS
- 11174 Cancer Research UK
- R01 CA100374 NCI NIH HHS
- P30 CA008748 NCI NIH HHS
- R01 CA128978 NCI NIH HHS
- R01 CA064277 NCI NIH HHS
- R01 CA083855 NCI NIH HHS
- R01 CA047147 NCI NIH HHS
- P30 CA014089 NCI NIH HHS
- U19 CA148537 NCI NIH HHS
- P30 CA051008 NCI NIH HHS
- R01 CA116167 NCI NIH HHS
- R01 CA148667 NCI NIH HHS
- P50 CA116201 NCI NIH HHS
- 16565 Cancer Research UK
- 15106 Cancer Research UK
- U01 CA113916 NCI NIH HHS
- R01 CA063464 NCI NIH HHS
- U10 CA037517 NCI NIH HHS
- N02CP65504 NCI NIH HHS
- U01 CA063464 NCI NIH HHS
- R01 CA077398 NCI NIH HHS
- R01 CA054281 NCI NIH HHS
- R01 CA132839 NCI NIH HHS
- P30 CA068485 NCI NIH HHS
- R01 CA102776 NCI NIH HHS
- U01 CA058860 NCI NIH HHS
- 10118 Cancer Research UK
- U19 CA148112 NCI NIH HHS
- R01 CA149429 NCI NIH HHS
- U01 CA098758 NCI NIH HHS
- N01 CN025403 NCI NIH HHS
- U19 CA148065 NCI NIH HHS
- R01 CA069664 NCI NIH HHS
- 001 World Health Organization
- UM1 CA182910 NCI NIH HHS
- U10 CA180822 NCI NIH HHS
- P30 CA006927 NCI NIH HHS
- R37 CA054281 NCI NIH HHS
- R01 CA047305 NCI NIH HHS
- 10119 Cancer Research UK
- National Institutes of Health
- Seventh Framework Programme
- National Cancer Institute
- U.S. Department of Defense
- Canadian Institutes of Health Research
- Susan G. Komen for the Cure
- Breast Cancer Research Foundation
- Ovarian Cancer Research Fund
- National Health and Medical Research Council
- New South Wales Cancer Council
- Victorian Health Promotion Foundation
- Victorian Breast Cancer Research Consortium
- Dutch Cancer Society
- Cancer Institute NSW
- National Breast Cancer Foundation
- Breast Cancer Research Trust
- Breakthrough Breast Cancer
- NIHR Comprehensive Biomedical Research Centre
- Guy's and St Thomas' NHS Foundation Trust
- Oxford Biomedical Research Centre
- Dietmar-Hopp Foundation
- Helmholtz Society
- Fondation de France
- Institut National Du Cancer
- Ligue Contre le Cancer
- Agence Nationale de la Recherche
- Danish Medical Research Council
- Instituto de Salud Carlos III
- Red Temática de Investigacióm Cooperativa en Cáncer
- Asociación Española Contra el Cáncer
- Fondo de Investigación Sanitario
- California Breast Cancer Research Fund
- Lon V Smith Foundation
- Baden-Württemberg Ministry of Science, Research and Arts
- Deutsche Krebshilfe
- Federal Ministry of Education and Research
- Deutsches Krebsforschungszentrum
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance
- Academy of Finland
- Finnish Cancer Society
- Ministry of Education, Culture, Sports, Science, and Technology
- Ministry of Health, Labour and Welfare
- Takeda Health Foundation
- German Federal Ministry of Research and Education
- Swedish Cancer Society
- Gustav V Jubilee Foundation
- Berth von Kantzows Stiftelse
- Cancer Fund of North Savo
- Finnish Cancer Organizations
- Queensland Cancer Fund
- Prostate Cancer Foundation of Australia (AU)
- Cancer Council of New South Wales
- Cancer Council of Victoria
- Cancer Council of Tasmania
- Cancer Council of South Australia
- U.S. Army Medical Research and Materiel Command
- National Health and Medical Research Council (AU)
- California Breast Cancer Research Program
- Stichting Tegen Kanker
- Hamburg Cancer Society
- Italian Associatin for Cancer Research
- David F and Margaret T Grohne Family Foundation
- Ting Tsung and Wei Fong Chao Foundation
- Robert and Kate Niehaus Clinical Cancer Genetics Initiative
- Quebec Breast Cancer Foundation
- Ministry of Economic Development, Innovation and Export Trade
- Malaysian Ministry of Science, Technology and Innovation
- Malaysian Ministry of Higher Education
- Cancer Resarch Initiatives Foundation
- Biomedical Research Council
- National Medical Research Council
- K G Jebsen Centre for Breast Cancer Research
- Research Council of Norway
- Researhc Council of Norway
- South Eastern Norway Health Authority
- Norwegian Cancer Socieety
- Finnish Cancer Foundation
