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1. Fine-mapping of the HNF1B multicancer locus identifies candidate variants that mediate endometrial cancer risk

Author

Painter, J.N., O'Mara, T.A., Batra, J., Cheng, T., Lose, F.A., Dennis, J., Michailidou, K., Tyrer, J.P., Ahmed, S., Ferguson, K., Healey, C.S., Kaufmann, S., Hillman, K.M., Walpole, C., Moya, L., Pollock, P., Jones, A., Howarth, K., Martin, L., Gorman, M., Hodgson, S., Magdalena Echeverry De Polanco, M., Sans, M., Carracedo, A., Castellvi-Bel, S., Rojas-Martinez, A., Santos, E., Teixeira, M.R., Carvajal-Carmona, L., Shu, X-O., Long, J., Zheng, W., Xiang, Y-B., Montgomery, G.W., Webb, P.M., Scott, R.J., McEvoy, M., Attia, J., Holliday, E., Martin, N.G., Nyholt, D.R., Henders, A.K., Fasching, P.A., Hein, A., Beckmann, M.W., Renner, S.P., Doerk, T., Hillemanns, P., Duerst, M., Runnebaum, I., Lambrechts, D., Coenegrachts, L., Schrauwen, S., Amant, F., Winterhoff, B., Dowdy, S.C., Goode, E.L., Teoman, A., Salvesen, H.B., Trovik, J., Njolstad, T.S., Werner, H.M.J., Ashton, K., Proietto, T., Otton, G., Tzortzatos, G., Mints, M., Tham, E., Hall, P., Czene, K., Liu, J., Li, J., Hopper, J.L., Southey, M.C., Ekici, A.B., Ruebner, M., Johnson, N., Peto, J., Burwinkel, B., Marme, F., Brenner, H., Dieffenbach, A.K., Meindl, A., Brauch, H., Lindblom, A., Depreeuw, J., Moisse, M., Chang-Claude, J., Rudolph, A., Couch, F.J., Olson, J.E., Giles, G.G., Bruinsma, F., Cunningham, J.M., Fridley, B.L., Borresen-Dale, A-L., Kristensen, V.N., Cox, A., Swerdlow, A.J., Orr, N., Bolla, M.K., Wang, Q., Weber, R.P., Chen, Z., Shah, M., French, J.D., Pharoah, P.D.P., Dunning, A.M., Tomlinson, I., Easton, D.F., Edwards, S.L., Thompson, D.J., Spurdle, A.B., Canc, N.S.E., Consortium, CHIBCHA, Canc, ANE, RENDOCAS, AOCS, Network, GENICA, Dennis, Joe [0000-0003-4591-1214], Tyrer, Jonathan [0000-0003-3724-4757], Pharoah, Paul [0000-0001-8494-732X], Dunning, Alison [0000-0001-6651-7166], Easton, Douglas [0000-0003-2444-3247], Thompson, Deborah [0000-0003-1465-5799], and Apollo - University of Cambridge Repository

Subjects
Genotype, Chromosome Mapping, Computational Biology, Genetic Variation, Polymorphism, Single Nucleotide, Linkage Disequilibrium, White People, Endometrial Neoplasms, Epigenesis, Genetic, Haplotypes, Genetic Loci, Risk Factors, Case-Control Studies, Cell Line, Tumor, Databases, Genetic, Humans, Female, RNA, Messenger, Promoter Regions, Genetic, Alleles, Genome-Wide Association Study, Hepatocyte Nuclear Factor 1-beta
Abstract

Common variants in the hepatocyte nuclear factor 1 homeobox B (HNF1B) gene are associated with the risk of type II diabetes and multiple cancers. Evidence to date indicates that cancer risk may be mediated via genetic or epigenetic effects on HNF1B gene expression. We previously found single nucleotide polymorphisms (SNPs) at the HNF1B locus to be associated with endometrial cancer, and now report extensive fine-mapping and in silico and laboratory analyses of this locus. Analysis of 1,184 genotyped and imputed SNPs in 6,608 Caucasian cases and 37,925 controls, and 895 Asian cases and 1,968 controls, revealed the best signal of association for SNP rs11263763 (P=8.4×10(-14), OR=0.86, 95% CI=0.82-0.89), located within HNF1B intron 1. Haplotype analysis and conditional analyses provide no evidence of further independent endometrial cancer risk variants at this locus. SNP rs11263763 genotype was associated with HNF1B mRNA expression but not with HNF1B methylation in endometrial tumour samples from The Cancer Genome Atlas. Genetic analyses prioritized rs11263763 and four other SNPs in high to moderate LD as the most likely causal SNPs. Three of these SNPs map to the extended HNF1B promoter based on chromatin marks extending from the minimal promoter region. Reporter assays demonstrated that this extended region reduces activity in combination with the minimal HNF1B promoter, and that the minor alleles of rs11263763 or rs8064454 are associated with decreased HNF1B promoter activity. Our findings provide evidence for a single signal associated with endometrial cancer risk at the HNF1B locus, and that risk is likely mediated via altered HNF1B gene expression. ispartof: Human Molecular Genetics vol:24 issue:5 pages:1478-92 ispartof: location:England status: published

Published
2015

2. Candidate locus analysis of the TERT-CLPTM1L cancer risk region on chromosome 5p15 identifies multiple independent variants associated with endometrial cancer risk

