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2. Breast Cancer Risk Genes — Association Analysis in More than 113,000 Women

Author

Dorling, L., Carvalho, S., Allen, J., Gonzalez-Neira, A., Luccarini, C., Wahlstrom, C., Pooley, K.A., Parsons, M.T., Fortuno, C., Wang, Q., Bolla, M.K., Dennis, J., Keeman, R., Alonso, M.R., Alvarez, N., Herraez, B., Fernandez, V., Nunez-Torres, R., Osorio, A., Valcich, J., Li, M., Torngren, T., Harrington, P.A., Baynes, C., Conroy, D.M., Decker, B., Fachal, L., Mavaddat, N., Ahearn, T., Aittomaki, K., Antonenkova, N.N., Arnold, N., Arveux, P., Ausems, M.G.E.M., Auvinen, P., Becher, H., Beckmann, M.W., Behrens, S., Bermisheva, M., Bialkowska, K., Blomqvist, C., Bogdanova, N.V., Bogdanova-Markov, N., Bojesen, S.E., Bonanni, B., Borresen-Dale, A.L., Brauch, H., Bremer, M., Briceno, I., Bruning, T., Burwinkel, B., Cameron, D.A., Camp, N.J., Campbell, A., Carracedo, A., Castelao, J.E., Cessna, M.H., Chanock, S.J., Christiansen, H., Collee, J.M., Cordina-Duverger, E., Cornelissen, S., Czene, K., Dork, T., Ekici, A.B., Engel, C., Eriksson, M., Fasching, P.A., Figueroa, J., Flyger, H., Forsti, A., Gabrielson, M., Gago-Dominguez, M., Georgoulias, V., Gil, F., Giles, G.G., Glendon, G., Garcia, E.B.G., Alnaes, G.I.G., Guenel, P., Hadjisavvas, A., Haeberle, L., Hahnen, E., Hall, P., Hamann, U., Harkness, E.F., Hartikainen, J.M., Hartman, M., He, W., Heemskerk-Gerritsen, B.A.M., Hillemanns, P., Hogervorst, F.B.L., Hollestelle, A., Ho, W.K., Hooning, M.J., Howell, A., Humphreys, K., Idris, F., Jakubowska, A., Jung, A., Kapoor, P.M., Kerin, M.J., Khusnutdinova, E., Kim, S.W., Ko, Y.D., Kosma, V.M., Kristensen, V.N., Kyriacou, K., Lakeman, I.M.M., Lee, J.W., Lee, M.H., Li, J.M., Lindblom, A., W.Y. lo, Loizidou, M.A., Lophatananon, A., Lubinski, J., MacInnis, R.J., Madsen, M.J., Mannermaa, A., Manoochehri, M., Manoukian, S., Margolin, S., Martinez, M.E., Maurer, T., Mavroudis, D., McLean, C., Meindl, A., Mensenkamp, A.R., Michailidou, K., Miller, N., Taib, N.A.M., Muir, K., Mulligan, A.M., Nevanlinna, H., Newman, W.G., Nordestgaard, B.G., Ng, P.S., Oosterwijk, J.C., Park, S.K., Park-Simon, T.W., Perez, J.I.A., Peterlongo, P., Porteous, D.J., Prajzendanc, K., Prokofyeva, D., Radice, P., Rashid, M.U., Rhenius, V., Rookus, M.A., Rudiger, T., Saloustros, E., Sawyer, E.J., Schmutzler, R.K., Schneeweiss, A., Schurmann, P., Shah, M., Sohn, C., Southey, M.C., Surowy, H., Suvanto, M., Thanasitthichai, S., Tomlinson, I., Torres, D., Truong, T., Tzardi, M., Valova, Y., Asperen, C.J. van, Dam, R.M. van, Ouweland, A.M.W. van den, Kolk, L.E. van der, Veen, E.M. van, Wendt, C., Williams, J.A., Yang, X.H.R., Yoon, S.Y., Zamora, M.P., Evans, D.G., Hoya, M. de la, Simard, J., Antoniou, A.C., Borg, A., Andrulis, I.L., Chang-Claude, J., Garcia-Closas, M., Chenevix-Trench, G., Milne, R.L., Pharoah, P.D.P., Schmidt, M.K., Spurdle, A.B., Vreeswijk, M.P.G., Benitez, J., Dunning, A.M., Kvist, A., Teo, S.H., Devilee, P., Easton, D.F., Breast Canc Assoc Consortium, Erasmus MC other, Medical Oncology, Clinical Genetics, Keeman, Renske [0000-0002-5452-9933], Decker, Brennan [0000-0003-4516-7421], Eriksson, Mikael [0000-0001-8135-4270], Martinez, Maria Elena [0000-0002-6728-1834], Surowy, Harald [0000-0002-3595-9188], Pharoah, Paul DP [0000-0001-8494-732X], Apollo - University of Cambridge Repository, Damage and Repair in Cancer Development and Cancer Treatment (DARE), Targeted Gynaecologic Oncology (TARGON), RS: GROW - R4 - Reproductive and Perinatal Medicine, MUMC+: DA KG Polikliniek (9), and Klinische Genetica

Subjects
Adult, Risk, Oncology, medicine.medical_specialty, Adolescent, PALB2, Genetic counseling, Genes, BRCA2, Mutation, Missense, Genes, BRCA1, Estrogen receptor, Breast Neoplasms, 030204 cardiovascular system & hematology, OVARIAN-CANCER, Article, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Breast cancer, SDG 3 - Good Health and Well-being, Internal medicine, Odds Ratio, medicine, Humans, Genetic Predisposition to Disease, 030212 general & internal medicine, skin and connective tissue diseases, CHEK2, Aged, Genetic testing, Genetic association, Aged, 80 and over, Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17], medicine.diagnostic_test, MUTATIONS, business.industry, Age Factors, Genetic Variation, Sequence Analysis, DNA, General Medicine, Odds ratio, Middle Aged, BRCA1, medicine.disease, 3. Good health, Logistic Models, Female, business
Abstract

BACKGROUNDGenetic testing for breast cancer susceptibility is widely used, but for many genes,evidence of an association with breast cancer is weak, underlying risk estimatesare imprecise, and reliable subtype-specific risk estimates are lacking.METHODSWe used a panel of 34 putative susceptibility genes to perform sequencing onsamples from 60,466 women with breast cancer and 53,461 controls. In separateanalyses for protein-truncating variants and rare missense variants in these genes,we estimated odds ratios for breast cancer overall and tumor subtypes. We evaluatedmissense-variant associations according to domain and classification of pathogenicity.RESULTSProtein-truncating variants in 5 genes (ATM, BRCA1, BRCA2, CHEK2, and PALB2)were associated with a risk of breast cancer overall with a P value of less than0.0001. Protein-truncating variants in 4 other genes (BARD1, RAD51C, RAD51D,and TP53) were associated with a risk of breast cancer overall with a P value ofless than 0.05 and a Bayesian false-discovery probability of less than 0.05. Forprotein-truncating variants in 19 of the remaining 25 genes, the upper limit ofthe 95% confidence interval of the odds ratio for breast cancer overall was lessthan 2.0. For protein-truncating variants in ATM and CHEK2, odds ratios werehigher for estrogen receptor (ER)–positive disease than for ER-negative disease;for protein-truncating variants in BARD1, BRCA1, BRCA2, PALB2, RAD51C, andRAD51D, odds ratios were higher for ER-negative disease than for ER-positivedisease. Rare missense variants (in aggregate) in ATM, CHEK2, and TP53 wereassociated with a risk of breast cancer overall with a P value of less than 0.001.For BRCA1, BRCA2, and TP53, missense variants (in aggregate) that would be classified as pathogenic according to standard criteria were associated with a riskof breast cancer overall, with the risk being similar to that of protein-truncatingvariants.CONCLUSIONSThe results of this study define the genes that are most clinically useful for inclusion on panels for the prediction of breast cancer risk, as well as provide estimatesof the risks associated with protein-truncating variants, to guide genetic counseling. (Funded by European Union Horizon 2020 programs and others.)

Published
2021

3. Breast cancer risks associated with missense variants in breast cancer susceptibility genes

Author

Dorling, L., Carvalho, S., Allen, J., Parsons, M.T., Fortuno, C., Gonzalez-Neira, A., Heijl, S.M., Adank, M.A., Ahearn, T.U., Andrulis, I.L., Auvinen, P., Becher, H., Beckmann, M.W., Behrens, S., Bermisheva, M., Bogdanova, N.V., Bojesen, S.E., Bolla, M.K., Bremer, M., Briceno, I., Camp, N.J., Campbell, A., Castelao, J.E., Chang-Claude, J., Chanock, S.J., Chenevix-Trench, G., Collee, J.M., Czene, K., Dennis, J., Dork, T., Eriksson, M., Evans, D.G., Fasching, P.A., Figueroa, J., Flyger, H., Gabrielson, M., Gago-Dominguez, M., Garcia-Closas, M., Giles, G.G., Glendon, G., Guenel, P., Gundert, M., Hadjisavvas, A., Hahnen, E., Hall, P., Hamann, U., Harkness, E.F., Hartman, M., Hogervorst, F.B.L., Hollestelle, A., Hoppe, R., Howell, A., Jakubowska, A., Jung, A., Khusnutdinova, E., Kim, S.W., Ko, Y.D., Kristensen, V.N., Lakeman, I.M.M., Li, J.M., Lindblom, A., Loizidou, M.A., Lophatananon, A., Lubinski, J., Luccarini, C., Madsen, M.J., Mannermaa, A., Manoochehri, M., Margolin, S., Mavroudis, D., Milne, R.L., Taib, N.A.M., Muir, K., Nevanlinna, H., Newman, W.G., Oosterwijk, J.C., Park, S.K., Peterlongo, P., Radice, P., Saloustros, E., Sawyer, E.J., Schmutzler, R.K., Shah, M.T., Sim, X., Southey, M.C., Surowy, H., Suvanto, M., Tomlinson, I., Torres, D., Truong, T., Asperen, C.J. van, Waltes, R., Wang, Q., Yang, X.H.R., Pharoah, P.D.P., Schmidt, M.K., Benitez, J., Vroling, B., Dunning, A.M., Teo, S.H., Kvist, A., Hoya, M. de la, Devilee, P., Spurdle, A.B., Vreeswijk, M.P.G., Easton, D.F., NBCS Collaborators, KConFab Investigators, SGBCC Investigators, Clinical Genetics, Medical Oncology, Apollo - University of Cambridge Repository, Dennis, Joe [0000-0003-4591-1214], Pharoah, Paul [0000-0001-8494-732X], Easton, Douglas [0000-0003-2444-3247], Targeted Gynaecologic Oncology (TARGON), Damage and Repair in Cancer Development and Cancer Treatment (DARE), University of Helsinki, Clinicum, Department of Obstetrics and Gynecology, HUS Gynecology and Obstetrics, Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Wellcome Trust, WT: 633784, v203477/Z/16/Z, Horizon 2020 Framework Programme, H2020, Cancer Research UK, CRUK: C1287/A16563, The sequencing and analysis for this project was funded by the European Union’s Horizon 2020 Research and Innovation Programme (BRIDGES: grant number 634935) and the Wellcome Trust [grant no: v203477/Z/16/Z]. BCAC co-ordination was additionally funded by the European Union’s Horizon 2020 Research and Innovation Programme (BRIDGES: grant number 634935, BCAST: grant number 633784) and by Cancer Research UK [C1287/A16563]. Study specific funding is given in the Additional Note., and HAL UVSQ, Équipe

Subjects
Mutation, Missense, Breast Neoplasms, [SDV.GEN.GH] Life Sciences [q-bio]/Genetics/Human genetics, Breast Neoplasms/genetics, Breast Cancer, Genetic Epidemiology, Missense Variants, Risk Prediction, CLASSIFICATION, Breast cancer, Missense variants, SDG 3 - Good Health and Well-being, 3123 Gynaecology and paediatrics, SEQUENCE VARIANTS, Genetics, Humans, Genetic Predisposition to Disease, Genetic epidemiology, ddc:610, skin and connective tissue diseases, Molecular Biology, Genetics (clinical), MUTATIONS, Research, UNKNOWN CLINICAL-SIGNIFICANCE, 1184 Genetics, developmental biology, physiology, FRAMEWORK, BRCA1, Risk prediction, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, SUBSTITUTIONS, Case-Control Studies, Mutation, Molecular Medicine, Female, Missense, PATHOGENICITY
Abstract

Background Protein truncating variants in ATM, BRCA1, BRCA2, CHEK2, and PALB2 are associated with increased breast cancer risk, but risks associated with missense variants in these genes are uncertain. Methods We analyzed data on 59,639 breast cancer cases and 53,165 controls from studies participating in the Breast Cancer Association Consortium BRIDGES project. We sampled training (80%) and validation (20%) sets to analyze rare missense variants in ATM (1146 training variants), BRCA1 (644), BRCA2 (1425), CHEK2 (325), and PALB2 (472). We evaluated breast cancer risks according to five in silico prediction-of-deleteriousness algorithms, functional protein domain, and frequency, using logistic regression models and also mixture models in which a subset of variants was assumed to be risk-associated. Results The most predictive in silico algorithms were Helix (BRCA1, BRCA2 and CHEK2) and CADD (ATM). Increased risks appeared restricted to functional protein domains for ATM (FAT and PIK domains) and BRCA1 (RING and BRCT domains). For ATM, BRCA1, and BRCA2, data were compatible with small subsets (approximately 7%, 2%, and 0.6%, respectively) of rare missense variants giving similar risk to those of protein truncating variants in the same gene. For CHEK2, data were more consistent with a large fraction (approximately 60%) of rare missense variants giving a lower risk (OR 1.75, 95% CI (1.47–2.08)) than CHEK2 protein truncating variants. There was little evidence for an association with risk for missense variants in PALB2. The best fitting models were well calibrated in the validation set. Conclusions These results will inform risk prediction models and the selection of candidate variants for functional assays and could contribute to the clinical reporting of gene panel testing for breast cancer susceptibility.