- Sigrid Juselius Foundation
- Biobanking and Biomolecular Resources Research Infrastructure
- Marit and Hans Rausings Initiative Against Breast Cancer
- Yorkshire Cancer Research
- Sheffield Experimental Cancer Medicine Centre
- Ministry of Education, Science and Technology
- National Cancer Institute Thailand
- Stefanie Spielman Breast Cancer Fund
- Hellenic Cooperative Oncology Group
- Research Council of Lithuania
- Cancer Association of South Africa
- NEYE Foundation
- Spanish Association Against Cancer
- German Cancer Aid
- Ligue Nationale Contre le Cancer
- Jess and Mildred Fisher Center for Familial Cancer Research
- Swing Fore the Cure
- Netherlands Organization of Scientific Research
- Pink Ribbons Project
- Hungarian Research Grants
- Norwegian EEA Financial Mechanism
- Instituto de Salud Carlos III (ES)
- Canadian Breast Cancer Research Alliance
- Ministry for Health, Welfare and Family Affairs
- Andrew Sabin Research Fund
- Russian Federation for Basic Research
- Istituto Toscano Tumori
- Ministry of Higher Education
- Dr. Ralph and Marian Falk Medical Research Trust
- Entertainment Industry Fund National Women's Cancer Research Alliance
- Frieda G and Saul F Shapira BRCA-Associated Cancer Research Program
- American Cancer Society
- National Center for Advancing Translational Sciences
Collapse
|
116
|
Bull CJ, Bonilla C, Holly JMP, Perks CM, Davies N, Haycock P, Yu OHY, Richards JB, Eeles R, Easton D, Kote‐Jarai Z, Amin Al Olama A, Benlloch S, Muir K, Giles GG, MacInnis RJ, Wiklund F, Gronberg H, Haiman CA, Schleutker J, Nordestgaard BG, Travis RC, Neal D, Pashayan N, Khaw K, Stanford JL, Blot WJ, Thibodeau S, Maier C, Kibel AS, Cybulski C, Cannon‐Albright L, Brenner H, Park J, Kaneva R, Batra J, Teixeira MR, Micheal A, Pandha H, Smith GD, Lewis SJ, Martin RM. Blood lipids and prostate cancer: a Mendelian randomization analysis. Cancer Med 2016; 5:1125-36. [PMID: 26992435 PMCID: PMC4924371 DOI: 10.1002/cam4.695] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 02/03/2016] [Accepted: 02/08/2016] [Indexed: 12/14/2022] Open
Abstract
Genetic risk scores were used as unconfounded instruments for specific lipid traits (Mendelian randomization) to assess whether circulating lipids causally influence prostate cancer risk. Data from 22,249 prostate cancer cases and 22,133 controls from 22 studies within the international PRACTICAL consortium were analyzed. Allele scores based on single nucleotide polymorphisms (SNPs) previously reported to be uniquely associated with each of low-density lipoprotein (LDL), high-density lipoprotein (HDL), and triglyceride (TG) levels, were first validated in an independent dataset, and then entered into logistic regression models to estimate the presence (and direction) of any causal effect of each lipid trait on prostate cancer risk. There was weak evidence for an association between the LDL genetic score and cancer grade: the odds ratio (OR) per genetically instrumented standard deviation (SD) in LDL, comparing high- (≥7 Gleason score) versus low-grade (<7 Gleason score) cancers was 1.50 (95% CI: 0.92, 2.46; P = 0.11). A genetically instrumented SD increase in TGs was weakly associated with stage: the OR for advanced versus localized cancer per unit increase in genetic risk score was 1.68 (95% CI: 0.95, 3.00; P = 0.08). The rs12916-T variant in 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) was inversely associated with prostate cancer (OR: 0.97; 95% CI: 0.94, 1.00; P = 0.03). In conclusion, circulating lipids, instrumented by our genetic risk scores, did not appear to alter prostate cancer risk. We found weak evidence that higher LDL and TG levels increase aggressive prostate cancer risk, and that a variant in HMGCR (that mimics the LDL lowering effect of statin drugs) reduces risk. However, inferences are limited by sample size and evidence of pleiotropy.