Author

Carvajal-Carmona, L.G., O'Mara, T.A., Painter, J.N.., Lose, F.A., Dennis, J., Michailidou, K., Tyrer, J.P., Ahmed, S., Ferguson, K., Healey, C.S., Pooley, K., Beesley, J., Cheng, T., Jones, A., Howarth, K., Martin, L., Gorman, M., Hodgson, S., Wentzensen, N., Fasching, P.A., Hein, A., Beckmann, M.W., Renner, S.P., Doerk, T., Hillemanns, P., Duerst, M., Runnebaum, I., Lambrechts, D., Coenegrachts, L., Schrauwen, S., Amant, F., Winterhoff, B., Dowdy, S.C., Goode, E.L., Teoman, A., Salvesen, H.B., Trovik, J., Njolstad, T.S., Werner, H.M.J., Scott, R.J., Ashton, K., Proietto, T., Otton, G., Wersaell, O., Mints, M., Tham, E., Hall, P., Czene, K., Liu, J., Li, J., Hopper, J.L., Southey, M.C., Ekici, A.B., Ruebner, M., Johnson, N., Peto, J., Burwinkel, B., Marme, F., Brenner, H., Dieffenbach, A.K., Meindl, A., Brauch, H., Lindblom, A., Depreeuw, J., Moisse, M., Chang-Claude, J., Rudolph, A., Couch, F.J., Olson, J.E., Giles, G.G., Bruinsma, F., Cunningham, J.M., Fridley, B.L., Borresen-Dale, A.-L., Kristensen, V.N., Cox, A., Swerdlow, A.J., Orr, N., Bolla, M.K., Wang, Q., Weber, R.P., Chen, Z., Shah, M., Pharoah, P.D.P., Dunning, A.M., Tomlinson, I., Easton, D.F., Spurdle, A.B., Thompson, D.J., NSECG, ANECS, RENDOCAS, AOCS, Network, GENICA, Dennis, Joe [0000-0003-4591-1214], Tyrer, Jonathan [0000-0003-3724-4757], Pooley, Karen [0000-0002-1274-9460], Wang, Jean [0000-0002-9139-0627], Pharoah, Paul [0000-0001-8494-732X], Dunning, Alison [0000-0001-6651-7166], Easton, Douglas [0000-0003-2444-3247], and Apollo - University of Cambridge Repository

Subjects
National Study of Endometrial Cancer Genetics Group, Australian Ovarian Cancer Study, Polymorphism, Single Nucleotide, Chromosomes, Promoter Regions, Paediatrics and Reproductive Medicine, Databases, Uterine Cancer, Genetic, Complementary and Alternative Medicine, Risk Factors, Models, Australian National Endometrial Cancer Study Group, Genetics, 2.1 Biological and endogenous factors, Humans, Genetic Testing, Aetiology, Polymorphism, Promoter Regions, Genetic, Telomerase, Cancer, Genetics & Heredity, Neoplastic, Models, Genetic, Nucleic Acid, RENDOCAS, Prevention, Human Genome, Membrane Proteins, Single Nucleotide, Neoplasm Proteins, Gene Expression Regulation, Neoplastic, Gene Expression Regulation, Haplotypes, Genetic Loci, Chromosomes, Human, Pair 5, Female, GENICA Network, Pair 5, Databases, Nucleic Acid, Human
Abstract

Several studies have reported associations between multiple cancer types and single-nucleotide polymorphisms (SNPs) on chromosome 5p15, which harbours TERT and CLPTM1L, but no such association has been reported with endometrial cancer. To evaluate the role of genetic variants at the TERT-CLPTM1L region in endometrial cancer risk, we carried out comprehensive fine-mapping analyses of genotyped and imputed SNPs using a custom Illumina iSelect array which includes dense SNP coverage of this region. We examined 396 SNPs (113 genotyped, 283 imputed) in 4,401 endometrial cancer cases and 28,758 controls. Single-SNP and forward/backward logistic regression models suggested evidence for three variants independently associated with endometrial cancer risk (P = 4.9 × 10(-6) to P = 7.7 × 10(-5)). Only one falls into a haplotype previously associated with other cancer types (rs7705526, in TERT intron 1), and this SNP has been shown to alter TERT promoter activity. One of the novel associations (rs13174814) maps to a second region in the TERT promoter and the other (rs62329728) is in the promoter region of CLPTM1L; neither are correlated with previously reported cancer-associated SNPs. Using TCGA RNASeq data, we found significantly increased expression of both TERT and CLPTM1L in endometrial cancer tissue compared with normal tissue (TERT P = 1.5 × 10(-18), CLPTM1L P = 1.5 × 10(-19)). Our study thus reports a novel endometrial cancer risk locus and expands the spectrum of cancer types associated with genetic variation at 5p15, further highlighting the importance of this region for cancer susceptibility. ispartof: Human Genetics vol:134 issue:2 pages:231-45 ispartof: location:Germany status: published

Published
2015

3. Refined histopathological predictors of BRCA1\ud and BRCA2 mutation status: a large-scale analysis\ud of breast cancer characteristics from the BCAC,\ud CIMBA, and ENIGMA consortia