Published
2022

4. Functional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element

Author

Baxter, J.S., Johnson, N., Tomczyk, K., Gillespie, A., Maguire, S., Brough, R., Fachal, L., Michailidou, K., Bolla, M.K., Wang, Q., Dennis, J., Ahearn, T.U., Andrulis, I.L., Anton-Culver, H., Antonenkova, N.N., Arndt, V., Aronson, K.J., Augustinsson, A., Becher, H., Beckmann, M.W., Behrens, S., Benitez, J., Bermisheva, M., Bogdanova, N.V., Bojesen, S.E., Brenner, H., Brucker, S.Y., Cai, Q.Y., Campa, D., Canzian, F., Castelao, J.E., Chan, T.L., Chang-Claude, J., Chanock, S.J., Chenevix-Trench, G., Choi, J.Y., Clarke, C.L., Collaborators, N., Colonna, S., Conroy, D.M., Couch, F.J., Cox, A., Cross, S.S., Czene, K., Daly, M.B., Devilee, P., Dork, T., Dossus, L., Dwek, M., Eccles, D.M., Ekici, A.B., Eliassen, A.H., Engel, C., Fasching, P.A., Figueroa, J., Flyger, H., Gago-Dominguez, M., Gao, C., Garcia-Closas, M., Garcia-Saenz, J.A., Ghoussaini, M., Giles, G.G., Goldberg, M.S., Gonzalez-Neira, A., Guenel, P., Gundert, M., Haeberle, L., Hahnen, E., Haiman, C.A., Hall, P., Hamann, U., Hartman, M., Hatse, S., Hauke, J., Hollestelle, A., Hoppe, R., Hopper, J.L., Hou, M.F., Ito, H., Iwasaki, M., Jager, A., Jakubowska, A., Janni, W., John, E.M., Joseph, V., Jung, A., Kaaks, R., Kang, D., Keeman, R., Khusnutdinova, E., Kim, S.W., Kosma, V.M., Kraft, P., Kristensen, V.N., Kubelka-Sabit, K., Kurian, A.W., Kwong, A., Lacey, J.V., Lambrechts, D., Larson, N.L., Larsson, S.C., Marchand, L. le, Lejbkowicz, F., Li, J.M., Long, J.R., Lophatananon, A., LubiNski, J., Mannermaa, A., Manoochehri, M., Manoukian, S., Margolin, S., Matsuo, K., Mavroudis, D., Mayes, R., Menon, U., Milne, R.L., Taib, N.A.M., Muir, K., Muranen, T.A., Murphy, R.A., Nevanlinna, H., O'Brien, K.M., Offit, K., Olson, J.E., Olsson, H., Park, S.K., Park-Simon, T.W., Patel, A.V., Peterlongo, P., Peto, J., Plaseska-Karanfilska, D., Presneau, N., Pylkas, K., Rack, B., Rennert, G., Romero, A., Ruebner, M., Rudiger, T., Saloustros, E., Sandler, D.P., Sawyer, E.J., Schmidt, M.K., Schmutzler, R.K., Schneeweiss, A., Schoemaker, M.J., Shah, M., Shen, C.Y., Shu, X.O., Simard, J., Southey, M.C., Stone, J., Surowy, H., Swerdlow, A.J., Tamimi, R.M., Tapper, W.J., Taylor, J.A., Teo, S.H., Teras, L.R., Terry, M.B., Toland, A.E., Tomlinson, I., Truong, T., Tseng, C.C., Untch, M., Vachon, C.M., Ouweland, A.M.W. van den, Wang, S.S., Weinberg, C.R., Wendt, C., Winham, S.J., Winqvist, R., Wolk, A., Wu, A.H., Yamaji, T., Zheng, W., Ziogas, A., Pharoah, P.D.P., Dunning, A.M., Easton, D.F., Pettitt, S.J., Lord, C.J., Haider, S., Orr, N., Fletcher, O., kConFab Investigators, ABCTB Investigators, Medical Oncology, Clinical Genetics, HUS Gynecology and Obstetrics, Department of Obstetrics and Gynecology, Biosciences, Dennis, Joe [0000-0003-4591-1214], 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
Basic medicine, breast cancer risk, 0302 clinical medicine, Transcription (biology), Risk Factors, WIDE ASSOCIATION, TRANSCRIPTION, Promoter Regions, Genetic, Genetics (clinical), Sequence Deletion, Genetics, Genetics & Heredity, 0303 health sciences, Chromosome Mapping, 3. Good health, 030220 oncology & carcinogenesis, Chromosomes, Human, Pair 2, Pair 2, Female, Medical Genetics, Life Sciences & Biomedicine, Human, Tumor suppressor gene, SUSCEPTIBILITY LOCI, In silico, 3122 Cancers, Locus (genetics), Breast Neoplasms, Biology, Chromosomes, Article, Cell Line, RNAS, Promoter Regions, 03 medical and health sciences, functional annotation, risk locus, CRISPR-Cas Systems, Genetic Association Studies, Genetic Variation, Humans, Insulin-Like Growth Factor Binding Protein 5, Molecular Sequence Annotation, 11Q13, Genetic, SDG 3 - Good Health and Well-being, Enhancer, Transcription factor, 030304 developmental biology, Medicinsk genetik, Reporter gene, Science & Technology, IDENTIFICATION, Clinical medicine, Estrogen receptor alpha
Abstract

A combination of genetic and functional approaches has identified three independent breast cancer risk loci at 2q35. A recent fine-scale mapping analysis to refine these associations resulted in 1 (signal 1), 5 (signal 2), and 42 (signal 3) credible causal variants at these loci. We used publicly available in silico DNase I and ChIP-seq data with in vitro reporter gene and CRISPR assays to annotate signals 2 and 3. We identified putative regulatory elements that enhanced cell-type-specific transcription from the IGFBP5 promoter at both signals (30- to 40-fold increased expression by the putative regulatory element at signal 2, 2- to 3-fold by the putative regulatory element at signal 3). We further identified one of the five credible causal variants at signal 2, a 1.4 kb deletion (esv3594306), as the likely causal variant; the deletion allele of this variant was associated with an average additional increase in IGFBP5 expression of 1.3-fold (MCF-7) and 2.2-fold (T-47D). We propose a model in which the deletion allele of esv3594306 juxtaposes two transcription factor binding regions (annotated by estrogen receptor alpha ChIP-seq peaks) to generate a single extended regulatory element. This regulatory element increases cell-type-specific expression of the tumor suppressor gene IGFBP5 and, thereby, reduces risk of estrogen receptor-positive breast cancer (odds ratio = 0.77, 95% CI 0.74-0.81, p = 3.1 × 10-31). ispartof: AMERICAN JOURNAL OF HUMAN GENETICS vol:108 issue:7 pages:1190-1203 ispartof: location:United States status: published

Published
2021

5. Breast cancer risk genes - Association analysis in more than 113,000 women.

Author

Cornelissen S., Michailidou K., Miller N., Taib N.A.M., Muir K., Mulligan A.M., Nevanlinna H., Newman W.G., Nordestgaard B.G., Ng P.-S., Oosterwijk J.C., Park S.K., Park-Simon T.-W., Perez J.I.A., Peterlongo P., Porteous D.J., Prajzendanc K., Prokofyeva D., Radice P., Rashid M.U., Rhenius V., Rookus M.A., Rudiger T., Saloustros E., Sawyer E.J., Schmutzler R.K., Schneeweiss A., Schurmann P., Shah M., Sohn C., Southey M.C., Surowy H., Suvanto M., Thanasitthichai S., Tomlinson I., Torres D., Truong T., Tzardi M., Valova Y., van Asperen C.J., van Dam R.M., van den Ouweland A.M.W., van der Kolk L.E., van Veen E.M., Wendt C., Williams J.A., Yang X.R., Yoon S.-Y., Zamora M.P., Evans D.G., de la Hoya M., Simard J., Antoniou A.C., Borg A., Andrulis I.L., Chang-Claude J., Garcia-Closas M., Chenevix-Trench G., Milne R.L., Pharoah P.D.P., Schmidt M.K., Spurdle A.B., Vreeswijk M.P.G., Benitez J., Dunning A.M., Kvist A., Teo S.H., Devilee P., Easton D.F., Dorling L., Carvalho S., Allen J., Gonzalez-Neira A., Luccarini C., Wahlstrom C., Pooley K.A., Parsons M.T., Fortuno C., Wang Q., Bolla M.K., Dennis J., Keeman R., Alonso M.R., Alvarez N., Herraez B., Fernandez V., Nunez-Torres R., Osorio A., Valcich J., Li M., Torngren T., Harrington P.A., Baynes C., Conroy D.M., Decker B., Fachal L., Mavaddat N., Ahearn T., Aittomaki K., Antonenkova N.N., Arnold N., Arveux P., Ausems M.G.E.M., Auvinen P., Becher H., Beckmann M.W., Behrens S., Bermisheva M., Bialkowska K., Blomqvist C., Bogdanova N.V., Bogdanova-Markov N., Bojesen S.E., Bonanni B., Borresen-Dale A.-L., Brauch H., Bremer M., Briceno I., Bruning T., Burwinkel B., Cameron D.A., Camp N.J., Campbell A., Carracedo A., Castelao J.E., Cessna M.H., Chanock S.J., Christiansen H., Collee J.M., Cordina-Duverger E., Czene K., Dork T., Ekici A.B., Engel C., Eriksson M., Fasching P.A., Figueroa J., Flyger H., Forsti A., Gabrielson M., Gago-Dominguez M., Georgoulias V., Gil F., Giles G.G., Glendon G., Gomez Garcia E.B., Grenaker Alnaes G.I., Guenel P., Hadjisavvas A., Haeberle L., Hahnen E., Hall P., Hamann U., Harkness E.F., Hartikainen J.M., Hartman M., He W., Heemskerk-Gerritsen B.A.M., Hillemanns P., Hogervorst F.B.L., Hollestelle A., Ho W.K., Hooning M.J., Howell A., Humphreys K., Idris F., Jakubowska A., Jung A., Kapoor P.M., Kerin M.J., Khusnutdinova E., Kim S.-W., Ko Y.-D., Kosma V.-M., Kristensen V.N., Kyriacou K., Lakeman I.M.M., Lee J.W., Lee M.H., Li J., Lindblom A., Lo W.-Y., Loizidou M.A., Lophatananon A., Lubinski J., MacInnis R.J., Madsen M.J., Mannermaa A., Manoochehri M., Manoukian S., Margolin S., Martinez M.E., Maurer T., Mavroudis D., McLean C., Meindl A., Mensenkamp A.R., Cornelissen S., Michailidou K., Miller N., Taib N.A.M., Muir K., Mulligan A.M., Nevanlinna H., Newman W.G., Nordestgaard B.G., Ng P.-S., Oosterwijk J.C., Park S.K., Park-Simon T.-W., Perez J.I.A., Peterlongo P., Porteous D.J., Prajzendanc K., Prokofyeva D., Radice P., Rashid M.U., Rhenius V., Rookus M.A., Rudiger T., Saloustros E., Sawyer E.J., Schmutzler R.K., Schneeweiss A., Schurmann P., Shah M., Sohn C., Southey M.C., Surowy H., Suvanto M., Thanasitthichai S., Tomlinson I., Torres D., Truong T., Tzardi M., Valova Y., van Asperen C.J., van Dam R.M., van den Ouweland A.M.W., van der Kolk L.E., van Veen E.M., Wendt C., Williams J.A., Yang X.R., Yoon S.-Y., Zamora M.P., Evans D.G., de la Hoya M., Simard J., Antoniou A.C., Borg A., Andrulis I.L., Chang-Claude J., Garcia-Closas M., Chenevix-Trench G., Milne R.L., Pharoah P.D.P., Schmidt M.K., Spurdle A.B., Vreeswijk M.P.G., Benitez J., Dunning A.M., Kvist A., Teo S.H., Devilee P., Easton D.F., Dorling L., Carvalho S., Allen J., Gonzalez-Neira A., Luccarini C., Wahlstrom C., Pooley K.A., Parsons M.T., Fortuno C., Wang Q., Bolla M.K., Dennis J., Keeman R., Alonso M.R., Alvarez N., Herraez B., Fernandez V., Nunez-Torres R., Osorio A., Valcich J., Li M., Torngren T., Harrington P.A., Baynes C., Conroy D.M., Decker B., Fachal L., Mavaddat N., Ahearn T., Aittomaki K., Antonenkova N.N., Arnold N., Arveux P., Ausems M.G.E.M., Auvinen P., Becher H., Beckmann M.W., Behrens S., Bermisheva M., Bialkowska K., Blomqvist C., Bogdanova N.V., Bogdanova-Markov N., Bojesen S.E., Bonanni B., Borresen-Dale A.-L., Brauch H., Bremer M., Briceno I., Bruning T., Burwinkel B., Cameron D.A., Camp N.J., Campbell A., Carracedo A., Castelao J.E., Cessna M.H., Chanock S.J., Christiansen H., Collee J.M., Cordina-Duverger E., Czene K., Dork T., Ekici A.B., Engel C., Eriksson M., Fasching P.A., Figueroa J., Flyger H., Forsti A., Gabrielson M., Gago-Dominguez M., Georgoulias V., Gil F., Giles G.G., Glendon G., Gomez Garcia E.B., Grenaker Alnaes G.I., Guenel P., Hadjisavvas A., Haeberle L., Hahnen E., Hall P., Hamann U., Harkness E.F., Hartikainen J.M., Hartman M., He W., Heemskerk-Gerritsen B.A.M., Hillemanns P., Hogervorst F.B.L., Hollestelle A., Ho W.K., Hooning M.J., Howell A., Humphreys K., Idris F., Jakubowska A., Jung A., Kapoor P.M., Kerin M.J., Khusnutdinova E., Kim S.-W., Ko Y.-D., Kosma V.-M., Kristensen V.N., Kyriacou K., Lakeman I.M.M., Lee J.W., Lee M.H., Li J., Lindblom A., Lo W.-Y., Loizidou M.A., Lophatananon A., Lubinski J., MacInnis R.J., Madsen M.J., Mannermaa A., Manoochehri M., Manoukian S., Margolin S., Martinez M.E., Maurer T., Mavroudis D., McLean C., Meindl A., and Mensenkamp A.R.