Collapse
|
117
|
Scott RA, Freitag DF, Li L, Chu AY, Surendran P, Young R, Grarup N, Stancáková A, Chen Y, Varga TV, Yaghootkar H, Luan J, Zhao JH, Willems SM, Wessel J, Wang S, Maruthur N, Michailidou K, Pirie A, van der Lee SJ, Gillson C, Al Olama AA, Amouyel P, Arriola L, Arveiler D, Aviles-Olmos I, Balkau B, Barricarte A, Barroso I, Garcia SB, Bis JC, Blankenberg S, Boehnke M, Boeing H, Boerwinkle E, Borecki IB, Bork-Jensen J, Bowden S, Caldas C, Caslake M, Cupples LA, Cruchaga C, Czajkowski J, den Hoed M, Dunn JA, Earl HM, Ehret GB, Ferrannini E, Ferrieres J, Foltynie T, Ford I, Forouhi NG, Gianfagna F, Gonzalez C, Grioni S, Hiller L, Jansson JH, Jørgensen ME, Jukema JW, Kaaks R, Kee F, Kerrison ND, Key TJ, Kontto J, Kote-Jarai Z, Kraja AT, Kuulasmaa K, Kuusisto J, Linneberg A, Liu C, Marenne G, Mohlke KL, Morris AP, Muir K, Müller-Nurasyid M, Munroe PB, Navarro C, Nielsen SF, Nilsson PM, Nordestgaard BG, Packard CJ, Palli D, Panico S, Peloso GM, Perola M, Peters A, Poole CJ, Quirós JR, Rolandsson O, Sacerdote C, Salomaa V, Sánchez MJ, Sattar N, Sharp SJ, Sims R, Slimani N, Smith JA, Thompson DJ, Trompet S, Tumino R, van der A DL, van der Schouw YT, Virtamo J, Walker M, Walter K, Abraham JE, Amundadottir LT, Aponte JL, Butterworth AS, Dupuis J, Easton DF, Eeles RA, Erdmann J, Franks PW, Frayling TM, Hansen T, Howson JMM, Jørgensen T, Kooner J, Laakso M, Langenberg C, McCarthy MI, Pankow JS, Pedersen O, Riboli E, Rotter JI, Saleheen D, Samani NJ, Schunkert H, Vollenweider P, O'Rahilly S, Deloukas P, Danesh J, Goodarzi MO, Kathiresan S, Meigs JB, Ehm MG, Wareham NJ, Waterworth DM. A genomic approach to therapeutic target validation identifies a glucose-lowering GLP1R variant protective for coronary heart disease. Sci Transl Med 2016; 8:341ra76. [PMID: 27252175 PMCID: PMC5219001 DOI: 10.1126/scitranslmed.aad3744] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 05/10/2016] [Indexed: 02/06/2023]
Abstract
Regulatory authorities have indicated that new drugs to treat type 2 diabetes (T2D) should not be associated with an unacceptable increase in cardiovascular risk. Human genetics may be able to guide development of antidiabetic therapies by predicting cardiovascular and other health endpoints. We therefore investigated the association of variants in six genes that encode drug targets for obesity or T2D with a range of metabolic traits in up to 11,806 individuals by targeted exome sequencing and follow-up in 39,979 individuals by targeted genotyping, with additional in silico follow-up in consortia. We used these data to first compare associations of variants in genes encoding drug targets with the effects of pharmacological manipulation of those targets in clinical trials. We then tested the association of those variants with disease outcomes, including coronary heart disease, to predict cardiovascular safety of these agents. A low-frequency missense variant (Ala316Thr; rs10305492) in the gene encoding glucagon-like peptide-1 receptor (GLP1R), the target of GLP1R agonists, was associated with lower fasting glucose and T2D risk, consistent with GLP1R agonist therapies. The minor allele was also associated with protection against heart disease, thus providing evidence that GLP1R agonists are not likely to be associated with an unacceptable increase in cardiovascular risk. Our results provide an encouraging signal that these agents may be associated with benefit, a question currently being addressed in randomized controlled trials. Genetic variants associated with metabolic traits and multiple disease outcomes can be used to validate therapeutic targets at an early stage in the drug development process.