Author

Spurdle, A.B., Couch, F.J., Parsons, M.T., McGuffog, L., Barrowdale, D., Bolla, M.K., Wang, Q., Healey, S., Schmutzler, R.K., Wappenschmidt, B., Rhiem, K., Hahnen, E., Engel, C., Meindl, A., Ditsch, N., Arnold, N., Plendl, H., Niederacher, D., Sutter, C., Wang-Gohrke, S., Steinemann, D., Preisler-Adams, S., Kast, K., Varon-Mateeva, R., Ellis, S., Frost, D., Platte, R., Perkins, J., Evans, D.G., Izatt, L., Eeles, R., Adlard, J., Davidson, R., Cole, T., Scuvera, G., Manoukian, S., Bonanni, B., Mariette, F., Fortuzzi, S., Viel, A., Pasini, B., Papi, L., Varesco, L., Balleine, R., Nathanson, K.L., Domchek, S.M., Offitt, K., Jakubowska, A., Lindor, N., Thomassen, M., Jensen, U.B., Rantala, J., Borg, A., Andrulis, I.L., Miron, A., Hansen, T.V.O., Caldes, T., Neuhausen, S.L., Toland, A.E., Nevanlinna, H., Montagna, M., Garber, J., Godwin, A.K., Osorio, A., Factor, R.E., Terry, M.B., Rebbeck, T.R., Karlan, B.Y., Southey, M., Rashid, M.U., Tung, N., Pharoah, P.D.P., Blows, F.M., Dunning, A.M., Provenzano, E., Hall, P., Czene, K., Schmidt, M.K., Broeks, A., Cornelissen, S., Verhoef, S., Fasching, P.A., Beckmann, M.W., Ekici, A.B., Slamon, D.J., Bojesen, S.E., Nordestgaard, B.G., Nielsen, S.F., Flyger, H., Chang-Claude, J., Flesch-Janys, D., Rudolph, A., Seibold, P., Aittomaki, K., Muranen, T.A., Heikkila, P., Blomqvist, C., Figueroa, J., Chanock, S.J., Brinton, L., Lissowska, J., Olson, J.E., Pankratz, V.S., John, E.M., Whittemore, A.S., West, D.W., Hamann, U., Torres, D., Ulmer, H.U., Rudiger, T., Devilee, P., Tollenaar, R.A.E.M., Seynaeve, C., Van Asperen, C.J., Eccles, D.M., Tapper, W.J., Durcan, L., Jones, L., Peto, J., dos-Santos-Silva, I., Fletcher, O., Johnson, N., Dwek, M., Swann, R., Bane, A.L., Glendon, G., Mulligan, A.M., Giles, G.G., Milne, R.L., Baglietto, L., McLean, C., Carpenter, J., Clarke, C., Scott, R., Brauch, H., Bruning, T., Ko, Y-D., Cox, A., Cross, S.S., Reed, M.W.R., Lubinski, J., Jaworska-Bieniek, K., Durda, K., Gronwald, J., Dork, T., Bogdanova, N., Park-Simon, T-W., Hillemanns, P., Haiman, C.A., Henderson, B.E., Schumacher, F., Le Marchand, L., Burwinkel, B., Marme, F., Surovy, H., Yang, R., Anton-Culver, H., Ziogas, A., Hooning, M.J., Collee, J.M., Martens, J.W.M., Tilanus-Linthorst, M.M.A., Brenner, H., Dieffenbach, A.K., Arndt, V., Stegmaier, C., Winqvist, R., Pylkas, K., Jukkola-Vuorinen, A., Grip, M., Lindblom, A., Margolin, S., Joseph, V., Robson, M., Rau-Murthy, R., Gonzalez-Neira, A., Arias, J.I., Zamora, P., Benitez, J., Mannermaa, A., Kataja, V., Kosma, V-M., Hartikainen, J.M., Peterlongo, P., Zaffaroni, D., Barile, M., Capra, F., Radice, P., Teo, S.H., Easton, D.F., Antoniou, A.C., Chenevix-Trench, G., Goldgar, D.E., Investigators, ABCTB, Group, EMBRACE, Network, GENICA, Group, HEBON, and Investigators, KConFab

Subjects
endocrine system diseases, skin and connective tissue diseases
Abstract

Introduction: The distribution of histopathological features of invasive breast tumors in BRCA1 or BRCA2 germline\ud mutation carriers differs from that of individuals with no known mutation. Histopathological features thus have\ud utility for mutation prediction, including statistical modeling to assess pathogenicity of BRCA1 or BRCA2 variants of\ud uncertain clinical significance. We analyzed large pathology datasets accrued by the Consortium of Investigators of\ud Modifiers of BRCA1/2 (CIMBA) and the Breast Cancer Association Consortium (BCAC) to reassess histopathological\ud predictors of BRCA1 and BRCA2 mutation status, and provide robust likelihood ratio (LR) estimates for statistical\ud modeling.\ud Methods: Selection criteria for study/center inclusion were estrogen receptor (ER) status or grade data available for\ud invasive breast cancer diagnosed younger than 70 years. The dataset included 4,477 BRCA1 mutation carriers, 2,565\ud BRCA2 mutation carriers, and 47,565 BCAC breast cancer cases. Country-stratified estimates of the likelihood of\ud mutation status by histopathological markers were derived using a Mantel-Haenszel approach.\ud Results: ER-positive phenotype negatively predicted BRCA1 mutation status, irrespective of grade (LRs from 0.08 to\ud 0.90). ER-negative grade 3 histopathology was more predictive of positive BRCA1 mutation status in women 50 years\ud or older (LR = 4.13 (3.70 to 4.62)) versus younger than 50 years (LR = 3.16 (2.96 to 3.37)). For BRCA2, ER-positive grade 3\ud phenotype modestly predicted positive mutation status irrespective of age (LR = 1.7-fold), whereas ER-negative grade 3\ud features modestly predicted positive mutation status at 50 years or older (LR = 1.54 (1.27 to 1.88)). Triple-negative tumor\ud status was highly predictive of BRCA1 mutation status for women younger than 50 years (LR = 3.73 (3.43 to 4.05)) and\ud 50 years or older (LR = 4.41 (3.86 to 5.04)), and modestly predictive of positive BRCA2 mutation status in women 50 years\ud or older (LR = 1.79 (1.42 to 2.24)).\ud Conclusions: These results refine likelihood-ratio estimates for predicting BRCA1 and BRCA2 mutation status by using\ud commonly measured histopathological features. Age at diagnosis is an important variable for most analyses, and grade is\ud more informative than ER status for BRCA2 mutation carrier prediction. The estimates will improve BRCA1 and BRCA2\ud variant classification and inform patient mutation testing and clinical management.