Abstract

BACKGROUND Genetic testing for breast cancer susceptibility is widely used, but for many genes, evidence of an association with breast cancer is weak, underlying risk estimates are imprecise, and reliable subtype-specific risk estimates are lacking. METHODS We used a panel of 34 putative susceptibility genes to perform sequencing on samples from 60,466 women with breast cancer and 53,461 controls. In separate analyses for protein-truncating variants and rare missense variants in these genes, we estimated odds ratios for breast cancer overall and tumor subtypes. We evaluated missense-variant associations according to domain and classification of pathogenicity. RESULTS Protein-truncating variants in 5 genes (ATM, BRCA1, BRCA2, CHEK2, and PALB2) were associated with a risk of breast cancer overall with a P value of less than 0.0001. Protein-truncating variants in 4 other genes (BARD1, RAD51C, RAD51D, and TP53) were associated with a risk of breast cancer overall with a P value of less than 0.05 and a Bayesian false-discovery probability of less than 0.05. For protein-truncating variants in 19 of the remaining 25 genes, the upper limit of the 95% confidence interval of the odds ratio for breast cancer overall was less than 2.0. For protein-truncating variants in ATM and CHEK2, odds ratios were higher for estrogen receptor (ER)-positive disease than for ER-negative disease; for protein-truncating variants in BARD1, BRCA1, BRCA2, PALB2, RAD51C, and RAD51D, odds ratios were higher for ER-negative disease than for ER-positive disease. Rare missense variants (in aggregate) in ATM, CHEK2, and TP53 were associated with a risk of breast cancer overall with a P value of less than 0.001. For BRCA1, BRCA2, and TP53, missense variants (in aggregate) that would be classified as pathogenic according to standard criteria were associated with a risk of breast cancer overall, with the risk being similar to that of protein-truncating variants. CONCLUSIONS The results of this study define

Published
2021

6. Gene-environment interactions relevant to estrogen and risk of breast cancer: Can gene-environment interactions be detected only among candidate snps from genome-wide association studies?.

Author

Park J.Y., Choi J.-Y., Choi J., Chung S., Song N., Park S.K., Han W., Noh D.-Y., Ahn S.-H., Lee J.W., Kim M.K., Jee S.H., Wen W., Bolla M.K., Wang Q., Dennis J., Michailidou K., Shah M., Conroy D.M., Harrington P.A., Mayes R., Czene K., Hall P., Teras L.R., Patel A.V., Couch F.J., Olson J.E., Sawyer E.J., Roylance R., Bojesen S.E., Flyger H., Lambrechts D., Baten A., Matsuo K., Ito H., Guenel P., Truong T., Keeman R., Schmidt M.K., Wu A.H., Tseng C.-C., Cox A., Cross S.S., Investigators K., Andrulis I.L., Hopper J.L., Southey M.C., Wu P.-E., Shen C.-Y., Fasching P.A., Ekici A.B., Muir K., Lophatananon A., Brenner H., Arndt V., Jones M.E., Swerdlow A.J., Hoppe R., Ko Y.-D., Hartman M., Li J., Mannermaa A., Hartikainen J.M., Benitez J., Gonzalez-Neira A., Haiman C.A., Dork T., Bogdanova N.V., Teo S.H., Taib N.A.M., Fletcher O., Johnson N., Grip M., Winqvist R., Blomqvist C., Nevanlinna H., Lindblom A., Wendt C., Kristensen V.N., Collaborators N.B.C.S., Tollenaar R.A.E.M., Heemskerk-Gerritsen B.A.M., Radice P., Bonanni B., Hamann U., Manoochehri M., Lacey J.V., Martinez M.E., Dunning A.M., Pharoah P.D.P., Easton D.F., Yoo K.-Y., Kang D., Park J.Y., Choi J.-Y., Choi J., Chung S., Song N., Park S.K., Han W., Noh D.-Y., Ahn S.-H., Lee J.W., Kim M.K., Jee S.H., Wen W., Bolla M.K., Wang Q., Dennis J., Michailidou K., Shah M., Conroy D.M., Harrington P.A., Mayes R., Czene K., Hall P., Teras L.R., Patel A.V., Couch F.J., Olson J.E., Sawyer E.J., Roylance R., Bojesen S.E., Flyger H., Lambrechts D., Baten A., Matsuo K., Ito H., Guenel P., Truong T., Keeman R., Schmidt M.K., Wu A.H., Tseng C.-C., Cox A., Cross S.S., Investigators K., Andrulis I.L., Hopper J.L., Southey M.C., Wu P.-E., Shen C.-Y., Fasching P.A., Ekici A.B., Muir K., Lophatananon A., Brenner H., Arndt V., Jones M.E., Swerdlow A.J., Hoppe R., Ko Y.-D., Hartman M., Li J., Mannermaa A., Hartikainen J.M., Benitez J., Gonzalez-Neira A., Haiman C.A., Dork T., Bogdanova N.V., Teo S.H., Taib N.A.M., Fletcher O., Johnson N., Grip M., Winqvist R., Blomqvist C., Nevanlinna H., Lindblom A., Wendt C., Kristensen V.N., Collaborators N.B.C.S., Tollenaar R.A.E.M., Heemskerk-Gerritsen B.A.M., Radice P., Bonanni B., Hamann U., Manoochehri M., Lacey J.V., Martinez M.E., Dunning A.M., Pharoah P.D.P., Easton D.F., Yoo K.-Y., and Kang D.

Abstract

In this study we aim to examine gene-environment interactions (GxEs) between genes involved with estrogen metabolism and environmental factors related to estrogen exposure. GxE analyses were conducted with 1970 Korean breast cancer cases and 2052 controls in the case-control study, the Seoul Breast Cancer Study (SEBCS). A total of 11,555 SNPs from the 137 candidate genes were included in the GxE analyses with eight established environmental factors. A replication test was conducted by using an independent population from the Breast Cancer Association Consortium (BCAC), with 62,485 Europeans and 9047 Asians. The GxE tests were performed by using two-step methods in GxEScan software. Two interactions were found in the SEBCS. The first interaction was shown between rs13035764 of NCOA1 and age at menarche in the GE2df model (p-2df = 1.2 x 10-3 ). The age at menarche before 14 years old was associated with the high risk of breast cancer, and the risk was higher when subjects had homozygous minor allele G. The second GxE was shown between rs851998 near ESR1 and height in the GE2df model (p-2df = 1.1 x 10-4 ). Height taller than 160 cm was associated with a high risk of breast cancer, and the risk increased when the minor allele was added. The findings were not replicated in the BCAC. These results would suggest specificity in Koreans for breast cancer risk.Copyright © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

Published
2021

7. Cancer risks associated with germline PALB2 pathogenic variants: An international study of 524 families.

Author

Hake C., Redman J., Kleibl Z., Kleiblova P., Konstantopoulou I., Kvist A., Laduca H., Lee A.S.G., Lesueur F., Maher E.R., Mannermaa A., Manoukian S., McFarland R., McKinnon W., Meindl A., Metcalfe K., Taib N.A.M., Moilanen J., Nathanson K.L., Neuhausen S., Ng P.S., Nguyen-Dumont T., Nielsen S.M., Obermair F., Offit K., Olopade O.I., Ottini L., Penkert J., Pylkas K., Radice P., Ramus S.J., Rudaitis V., Side L., Silva-Smith R., Silvestri V., Skytte A.-B., Slavin T., Soukupova J., Tondini C., Trainer A.H., Unzeitig G., Usha L., Van Overeem Hansen T., Whitworth J., Wood M., Yip C.H., Yoon S.-Y., Yussuf A., Zogopoulos G., Goldgar D., Hopper J.L., Chenevix-Trench G., Pharoah P., George S.H.L., Balmana J., Houdayer C., James P., El-Haffaf Z., Ehrencrona H., Janatova M., Peterlongo P., Nevanlinna H., Schmutzler R., Teo S.-H., Robson M., Pal T., Couch F., Weitzel J.N., Elliott A., Southey M., Winqvist R., Easton D.F., Foulkes W.D., Antoniou A.C., Tischkowitz M., Yang X., Leslie G., Doroszuk A., Schneider S., Allen J., Decker B., Dunning A.M., Scarth J., Plaskocinska I., Luccarini C., Shah M., Pooley K., Dorling L., Leei A., Adank M.A., Adlard J., Aittomaki K., Andrulis I.L., Ang P., Barwell J., Bernstein J.L., Bobolis K., Borg A., Blomqvist C., Claes K.B.M., Concannon P., Cuggia A., Culver J.O., Damiola F., De Pauw A., Diez O., Dolinsky J.S., Domchek S.M., Engel C., Evans D.G., Fostira F., Garber J., Golmard L., Goode E.L., Gruber S.B., Hahnen E., Heikkinen T., Hurley J.E., Janavicius R., Hake C., Redman J., Kleibl Z., Kleiblova P., Konstantopoulou I., Kvist A., Laduca H., Lee A.S.G., Lesueur F., Maher E.R., Mannermaa A., Manoukian S., McFarland R., McKinnon W., Meindl A., Metcalfe K., Taib N.A.M., Moilanen J., Nathanson K.L., Neuhausen S., Ng P.S., Nguyen-Dumont T., Nielsen S.M., Obermair F., Offit K., Olopade O.I., Ottini L., Penkert J., Pylkas K., Radice P., Ramus S.J., Rudaitis V., Side L., Silva-Smith R., Silvestri V., Skytte A.-B., Slavin T., Soukupova J., Tondini C., Trainer A.H., Unzeitig G., Usha L., Van Overeem Hansen T., Whitworth J., Wood M., Yip C.H., Yoon S.-Y., Yussuf A., Zogopoulos G., Goldgar D., Hopper J.L., Chenevix-Trench G., Pharoah P., George S.H.L., Balmana J., Houdayer C., James P., El-Haffaf Z., Ehrencrona H., Janatova M., Peterlongo P., Nevanlinna H., Schmutzler R., Teo S.-H., Robson M., Pal T., Couch F., Weitzel J.N., Elliott A., Southey M., Winqvist R., Easton D.F., Foulkes W.D., Antoniou A.C., Tischkowitz M., Yang X., Leslie G., Doroszuk A., Schneider S., Allen J., Decker B., Dunning A.M., Scarth J., Plaskocinska I., Luccarini C., Shah M., Pooley K., Dorling L., Leei A., Adank M.A., Adlard J., Aittomaki K., Andrulis I.L., Ang P., Barwell J., Bernstein J.L., Bobolis K., Borg A., Blomqvist C., Claes K.B.M., Concannon P., Cuggia A., Culver J.O., Damiola F., De Pauw A., Diez O., Dolinsky J.S., Domchek S.M., Engel C., Evans D.G., Fostira F., Garber J., Golmard L., Goode E.L., Gruber S.B., Hahnen E., Heikkinen T., Hurley J.E., and Janavicius R.

Abstract

PURPOSE To estimate age-specific relative and absolute cancer risks of breast cancer and to estimate risks of ovarian, pancreatic, male breast, prostate, and colorectal cancers associated with germline PALB2 pathogenic variants (PVs) because these risks have not been extensively characterized. METHODS We analyzed data from 524 families with PALB2 PVs from 21 countries. Complex segregation analysis was used to estimate relative risks (RRs; relative to country-specific population incidences) and absolute risks of cancers. The models allowed for residual familial aggregation of breast and ovarian cancer and were adjusted for the family-specific ascertainment schemes. RESULTS We found associations between PALB2 PVs and risk of female breast cancer (RR, 7.18; 95% CI, 5.82 to 8.85; P = 6.5 x 10-76), ovarian cancer (RR, 2.91; 95% CI, 1.40 to 6.04; P = 4.1 x 10-3), pancreatic cancer (RR, 2.37; 95% CI, 1.24 to 4.50; P = 8.7 x 10-3), and male breast cancer (RR, 7.34; 95% CI, 1.28 to 42.18; P = 2.6 3 1022). There was no evidence for increased risks of prostate or colorectal cancer. The breast cancer RRs declined with age (P for trend = 2.0 x 10-3). After adjusting for family ascertainment, breast cancer risk estimates on the basis of multiple case families were similar to the estimates from families ascertained through population-based studies (P for difference = .41). On the basis of the combined data, the estimated risks to age 80 years were 53% (95% CI, 44% to 63%) for female breast cancer, 5% (95% CI, 2% to 10%) for ovarian cancer, 2%-3% (95% CI females, 1% to 4%; 95% CI males, 2% to 5%) for pancreatic cancer, and 1% (95% CI, 0.2% to 5%) for male breast cancer. CONCLUSION These results confirm PALB2 as a major breast cancer susceptibility gene and establish substantial associations between germline PALB2 PVs and ovarian, pancreatic, and male breast cancers. These findings will facilitate incorporation of PALB2 into risk prediction models and optimize the clinical cancer ri