Collapse
|
118
|
Zhao Z, Wen W, Michailidou K, Bolla MK, Wang Q, Zhang B, Long J, Shu XO, Schmidt MK, Milne RL, García-Closas M, Chang-Claude J, Lindstrom S, Bojesen SE, Ahsan H, Aittomäki K, Andrulis IL, Anton-Culver H, Arndt V, Beckmann MW, Beeghly-Fadiel A, Benitez J, Blomqvist C, Bogdanova NV, Børresen-Dale AL, Brand J, Brauch H, Brenner H, Burwinkel B, Cai Q, Casey G, Chenevix-Trench G, Couch FJ, Cox A, Cross SS, Czene K, Dörk T, Dumont M, Fasching PA, Figueroa J, Flesch-Janys D, Fletcher O, Flyger H, Fostira F, Gammon M, Giles GG, Guénel P, Haiman CA, Hamann U, Harrington P, Hartman M, Hooning MJ, Hopper JL, Jakubowska A, Jasmine F, John EM, Johnson N, Kabisch M, Khan S, Kibriya M, Knight JA, Kosma VM, Kriege M, Kristensen V, Le Marchand L, Lee E, Li J, Lindblom A, Lophatananon A, Luben R, Lubinski J, Malone KE, Mannermaa A, Manoukian S, Margolin S, Marme F, McLean C, Meijers-Heijboer H, Meindl A, Miao H, Muir K, Neuhausen SL, Nevanlinna H, Neven P, Olson JE, Perkins B, Peterlongo P, Phillips KA, Pylkäs K, Rudolph A, Santella R, Sawyer EJ, Schmutzler RK, Schoemaker M, Shah M, Shrubsole M, Southey MC, Swerdlow AJ, Toland AE, Tomlinson I, Torres D, Truong T, Ursin G, Van Der Luijt RB, Verhoef S, Wang-Gohrke S, Whittemore AS, Winqvist R, Pilar Zamora M, Zhao H, Dunning AM, Simard J, Hall P, Kraft P, Pharoah P, Hunter D, Easton DF, Zheng W. Association of genetic susceptibility variants for type 2 diabetes with breast cancer risk in women of European ancestry. Cancer Causes Control 2016; 27:679-93. [PMID: 27053251 PMCID: PMC5029371 DOI: 10.1007/s10552-016-0741-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 03/25/2016] [Indexed: 12/29/2022]
Abstract
PURPOSE Type 2 diabetes (T2D) has been reported to be associated with an elevated risk of breast cancer. It is unclear, however, whether this association is due to shared genetic factors. METHODS We constructed a genetic risk score (GRS) using risk variants from 33 known independent T2D susceptibility loci and evaluated its relation to breast cancer risk using the data from two consortia, including 62,328 breast cancer patients and 83,817 controls of European ancestry. Unconditional logistic regression models were used to derive adjusted odds ratios (ORs) and 95 % confidence intervals (CIs) to measure the association of breast cancer risk with T2D GRS or T2D-associated genetic risk variants. Meta-analyses were conducted to obtain summary ORs across all studies. RESULTS The T2D GRS was not found to be associated with breast cancer risk, overall, by menopausal status, or for estrogen receptor positive or negative breast cancer. Three T2D associated risk variants were individually associated with breast cancer risk after adjustment for multiple comparisons using the Bonferroni method (at p < 0.001), rs9939609 (FTO) (OR 0.94, 95 % CI = 0.92-0.95, p = 4.13E-13), rs7903146 (TCF7L2) (OR 1.04, 95 % CI = 1.02-1.06, p = 1.26E-05), and rs8042680 (PRC1) (OR 0.97, 95 % CI = 0.95-0.99, p = 8.05E-04). CONCLUSIONS We have shown that several genetic risk variants were associated with the risk of both T2D and breast cancer. However, overall genetic susceptibility to T2D may not be related to breast cancer risk.