Published
2014

4. Genetic Predisposition to In Situ and Invasive Lobular\ud Carcinoma of the Breast

Author

Sawyer, E., Roylance, R., Petridis, C., Brook, M.N., Nowinski, S., Papouli, E., Fletcher, O., Pinder, S., Hanby, A., Kohut, K., Gorman, P., Caneppele, M., Peto, J., Silva, I.D.S., Johnson, N., Swann, R., Dwek, M., Perkins, K-A., Gillett, C., Houlston, R., Ross, G., De Ieso, P., Southey, M.C., Hopper, J.L., Provenzano, E., Apicella, C., Wesseling, J., Cornelissen, S., Keeman, R., Fasching, P.A., Jud, S.M., Ekici, A.B., Beckmann, M.W., Kerin, M.J., Marme, F., Schneeweiss, A., Sohn, C., Burwinkel, B., Guenel, P., Truong, T., Laurent-Puig, P., Kerbrat, P., Bojesen, S.E., Nordestgaard, B.G., Nielsen, S.F., Flyger, H., Milne, R.L., Perez, J.I.A., Menendez, P., Benitez, J., Brenner, H., Dieffenbach, A.K., Arndt, V., Stegmaier, C., Meindl, A., Lichtner, P., Schmutzler, R.K., Lochmann, M., Brauch, H., Fischer, H-P., Ko, Y-D., Nevanlinna, H., Muranen, T.A., Aittomaki, K., Blomqvist, C., Bogdanova, N.V., Dork, T., Lindblom, A., Margolin, S., Mannermaa, A., Kataja, V., Kosma, V-M., Hartikainen, J.M., Chenevix-Trench, G., Lambrechts, D., Weltens, C., Van Limbergen, E., Hatse, S., Chang-Claude, J., Rudolph, A., Seibold, P., Flesch-Janys, D., Radice, P., Peterlongo, P., Bonanni, B., Volorio, S., Giles, G.G., Severi, G., Baglietto, L., Mclean, C.A., Haiman, C.A., Henderson, B.E., Schumacher, F., Le Marchand, L., Simard, J., Goldberg, M.S., Labreche, F., Dumont, M., Kristensen, V., Winqvist, R., Pylkas, K., Jukkola-Vuorinen, A., Kauppila, S., Andrulis, I.L., Knight, J.A., Glendon, G., Mulligan, A.M., Devillee, P., Tollenaar, R.A.E.M., Seynaeve, C.M., Kriege, M., Figueroa, J., Chanock, S.J., Sherman, M.E., Hooning, M.J., Hollestelle, A., van den Ouweland, A.M.W., van Deurzen, C.H.M., Li, J., Czene, K., Humphreys, K., Cox, A., Cross, S.S., Reed, M.W.R., Shah, M., Jakubowska, A., Lubinski, J., Jaworska-Bieniek, K., Durda, K., Swerdlow, A., Ashworth, A., Orr, N., Schoemaker, M., Couch, F.J., Hallberg, E., Gonzalez-Neira, A., Pita, G., Alonso, M.R., Tessier, D.C., Vincent, D., Bacot, F., Bolla, M.K., Wang, Q., Dennis, J., Michailidou, K., Dunning, A.M., Hall, P., Easton, D., Pharoah, P., Schmidt, M.K., Tomlinson, I., Garcia-Closas, M., Network, GENICA, and Investigators, K

Subjects
body regions, skin and connective tissue diseases
Abstract

Invasive lobular breast cancer (ILC) accounts for 10–15% of all invasive breast carcinomas. It is generally ER positive (ER+) and\ud often associated with lobular carcinoma in situ (LCIS). Genome-wide association studies have identified more than 70 common\ud polymorphisms that predispose to breast cancer, but these studies included predominantly ductal (IDC) carcinomas. To\ud identify novel common polymorphisms that predispose to ILC and LCIS, we pooled data from 6,023 cases (5,622 ILC, 401 pure\ud LCIS) and 34,271 controls from 36 studies genotyped using the iCOGS chip. Six novel SNPs most strongly associated with ILC/\ud LCIS in the pooled analysis were genotyped in a further 516 lobular cases (482 ILC, 36 LCIS) and 1,467 controls. These analyses\ud identified a lobular-specific SNP at 7q34 (rs11977670, OR (95%CI) for ILC = 1.13 (1.09–1.18), P = 6.0610210; P-het for ILC vs IDC\ud ER+ tumors = 1.861024\ud ). Of the 75 known breast cancer polymorphisms that were genotyped, 56 were associated with ILC and\ud 15 with LCIS at P,0.05. Two SNPs showed significantly stronger associations for ILC than LCIS (rs2981579/10q26/FGFR2, Phet\ud = 0.04 and rs889312/5q11/MAP3K1, P-het = 0.03); and two showed stronger associations for LCIS than ILC (rs6678914/1q32/\ud LGR6, P-het = 0.001 and rs1752911/6q14, P-het = 0.04). In addition, seven of the 75 known loci showed significant differences\ud between ER+ tumors with IDC and ILC histology, three of these showing stronger associations for ILC (rs11249433/1p11,\ud rs2981579/10q26/FGFR2 and rs10995190/10q21/ZNF365) and four associated only with IDC (5p12/rs10941679; rs2588809/\ud 14q24/RAD51L1, rs6472903/8q21 and rs1550623/2q31/CDCA7). In conclusion, we have identified one novel lobular breast\ud cancer specific predisposition polymorphism at 7q34, and shown for the first time that common breast cancer polymorphisms\ud predispose to LCIS. We have shown that many of the ER+ breast cancer predisposition loci also predispose to ILC, although\ud there is some heterogeneity between ER+ lobular and ER+ IDC tumors. These data provide evidence for overlapping, but\ud distinct etiological pathways within ER+ breast cancer between morphological subtypes.