Published
2020

8. Two truncating variants in FANCC and breast cancer risk

Author

Dork, T., Peterlongo, P., Mannermaa, A., Bolla, M.K., Wang, Q., Dennis, J., Ahearn, T., Andrulis, I.L., Anton-Culver, H., Arndt, V., Aronson, K.J., Augustinsson, A., Freeman, L.E.B., Beckmann, M.W., Beeghly-Fadiel, A., Behrens, S., Bermisheva, M., Blomqvist, C., Bogdanova, N., Bojesen, S.E., Brauch, H., Brenner, H., Burwinkel, B., Canzian, F., Chan, T.L., Chang-Claude, J., Chanock, S.J., Choi, J.Y., Christiansen, H., Clarke, C.L., Couch, F.J., Czene, K., Daly, M.B., dos-Santos-Silva, I., Dwek, M., Eccles, D.M., Ekici, A.B., Eriksson, M., Evans, D.G., Fasching, P.A., Figueroa, J., Flyger, H., Fritschisl, L., Gabrielson, M., Gago-Dominguez, M., Gao, C., Gapstur, S.M., Garcia-Closas, M., Garcia-Saenz, J.A., Gaudet, M.M., Giles, G.G., Goldberg, M.S., Goldgar, D.E., Guenel, P., Haeberle, L., Haiman, C.A., Hakansson, N., Hall, P., Hamann, U., Hartman, M., Hauke, J., Hein, A., Hillemanns, P., Hogervorst, F.B.L., Hooning, M.J., Hopper, J.L., Howell, T., Huo, D.Z., Ito, H., Iwasaki, M., Jakubowska, A., Janni, W., John, E.M., Jung, A., Kaaks, R., Kang, D., Kapoor, P.M., Khusnutdinova, E., Kim, S.W., Kitahara, C.M., Koutros, S., Kraft, P., Kristensen, V.N., Kwon, A., Lambrechts, D., Marchand, L. le, Li, J.M., Lindstrom, S., Linet, M., W.Y. lo, Long, J.R., Lophatananon, A., Lubinski, J., Manoochehri, M., Manoukian, S., Margolin, S., Martinez, E., Matsuo, K., Mavroudis, D., Meindl, A., Menon, U., Milne, R.L., Taib, N.A.M., Muir, K., Mulligan, A.M., Neuhausen, S.L., Nevanlinna, H., Neven, P., Newman, W.G., Offit, K., Olopade, O.I., Olshan, A.F., Olson, J.E., Olsson, H., Park, S.K., Park-Simon, T.W., Peto, J., Plaseska-Karanfilska, D., Pohl-Rescigno, E., Presneau, N., Rack, B., Radice, P., Rashid, M.U., Rennert, G., Rennert, H.S., Romero, A., Ruebner, M., Saloustros, E., Schmidt, M.K., Schmutzler, R.K., Schneider, M.O., Schoemaker, M.J., Scott, C., Shen, C.Y., Shu, X.O., Simard, J., Slager, S., Smichkoska, S., Southey, M.C., Spinelli, J.J., Stone, J., Surowy, H., Swerdlow, A.J., Tamimi, R.M., Tapper, W.J., Teo, S.H., Terry, M.B., Toland, A.E., Tollenaar, R.A.E.M., Torres, D., Torres-Mejia, G., Troester, M.A., Truong, T., Tsugane, S., Untch, M., Vachon, C.M., Ouweland, A.M.W. van den, Veen, E.M. van, Vijai, J., Wendt, C., Wolk, A., Yu, J.C., Zheng, W., Ziogas, A., Ziv, E., Dunning, A.M., Pharoah, P.D.P., Schindler, D., Devilee, P., Easton, D.F., Balleine, R., Baxter, R., Braye, S., Carpenter, J., Dahlstrom, J., Forbes, J., Lee, C.S., Marsh, D., Morey, A., Pathmanathan, N., Scott, R., Simpson, P., Spigelman, A., Wilcken, N., Yip, D., Zeps, N., Borresen-Dale, A.L., Alnaes, G.I.G., Sahlberg, K.K., Ottestad, L., Karesen, R., Schlichting, E., Holmen, M.M., Sauer, T., Haakensen, V., Engebraten, O., Naume, B., Fossa, A., Kiserud, C.E., Reinertsen, K.V., Helland, A., Riis, M., Geisler, J., ABCTB Investigators, NBCS Collaborators, Andrulis, Irene L [0000-0002-4226-6435], Arndt, Volker [0000-0001-9320-8684], Brauch, Hiltrud [0000-0001-7531-2736], Dwek, Miriam [0000-0001-7184-2932], Ekici, Arif B [0000-0001-6099-7066], Fasching, Peter A [0000-0003-4885-8471], Figueroa, Jonine [0000-0002-5100-623X], Hein, Alexander [0000-0003-2601-3398], Ito, Hidemi [0000-0002-8023-4581], Matsuo, Keitaro [0000-0003-1761-6314], Menon, Usha [0000-0003-3708-1732], Milne, Roger L [0000-0001-5764-7268], Muir, Kenneth [0000-0001-6429-988X], Nevanlinna, Heli [0000-0002-0916-2976], Newman, William G [0000-0002-6382-4678], Peto, Julian [0000-0002-1685-8912], Rennert, Gad [0000-0002-8512-068X], Romero, Atocha [0000-0002-1634-7397], Schmidt, Marjanka K [0000-0002-2228-429X], Scott, Christopher [0000-0003-1340-0647], Stone, Jennifer [0000-0001-5077-0124], Truong, Thérèse [0000-0002-2943-6786], Tsugane, Shoichiro [0000-0003-4105-2774], Ziogas, Argyrios [0000-0003-4529-3727], Dunning, Alison M [0000-0001-6651-7166], Pharoah, Paul DP [0000-0001-8494-732X], Devilee, Peter [0000-0002-8023-2009], Easton, Douglas F [0000-0003-2444-3247], Apollo - University of Cambridge Repository, Andrulis, Irene L. [0000-0002-4226-6435], Ekici, Arif B. [0000-0001-6099-7066], Fasching, Peter A. [0000-0003-4885-8471], Milne, Roger L. [0000-0001-5764-7268], Newman, William G. [0000-0002-6382-4678], Schmidt, Marjanka K. [0000-0002-2228-429X], Dunning, Alison M. [0000-0001-6651-7166], Pharoah, Paul D. P. [0000-0001-8494-732X], Easton, Douglas F. [0000-0003-2444-3247], HUS Comprehensive Cancer Center, Clinicum, University Management, Department of Oncology, University of Helsinki, Department of Obstetrics and Gynecology, HUS Gynecology and Obstetrics, Medical Oncology, and Clinical Genetics

Subjects
0301 basic medicine, Oncology, PROTEIN, lcsh:Medicine, 45/47, 0302 clinical medicine, Fanconi anemia, Genotype, lcsh:Science, Sequence Deletion, Multidisciplinary, BRCA1 Protein, Fanconi Anemia Complementation Group C Protein, 1184 Genetics, developmental biology, physiology, BRCA2 Protein, 3. Good health, BIALLELIC MUTATIONS, DNA-REPAIR, Female, 692/499, Medical Genetics, medicine.medical_specialty, PALB2, 3122 Cancers, ABCTB Investigators, Breast Neoplasms, FANCONIS ANEMIA, Article, 692/4028, NBCS Collaborators, 03 medical and health sciences, Breast cancer, SDG 3 - Good Health and Well-being, Internal medicine, medicine, Humans, NONSENSE MUTATION, Genetic Predisposition to Disease, Medicinsk genetik, 45, business.industry, Genetic heterogeneity, lcsh:R, Case-control study, Genetic Variation, Odds ratio, medicine.disease, GENE, Fanconi Anemia, 030104 developmental biology, Risk factors, Case-Control Studies, lcsh:Q, 3111 Biomedicine, business, 030217 neurology & neurosurgery
Abstract

Fanconi anemia (FA) is a genetically heterogeneous disorder with 22 disease-causing genes reported to date. In some FA genes, monoallelic mutations have been found to be associated with breast cancer risk, while the risk associations of others remain unknown. The gene for FA type C, FANCC, has been proposed as a breast cancer susceptibility gene based on epidemiological and sequencing studies. We used the Oncoarray project to genotype two truncating FANCC variants (p.R185X and p.R548X) in 64,760 breast cancer cases and 49,793 controls of European descent. FANCC mutations were observed in 25 cases (14 with p.R185X, 11 with p.R548X) and 26 controls (18 with p.R185X, 8 with p.R548X). There was no evidence of an association with the risk of breast cancer, neither overall (odds ratio 0.77, 95%CI 0.44–1.33, p = 0.4) nor by histology, hormone receptor status, age or family history. We conclude that the breast cancer risk association of these two FANCC variants, if any, is much smaller than for BRCA1, BRCA2 or PALB2 mutations. If this applies to all truncating variants in FANCC it would suggest there are differences between FA genes in their roles on breast cancer risk and demonstrates the merit of large consortia for clarifying risk associations of rare variants.

Published
2019

9. Fine-mapping of the 1p11.2 breast cancer susceptibility locus

Author

Horne, H.N. (Hisani N.), Chung, C.C. (Charles C.), Zhang, H. (Han), Yu, K. (Kai), Prokunina-Olsson, L. (Ludmila), Michailidou, K. (Kyriaki), Bolla, M.K. (Manjeet K.), Wang, Q. (Qing), Dennis, J. (Joe), Hopper, J.L. (John), Southey, M.C. (Melissa), Schmidt, M.K. (Marjanka), Broeks, A. (Annegien), Muir, K.R. (K.), Lophatananon, A. (Artitaya), Fasching, P.A. (Peter), Beckmann, M.W. (Matthias), Fletcher, O. (Olivia), Johnson, N. (Nichola), Sawyer, E.J. (Elinor), Tomlinson, I.P. (Ian), Burwinkel, B. (Barbara), Marme, F. (Frederik), Guénel, P. (Pascal), Truong, T. (Thérèse), Bojesen, S.E. (Stig), Flyger, H. (Henrik), Benítez, J. (Javier), González-Neira, A. (Anna), Anton-Culver, H. (Hoda), Neuhausen, S.L. (Susan), Brenner, H. (Hermann), Arndt, V. (Volker), Meindl, A. (Alfons), Schmutzler, R.K. (Rita), Brauch, H. (Hiltrud), Hamann, U. (Ute), Nevanlinna, H. (Heli), Khan, S. (Sofia), Matsuo, K. (Keitaro), Iwata, H. (Hiroji), Dörk, T. (Thilo), Bogdanova, N.V. (Natalia), Lindblom, A. (Annika), Margolin, S. (Sara), Mannermaa, A. (Arto), Kosma, V-M. (Veli-Matti), Chenevix-Trench, G. (Georgia), Wu, A.H. (Anna), Ven Den Berg, D. (David), Smeets, A. (Ann), Zhao, H. (Hui), Chang-Claude, J. (Jenny), Rudolph, A. (Anja), Radice, P. (Paolo), Barile, M. (Monica), Couch, F.J. (Fergus), Vachon, C. (Celine), Giles, G.G. (Graham G.), Milne, R.L. (Roger), Haiman, C.A. (Christopher A.), Le Marchand, L. (Loic), Goldberg, M.S. (Mark), Teo, S.-H. (Soo-Hwang), Taib, N.A.M. (Nur Aishah Mohd), Kristensen, V. (Vessela), Borresen-Dale, A.-L. (Anne-Lise), Zheng, W. (Wei), Shrubsole, M. (Martha), Winqvist, R. (Robert), Jukkola-Vuorinen, A. (Arja), Andrulis, I.L. (Irene), Knight, J.A. (Julia), Devilee, P. (Peter), Seynaeve, C.M. (Caroline), García-Closas, M. (Montserrat), Czene, K. (Kamila), Darabi, H. (Hatef), Hollestelle, A. (Antoinette), Martens, J.W.M. (John), Li, J. (Jingmei), Lu, W. (Wei), Shu, X.-O. (Xiao-Ou), Cox, A. (Angela), Cross, S.S. (Simon), Blot, W.J. (William), Cai, Q. (Qiuyin), Shah, M. (Mitul), Luccarini, C. (Craig), Baynes, C. (Caroline), harrington, P. (Patricia), Kang, D. (Daehee), Choi, J.-Y. (Ji-Yeob), Hartman, J.M. (Joost), Chia, K.S. (Kee Seng), Kabisch, M. (Maria), Torres, D. (Diana), Jakubowska, A. (Anna), Lubinski, J. (Jan), Sangrajrang, S. (Suleeporn), Brennan, P. (Paul), Slager, S. (Susan), Yannoukakos, D. (Drakoulis), Shen, C.-Y. (Chen-Yang), Hou, M.-F. (Ming-Feng), Swerdlow, A.J. (Anthony ), Orr, N. (Nick), Simard, J. (Jacques), Hall, P. (Per), Pharoah, P.D.P. (Paul), Easton, D.F. (Douglas F.), Chanock, S.J. (Stephen J.), Dunning, A.M. (Alison), Figueroa, J.D. (Jonine), Horne, H.N. (Hisani N.), Chung, C.C. (Charles C.), Zhang, H. (Han), Yu, K. (Kai), Prokunina-Olsson, L. (Ludmila), Michailidou, K. (Kyriaki), Bolla, M.K. (Manjeet K.), Wang, Q. (Qing), Dennis, J. (Joe), Hopper, J.L. (John), Southey, M.C. (Melissa), Schmidt, M.K. (Marjanka), Broeks, A. (Annegien), Muir, K.R. (K.), Lophatananon, A. (Artitaya), Fasching, P.A. (Peter), Beckmann, M.W. (Matthias), Fletcher, O. (Olivia), Johnson, N. (Nichola), Sawyer, E.J. (Elinor), Tomlinson, I.P. (Ian), Burwinkel, B. (Barbara), Marme, F. (Frederik), Guénel, P. (Pascal), Truong, T. (Thérèse), Bojesen, S.E. (Stig), Flyger, H. (Henrik), Benítez, J. (Javier), González-Neira, A. (Anna), Anton-Culver, H. (Hoda), Neuhausen, S.L. (Susan), Brenner, H. (Hermann), Arndt, V. (Volker), Meindl, A. (Alfons), Schmutzler, R.K. (Rita), Brauch, H. (Hiltrud), Hamann, U. (Ute), Nevanlinna, H. (Heli), Khan, S. (Sofia), Matsuo, K. (Keitaro), Iwata, H. (Hiroji), Dörk, T. (Thilo), Bogdanova, N.V. (Natalia), Lindblom, A. (Annika), Margolin, S. (Sara), Mannermaa, A. (Arto), Kosma, V-M. (Veli-Matti), Chenevix-Trench, G. (Georgia), Wu, A.H. (Anna), Ven Den Berg, D. (David), Smeets, A. (Ann), Zhao, H. (Hui), Chang-Claude, J. (Jenny), Rudolph, A. (Anja), Radice, P. (Paolo), Barile, M. (Monica), Couch, F.J. (Fergus), Vachon, C. (Celine), Giles, G.G. (Graham G.), Milne, R.L. (Roger), Haiman, C.A. (Christopher A.), Le Marchand, L. (Loic), Goldberg, M.S. (Mark), Teo, S.-H. (Soo-Hwang), Taib, N.A.M. (Nur Aishah Mohd), Kristensen, V. (Vessela), Borresen-Dale, A.-L. (Anne-Lise), Zheng, W. (Wei), Shrubsole, M. (Martha), Winqvist, R. (Robert), Jukkola-Vuorinen, A. (Arja), Andrulis, I.L. (Irene), Knight, J.A. (Julia), Devilee, P. (Peter), Seynaeve, C.M. (Caroline), García-Closas, M. (Montserrat), Czene, K. (Kamila), Darabi, H. (Hatef), Hollestelle, A. (Antoinette), Martens, J.W.M. (John), Li, J. (Jingmei), Lu, W. (Wei), Shu, X.-O. (Xiao-Ou), Cox, A. (Angela), Cross, S.S. (Simon), Blot, W.J. (William), Cai, Q. (Qiuyin), Shah, M. (Mitul), Luccarini, C. (Craig), Baynes, C. (Caroline), harrington, P. (Patricia), Kang, D. (Daehee), Choi, J.-Y. (Ji-Yeob), Hartman, J.M. (Joost), Chia, K.S. (Kee Seng), Kabisch, M. (Maria), Torres, D. (Diana), Jakubowska, A. (Anna), Lubinski, J. (Jan), Sangrajrang, S. (Suleeporn), Brennan, P. (Paul), Slager, S. (Susan), Yannoukakos, D. (Drakoulis), Shen, C.-Y. (Chen-Yang), Hou, M.-F. (Ming-Feng), Swerdlow, A.J. (Anthony ), Orr, N. (Nick), Simard, J. (Jacques), Hall, P. (Per), Pharoah, P.D.P. (Paul), Easton, D.F. (Douglas F.), Chanock, S.J. (Stephen J.), Dunning, A.M. (Alison), and Figueroa, J.D. (Jonine)

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). Perallelic 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 silic

Published
2016
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10. PassivelyQ-switched flashlamp pumped Nd:YAG laser using liquid graphene oxide as saturable absorber

Author

Adnan, N.N., Bidin, N., Taib, N.A.M., Haris, H., Fakaruddin, M., Hashim, A.M., Krishnan, G., Harun, S.W., Adnan, N.N., Bidin, N., Taib, N.A.M., Haris, H., Fakaruddin, M., Hashim, A.M., Krishnan, G., and Harun, S.W.