Collapse
|
119
|
Easton DF, Lesueur F, Decker B, Michailidou K, Li J, Allen J, Luccarini C, Pooley KA, Shah M, Bolla MK, Wang Q, Dennis J, Ahmad J, Thompson ER, Damiola F, Pertesi M, Voegele C, Mebirouk N, Robinot N, Durand G, Forey N, Luben RN, Ahmed S, Aittomäki K, Anton-Culver H, Arndt V, Baynes C, Beckman MW, Benitez J, Van Den Berg D, Blot WJ, Bogdanova NV, Bojesen SE, Brenner H, Chang-Claude J, Chia KS, Choi JY, Conroy DM, Cox A, Cross SS, Czene K, Darabi H, Devilee P, Eriksson M, Fasching PA, Figueroa J, Flyger H, Fostira F, García-Closas M, Giles GG, Glendon G, González-Neira A, Guénel P, Haiman CA, Hall P, Hart SN, Hartman M, Hooning MJ, Hsiung CN, Ito H, Jakubowska A, James PA, John EM, Johnson N, Jones M, Kabisch M, Kang D, Kosma VM, Kristensen V, Lambrechts D, Li N, Lindblom A, Long J, Lophatananon A, Lubinski J, Mannermaa A, Manoukian S, Margolin S, Matsuo K, Meindl A, Mitchell G, Muir K, Nevelsteen I, van den Ouweland A, Peterlongo P, Phuah SY, Pylkäs K, Rowley SM, Sangrajrang S, Schmutzler RK, Shen CY, Shu XO, Southey MC, Surowy H, Swerdlow A, Teo SH, Tollenaar RAEM, Tomlinson I, Torres D, Truong T, Vachon C, Verhoef S, Wong-Brown M, Zheng W, Zheng Y, Nevanlinna H, Scott RJ, Andrulis IL, Wu AH, Hopper JL, Couch FJ, Winqvist R, Burwinkel B, Sawyer EJ, Schmidt MK, Rudolph A, Dörk T, Brauch H, Hamann U, Neuhausen SL, Milne RL, Fletcher O, Pharoah PDP, Campbell IG, Dunning AM, Le Calvez-Kelm F, Goldgar DE, Tavtigian SV, Chenevix-Trench G. No evidence that protein truncating variants in BRIP1 are associated with breast cancer risk: implications for gene panel testing. J Med Genet 2016; 53:298-309. [PMID: 26921362 PMCID: PMC4938802 DOI: 10.1136/jmedgenet-2015-103529] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/16/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND BRCA1 interacting protein C-terminal helicase 1 (BRIP1) is one of the Fanconi Anaemia Complementation (FANC) group family of DNA repair proteins. Biallelic mutations in BRIP1 are responsible for FANC group J, and previous studies have also suggested that rare protein truncating variants in BRIP1 are associated with an increased risk of breast cancer. These studies have led to inclusion of BRIP1 on targeted sequencing panels for breast cancer risk prediction. METHODS We evaluated a truncating variant, p.Arg798Ter (rs137852986), and 10 missense variants of BRIP1, in 48 144 cases and 43 607 controls of European origin, drawn from 41 studies participating in the Breast Cancer Association Consortium (BCAC). Additionally, we sequenced the coding regions of BRIP1 in 13 213 cases and 5242 controls from the UK, 1313 cases and 1123 controls from three population-based studies as part of the Breast Cancer Family Registry, and 1853 familial cases and 2001 controls from Australia. RESULTS The rare truncating allele of rs137852986 was observed in 23 cases and 18 controls in Europeans in BCAC (OR 1.09, 95% CI 0.58 to 2.03, p=0.79). Truncating variants were found in the sequencing studies in 34 cases (0.21%) and 19 controls (0.23%) (combined OR 0.90, 95% CI 0.48 to 1.70, p=0.75). CONCLUSIONS These results suggest that truncating variants in BRIP1, and in particular p.Arg798Ter, are not associated with a substantial increase in breast cancer risk. Such observations have important implications for the reporting of results from breast cancer screening panels.