Published
2014

5. Comparison of 6q25 Breast Cancer Hits from Asian and\ud European Genome Wide Association Studies in the\ud Breast Cancer Association Consortium (BCAC)

Author

Hein, R., Maranian, M., Hopper, J.L., Kapuscinski, M.K., Southey, M.C., Park, D.J., Schmidt, M.K., Broeks, A., Hogervorst, F.B.L., Bueno-de-Mesquit, H.B., Muir, K.R., Lophatananon, A., Rattanamongkongul, S., Puttawibul, P., Fasching, P.A., Hein, A., Ekici, A.B., Beckmann, M.W., Fletcher, O., Johnson, N., Silva, I.D.S., Peto, J., Sawyer, E., Tomlinson, I., Kerin, M., Miller, N., Marmee, F., Schneeweiss, A., Sohn, C., Burwinkel, B., Guenel, P., Cordina-Duverger, E., Menegaux, F., Truong, T., Bojesen, S.E., Nordestgaard, B.G., Flyger, H., Milne, R.L., Arias Perez, J.I., Pilar Zamora, M., Benitez, J., Anton-Culver, H., Ziogas, A., Bernstein, L., Clarke, C.A., Brenner, H., Mueller, H., Arndt, V., Stegmaier, C., Rahman, N., Seal, S., Turnbull, C., Renwick, A., Meindl, A., Schott, S., Bartram, C.R., Schmutzler, R.K., Brauch, H., Hamann, U., Ko, Y-D., Wang-Gohrke, S., Doerk, T., Schuermann, P., Karstens, J.H., Hillemanns, P., Nevanlinna, H., Heikkinen, T., Aittomaki, K., Blomqvist, C., Bogdanova, N.V., Zalutsky, I.V., Antonenkova, N.N., Bermisheva, M., Prokovieva, D., Farahtdinova, A., Khusnutdinova, E., Lindblom, A., Margolin, S., Mannermaa, A., Kataja, V., Kosma, V-M., Hartikainen, J., Chen, X., Beesley, J., Lambrechts, D., Zhao, H., Neven, P., Wildiers, H., Nickels, S., Flesch-Janys, D., Radice, P., Peterlongo, P., Manoukian, S., Barile, M., Couch, F.J., Olson, J.E., Wang, X., Fredericksen, Z., Giles, G.G., Baglietto, L., McLean, C.A., Severi, G., Offit, K., Robson, M., Gaudet, M.M., Vijai, J., Alnaes, G.G., Kristensen, V., Borresen-Dale, A-L., John, E.M., Miron, A., Winqvist, R., Pylkas, K., Jukkola-Vuorinen, A., Grip, M., Andrulis, I.L., Knight, J.A., Glendon, G., Mulligan, A.M., Figueroa, J.D., Garcia-Closas, M., Lissowska, J., Sherman, M.E., Hooning, M., Martens, J.W.M., Seynaeve, C., Collee, M., Hall, P., Humpreys, K., Czene, K., Liu, J., Cox, A., Brock, I.W., Cross, S.S., Reed, M.W.R., Ahmed, S., Ghoussaini, M., Pharoah, P.D.P., Kang, D., Yoo, K-Y., Noh, D-Y., Jakubowska, A., Jaworska, K., Durda, K., Zlowocka, E., Sangrajrang, S., Gaborieau, V., Brennan, P., McKay, J., Shen, C-Y., Yu, J-C., Hsu, H-M., Hou, M-F., Orr, N., Schoemaker, M., Ashworth, A., Swerdlow, A., Trentham-Dietz, A., Newcomb, P.A., Titus, L., Egan, K.M., Chenevix-Trench, G., Antoniou, A.C., Humphreys, M.K., Morrison, J., Chang-Claude, J., Easton, D.F., Dunning, A.M., Network, GENICA, Investigators, K, and Group, AOCS