Abstract

The performance of passively Q-switched Nd:YAG laser operating at 1060 nm is demonstrated using liquid graphene oxide (GO) composite solution as saturable absorber for the first time. The Q-switched Nd:YAG laser is pumped by a xenon flashlamp. The GO was prepared using the simplified Hummer's method and then mixed with polyethylene oxide to form a composite solution. The Q-switched pulsed laser operates at wavelength of 1064.5 nm with a threshold pump energy of 33.64 J. The maximum output Q-switched laser energy of 41.6 mJ achieved at the maximum pump energy of 81 J. The corresponding pulse width is 98.67 ns.

Published
2016

11. Assessment of variation in immunosuppressive pathway genes reveals TGFBR2 to be associated with prognosis of estrogen receptor-negative breast cancer after chemotherapy

Author

Lei, J. (Jieping), Rudolph, A. (Anja), Moysich, K.B. (Kirsten), Rafiq, M. (Meena), Behrens, T.W. (Timothy), Goode, E.L. (Ellen), Pharoah, P.D.P. (Paul), Seibold, P. (Petra), Fasching, P.A. (Peter), Andrulis, I.L. (Irene), Kristensen, V. (Vessela), Couch, F.J. (Fergus), Hamann, U. (Ute), Hooning, M.J. (Maartje), Nevanlinna, H. (Heli), Eilber, U. (Ursula), Bolla, M.K. (Manjeet), Dennis, J. (Joe), Wang, Q. (Qing), Lindblom, A. (Annika), Mannermaa, A. (Arto), Lambrechts, D. (Diether), García-Closas, M. (Montserrat), Hall, P. (Per), Chenevix-Trench, G. (Georgia), Shah, M. (Mitul), Luben, R.N. (Robert), Haeberle, L. (Lothar), Ekici, A.B. (Arif), Beckmann, M.W. (Matthias), Knight, J.A. (Julia), Glendon, G. (Gord), Tchatchou, S. (Sandrine), Alnæs, G.G. (Grethe), Borresen-Dale, A.-L. (Anne-Lise), Nord, S. (Silje), Olson, J.E. (Janet), Hallberg, B. (Boubou), Vachon, C. (Celine), Torres, D. (Diana), Ulmer, H.U. (Hans), Rud̈iger, T. (Thomas), Jager, A. (Agnes), Deurzen, C.H.M. (Carolien) van, Tilanus-Linthorst, M.M.A. (Madeleine), Muranen, T.A. (Taru), Aittomäki, K. (Kristiina), Blomqvist, C. (Carl), Margolin, S. (Sara), Kosma, V-M. (Veli-Matti), Hartikainen, J.M. (J.), Kataja, V. (Vesa), Hatse, S. (Sigrid), Wildiers, H. (Hans), Smeets, A. (Ann), Figueroa, J.D. (Jonine), Chanock, S.J. (Stephen), Lissowska, J. (Jolanta), Li, J. (Jingmei), Humphreys, M.K. (Manjeet), Phillips, K.-A. (Kelly-Anne), Linn, S.C. (Sabine), Cornelissen, S. (Sten), van den Broek, S.A.J. (Sandra Alexandra), Kang, D. (Daehee), Choi, J.-Y. (J.), Park, S.K. (Sue), Yoo, K.Y., Hsiung, C.-N. (Chia-Ni), Wu, P.-E. (Pei-Ei), Hou, M.-F. (Ming-Feng), Shen, C-Y. (Chen-Yang), Teo, S.-H. (Soo-Hwang), Taib, N.A.M. (Nur Aishah Mohd), Yip, C.-H. (Cheng-Har), Ho, G.F. (Gwo Fuang), Matsuo, K. (Keitaro), Ito, H. (Hidemi), Iwata, H. (Hisato), Tajima, K. (Kazuo), Dunning, A.M. (Alison), Benítez, J. (Javier), Czene, K. (Kamila), Sucheston, L. (Lara), Maishman, T. (Tom), Tapper, W. (William), Eccles, D. (Diana), Easton, D.F. (Douglas), Schmidt, M.K. (Marjanka), Chang-Claude, J. (Jenny), Lei, J. (Jieping), Rudolph, A. (Anja), Moysich, K.B. (Kirsten), Rafiq, M. (Meena), Behrens, T.W. (Timothy), Goode, E.L. (Ellen), Pharoah, P.D.P. (Paul), Seibold, P. (Petra), Fasching, P.A. (Peter), Andrulis, I.L. (Irene), Kristensen, V. (Vessela), Couch, F.J. (Fergus), Hamann, U. (Ute), Hooning, M.J. (Maartje), Nevanlinna, H. (Heli), Eilber, U. (Ursula), Bolla, M.K. (Manjeet), Dennis, J. (Joe), Wang, Q. (Qing), Lindblom, A. (Annika), Mannermaa, A. (Arto), Lambrechts, D. (Diether), García-Closas, M. (Montserrat), Hall, P. (Per), Chenevix-Trench, G. (Georgia), Shah, M. (Mitul), Luben, R.N. (Robert), Haeberle, L. (Lothar), Ekici, A.B. (Arif), Beckmann, M.W. (Matthias), Knight, J.A. (Julia), Glendon, G. (Gord), Tchatchou, S. (Sandrine), Alnæs, G.G. (Grethe), Borresen-Dale, A.-L. (Anne-Lise), Nord, S. (Silje), Olson, J.E. (Janet), Hallberg, B. (Boubou), Vachon, C. (Celine), Torres, D. (Diana), Ulmer, H.U. (Hans), Rud̈iger, T. (Thomas), Jager, A. (Agnes), Deurzen, C.H.M. (Carolien) van, Tilanus-Linthorst, M.M.A. (Madeleine), Muranen, T.A. (Taru), Aittomäki, K. (Kristiina), Blomqvist, C. (Carl), Margolin, S. (Sara), Kosma, V-M. (Veli-Matti), Hartikainen, J.M. (J.), Kataja, V. (Vesa), Hatse, S. (Sigrid), Wildiers, H. (Hans), Smeets, A. (Ann), Figueroa, J.D. (Jonine), Chanock, S.J. (Stephen), Lissowska, J. (Jolanta), Li, J. (Jingmei), Humphreys, M.K. (Manjeet), Phillips, K.-A. (Kelly-Anne), Linn, S.C. (Sabine), Cornelissen, S. (Sten), van den Broek, S.A.J. (Sandra Alexandra), Kang, D. (Daehee), Choi, J.-Y. (J.), Park, S.K. (Sue), Yoo, K.Y., Hsiung, C.-N. (Chia-Ni), Wu, P.-E. (Pei-Ei), Hou, M.-F. (Ming-Feng), Shen, C-Y. (Chen-Yang), Teo, S.-H. (Soo-Hwang), Taib, N.A.M. (Nur Aishah Mohd), Yip, C.-H. (Cheng-Har), Ho, G.F. (Gwo Fuang), Matsuo, K. (Keitaro), Ito, H. (Hidemi), Iwata, H. (Hisato), Tajima, K. (Kazuo), Dunning, A.M. (Alison), Benítez, J. (Javier), Czene, K. (Kamila), Sucheston, L. (Lara), Maishman, T. (Tom), Tapper, W. (William), Eccles, D. (Diana), Easton, D.F. (Douglas), Schmidt, M.K. (Marjanka), and Chang-Claude, J. (Jenny)

Abstract

Introduction: Tumor lymphocyte infiltration is associated with clinical response to chemotherapy in estrogen receptor (ER) negative breast cancer. To identify variants in immunosuppressive pathway genes associated with prognosis after adjuvant chemotherapy for ER-negative patients, we studied stage I-III invasive breast cancer patients of European ancestry, including 9,334 ER-positive (3,151 treated with chemotherapy) and 2,334 ER-negative patients (1,499 treated with chemotherapy). Methods: We pooled data from sixteen studies from the Breast Cancer Association Consortium (BCAC), and employed two independent studies for replications. Overall 3,610 single nucleotide polymorphisms (SNPs) in 133 genes were genotyped as part of the Collaborative Oncological Gene-environment Study, in which phenotype and clinical data were collected and harmonized. Multivariable Cox proportional hazard regression was used to assess genetic associations with overall survival (OS) and breast c

Published
2015
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12. Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer

Author

Michailidou, K. (Kyriaki), Beesley, J. (Jonathan), Lindstrom, S. (Stephen), Canisius, S. (Sander), Dennis, J. (Joe), Lush, M. (Michael), Maranian, M. (Melanie), Bolla, M.K. (Manjeet), Wang, Q. (Qing), Shah, M. (Mitul), Perkins, B. (Barbara), Czene, K. (Kamila), Eriksson, M. (Mikael), Darabi, H. (Hatef), Brand, J.S. (Judith S.), Bojesen, S.E. (Stig), Nordestgaard, B.G. (Børge), Flyger, H. (Henrik), Nielsen, S.F. (Sune), Rahman, N. (Nazneen), Turnbull, C. (Clare), Fletcher, O. (Olivia), Peto, J. (Julian), Gibson, L.J. (Lorna), Santos Silva, I. (Isabel) dos, Chang-Claude, J. (Jenny), Flesch-Janys, D. (Dieter), Rudolph, A. (Anja), Eilber, U. (Ursula), Behrens, T.W. (Timothy), Nevanlinna, H. (Heli), Muranen, T.A. (Taru), Aittomäki, K. (Kristiina), Blomqvist, C. (Carl), Khan, S. (Sofia), Aaltonen, K. (Kirsimari), Ahsan, H. (Habibul), Kibriya, M.G. (Muhammad), Whittemore, A.S. (Alice S.), John, E.M. (Esther M.), Malone, K.E. (Kathleen E.), Gammon, M.D. (Marilie), Santella, R.M. (Regina M.), Ursin, G. (Giske), Makalic, E. (Enes), Schmidt, D.F. (Daniel), Casey, G. (Graham), Hunter, D.J. (David J.), Gapstur, S.M. (Susan M.), Gaudet, M.M. (Mia), Diver, W.R. (Ryan), Haiman, C.A. (Christopher A.), Schumacher, F.R. (Fredrick), Henderson, B.E. (Brian), Le Marchand, L. (Loic), Berg, C.D. (Christine), Chanock, S.J. (Stephen), Figueroa, J.D. (Jonine), Hoover, R.N. (Robert N.), Lambrechts, D. (Diether), Neven, P. (Patrick), Wildiers, H. (Hans), Limbergen, E. (Erik) van, Schmidt, M.K. (Marjanka), Broeks, A. (Annegien), Verhoef, S., Cornelissen, S. (Sten), Couch, F.J. (Fergus), Olson, J.E. (Janet), Hallberg, B. (Boubou), Vachon, C. (Celine), Waisfisz, Q. (Quinten), Meijers-Heijboer, E.J. (Hanne), Adank, M.A. (Muriel), Luijt, R.B. (Rob) van der, Li, J. (Jingmei), Liu, J. (Jianjun), Humphreys, M.K. (Manjeet), Kang, D. (Daehee), Choi, J.-Y. (Ji-Yeob), Park, S.K. (Sue K.), Yoo, K.Y., Matsuo, K. (Keitaro), Ito, H. (Hidemi), Iwata, H. (Hiroji), Tajima, K. (Kazuo), Guénel, P. (Pascal), Truong, T. (Thérèse), Mulot, C. (Claire), Sanchez, M. (Marie), Burwinkel, B. (Barbara), Marme, F. (Federick), Surowy, H. (Harald), Sohn, C. (Christof), Wu, A.H. (Anna H), Tseng, C.-C. (Chiu-chen), Van Den Berg, D. (David), Stram, D.O. (Daniel O.), González-Neira, A. (Anna), Benítez, J. (Javier), Zamora, M.P. (Pilar), Perez, J.I.A. (Jose Ignacio Arias), Shu, X.-O. (Xiao-Ou), Lu, W. (Wei), Gao, Y. (Ying), Cai, H. (Hui), Cox, A. (Angela), Cross, S.S. (Simon), Reed, M.W.R. (Malcolm), Andrulis, I.L. (Irene), Knight, J.A. (Julia), Glendon, G. (Gord), Mulligan, A.-M. (Anna-Marie), Sawyer, E.J. (Elinor), Tomlinson, I.P. (Ian), Kerin, M. (Michael), Miller, N. (Nicola), Lindblom, A. (Annika), Margolin, S. (Sara), Teo, S.H. (Soo Hwang), Yip, C.H. (Cheng Har), Taib, N.A.M. (Nur Aishah Mohd), Tan, G.-H. (Gie-Hooi), Hooning, M.J. (Maartje), Hollestelle, A. (Antoinette), Martens, J.W.M. (John), Collée, J.M. (Margriet), Blot, W.J. (William), Signorello, L.B. (Lisa B.), Cai, Q. (Qiuyin), Hopper, J. (John), Southey, M.C. (Melissa), Tsimiklis, H. (Helen), Apicella, C. (Carmel), Shen, C-Y. (Chen-Yang), Hsiung, C.-N. (Chia-Ni), Wu, P.-E. (Pei-Ei), Hou, M.-F. (Ming-Feng), Kristensen, V. (Vessela), Nord, S. (Silje), Alnæs, G.G. (Grethe), Giles, G.G. (Graham G.), Milne, R.L. (Roger), McLean, C.A. (Catriona Ann), Canzian, F. (Federico), Trichopoulos, D. (Dimitrios), Peeters, P.H.M., Lund, E. (Eiliv), Sund, R. (Reijo), Khaw, K.T., Gunter, M.J. (Marc J.), Palli, D. (Domenico), Mortensen, L.M. (Lotte Maxild), Dossus, L. (Laure), Huerta, J.-M. (Jose-Maria), Meindl, A. (Alfons), Schmutzler, R.K. (Rita), Sutter, C. (Christian), Yang, R. (Rongxi), Muir, K. (Kenneth), Lophatananon, A. (Artitaya), Stewart-Brown, S. (Sarah), Siriwanarangsan, P. (Pornthep), Hartman, J.M. (Joost), Miao, X., Chia, K.S. (Kee Seng), Chan, C.W. (Ching Wan), Fasching, P.A. (Peter), Hein, R. (Rebecca), Beckmann, M.W. (Matthias), Haeberle, L. (Lothar), Brenner, H. (Hermann), Dieffenbach, A.K. (Aida Karina), Arndt, V. (Volker), Stegmaier, C. (Christa), Ashworth, A. (Alan), Orr, N. (Nick), Schoemaker, M. (Minouk), Swerdlow, A.J. (Anthony ), Brinton, L.A. (Louise), García-Closas, M. (Montserrat), Zheng, W. (Wei), Halverson, S.L. (Sandra L.), Shrubsole, M. (Martha), Long, J. (Jirong), Goldberg, M.S. (Mark), Labrèche, F. (France), Dumont, M. (Martine), Winqvist, R. (Robert), Pykäs, K. (Katri), Jukkola-Vuorinen, A. (Arja), Grip, M. (Mervi), Brauch, H. (Hiltrud), Hamann, U. (Ute), Brüning, T. (Thomas), Radice, P. (Paolo), Peterlongo, P. (Paolo), Manoukian, S. (Siranoush), Bernard, L. (Loris), Bogdanova, N.V. (Natalia), Dörk, T. (Thilo), Mannermaa, A. (Arto), Kataja, V. (Vesa), Kosma, V-M. (Veli-Matti), Hartikainen, J.M. (J.), Devilee, P. (Peter), Tollenaar, R.A.E.M. (Rob), Seynaeve, C.M. (Caroline), Asperen, C.J. (Christi) van, Jakubowska, A. (Anna), Lubinski, J. (Jan), Jaworska, K. (Katarzyna), Huzarski, T. (Tomasz), Sangrajrang, S. (Suleeporn), Gaborieau, V. (Valerie), Brennan, P. (Paul), McKay, J.D. (James), Slager, S. (Susan), Toland, A.E. (Amanda), Ambrosone, C.B. (Christine), Yannoukakos, D. (Drakoulis), Kabisch, M. (Maria), Torres, D. (Diana), Neuhausen, S.L. (Susan), Anton-Culver, H. (Hoda), Luccarini, C. (Craig), Baynes, C. (Caroline), Ahmed, S. (Shahana), Healey, S. (Sue), Tessier, D.C. (Daniel C.), Vincent, D. (Daniel), Bacot, F. (Francois), Pita, G. (Guillermo), Alonso, M.R. (Rosario), Álvarez, N. (Nuria), Herrero, D. (Daniel), Simard, J. (Jacques), Pharoah, P.P.D.P. (Paul P.D.P.), Kraft, P. (Peter), Dunning, A.M. (Alison), Chenevix-Trench, G. (Georgia), Hall, P. (Per), Easton, D.F. (Douglas), Michailidou, K. (Kyriaki), Beesley, J. (Jonathan), Lindstrom, S. (Stephen), Canisius, S. (Sander), Dennis, J. (Joe), Lush, M. (Michael), Maranian, M. (Melanie), Bolla, M.K. (Manjeet), Wang, Q. (Qing), Shah, M. (Mitul), Perkins, B. (Barbara), Czene, K. (Kamila), Eriksson, M. (Mikael), Darabi, H. (Hatef), Brand, J.S. (Judith S.), Bojesen, S.E. (Stig), Nordestgaard, B.G. (Børge), Flyger, H. (Henrik), Nielsen, S.F. (Sune), Rahman, N. (Nazneen), Turnbull, C. (Clare), Fletcher, O. (Olivia), Peto, J. (Julian), Gibson, L.J. (Lorna), Santos Silva, I. (Isabel) dos, Chang-Claude, J. (Jenny), Flesch-Janys, D. (Dieter), Rudolph, A. (Anja), Eilber, U. (Ursula), Behrens, T.W. (Timothy), Nevanlinna, H. (Heli), Muranen, T.A. (Taru), Aittomäki, K. (Kristiina), Blomqvist, C. (Carl), Khan, S. (Sofia), Aaltonen, K. (Kirsimari), Ahsan, H. (Habibul), Kibriya, M.G. (Muhammad), Whittemore, A.S. (Alice S.), John, E.M. (Esther M.), Malone, K.E. (Kathleen E.), Gammon, M.D. (Marilie), Santella, R.M. (Regina M.), Ursin, G. (Giske), Makalic, E. (Enes), Schmidt, D.F. (Daniel), Casey, G. (Graham), Hunter, D.J. (David J.), Gapstur, S.M. (Susan M.), Gaudet, M.M. (Mia), Diver, W.R. (Ryan), Haiman, C.A. (Christopher A.), Schumacher, F.R. (Fredrick), Henderson, B.E. (Brian), Le Marchand, L. (Loic), Berg, C.D. (Christine), Chanock, S.J. (Stephen), Figueroa, J.D. (Jonine), Hoover, R.N. (Robert N.), Lambrechts, D. (Diether), Neven, P. (Patrick), Wildiers, H. (Hans), Limbergen, E. (Erik) van, Schmidt, M.K. (Marjanka), Broeks, A. (Annegien), Verhoef, S., Cornelissen, S. (Sten), Couch, F.J. (Fergus), Olson, J.E. (Janet), Hallberg, B. (Boubou), Vachon, C. (Celine), Waisfisz, Q. (Quinten), Meijers-Heijboer, E.J. (Hanne), Adank, M.A. (Muriel), Luijt, R.B. (Rob) van der, Li, J. (Jingmei), Liu, J. (Jianjun), Humphreys, M.K. (Manjeet), Kang, D. (Daehee), Choi, J.-Y. (Ji-Yeob), Park, S.K. (Sue K.), Yoo, K.Y., Matsuo, K. (Keitaro), Ito, H. (Hidemi), Iwata, H. (Hiroji), Tajima, K. (Kazuo), Guénel, P. (Pascal), Truong, T. (Thérèse), Mulot, C. (Claire), Sanchez, M. (Marie), Burwinkel, B. (Barbara), Marme, F. (Federick), Surowy, H. (Harald), Sohn, C. (Christof), Wu, A.H. (Anna H), Tseng, C.-C. (Chiu-chen), Van Den Berg, D. (David), Stram, D.O. (Daniel O.), González-Neira, A. (Anna), Benítez, J. (Javier), Zamora, M.P. (Pilar), Perez, J.I.A. (Jose Ignacio Arias), Shu, X.-O. (Xiao-Ou), Lu, W. (Wei), Gao, Y. (Ying), Cai, H. (Hui), Cox, A. (Angela), Cross, S.S. (Simon), Reed, M.W.R. (Malcolm), Andrulis, I.L. (Irene), Knight, J.A. (Julia), Glendon, G. (Gord), Mulligan, A.-M. (Anna-Marie), Sawyer, E.J. (Elinor), Tomlinson, I.P. (Ian), Kerin, M. (Michael), Miller, N. (Nicola), Lindblom, A. (Annika), Margolin, S. (Sara), Teo, S.H. (Soo Hwang), Yip, C.H. (Cheng Har), Taib, N.A.M. (Nur Aishah Mohd), Tan, G.-H. (Gie-Hooi), Hooning, M.J. (Maartje), Hollestelle, A. (Antoinette), Martens, J.W.M. (John), Collée, J.M. (Margriet), Blot, W.J. (William), Signorello, L.B. (Lisa B.), Cai, Q. (Qiuyin), Hopper, J. (John), Southey, M.C. (Melissa), Tsimiklis, H. (Helen), Apicella, C. (Carmel), Shen, C-Y. (Chen-Yang), Hsiung, C.-N. (Chia-Ni), Wu, P.-E. (Pei-Ei), Hou, M.-F. (Ming-Feng), Kristensen, V. (Vessela), Nord, S. (Silje), Alnæs, G.G. (Grethe), Giles, G.G. (Graham G.), Milne, R.L. (Roger), McLean, C.A. (Catriona Ann), Canzian, F. (Federico), Trichopoulos, D. (Dimitrios), Peeters, P.H.M., Lund, E. (Eiliv), Sund, R. (Reijo), Khaw, K.T., Gunter, M.J. (Marc J.), Palli, D. (Domenico), Mortensen, L.M. (Lotte Maxild), Dossus, L. (Laure), Huerta, J.-M. (Jose-Maria), Meindl, A. (Alfons), Schmutzler, R.K. (Rita), Sutter, C. (Christian), Yang, R. (Rongxi), Muir, K. (Kenneth), Lophatananon, A. (Artitaya), Stewart-Brown, S. (Sarah), Siriwanarangsan, P. (Pornthep), Hartman, J.M. (Joost), Miao, X., Chia, K.S. (Kee Seng), Chan, C.W. (Ching Wan), Fasching, P.A. (Peter), Hein, R. (Rebecca), Beckmann, M.W. (Matthias), Haeberle, L. (Lothar), Brenner, H. (Hermann), Dieffenbach, A.K. (Aida Karina), Arndt, V. (Volker), Stegmaier, C. (Christa), Ashworth, A. (Alan), Orr, N. (Nick), Schoemaker, M. (Minouk), Swerdlow, A.J. (Anthony ), Brinton, L.A. (Louise), García-Closas, M. (Montserrat), Zheng, W. (Wei), Halverson, S.L. (Sandra L.), Shrubsole, M. (Martha), Long, J. (Jirong), Goldberg, M.S. (Mark), Labrèche, F. (France), Dumont, M. (Martine), Winqvist, R. (Robert), Pykäs, K. (Katri), Jukkola-Vuorinen, A. (Arja), Grip, M. (Mervi), Brauch, H. (Hiltrud), Hamann, U. (Ute), Brüning, T. (Thomas), Radice, P. (Paolo), Peterlongo, P. (Paolo), Manoukian, S. (Siranoush), Bernard, L. (Loris), Bogdanova, N.V. (Natalia), Dörk, T. (Thilo), Mannermaa, A. (Arto), Kataja, V. (Vesa), Kosma, V-M. (Veli-Matti), Hartikainen, J.M. (J.), Devilee, P. (Peter), Tollenaar, R.A.E.M. (Rob), Seynaeve, C.M. (Caroline), Asperen, C.J. (Christi) van, Jakubowska, A. (Anna), Lubinski, J. (Jan), Jaworska, K. (Katarzyna), Huzarski, T. (Tomasz), Sangrajrang, S. (Suleeporn), Gaborieau, V. (Valerie), Brennan, P. (Paul), McKay, J.D. (James), Slager, S. (Susan), Toland, A.E. (Amanda), Ambrosone, C.B. (Christine), Yannoukakos, D. (Drakoulis), Kabisch, M. (Maria), Torres, D. (Diana), Neuhausen, S.L. (Susan), Anton-Culver, H. (Hoda), Luccarini, C. (Craig), Baynes, C. (Caroline), Ahmed, S. (Shahana), Healey, S. (Sue), Tessier, D.C. (Daniel C.), Vincent, D. (Daniel), Bacot, F. (Francois), Pita, G. (Guillermo), Alonso, M.R. (Rosario), Álvarez, N. (Nuria), Herrero, D. (Daniel), Simard, J. (Jacques), Pharoah, P.P.D.P. (Paul P.D.P.), Kraft, P. (Peter), Dunning, A.M. (Alison), Chenevix-Trench, G. (Georgia), Hall, P. (Per), and Easton, D.F. (Douglas)

Abstract

Genome-wide association studies (GWAS) and large-scale replication studies have identified common variants in 79 loci associated with breast cancer, explaining ∼14% of the familial risk of the disease. To identify new susceptibility loci, we performed a meta-analysis of 11 GWAS, comprising 15,748 breast cancer cases and 18,084 controls together with 46,785 cases and 42,892 controls from 41 studies genotyped on a 211,155-marker custom array (iCOGS). Analyses were restricted to women of European ancestry. We generated genotypes for more than 11 million SNPs by imputation using the 1000 Genomes Project reference panel, and we identified 15 new loci associated with breast cancer at P < 5 × 10 â '8. Combining association analysis with ChIP-seq chromatin binding data in mammary cell lines and ChIA-PET chromatin interaction data from ENCODE, we identified likely target genes in two regions: SETBP1 at 18q12.3 and RNF115 and PDZK1 at 1q21.1. One association appears to be driven by an amino acid substitution encoded in EXO1.