Collapse
|
120
|
Gusev A, Shi H, Kichaev G, Pomerantz M, Li F, Long HW, Ingles SA, Kittles RA, Strom SS, Rybicki BA, Nemesure B, Isaacs WB, Zheng W, Pettaway CA, Yeboah ED, Tettey Y, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Chokkalingam AP, John EM, Murphy AB, Signorello LB, Carpten J, Leske MC, Wu SY, Hennis AJM, Neslund-Dudas C, Hsing AW, Chu L, Goodman PJ, Klein EA, Witte JS, Casey G, Kaggwa S, Cook MB, Stram DO, Blot WJ, Eeles RA, Easton D, Kote-Jarai ZS, Al Olama AA, Benlloch S, Muir K, Giles GG, Southey MC, Fitzgerald LM, Gronberg H, Wiklund F, Aly M, Henderson BE, Schleutker J, Wahlfors T, Tammela TLJ, Nordestgaard BG, Key TJ, Travis RC, Neal DE, Donovan JL, Hamdy FC, Pharoah P, Pashayan N, Khaw KT, Stanford JL, Thibodeau SN, McDonnell SK, Schaid DJ, Maier C, Vogel W, Luedeke M, Herkommer K, Kibel AS, Cybulski C, Wokolorczyk D, Kluzniak W, Cannon-Albright L, Teerlink C, Brenner H, Dieffenbach AK, Arndt V, Park JY, Sellers TA, Lin HY, Slavov C, Kaneva R, Mitev V, Batra J, Spurdle A, Clements JA, Teixeira MR, Pandha H, Michael A, Paulo P, Maia S, Kierzek A, Conti DV, Albanes D, Berg C, Berndt SI, Campa D, Crawford ED, Diver WR, Gapstur SM, Gaziano JM, Giovannucci E, Hoover R, Hunter DJ, Johansson M, Kraft P, Le Marchand L, Lindström S, Navarro C, Overvad K, Riboli E, Siddiq A, Stevens VL, Trichopoulos D, Vineis P, Yeager M, Trynka G, Raychaudhuri S, Schumacher FR, Price AL, Freedman ML, Haiman CA, Pasaniuc B. Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation. Nat Commun 2016; 7:10979. [PMID: 27052111 PMCID: PMC4829663 DOI: 10.1038/ncomms10979] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 02/03/2016] [Indexed: 12/22/2022] Open
Abstract
Although genome-wide association studies have identified over 100 risk loci that explain ∼33% of familial risk for prostate cancer (PrCa), their functional effects on risk remain largely unknown. Here we use genotype data from 59,089 men of European and African American ancestries combined with cell-type-specific epigenetic data to build a genomic atlas of single-nucleotide polymorphism (SNP) heritability in PrCa. We find significant differences in heritability between variants in prostate-relevant epigenetic marks defined in normal versus tumour tissue as well as between tissue and cell lines. The majority of SNP heritability lies in regions marked by H3k27 acetylation in prostate adenoc7arcinoma cell line (LNCaP) or by DNaseI hypersensitive sites in cancer cell lines. We find a high degree of similarity between European and African American ancestries suggesting a similar genetic architecture from common variation underlying PrCa risk. Our findings showcase the power of integrating functional annotation with genetic data to understand the genetic basis of PrCa.
Collapse
|
121
|
Bonilla C, Lewis SJ, Martin RM, Donovan JL, Hamdy FC, Neal DE, Eeles R, Easton D, Kote-Jarai Z, Al Olama AA, Benlloch S, Muir K, Giles GG, Wiklund F, Gronberg H, Haiman CA, Schleutker J, Nordestgaard BG, Travis RC, Pashayan N, Khaw KT, Stanford JL, Blot WJ, Thibodeau S, Maier C, Kibel AS, Cybulski C, Cannon-Albright L, Brenner H, Park J, Kaneva R, Batra J, Teixeira MR, Pandha H, Lathrop M, Davey Smith G. Pubertal development and prostate cancer risk: Mendelian randomization study in a population-based cohort. BMC Med 2016; 14:66. [PMID: 27044414 PMCID: PMC4820939 DOI: 10.1186/s12916-016-0602-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/16/2016] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Epidemiological studies have observed a positive association between an earlier age at sexual development and prostate cancer, but markers of sexual maturation in boys are imprecise and observational estimates are likely to suffer from a degree of uncontrolled confounding. To obtain causal estimates, we examined the role of pubertal development in prostate cancer using genetic polymorphisms associated with Tanner stage in adolescent boys in a Mendelian randomization (MR) approach. METHODS We derived a weighted genetic risk score for pubertal development, combining 13 SNPs associated with male Tanner stage. A higher score indicated a later puberty onset. We examined the association of this score with prostate cancer risk, stage and grade in the UK-based ProtecT case-control study (n = 2,927), and used the PRACTICAL consortium (n = 43,737) as a replication sample. RESULTS In ProtecT, the puberty genetic score was inversely associated with prostate cancer grade (odds ratio (OR) of high- vs. low-grade cancer, per tertile of the score: 0.76; 95 % CI, 0.64-0.89). In an instrumental variable estimation of the causal OR, later physical development in adolescence (equivalent to a difference of one Tanner stage between pubertal boys of the same age) was associated with a 77 % (95 % CI, 43-91 %) reduced odds of high Gleason prostate cancer. In PRACTICAL, the puberty genetic score was associated with prostate cancer stage (OR of advanced vs. localized cancer, per tertile: 0.95; 95 % CI, 0.91-1.00) and prostate cancer-specific mortality (hazard ratio amongst cases, per tertile: 0.94; 95 % CI, 0.90-0.98), but not with disease grade. CONCLUSIONS Older age at sexual maturation is causally linked to a reduced risk of later prostate cancer, especially aggressive disease.