Abstract

The 6q25.1 locus was first identified via a genome-wide association study (GWAS) in Chinese women and marked by single\ud nucleotide polymorphism (SNP) rs2046210, approximately 180 Kb upstream of ESR1. There have been conflicting reports\ud about the association of this locus with breast cancer in Europeans, and a GWAS in Europeans identified a different SNP,\ud tagged here by rs12662670. We examined the associations of both SNPs in up to 61,689 cases and 58,822 controls from fortyfour\ud studies collaborating in the Breast Cancer Association Consortium, of which four studies were of Asian and 39 of European\ud descent. Logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CI). Case-only analyses were\ud used to compare SNP effects in Estrogen Receptor positive (ER+) versus negative (ER2) tumours. Models including both SNPs\ud were fitted to investigate whether the SNP effects were independent. Both SNPs are significantly associated with breast cancer\ud risk in both ethnic groups. Per-allele ORs are higher in Asian than in European studies [rs2046210: OR (A/G) = 1.36 (95% CI 1.26–\ud 1.48), p = 7.6610214 in Asians and 1.09 (95% CI 1.07–1.11), p = 6.8610218 in Europeans. rs12662670: OR (G/T) = 1.29 (95% CI\ud 1.19–1.41), p = 1.261029 in Asians and 1.12 (95% CI 1.08–1.17), p = 3.861029 in Europeans]. SNP rs2046210 is associated with a\ud significantly greater risk of ER2 than ER+ tumours in Europeans [OR (ER2) = 1.20 (95% CI 1.15–1.25), p = 1.8610217 versus OR\ud (ER+) = 1.07 (95% CI 1.04–1.1), p = 1.361027\ud , pheterogeneity = 5.161026\ud ]. In these Asian studies, by contrast, there is no clear\ud evidence of a differential association by tumour receptor status. Each SNP is associated with risk after adjustment for the other\ud SNP. These results suggest the presence of two variants at 6q25.1 each independently associated with breast cancer risk in\ud Asians and in Europeans. Of these two, the one tagged by rs2046210 is associated with a greater risk of ER2 tumours.

Published
2012

6. Assessing interactions between the associations\ud of common genetic susceptibility variants,\ud reproductive history and body mass index with\ud breast cancer risk in the breast cancer association\ud consortium: a combined case-control study

Author

Milne, R.L., Gaudet, M.M., Spurdle, A.B., Fasching, P.A., Couch, F.J., Benitez, J., Perez, J.I.A., Zamora, M.P., Malats, N., Silva, I.D., Gibson, L.J., Fletcher, O., Johnson, N., Anton-Culver, H., Ziogas, A., Figueroa, J., Brinton, L., Sherman, M.E., Lissowska, J., Hopper, J.L., Dite, G.S., Apicella, C., Southey, M.C., Sigurdson, A.J., Linet, M.S., Schonfeld, S.J., Freedman, D.M., Mannermaa, A., Kosma, V.M., Kataja, V., Auvinen, P., Andrulis, I.L., Glendon, G., Knight, J.A., Weerasooriya, N., Cox, A., Reed, M.W.R., Cross, S.S., Dunning, A.M., Ahmed, S., Shah, M., Brauch, H., Ko, Y.D., Bruning, T., Lambrechts, D., Reumers, J., Smeets, A., Wang-Gohrke, S., Hall, P., Czene, K., Liu, J.J., Irwanto, A.K., Chenevix-Trench, G., Holland, H., Giles, G.G., Baglietto, L., Severi, G., Bojensen, S.E., Nordestgaard, B.G., Flyger, H., John, E.M., West, D.W., Whittemore, A.S., Vachon, C., Olson, J.E., Fredericksen, Z., Kosel, M., Hein, R., Vrieling, A., Flesch-Janys, D., Heinz, J., Beckmann, M.W., Heusinger, K., Ekici, A.B., Haeberle, L., Humphreys, M.K., Morrison, J., Easton, D.F., Pharoah, P.D., Garcia-Closas, M., Goode, E.L., Chang-Claude, J., Network, GENICA, Investigators, KConFab, and Group, AOCS

Abstract

Introduction: Several common breast cancer genetic susceptibility variants have recently been identified. We\ud aimed to determine how these variants combine with a subset of other known risk factors to influence breast\ud cancer risk in white women of European ancestry using case-control studies participating in the Breast Cancer\ud Association Consortium.\ud Methods: We evaluated two-way interactions between each of age at menarche, ever having had a live birth,\ud number of live births, age at first birth and body mass index (BMI) and each of 12 single nucleotide\ud polymorphisms (SNPs) (10q26-rs2981582 (FGFR2), 8q24-rs13281615, 11p15-rs3817198 (LSP1), 5q11-rs889312\ud (MAP3K1), 16q12-rs3803662 (TOX3), 2q35-rs13387042, 5p12-rs10941679 (MRPS30), 17q23-rs6504950 (COX11), 3p24-rs4973768 (SLC4A7), CASP8-rs17468277, TGFB1-rs1982073 and ESR1-rs3020314). Interactions were tested for by\ud fitting logistic regression models including per-allele and linear trend main effects for SNPs and risk factors,\ud respectively, and single-parameter interaction terms for linear departure from independent multiplicative effects.\ud Results: These analyses were applied to data for up to 26,349 invasive breast cancer cases and up to 32,208\ud controls from 21 case-control studies. No statistical evidence of interaction was observed beyond that expected by\ud chance. Analyses were repeated using data from 11 population-based studies, and results were very similar.\ud Conclusions: The relative risks for breast cancer associated with the common susceptibility variants identified to\ud date do not appear to vary across women with different reproductive histories or body mass index (BMI). The\ud assumption of multiplicative combined effects for these established genetic and other risk factors in risk prediction\ud models appears justified.

