Fine-mapping identifies two additional breast cancer susceptibility loci at 9q31.2. Orr, N., Dudbridge, F., Dryden, N., Maguire, S., Novo, D., Perrakis, E., Johnson, N., Ghoussaini, M., Hopper, J. L., Southey, M. C., Apicella, C., Stone, J., Schmidt, M. K., Broeks, A., Van't Veer, L. J., Hogervorst, F. B., Fasching, P. A., Haeberle, L., Ekici, A. B., Beckmann, M. W., Gibson, L., Aitken, Z., Warren, H., Sawyer, E., Tomlinson, I., Kerin, M. J., Miller, N., Burwinkel, B., Marme, F., Schneeweiss, A., Sohn, C., Guénel, P., Truong, T., Cordina-Duverger, E., Sanchez, M., Bojesen, S. E., Nordestgaard, B. G., Nielsen, S. F., Flyger, H., Benitez, J., Zamora, M. P., Arias Perez, J. I., Menéndez, P., Anton-Culver, H., Neuhausen, S. L., Brenner, H., Dieffenbach, A. K., Arndt, V., Stegmaier, C., Hamann, U., Brauch, H., Justenhoven, C., Brüning, T., Ko, Y., Nevanlinna, H., Aittomäki, K., Blomqvist, C., Khan, S., Bogdanova, N., Dörk, T., Lindblom, A., Margolin, S., Mannermaa, A., Kataja, V., Kosma, V., Hartikainen, J. M., Chenevix-Trench, G., Beesley, J., Lambrechts, D., Moisse, M., Floris, G., Beuselinck, B., Chang-Claude, J., Rudolph, A., Seibold, P., Flesch-Janys, D., Radice, P., Peterlongo, P., Peissel, B., Pensotti, V., Couch, F. J., Olson, J. E., Slettedahl, S., Vachon, C., Giles, G. G., Milne, R. L., McLean, C., Haiman, C. A., Henderson, B. E., Schumacher, F., Le Marchand, L., Simard, J., Goldberg, M. S., Labrèche, F., Dumont, M., Kristensen, V., Alnæs, G. G., Nord, S., Borresen-Dale, A., Zheng, W., Deming-Halverson, S., Shrubsole, M., Long, J., Winqvist, R., Pylkäs, K., Jukkola-Vuorinen, A., Grip, M., Andrulis, I. L., Knight, J. A., Glendon, G., Tchatchou, S., Devilee, P., Tollenaar, R. A. E. M., Seynaeve, C. M., Van Asperen, C. J., Garcia-Closas, M., Figueroa, J., Chanock, S. J., Lissowska, J., Czene, K., Darabi, H., Eriksson, M., Klevebring, D., Hooning, M. J., Hollestelle, A., van Deurzen, C. H. M., Kriege, M., Hall, P., Li, J., Liu, J., Humphreys, K., Cox, A., Cross, S. S., Reed, M. W. R., Pharoah, P. D. P., Dunning, A. M., Shah, M., Perkins, B. J., Jakubowska, A., Lubinski, J., Jaworska-Bieniek, K., Durda, K., Ashworth, A., Swerdlow, A., Jones, M., Schoemaker, M. J., Meindl, A., Schmutzler, R. K., Olswold, C., Slager, S., Toland, A. E., Yannoukakos, D., Muir, K., Lophatananon, A., Stewart-Brown, S., Siriwanarangsan, P., Matsuo, K., Ito, H., Iwata, H., Ishiguro, J., Wu, A. H., Tseng, C., Van Den Berg, D., Stram, D. O., Teo, S. H., Yip, C. H., Kang, P., Ikram, M. K., Shu, X., Lu, W., Gao, Y., Cai, H., Kang, D., Choi, J., Park, S. K., Noh, D., Hartman, M., Miao, H., Lim, W. Y., Lee, S. C., Sangrajrang, S., Gaborieau, V., Brennan, P., Mckay, J., Wu, P., Hou, M., Yu, J., Shen, C., Blot, W., Cai, Q., Signorello, L. B., Luccarini, C., Bayes, C., Ahmed, S., Maranian, M., Healey, C. S., González-Neira, A., Pita, G., Alonso, M. R., Álvarez, N., Herrero, D., Tessier, D. C., Vincent, D., Bacot, F., Hunter, D. J., Lindstrom, S., Dennis, J., Michailidou, K., Bolla, M. K., Easton, D. F., dos Santos Silva, I., Fletcher, O., Peto, J., GENICA Network, kConFab Investigators, & Australian Ovarian Cancer Study Group Human Molecular Genetics, 24(10):2966–2984, May, 2015.