Collapse
|
122
|
Dunning AM, Michailidou K, Kuchenbaecker KB, Thompson D, French JD, Beesley J, Healey CS, Kar S, Pooley KA, Lopez-Knowles E, Dicks E, Barrowdale D, Sinnott-Armstrong NA, Sallari RC, Hillman KM, Kaufmann S, Sivakumaran H, Moradi Marjaneh M, Lee JS, Hills M, Jarosz M, Drury S, Canisius S, Bolla MK, Dennis J, Wang Q, Hopper JL, Southey MC, Broeks A, Schmidt MK, Lophatananon A, Muir K, Beckmann MW, Fasching PA, Dos-Santos-Silva I, Peto J, Sawyer EJ, Tomlinson I, Burwinkel B, Marme F, Guénel P, Truong T, Bojesen SE, Flyger H, González-Neira A, Perez JIA, Anton-Culver H, Eunjung L, Arndt V, Brenner H, Meindl A, Schmutzler RK, Brauch H, Hamann U, Aittomäki K, Blomqvist C, Ito H, Matsuo K, Bogdanova N, Dörk T, Lindblom A, Margolin S, Kosma VM, Mannermaa A, Tseng CC, Wu AH, Lambrechts D, Wildiers H, Chang-Claude J, Rudolph A, Peterlongo P, Radice P, Olson JE, Giles GG, Milne RL, Haiman CA, Henderson BE, Goldberg MS, Teo SH, Yip CH, Nord S, Borresen-Dale AL, Kristensen V, Long J, Zheng W, Pylkäs K, Winqvist R, Andrulis IL, Knight JA, Devilee P, Seynaeve C, Figueroa J, Sherman ME, Czene K, Darabi H, Hollestelle A, van den Ouweland AMW, Humphreys K, Gao YT, Shu XO, Cox A, Cross SS, Blot W, Cai Q, Ghoussaini M, Perkins BJ, Shah M, Choi JY, Kang D, Lee SC, Hartman M, Kabisch M, Torres D, Jakubowska A, Lubinski J, Brennan P, Sangrajrang S, Ambrosone CB, Toland AE, Shen CY, Wu PE, Orr N, Swerdlow A, McGuffog L, Healey S, Lee A, Kapuscinski M, John EM, Terry MB, Daly MB, Goldgar DE, Buys SS, Janavicius R, Tihomirova L, Tung N, Dorfling CM, van Rensburg EJ, Neuhausen SL, Ejlertsen B, Hansen TVO, Osorio A, Benitez J, Rando R, Weitzel JN, Bonanni B, Peissel B, Manoukian S, Papi L, Ottini L, Konstantopoulou I, Apostolou P, Garber J, Rashid MU, Frost D, Izatt L, Ellis S, Godwin AK, Arnold N, Niederacher D, Rhiem K, Bogdanova-Markov N, Sagne C, Stoppa-Lyonnet D, Damiola F, Sinilnikova OM, Mazoyer S, Isaacs C, Claes KBM, De Leeneer K, de la Hoya M, Caldes T, Nevanlinna H, Khan S, Mensenkamp AR, Hooning MJ, Rookus MA, Kwong A, Olah E, Diez O, Brunet J, Pujana MA, Gronwald J, Huzarski T, Barkardottir RB, Laframboise R, Soucy P, Montagna M, Agata S, Teixeira MR, Park SK, Lindor N, Couch FJ, Tischkowitz M, Foretova L, Vijai J, Offit K, Singer CF, Rappaport C, Phelan CM, Greene MH, Mai PL, Rennert G, Imyanitov EN, Hulick PJ, Phillips KA, Piedmonte M, Mulligan AM, Glendon G, Bojesen A, Thomassen M, Caligo MA, Yoon SY, Friedman E, Laitman Y, Borg A, von Wachenfeldt A, Ehrencrona H, Rantala J, Olopade OI, Ganz PA, Nussbaum RL, Gayther SA, Nathanson KL, Domchek SM, Arun BK, Mitchell G, Karlan BY, Lester J, Maskarinec G, Woolcott C, Scott C, Stone J, Apicella C, Tamimi R, Luben R, Khaw KT, Helland Å, Haakensen V, Dowsett M, Pharoah PDP, Simard J, Hall P, García-Closas M, Vachon C, Chenevix-Trench G, Antoniou AC, Easton DF, Edwards SL. Breast cancer risk variants at 6q25 display different phenotype associations and regulate ESR1, RMND1 and CCDC170. Nat Genet 2016; 48:374-86. [PMID: 26928228 PMCID: PMC4938803 DOI: 10.1038/ng.3521] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 02/05/2016] [Indexed: 12/14/2022]
Abstract
We analyzed 3,872 common genetic variants across the ESR1 locus (encoding estrogen receptor α) in 118,816 subjects from three international consortia. We found evidence for at least five independent causal variants, each associated with different phenotype sets, including estrogen receptor (ER(+) or ER(-)) and human ERBB2 (HER2(+) or HER2(-)) tumor subtypes, mammographic density and tumor grade. The best candidate causal variants for ER(-) tumors lie in four separate enhancer elements, and their risk alleles reduce expression of ESR1, RMND1 and CCDC170, whereas the risk alleles of the strongest candidates for the remaining independent causal variant disrupt a silencer element and putatively increase ESR1 and RMND1 expression.