Published
2010

7. Fine-Scale Mapping of the FGFR2 Breast Cancer Risk Locus:Putative Functional Variants Differentially Bind FOXA1 and E2F1

Author

Meyer, Kerstin B, O'Reilly, Martin, Michailidou, Kyriaki, Carlebur, Saskia, Edwards, Stacey L, French, Juliet D, Prathalingham, Radhika, Dennis, Joe, Bolla, Manjeet K, Wang, Qin, de Santiago, Ines, Hopper, John L, Tsimiklis, Helen, Apicella, Carmel, Southey, Melissa C, Schmidt, Marjanka K, Broeks, Annegien, Van 't Veer, Laura J, Hogervorst, Frans B, Muir, Kenneth, Lophatananon, Artitaya, Stewart-Brown, Sarah, Siriwanarangsan, Pornthep, Fasching, Peter A, Lux, Michael P, Ekici, Arif B, Beckmann, Matthias W, Peto, Julian, Dos Santos Silva, Isabel, Fletcher, Olivia, Johnson, Nichola, Sawyer, Elinor J, Tomlinson, Ian, Kerin, Michael J, Miller, Nicola, Marme, Federick, Schneeweiss, Andreas, Sohn, Christof, Burwinkel, Barbara, Guénel, Pascal, Truong, Thérèse, Laurent-Puig, Pierre, Menegaux, Florence, Bojesen, Stig E, Nordestgaard, Børge G, Nielsen, Sune F, Flyger, Henrik, Milne, Roger L, Zamora, M Pilar, Arias, Jose I, Benitez, Javier, Neuhausen, Susan, Anton-Culver, Hoda, Ziogas, Argyrios, Dur, Christina C, Brenner, Hermann, Müller, Heiko, Arndt, Volker, Stegmaier, Christa, Meindl, Alfons, Schmutzler, Rita K, Engel, Christoph, Ditsch, Nina, Brauch, Hiltrud, Brüning, Thomas, Ko, Yon-Dschun, Nevanlinna, Heli, Muranen, Taru A, Aittomäki, Kristiina, Blomqvist, Carl, Matsuo, Keitaro, Ito, Hidemi, Iwata, Hiroji, Yatabe, Yasushi, Dörk, Thilo, Helbig, Sonja, Bogdanova, Natalia V, Lindblom, Annika, Margolin, Sara, Mannermaa, Arto, Kataja, Vesa, Kosma, Veli-Matti, Hartikainen, Jaana M, Chenevix-Trench, Georgia, Wu, Anna H, Tseng, Chiu-Chen, Van Den Berg, David, Stram, Daniel O, Lambrechts, Diether, Thienpont, Bernard, Christiaens, Marie-Rose, Smeets, Ann, Chang-Claude, Jenny, Rudolph, Anja, Seibold, Petra, Flesch-Janys, Dieter, Radice, Paolo, Peterlongo, Paolo, Bonanni, Bernardo, Bernard, Loris, Couch, Fergus J, Olson, Janet E, Wang, Xianshu, Purrington, Kristen, Giles, Graham G, Severi, Gianluca, Baglietto, Laura, McLean, Catriona, Haiman, Christopher A, Henderson, Brian E, Schumacher, Fredrick, Le Marchand, Loic, Simard, Jacques, Goldberg, Mark S, Labrèche, France, Dumont, Martine, Teo, Soo-Hwang, Yip, Cheng-Har, Phuah, Sze-Yee, Kristensen, Vessela, Grenaker Alnæs, Grethe, Børresen-Dale, Anne-Lise, Zheng, Wei, Deming-Halverson, Sandra, Shrubsole, Martha, Long, Jirong, Winqvist, Robert, Pylkäs, Katri, Jukkola-Vuorinen, Arja, Kauppila, Saila, Andrulis, Irene L, Knight, Julia A, Glendon, Gord, Tchatchou, Sandrine, Devilee, Peter, Tollenaar, Robert A E M, Seynaeve, Caroline M, García-Closas, Montserrat, Figueroa, Jonine, Chanock, Stephen J, Lissowska, Jolanta, Czene, Kamila, Darabi, Hartef, Eriksson, Kimael, Hooning, Maartje J, Martens, John W M, van den Ouweland, Ans M W, van Deurzen, Carolien H M, Hall, Per, Li, Jingmei, Liu, Jianjun, Humphreys, Keith, Shu, Xiao-Ou, Lu, Wei, Gao, Yu-Tang, Cai, Hui, Cox, Angela, Reed, Malcolm W R, Blot, William, Signorello, Lisa B, Cai, Qiuyin, Pharoah, Paul D P, Ghoussaini, Maya, Harrington, Patricia, Tyrer, Jonathan, Kang, Daehee, Choi, Ji-Yeob, Park, Sue K, Noh, Dong-Young, Hartman, Mikael, Hui, Miao, Lim, Wei-Yen, Buhari, Shaik A, Hamann, Ute, Försti, Asta, Rüdiger, Thomas, Ulmer, Hans-Ulrich, Jakubowska, Anna, Lubinski, Jan, Jaworska, Katarzyna, Durda, Katarzyna, Sangrajrang, Suleeporn, Gaborieau, Valerie, Brennan, Paul, McKay, James, Vachon, Celine, Slager, Susan, Fostira, Florentia, Pilarski, Robert, Shen, Chen-Yang, Hsiung, Chia-Ni, Wu, Pei-Ei, Hou, Ming-Feng, Swerdlow, Anthony, Ashworth, Alan, Orr, Nick, Schoemaker, Minouk J, Ponder, Bruce A J, Dunning, Alison