doi  abstract   bibtex   
We recently identified a novel susceptibility variant, rs865686, for estrogen-receptor positive breast cancer at 9q31.2. Here, we report a fine-mapping analysis of the 9q31.2 susceptibility locus using 43 160 cases and 42 600 controls of European ancestry ascertained from 52 studies and a further 5795 cases and 6624 controls of Asian ancestry from nine studies. Single nucleotide polymorphism (SNP) rs676256 was most strongly associated with risk in Europeans (odds ratios [OR] = 0.90 [0.88-0.92]; P-value = 1.58 × 10(-25)). This SNP is one of a cluster of highly correlated variants, including rs865686, that spans ∼14.5 kb. We identified two additional independent association signals demarcated by SNPs rs10816625 (OR = 1.12 [1.08-1.17]; P-value = 7.89 × 10(-09)) and rs13294895 (OR = 1.09 [1.06-1.12]; P-value = 2.97 × 10(-11)). SNP rs10816625, but not rs13294895, was also associated with risk of breast cancer in Asian individuals (OR = 1.12 [1.06-1.18]; P-value = 2.77 × 10(-05)). Functional genomic annotation using data derived from breast cancer cell-line models indicates that these SNPs localise to putative enhancer elements that bind known drivers of hormone-dependent breast cancer, including ER-α, FOXA1 and GATA-3. In vitro analyses indicate that rs10816625 and rs13294895 have allele-specific effects on enhancer activity and suggest chromatin interactions with the KLF4 gene locus. These results demonstrate the power of dense genotyping in large studies to identify independent susceptibility variants. Analysis of associations using subjects with different ancestry, combined with bioinformatic and genomic characterisation, can provide strong evidence for the likely causative alleles and their functional basis.
@article{orr_fine-mapping_2015,
	title = {Fine-mapping identifies two additional breast cancer susceptibility loci at 9q31.2},
	volume = {24},
	issn = {1460-2083},
	doi = {10.1093/hmg/ddv035},
	abstract = {We recently identified a novel susceptibility variant, rs865686, for estrogen-receptor positive breast cancer at 9q31.2. Here, we report a fine-mapping analysis of the 9q31.2 susceptibility locus using 43 160 cases and 42 600 controls of European ancestry ascertained from 52 studies and a further 5795 cases and 6624 controls of Asian ancestry from nine studies. Single nucleotide polymorphism (SNP) rs676256 was most strongly associated with risk in Europeans (odds ratios [OR] = 0.90 [0.88-0.92]; P-value = 1.58 × 10(-25)). This SNP is one of a cluster of highly correlated variants, including rs865686, that spans ∼14.5 kb. We identified two additional independent association signals demarcated by SNPs rs10816625 (OR = 1.12 [1.08-1.17]; P-value = 7.89 × 10(-09)) and rs13294895 (OR = 1.09 [1.06-1.12]; P-value = 2.97 × 10(-11)). SNP rs10816625, but not rs13294895, was also associated with risk of breast cancer in Asian individuals (OR = 1.12 [1.06-1.18]; P-value = 2.77 × 10(-05)). Functional genomic annotation using data derived from breast cancer cell-line models indicates that these SNPs localise to putative enhancer elements that bind known drivers of hormone-dependent breast cancer, including ER-α, FOXA1 and GATA-3. In vitro analyses indicate that rs10816625 and rs13294895 have allele-specific effects on enhancer activity and suggest chromatin interactions with the KLF4 gene locus. These results demonstrate the power of dense genotyping in large studies to identify independent susceptibility variants. Analysis of associations using subjects with different ancestry, combined with bioinformatic and genomic characterisation, can provide strong evidence for the likely causative alleles and their functional basis.},
	language = {eng},
	number = {10},
	journal = {Human Molecular Genetics},
	author = {Orr, Nick and Dudbridge, Frank and Dryden, Nicola and Maguire, Sarah and Novo, Daniela and Perrakis, Eleni and Johnson, Nichola and Ghoussaini, Maya and Hopper, John L. and Southey, Melissa C. and Apicella, Carmel and Stone, Jennifer and Schmidt, Marjanka K. and Broeks, Annegien and Van't Veer, Laura J. and Hogervorst, Frans B. and Fasching, Peter A. and Haeberle, Lothar and Ekici, Arif B. and Beckmann, Matthias W. and Gibson, Lorna and Aitken, Zoe and Warren, Helen and Sawyer, Elinor and Tomlinson, Ian and Kerin, Michael J. and Miller, Nicola and Burwinkel, Barbara and Marme, Frederik and Schneeweiss, Andreas and Sohn, Chistof and Guénel, Pascal and Truong, Thérèse and Cordina-Duverger, Emilie and