Published
2015
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13. Fine-scale mapping of the 4q24 locus identifies & pr two Independent loci associated with breast cancer risk

Author

Guo, X. (Xingyi), Long, J. (Jirong), Zeng, C. (Chenjie), Michailidou, K. (Kyriaki), Ghoussaini, M. (Maya), Bolla, M.K. (Manjeet), Wang, Q. (Qing), Milne, R.L. (Roger L.), Shu, X.-O. (Xiao-Ou), Cai, Q. (Qiuyin), Beesley, J. (Jonathan), Kar, S. (Siddhartha), Andrulis, I.L. (Irene), Anton-Culver, H. (Hoda), Arndt, V. (Volker), Beckmann, M.W. (Matthias), Beeghly-Fadiel, A. (Alicia), Benítez, J. (Javier), Blot, W.J. (William), Bogdanova, N.V. (Natalia), Bojesen, S.E. (Stig), Brauch, H. (Hiltrud), Brenner, H. (Hermann), Brinton, L.A. (Louise), Broekss, A. (Annegien), Brüning, T. (Thomas), Burwinkel, B. (Barbara), Cai, H. (Hui), Canisius, S. (Sander), Chang-Claude, J. (Jenny), Choi, J.-Y. (J.), Couch, F.J. (Fergus), Cox, A. (Angela), Cross, S.S. (Simon), Czene, K. (Kamila), Darabi, H. (Hatef), Devilee, P. (Peter), Droit, A. (Arnaud), Dörk, T. (Thilo), Fasching, P.A. (Peter), Fletcher, O. (Olivia), Flyger, H. (Henrik), Fostira, F. (Florentia), Gaborieau, V. (Valerie), García-Closas, M. (Montserrat), Giles, G.G. (Graham G.), Grip, M. (Mervi), Guénel, P. (Pascal), Haiman, C.A. (Christopher A.), Hamann, U. (Ute), Hartman, J.M. (Joost), Hollestelle, A. (Antoinette), Hopper, J.L. (John L.), Hsiung, C.-N. (Chia-Ni), Ito, H. (Hidemi), Jakubowska, A. (Anna), Johnson, N. (Nichola), Kabisch, M. (Maria), Kang, D. (Daehee), Khan, S. (Sofia), Knight, J.A. (Julia), Kosma, V-M. (Veli-Matti), Lambrechts, D. (Diether), Le Marchand, L. (Loic), Li, J. (Jingmei), Lindblom, A. (Annika), Lophatananon, A. (Artitaya), Lubinski, J. (Jan), Mannermaa, A. (Arto), Manoukian, S. (Siranoush), Margolin, S. (Sara), Marme, F. (Federick), Matsuo, K. (Keitaro), McLean, C.A. (Catriona Ann), Meindl, A. (Alfons), Muir, K. (Kenneth), Neuhausen, S.L. (Susan), Nevanlinna, H. (Heli), Nord, S. (Silje), Olson, J.E. (Janet), Orr, N. (Nick), Peterlongo, P. (Paolo), Putti, T.C. (Thomas Choudary), Rudolph, A. (Anja), Sangrajrang, S. (Suleeporn), Sawyer, E.J. (Elinor), Schmidt, M.K. (Marjanka), Schmutzler, R.K. (Rita), Shen, C-Y. (Chen-Yang), Shi, J. (Jiajun), Shrubsole, M. (Martha), Southey, M.C. (Melissa), Swerdlow, A.J. (Anthony ), Teo, S.H. (Soo Hwang), Thienpont, B. (Bernard), Toland, A.E. (Amanda), Tollenaar, R.A.E.M. (Rob), Tomlinson, I. (Ian), Truong, T. (Thérèse), Tseng, C.-C. (Chiu-chen), Ouweland, A.M.W. (Ans) van den, Wen, W. (Wanqing), Winqvist, R. (Robert), Wu, A. (Anna), Yip, C.H. (Cheng Har), Zamora, M.P. (Pilar), Zheng, Y. (Ying), Hall, P. (Per), Pharoah, P.D.P. (Paul), Simard, J. (Jacques), Chenevix-Trench, G. (Georgia), Dunning, A.M. (Alison), Easton, D.F. (Douglas F.), Zheng, W. (Wei), Eeles, R. (Rosalind), Al Olama, A.A. (Ali Amin), Kote-Jarai, Z., Benlloch, S. (Sara), Antoniou, A.C. (Antonis), McGuffog, L. (Lesley), Offit, K. (Kenneth), Lee, A. (Andrew), Dicks, E. (Ed), Luccarini, C. (Craig), Tessier, D.C. (Daniel C.), Bacot, F. (Francois), Vincent, D. (Daniel), La Boissière, S. (Sylvie), Robidoux, F. (Frederic), Nielsen, S.F. (Sune), Cunningham, J.M. (Julie), Windebank, S.A. (Sharon A.), Hilker, C.A. (Christopher A.), Meyer, J. (Jeffrey), Angelakos, M. (Maggie), Maskiell, J. (Judi), Rutgers, E.J. (Emiel J.), Verhoef, S., Hogervorst, F.B.L. (Frans), Boonyawongviroj, P. (Prat), Siriwanarungsan, P. (Pornthep), Schrauder, A. (André), Rübner, M. (Matthias), Oeser, S. (Sonja), Landrith, S. (Silke), Williams, E. (Eileen), Ryder-Mills, E. (Elaine), Sargus, K. (Kara), McInerney, N. (Niall), Colleran, G. (Gabrielle), Rowan, A. (Andrew), Jones, A. (Angela), Sohn, C. (Christof), Schneeweiß, A. (Andeas), Bugert, P. (Peter), Álvarez, N. (Nuria), Bernstein, L. (Leslie), Lacey, J. (James), Wang, S. (Sophia), Ma, H. (Huiyan), Lu, Y. (Yani), Clague De Hart, J. (Jessica), Deapen, D. (Dennis), Pinder, R. (Rich), Lee, E. (Eunjung), Schumacher, F.R. (Fredrick), Horn-Ross, P. (Pam), Reynolds, P. (Peggy), Nelson, D. (David), Park, H. (Hannah), Ziegler, H. (Hartwig), Wolf, S. (Sonja), Hermann, V. (Volker), Lo, W.-Y. (Wing-Yee), Justenhoven, C. (Christina), Ko, Y.-D. (Yon-Dschun), Baisch, C. (Christian), Fischer, H.-P. (Hans-Peter), Pesch, B. (Beate), Rabstein, S. (Sylvia), Lotz, A. (Anne), Harth, V. (Volker), Heikkinen, T. (Tuomas), Erkkilä, I. (Irja), Aaltonen, K. (Kirsimari), Smitten, K. (Karl) von, Antonenkova, N.N. (Natalia), Hillemanns, P. (Peter), Christiansen, H. (Hans), Myöhänen, E. (Eija), Kemiläinen, H. (Helena), Thorne, H. (Heather), Niedermayr, E. (Eveline), Bowtell, D., De Fazio, A. (Anna), Gertig, D., Green, A., Webb, P. (Penny), Parsons, P., Hayward, N., Webb, P.M. (P.), Whiteman, D., Fung, A. (Annie), Yashiki, J. (June), Peuteman, G. (Gilian), Smeets, D. (Dominiek), Van Brussel, T. (Thomas), Corthouts, K. (Kathleen), Obi, N. (Nadia), Heinz, J. (Judith), Behrens, T.W. (Timothy), Eilber, U. (Ursula), Celik, M. (Muhabbet), Olchers, T. (Til), Peissel, B. (Bernard), Scuvera, G. (Giulietta), Zaffaroni, D. (Daniela), Bonnani, B. (Bernardo), Feroce, I. (Irene), Maniscalco, A. (Angela), Rossi, A. (Alessandra), Bernard, L. (Loris), Tranchant, M. (Martine), Valois, M.-F. (Marie-France), Turgeon, A. (Annie), Heguy, L. (Lea), Yee, P.S. (Phuah Sze), Kang, P. (Peter), Nee, K.I. (Kang In), Mariapun, S. (Shivaani), Sook-Yee, Y. (Yoon), Lee, D.S.C. (Daphne S.C.), Ching, T.Y. (Teh Yew), Taib, N.A.M. (Nur Aishah Mohd), Otsukka, M. (Meeri), Mononen, K. (Kari), Selander, T. (Teresa), Weerasooriya, N. (Nayana), Krol-Warmerdam, E.M.M. (Elly), Molenaar, J., Blom, J., Szeszenia-Dabrowska, N. (Neonilia), Peplonska, B. (Beata), Zatonski, W. (Witold), Chao, P. (Pei), Stagner, M. (Michael), Bos, P. (Petra), Blom, J. (Jannet), Crepin, E. (Ellen), Nieuwlaat, A. (Anja), Heemskerk, A. (Annette), Higham, S. (Sue), Cramp, H.E. (Helen), Connley, D. (Daniel), Balasubramanian, S. (Sabapathy), Brock, I.W. (Ian), Kerin, M. (Michael), Miller, N. (Nicola), Kerbrat, P. (Pierre), Arveux, P. (Patrick), Le Scodan, R. (Romuald), Raoul, Y. (Yves), Laurent-Puig, P. (Pierre), Mulot, C. (Claire), Stegmaier, C. (Christa), Butterbach, K. (Katja), Karstens, J.H. (Johann), Flesch-Janys, D. (Dieter), Seibold, P. (Petra), Vrieling, A. (Alina), Nickels, S. (Stefan), Radice, P. (Paolo), Pykäs, K. (Katri), Jukkola-Vuorinen, A. (Arja), Kauppila, S. (Saila), Conroy, D. (Don), Baynes, C. (Caroline), Chua, K. (Kimberley), Pilarski, R. (Robert), Guo, X. (Xingyi), Long, J. (Jirong), Zeng, C. (Chenjie), Michailidou, K. (Kyriaki), Ghoussaini, M. (Maya), Bolla, M.K. (Manjeet), Wang, Q. (Qing), Milne, R.L. (Roger L.), Shu, X.-O. (Xiao-Ou), Cai, Q. (Qiuyin), Beesley, J. (Jonathan), Kar, S. (Siddhartha), Andrulis, I.L. (Irene), Anton-Culver, H. (Hoda), Arndt, V. (Volker), Beckmann, M.W. (Matthias), Beeghly-Fadiel, A. (Alicia), Benítez, J. (Javier), Blot, W.J. (William), Bogdanova, N.V. (Natalia), Bojesen, S.E. (Stig), Brauch, H. (Hiltrud), Brenner, H. (Hermann), Brinton, L.A. (Louise), Broekss, A. (Annegien), Brüning, T. (Thomas), Burwinkel, B. (Barbara), Cai, H. (Hui), Canisius, S. (Sander), Chang-Claude, J. (Jenny), Choi, J.-Y. (J.), Couch, F.J. (Fergus), Cox, A. (Angela), Cross, S.S. (Simon), Czene, K. (Kamila), Darabi, H. (Hatef), Devilee, P. (Peter), Droit, A. (Arnaud), Dörk, T. (Thilo), Fasching, P.A. (Peter), Fletcher, O. (Olivia), Flyger, H. (Henrik), Fostira, F. (Florentia), Gaborieau, V. (Valerie), García-Closas, M. (Montserrat), Giles, G.G. (Graham G.), Grip, M. (Mervi), Guénel, P. (Pascal), Haiman, C.A. (Christopher A.), Hamann, U. (Ute), Hartman, J.M. (Joost), Hollestelle, A. (Antoinette), Hopper, J.L. (John L.), Hsiung, C.-N. (Chia-Ni), Ito, H. (Hidemi), Jakubowska, A. (Anna), Johnson, N. (Nichola), Kabisch, M. (Maria), Kang, D. (Daehee), Khan, S. (Sofia), Knight, J.A. (Julia), Kosma, V-M. (Veli-Matti), Lambrechts, D. (Diether), Le Marchand, L. (Loic), Li, J. (Jingmei), Lindblom, A. (Annika), Lophatananon, A. (Artitaya), Lubinski, J. (Jan), Mannermaa, A. (Arto), Manoukian, S. (Siranoush), Margolin, S. (Sara), Marme, F. (Federick), Matsuo, K. (Keitaro), McLean, C.A. (Catriona Ann), Meindl, A. (Alfons), Muir, K. (Kenneth), Neuhausen, S.L. (Susan), Nevanlinna, H. (Heli), Nord, S. (Silje), Olson, J.E. (Janet), Orr, N. (Nick), Peterlongo, P. (Paolo), Putti, T.C. (Thomas Choudary), Rudolph, A. (Anja), Sangrajrang, S. (Suleeporn), Sawyer, E.J. (Elinor), Schmidt, M.K. (Marjanka), Schmutzler, R.K. (Rita), Shen, C-Y. (Chen-Yang), Shi, J. (Jiajun), Shrubsole, M. (Martha), Southey, M.C. (Melissa), Swerdlow, A.J. (Anthony ), Teo, S.H. (Soo Hwang), Thienpont, B. (Bernard), Toland, A.E. (Amanda), Tollenaar, R.A.E.M. (Rob), Tomlinson, I. (Ian), Truong, T. (Thérèse), Tseng, C.-C. (Chiu-chen), Ouweland, A.M.W. (Ans) van den, Wen, W. (Wanqing), Winqvist, R. (Robert), Wu, A. (Anna), Yip, C.H. (Cheng Har), Zamora, M.P. (Pilar), Zheng, Y. (Ying), Hall, P. (Per), Pharoah, P.D.P. (Paul), Simard, J. (Jacques), Chenevix-Trench, G. (Georgia), Dunning, A.M. (Alison), Easton, D.F. (Douglas F.), Zheng, W. (Wei), Eeles, R. (Rosalind), Al Olama, A.A. (Ali Amin), Kote-Jarai, Z., Benlloch, S. (Sara), Antoniou, A.C. (Antonis), McGuffog, L. (Lesley), Offit, K. (Kenneth), Lee, A. (Andrew), Dicks, E. (Ed), Luccarini, C. (Craig), Tessier, D.C. (Daniel C.), Bacot, F. (Francois), Vincent, D. (Daniel), La Boissière, S. (Sylvie), Robidoux, F. (Frederic), Nielsen, S.F. (Sune), Cunningham, J.M. (Julie), Windebank, S.A. (Sharon A.), Hilker, C.A. (Christopher A.), Meyer, J. (Jeffrey), Angelakos, M. (Maggie), Maskiell, J. (Judi), Rutgers, E.J. (Emiel J.), Verhoef, S., Hogervorst, F.B.L. (Frans), Boonyawongviroj, P. (Prat), Siriwanarungsan, P. (Pornthep), Schrauder, A. (André), Rübner, M. (Matthias), Oeser, S. (Sonja), Landrith, S. (Silke), Williams, E. (Eileen), Ryder-Mills, E. (Elaine), Sargus, K. (Kara), McInerney, N. (Niall), Colleran, G. (Gabrielle), Rowan, A. (Andrew), Jones, A. (Angela), Sohn, C. (Christof), Schneeweiß, A. (Andeas), Bugert, P. (Peter), Álvarez, N. (Nuria), Bernstein, L. (Leslie), Lacey, J. (James), Wang, S. (Sophia), Ma, H. (Huiyan), Lu, Y. (Yani), Clague De Hart, J. (Jessica), Deapen, D. (Dennis), Pinder, R. (Rich), Lee, E. (Eunjung), Schumacher, F.R. (Fredrick), Horn-Ross, P. (Pam), Reynolds, P. (Peggy), Nelson, D. (David), Park, H. (Hannah), Ziegler, H. (Hartwig), Wolf, S. (Sonja), Hermann, V. (Volker), Lo, W.-Y. (Wing-Yee), Justenhoven, C. (Christina), Ko, Y.-D. (Yon-Dschun), Baisch, C. (Christian), Fischer, H.-P. (Hans-Peter), Pesch, B. (Beate), Rabstein, S. (Sylvia), Lotz, A. (Anne), Harth, V. (Volker), Heikkinen, T. (Tuomas), Erkkilä, I. (Irja), Aaltonen, K. (Kirsimari), Smitten, K. (Karl) von, Antonenkova, N.N. (Natalia), Hillemanns, P. (Peter), Christiansen, H. (Hans), Myöhänen, E. (Eija), Kemiläinen, H. (Helena), Thorne, H. (Heather), Niedermayr, E. (Eveline), Bowtell, D., De Fazio, A. (Anna), Gertig, D., Green, A., Webb, P. (Penny), Parsons, P., Hayward, N., Webb, P.M. (P.), Whiteman, D., Fung, A. (Annie), Yashiki, J. (June), Peuteman, G. (Gilian), Smeets, D. (Dominiek), Van Brussel, T. (Thomas), Corthouts, K. (Kathleen), Obi, N. (Nadia), Heinz, J. (Judith), Behrens, T.W. (Timothy), Eilber, U. (Ursula), Celik, M. (Muhabbet), Olchers, T. (Til), Peissel, B. (Bernard), Scuvera, G. (Giulietta), Zaffaroni, D. (Daniela), Bonnani, B. (Bernardo), Feroce, I. (Irene), Maniscalco, A. (Angela), Rossi, A. (Alessandra), Bernard, L. (Loris), Tranchant, M. (Martine), Valois, M.-F. (Marie-France), Turgeon, A. (Annie), Heguy, L. (Lea), Yee, P.S. (Phuah Sze), Kang, P. (Peter), Nee, K.I. (Kang In), Mariapun, S. (Shivaani), Sook-Yee, Y. (Yoon), Lee, D.S.C. (Daphne S.C.), Ching, T.Y. (Teh Yew), Taib, N.A.M. (Nur Aishah Mohd), Otsukka, M. (Meeri), Mononen, K. (Kari), Selander, T. (Teresa), Weerasooriya, N. (Nayana), Krol-Warmerdam, E.M.M. (Elly), Molenaar, J., Blom, J., Szeszenia-Dabrowska, N. (Neonilia), Peplonska, B. (Beata), Zatonski, W. (Witold), Chao, P. (Pei), Stagner, M. (Michael), Bos, P. (Petra), Blom, J. (Jannet), Crepin, E. (Ellen), Nieuwlaat, A. (Anja), Heemskerk, A. (Annette), Higham, S. (Sue), Cramp, H.E. (Helen), Connley, D. (Daniel), Balasubramanian, S. (Sabapathy), Brock, I.W. (Ian), Kerin, M. (Michael), Miller, N. (Nicola), Kerbrat, P. (Pierre), Arveux, P. (Patrick), Le Scodan, R. (Romuald), Raoul, Y. (Yves), Laurent-Puig, P. (Pierre), Mulot, C. (Claire), Stegmaier, C. (Christa), Butterbach, K. (Katja), Karstens, J.H. (Johann), Flesch-Janys, D. (Dieter), Seibold, P. (Petra), Vrieling, A. (Alina), Nickels, S. (Stefan), Radice, P. (Paolo), Pykäs, K. (Katri), Jukkola-Vuorinen, A. (Arja), Kauppila, S. (Saila), Conroy, D. (Don), Baynes, C. (Caroline), Chua, K. (Kimberley), and Pilarski, R. (Robert)