M, Easton, Douglas F, Network, GENICA, Meyer, Kerstin B, O'Reilly, Martin, Michailidou, Kyriaki, Carlebur, Saskia, Edwards, Stacey L, French, Juliet D, Prathalingham, Radhika, Dennis, Joe, Bolla, Manjeet K, Wang, Qin, de Santiago, Ines, Hopper, John L, Tsimiklis, Helen, Apicella, Carmel, Southey, Melissa C, Schmidt, Marjanka K, Broeks, Annegien, Van 't Veer, Laura J, Hogervorst, Frans B, Muir, Kenneth, Lophatananon, Artitaya, Stewart-Brown, Sarah, Siriwanarangsan, Pornthep, Fasching, Peter A, Lux, Michael P, Ekici, Arif B, Beckmann, Matthias W, Peto, Julian, Dos Santos Silva, Isabel, Fletcher, Olivia, Johnson, Nichola, Sawyer, Elinor J, Tomlinson, Ian, Kerin, Michael J, Miller, Nicola, Marme, Federick, Schneeweiss, Andreas, Sohn, Christof, Burwinkel, Barbara, Guénel, Pascal, Truong, Thérèse, Laurent-Puig, Pierre, Menegaux, Florence, Bojesen, Stig E, Nordestgaard, Børge G, Nielsen, Sune F, Flyger, Henrik, Milne, Roger L, Zamora, M Pilar, Arias, Jose I, Benitez, Javier, Neuhausen, Susan, Anton-Culver, Hoda, Ziogas, Argyrios, Dur, Christina C, Brenner, Hermann, Müller, Heiko, Arndt, Volker, Stegmaier, Christa, Meindl, Alfons, Schmutzler, Rita K, Engel, Christoph, Ditsch, Nina, Brauch, Hiltrud, Brüning, Thomas, Ko, Yon-Dschun, Nevanlinna, Heli, Muranen, Taru A, Aittomäki, Kristiina, Blomqvist, Carl, Matsuo, Keitaro, Ito, Hidemi, Iwata, Hiroji, Yatabe, Yasushi, Dörk, Thilo, Helbig, Sonja, Bogdanova, Natalia V, Lindblom, Annika, Margolin, Sara, Mannermaa, Arto, Kataja, Vesa, Kosma, Veli-Matti, Hartikainen, Jaana M, Chenevix-Trench, Georgia, Wu, Anna H, Tseng, Chiu-Chen, Van Den Berg, David, Stram, Daniel O, Lambrechts, Diether, Thienpont, Bernard, Christiaens, Marie-Rose, Smeets, Ann, Chang-Claude, Jenny, Rudolph, Anja, Seibold, Petra, Flesch-Janys, Dieter, Radice, Paolo, Peterlongo, Paolo, Bonanni, Bernardo, Bernard, Loris, Couch, Fergus J, Olson, Janet E, Wang, Xianshu, Purrington, Kristen, Giles, Graham G, Severi, Gianluca, Baglietto, Laura, McLean, Catriona, Haiman, Christopher A, Henderson, Brian E, Schumacher, Fredrick, Le Marchand, Loic, Simard, Jacques, Goldberg, Mark S, Labrèche, France, Dumont, Martine, Teo, Soo-Hwang, Yip, Cheng-Har, Phuah, Sze-Yee, Kristensen, Vessela, Grenaker Alnæs, Grethe, Børresen-Dale, Anne-Lise, Zheng, Wei, Deming-Halverson, Sandra, Shrubsole, Martha, Long, Jirong, Winqvist, Robert, Pylkäs, Katri, Jukkola-Vuorinen, Arja, Kauppila, Saila, Andrulis, Irene L, Knight, Julia A, Glendon, Gord, Tchatchou, Sandrine, Devilee, Peter, Tollenaar, Robert A E M, Seynaeve, Caroline M, García-Closas, Montserrat, Figueroa, Jonine, Chanock, Stephen J, Lissowska, Jolanta, Czene, Kamila, Darabi, Hartef, Eriksson, Kimael, Hooning, Maartje J, Martens, John W M, van den Ouweland, Ans M W, van Deurzen, Carolien H M, Hall, Per, Li, Jingmei, Liu, Jianjun, Humphreys, Keith, Shu, Xiao-Ou, Lu, Wei, Gao, Yu-Tang, Cai, Hui, Cox, Angela, Reed, Malcolm W R, Blot, William, Signorello, Lisa B, Cai, Qiuyin, Pharoah, Paul D P, Ghoussaini, Maya, Harrington, Patricia, Tyrer, Jonathan, Kang, Daehee, Choi, Ji-Yeob, Park, Sue K, Noh, Dong-Young, Hartman, Mikael, Hui, Miao, Lim, Wei-Yen, Buhari, Shaik A, Hamann, Ute, Försti, Asta, Rüdiger, Thomas, Ulmer, Hans-Ulrich, Jakubowska, Anna, Lubinski, Jan, Jaworska, Katarzyna, Durda, Katarzyna, Sangrajrang, Suleeporn, Gaborieau, Valerie, Brennan, Paul, McKay, James, Vachon, Celine, Slager, Susan, Fostira, Florentia, Pilarski, Robert, Shen, Chen-Yang, Hsiung, Chia-Ni, Wu, Pei-Ei, Hou, Ming-Feng, Swerdlow, Anthony, Ashworth, Alan, Orr, Nick, Schoemaker, Minouk J, Ponder, Bruce A J, Dunning, Alison M, Easton, Douglas F, and Network, GENICA

Published
2013

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