Collapse
|
123
|
George AJT, Collett C, Carr AJ, Holm S, Bale C, Burton S, Campbell M, Coles A, Gottlieb G, Muir K, Parroy S, Price J, Rice ASC, Sinden J, Stephenson C, Wartolowska K, Whittall H. When should placebo surgery as a control in clinical trials be carried out? ACTA ACUST UNITED AC 2016. [DOI: 10.1308/rcsbull.2016.75] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Placebo surgery – often maligned as ‘sham surgery’ – is a tough sell to patients and to many clinicians. But could surgical research benefit from increased use of placebo control groups?
Collapse
|
124
|
Abhishek A, Doherty S, Maciewicz RA, Muir K, Zhang W, Doherty M. Does Chondrocalcinosis Associate With a Distinct Radiographic Phenotype of Osteoarthritis in Knees and Hips? A Case-Control Study. Arthritis Care Res (Hoboken) 2016. [DOI: 10.1002/acr.22652] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
125
|
Scarbrough PM, Weber RP, Iversen ES, Brhane Y, Amos CI, Kraft P, Hung RJ, Sellers TA, Witte JS, Pharoah P, Henderson BE, Gruber SB, Hunter DJ, Garber JE, Joshi AD, McDonnell K, Easton DF, Eeles R, Kote-Jarai Z, Muir K, Doherty JA, Schildkraut JM. A Cross-Cancer Genetic Association Analysis of the DNA Repair and DNA Damage Signaling Pathways for Lung, Ovary, Prostate, Breast, and Colorectal Cancer. Cancer Epidemiol Biomarkers Prev 2016; 25:193-200. [PMID: 26637267 PMCID: PMC4713268 DOI: 10.1158/1055-9965.epi-15-0649] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/05/2015] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND DNA damage is an established mediator of carcinogenesis, although genome-wide association studies (GWAS) have identified few significant loci. This cross-cancer site, pooled analysis was performed to increase the power to detect common variants of DNA repair genes associated with cancer susceptibility. METHODS We conducted a cross-cancer analysis of 60,297 single nucleotide polymorphisms, at 229 DNA repair gene regions, using data from the NCI Genetic Associations and Mechanisms in Oncology (GAME-ON) Network. Our analysis included data from 32 GWAS and 48,734 controls and 51,537 cases across five cancer sites (breast, colon, lung, ovary, and prostate). Because of the unavailability of individual data, data were analyzed at the aggregate level. Meta-analysis was performed using the Association analysis for SubSETs (ASSET) software. To test for genetic associations that might escape individual variant testing due to small effect sizes, pathway analysis of eight DNA repair pathways was performed using hierarchical modeling. RESULTS We identified three susceptibility DNA repair genes, RAD51B (P < 5.09 × 10(-6)), MSH5 (P < 5.09 × 10(-6)), and BRCA2 (P = 5.70 × 10(-6)). Hierarchical modeling identified several pleiotropic associations with cancer risk in the base excision repair, nucleotide excision repair, mismatch repair, and homologous recombination pathways. CONCLUSIONS Only three susceptibility loci were identified, which had all been previously reported. In contrast, hierarchical modeling identified several pleiotropic cancer risk associations in key DNA repair pathways. IMPACT Results suggest that many common variants in DNA repair genes are likely associated with cancer susceptibility through small effect sizes that do not meet stringent significance testing criteria.
Collapse
|