Abstract

Background: A recent association study identified a common variant (rs9790517) at 4q24 to be associated with breast cancer risk. Independent association signals and potential functional variants in this locus have not been explored. Methods: We conducted a fine-mapping analysis in 55,540 breast cancer cases and 51,168 controls from the Breast Cancer Association Consortium. Results: Conditional analyses identified two independent association signals among women of European ancestry, represented by rs9790517 [conditional P=2.51 × 10-4; OR, 1.04; 95% confidence interval (CI), 1.02-1.07] and rs77928427 (P=1.86 × 10-4; OR, 1.04; 95% CI, 1.02-1.07). Functional annotation using data from the Encyclopedia of DNA Elements (ENCODE) project revealed two putative functional variants, rs62331150 and rs73838678 in linkage disequilibrium (LD) with rs9790517 (r2≥ 0.90) residing in the active promoter or enhancer, respectively, of the nearest gene, TET2. Both variants are located in DNase I hypersensitivity and transcription factor-binding sites. Using data from both The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), we showed that rs62331150 was associated with level of expression of TET2 in breast normal and tumor tissue. Conclusion: Our study identified two independent association signals at 4q24 in relation to breast cancer risk and suggested that observed association in this locus may be mediated through the regulation of TET2. Impact: Fine-mapping study with large sample size warranted for identification of independent loci for breast cancer risk.

Published
2015
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17. 2q36.3 is associated with prognosis for oestrogen receptor-negative breast cancer patients treated with chemotherapy

Author

Li, J. (Jingmei), Lindström, L.S. (Linda), Foo, J.N. (Jia), Rafiq, M. (Meena), Schmidt, M.K. (Marjanka), Pharoah, P.D.P. (Paul), Michailidou, K. (Kyriaki), Dennis, J. (Joe), Bolla, M.K. (Manjeet), Wang, Q. (Qing), Veer, L.J. (Laura) van 't, Cornelissen, S. (Sten), Rutgers, E.J.T. (Emiel), Southey, M.C. (Melissa), Apicella, C. (Carmel), Dite, G.S. (Gillian), Hopper, J.L. (John), Fasching, P.A. (Peter), Haeberle, L. (Lothar), Ekici, A.B. (Arif), Beckmann, M.W. (Matthias), Blomqvist, C. (Carl), Muranen, T.A. (Taru), Aittomäki, K. (Kristiina), Lindblom, A. (Annika), Margolin, S. (Sara), Mannermaa, A. (Arto), Kosma, V-M. (Veli-Matti), Hartikainen, J. (Jaana), Kataja, V. (Vesa), Chenevix-Trench, G. (Georgia), Investigators, K. (Kconfab), Phillips, K.-A. (Kelly-Anne), McLachlan, S.-A. (Sue-Anne), Lambrechts, D. (Diether), Thienpont, B. (Bernard), Smeets, A. (Ann), Wildiers, H. (Hans), Chang-Claude, J. (Jenny), Flesch-Janys, D. (Dieter), Seibold, P. (Petra), Rudolph, A. (Anja), Giles, G.G. (Graham), Baglietto, L. (Laura), Severi, G. (Gianluca), Haiman, C.A. (Christopher), Henderson, B.E. (Brian), Schumacher, F.R. (Fredrick), Le Marchand, L. (Loic), Kristensen, V. (Vessela), Alnæs, G.G. (Grethe), Borresen-Dale, A.-L. (Anne-Lise), Nord, S. (Silje), Winqvist, R. (Robert), Pykäs, K. (Katri), Jukkola-Vuorinen, A. (Arja), Grip, M. (Mervi), Andrulis, I.L. (Irene), Knight, J.A. (Julia), Glendon, G. (Gord), Tchatchou, S. (Sandrine), Devilee, P. (Peter), Tollenaar, R.A.E.M. (Rob), Seynaeve, C.M. (Caroline), Hooning, M.J. (Maartje), Kriege, M. (Mieke), Hollestelle, A. (Antoinette), Ouweland, A.M.W. (Ans) van den, Li, Y. (Yi), Hamann, U. (Ute), Torres, D. (Diana), Ulmer, H.U. (Hans), Rüdiger, T. (Thomas), Shen, C-Y. (Chen-Yang), Hsiung, C.-N. (Chia-Ni), Wu, P.-E. (Pei-Ei), Chen, S.-T. (Shou-Tung), Teo, S.-H. (Soo-Hwang), Taib, N.A.M. (Nur Aishah Mohd), Har Yip, C. (Cheng), Fuang Ho, G. (Gwo), Matsuo, K. (Keitaro), Ito, H. (Hidemi), Iwata, H. (Hisato), Tajima, K. (Kazuo), Kang, D. (Daehee), Choi, J.-Y. (Ji-Yeob), Park, S.K. (Sue), Yoo, K-Y. (Keun-Young), Maishman, T. (Tom), Tapper, W. (William), Dunning, A.M. (Alison), Shah, M. (Mitul), Luben, R.N. (Robert), Brown, J. (Judith), Chuen Khor, C. (Chiea), Eccles, D. (Diana), Nevanlinna, H. (Heli), Easton, D.F. (Douglas), Humphreys, M.K. (Manjeet), Liu, J. (Jianjun), Hall, P. (Per), Czene, K. (Kamila), Li, J. (Jingmei), Lindström, L.S. (Linda), Foo, J.N. (Jia), Rafiq, M. (Meena), Schmidt, M.K. (Marjanka), Pharoah, P.D.P. (Paul), Michailidou, K. (Kyriaki), Dennis, J. (Joe), Bolla, M.K. (Manjeet), Wang, Q. (Qing), Veer, L.J. (Laura) van 't, Cornelissen, S. (Sten), Rutgers, E.J.T. (Emiel), Southey, M.C. (Melissa), Apicella, C. (Carmel), Dite, G.S. (Gillian), Hopper, J.L. (John), Fasching, P.A. (Peter), Haeberle, L. (Lothar), Ekici, A.B. (Arif), Beckmann, M.W. (Matthias), Blomqvist, C. (Carl), Muranen, T.A. (Taru), Aittomäki, K. (Kristiina), Lindblom, A. (Annika), Margolin, S. (Sara), Mannermaa, A. (Arto), Kosma, V-M. (Veli-Matti), Hartikainen, J. (Jaana), Kataja, V. (Vesa), Chenevix-Trench, G. (Georgia), Investigators, K. (Kconfab), Phillips, K.-A. (Kelly-Anne), McLachlan, S.-A. (Sue-Anne), Lambrechts, D. (Diether), Thienpont, B. (Bernard), Smeets, A. (Ann), Wildiers, H. (Hans), Chang-Claude, J. (Jenny), Flesch-Janys, D. (Dieter), Seibold, P. (Petra), Rudolph, A. (Anja), Giles, G.G. (Graham), Baglietto, L. (Laura), Severi, G. (Gianluca), Haiman, C.A. (Christopher), Henderson, B.E. (Brian), Schumacher, F.R. (Fredrick), Le Marchand, L. (Loic), Kristensen, V. (Vessela), Alnæs, G.G. (Grethe), Borresen-Dale, A.-L. (Anne-Lise), Nord, S. (Silje), Winqvist, R. (Robert), Pykäs, K. (Katri), Jukkola-Vuorinen, A. (Arja), Grip, M. (Mervi), Andrulis, I.L. (Irene), Knight, J.A. (Julia), Glendon, G. (Gord), Tchatchou, S. (Sandrine), Devilee, P. (Peter), Tollenaar, R.A.E.M. (Rob), Seynaeve, C.M. (Caroline), Hooning, M.J. (Maartje), Kriege, M. (Mieke), Hollestelle, A. (Antoinette), Ouweland, A.M.W. (Ans) van den, Li, Y. (Yi), Hamann, U. (Ute), Torres, D. (Diana), Ulmer, H.U. (Hans), Rüdiger, T. (Thomas), Shen, C-Y. (Chen-Yang), Hsiung, C.-N. (Chia-Ni), Wu, P.-E. (Pei-Ei), Chen, S.-T. (Shou-Tung), Teo, S.-H. (Soo-Hwang), Taib, N.A.M. (Nur Aishah Mohd), Har Yip, C. (Cheng), Fuang Ho, G. (Gwo), Matsuo, K. (Keitaro), Ito, H. (Hidemi), Iwata, H. (Hisato), Tajima, K. (Kazuo), Kang, D. (Daehee), Choi, J.-Y. (Ji-Yeob), Park, S.K. (Sue), Yoo, K-Y. (Keun-Young), Maishman, T. (Tom), Tapper, W. (William), Dunning, A.M. (Alison), Shah, M. (Mitul), Luben, R.N. (Robert), Brown, J. (Judith), Chuen Khor, C. (Chiea), Eccles, D. (Diana), Nevanlinna, H. (Heli), Easton, D.F. (Douglas), Humphreys, M.K. (Manjeet), Liu, J. (Jianjun), Hall, P. (Per), and Czene, K. (Kamila)

Abstract

Large population-based registry studies have shown that breast cancer prognosis is inherited. Here we analyse single-nucleotide polymorphisms (SNPs) of genes implicated in human immunology and inflammation as candidates for prognostic markers of breast cancer survival involving 1,804 oestrogen receptor (ER)-negative patients treated with chemotherapy (279 events) from 14 European studies in a prior large-scale genotyping experiment, which is part of the Collaborative Oncological Gene-environment Study (COGS) initiative. We carry out replication using Asian COGS samples (n=522, 53 events) and the Prospective Study of Outcomes in Sporadic versus Hereditary breast cancer (POSH) study (n=315, 108 events). Rs4458204-A near CCL20 (2q36.3) is found to be associated with breast cancer-specific death at a genome-wide significant level (n=2,641, 440 events, combined allelic hazard ratio (HR)=1.81 (1.49-2.19); P for trend=1.90 × 10 â ̂'9). Such survival-associated variants can represent ideal targets for tailored therapeutics, and may also enhance our current prognostic prediction capabilities.

Published
2014
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19. 22P Impact of an online Asian genetic risk calculator on risk perception: Cancer-related distress and uptake of genetic counselling among Malaysian breast cancer patients (The ARiCa Study).

Author

Padmanabhan, H., Hassan, N.T.T., Yip, C.H., Taib, N.A.M., Abdul Aziz, A.F., Wong, M.W., Ho, W.K., Ang, B.H., Lee, V.Y.M., Lee, Y.Q., Thong, M-K., Yoon, S.Y., and Teo, S-H.

Subjects
*GENETIC counseling, *RISK perception, *BREAST cancer, *CANCER patients, *CALCULATORS, *METASTATIC breast cancer
Published
2023
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