Sanchez, Marie and Bojesen, Stig E. and Nordestgaard, Børge G. and Nielsen, Sune F. and Flyger, Henrik and Benitez, Javier and Zamora, Maria Pilar and Arias Perez, Jose Ignacio and Menéndez, Primitiva and Anton-Culver, Hoda and Neuhausen, Susan L. and Brenner, Hermann and Dieffenbach, Aida Karina and Arndt, Volker and Stegmaier, Christa and Hamann, Ute and Brauch, Hiltrud and Justenhoven, Christina and Brüning, Thomas and Ko, Yon-Dschun and Nevanlinna, Heli and Aittomäki, Kristiina and Blomqvist, Carl and Khan, Sofia and Bogdanova, Natalia and Dörk, Thilo and Lindblom, Annika and Margolin, Sara and Mannermaa, Arto and Kataja, Vesa and Kosma, Veli-Matti and Hartikainen, Jaana M. and Chenevix-Trench, Georgia and Beesley, Jonathan and Lambrechts, Diether and Moisse, Matthieu and Floris, Guiseppe and Beuselinck, Benoit and Chang-Claude, Jenny and Rudolph, Anja and Seibold, Petra and Flesch-Janys, Dieter and Radice, Paolo and Peterlongo, Paolo and Peissel, Bernard and Pensotti, Valeria and Couch, Fergus J. and Olson, Janet E. and Slettedahl, Seth and Vachon, Celine and Giles, Graham G. and Milne, Roger L. and McLean, Catriona and Haiman, Christopher A. and Henderson, Brian E. and Schumacher, Fredrick and Le Marchand, Loic and Simard, Jacques and Goldberg, Mark S. and Labrèche, France and Dumont, Martine and Kristensen, Vessela and Alnæs, Grethe Grenaker and Nord, Silje and Borresen-Dale, Anne-Lise and Zheng, Wei and Deming-Halverson, Sandra and Shrubsole, Martha and Long, Jirong and Winqvist, Robert and Pylkäs, Katri and Jukkola-Vuorinen, Arja and Grip, Mervi and Andrulis, Irene L. and Knight, Julia A. and Glendon, Gord and Tchatchou, Sandrine and Devilee, Peter and Tollenaar, Robertus A. E. M. and Seynaeve, Caroline M. and Van Asperen, Christi J. and Garcia-Closas, Montserrat and Figueroa, Jonine and Chanock, Stephen J. and Lissowska, Jolanta and Czene, Kamila and Darabi, Hatef and Eriksson, Mikael and Klevebring, Daniel and Hooning, Maartje J. and Hollestelle, Antoinette and van Deurzen, Carolien H. M. and Kriege, Mieke and Hall, Per and Li, Jingmei and Liu, Jianjun and Humphreys, Keith and Cox, Angela and Cross, Simon S. and Reed, Malcolm W. R. and Pharoah, Paul D. P. and Dunning, Alison M. and Shah, Mitul and Perkins, Barbara J. and Jakubowska, Anna and Lubinski, Jan and Jaworska-Bieniek, Katarzyna and Durda, Katarzyna and Ashworth, Alan and Swerdlow, Anthony and Jones, Michael and Schoemaker, Minouk J. and Meindl, Alfons and Schmutzler, Rita K. and Olswold, Curtis and Slager, Susan and Toland, Amanda E. and Yannoukakos, Drakoulis and Muir, Kenneth and Lophatananon, Artitaya and Stewart-Brown, Sarah and Siriwanarangsan, Pornthep and Matsuo, Keitaro and Ito, Hidema and Iwata, Hiroji and Ishiguro, Junko and Wu, Anna H. and Tseng, Chiu-Chen and Van Den Berg, David and Stram, Daniel O. and Teo, Soo Hwang and Yip, Cheng Har and Kang, Peter and Ikram, Mohammad Kamran and Shu, Xiao-Ou and Lu, Wei and Gao, Yu-Tang and Cai, Hui and Kang, Daehee and Choi, Ji-Yeob and Park, Sue K. and Noh, Dong-Young and Hartman, Mikael and Miao, Hui and Lim, Wei Yen and Lee, Soo Chin and Sangrajrang, Suleeporn and Gaborieau, Valerie and Brennan, Paul and Mckay, James and Wu, Pei-Ei and Hou, Ming-Feng and Yu, Jyh-Cherng and Shen, Chen-Yang and Blot, William and Cai, Qiuyin and Signorello, Lisa B. and Luccarini, Craig and Bayes, Caroline and Ahmed, Shahana and Maranian, Mel and Healey, Catherine S. and González-Neira, Anna and Pita, Guillermo and Alonso, M. Rosario and Álvarez, Nuria and Herrero, Daniel and Tessier, Daniel C. and Vincent, Daniel and Bacot, Francois and Hunter, David J. and Lindstrom, Sara and Dennis, Joe and Michailidou, Kyriaki and Bolla, Manjeet K. and Easton, Douglas F. and dos Santos Silva, Isabel and Fletcher, Olivia and Peto, Julian and {GENICA Network} and {kConFab Investigators} and {Australian Ovarian Cancer Study Group}},
	month = may,
	year = {2015},
	pmid = {25652398},
	pmcid = {PMC4406292},
	keywords = {Adult, Aged, Asian Continental Ancestry Group, Breast Neoplasms, Chromosome Mapping, Chromosomes, Human, Pair 9, Enhancer Elements, Genetic, Estrogen Receptor alpha, European Continental Ancestry Group, Female, GATA3 Transcription Factor, Genetic Association Studies, Genetic Loci, Genetic Predisposition to Disease, Hepatocyte Nuclear Factor 3-alpha, Humans, Kruppel-Like Transcription Factors, Middle Aged, Polymorphism, Single Nucleotide, Risk},
	pages = {2966--2984},
}
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