Fine scale mapping of the breast cancer 16q12 locus

Human Molecular Genetics

Volumn 19, Issue 12, 2010, Pages 2507-2515

  Udler, Miriam S ^a,b,c   Ahmed, Shahana ^a   Healey, Catherine S ^a   Meyer, Kerstin ^c   Struewing, Jeffrey ^b,d   Maranian, Melanie ^a   Kwon, Erika M ^b   Zhang, Jinghui ^d   Tyrer, Jonathan ^a   Karlins, Eric ^b   Platte, Radka ^a   Kalmyrzaev, Bolot ^a   Dicks, Ed ^a   Field, Helen ^a   Maia, Ana Teresa ^c   Prathalingam, Radhika ^c   Teschendorff, Andrew ^c,e   McArthur, Stewart ^c   Doody, David R ^f   Luben, Robert ^a   Caldas, Carlos ^c   Bernstein, Leslie ^g   Kolonel, Laurence K ^h   Henderson, Brian E ⁱ   Wu, Anna H ⁱ   Le Marchand, Loic ^h   Ursin, Giske ^i,j   Press, Michael F ^k   Lindblom, Annika ^l   Margolin, Sara ^l   Shen, Chen Yang ^m   Yang, Show Lin ^m   Hsiung, Chia Ni ^m   Kang, Daehee ⁿ   Yoo, Keun Young ⁿ   Noh, Dong Young ⁿ   Ahn, Sei Hyun ^o   Malone, Kathleen E ^f   Haiman, Christopher A ⁱ   Pharoah, Paul D ^a   Ponder, Bruce A J ^a,c   Ostrander, Elaine A ^b   Easton, Douglas F ^a   Dunning, Alison M ^a   more..

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^c CANCER RESEARCH UK CAMBRIDGE RESEARCH INSTITUTE   (United Kingdom)

^d NATIONAL CANCER INSTITUTE   (United States)

^e UNIVERSITY COLLEGE LONDON   (United Kingdom)

^f Fred Hutchinson Cancer Research Center   (United States)

^g CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

^h UNIVERSITY OF HAWAII CANCER CENTER   (United States)

ⁱ UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^j UNIVERSITY OF OSLO   (Norway)

^k UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^l KAROLINSKA INSTITUTE   (Sweden)

^m INSTITUTE OF BIOMEDICAL SCIENCES   (Taiwan)

ⁿ Seoul National University College of Medicine   (South Korea)

^o University of Ulsan   (South Korea)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ASIAN; BREAST CANCER; CANCER RISK; CAUCASIAN; CHROMOSOME 16P; GENE; GENE LOCATION; GENE LOCUS; GENE MAPPING; GENETIC RISK; HAPLOTYPE; HUMAN; MAJOR CLINICAL STUDY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; TOX3 GENE;

BREAST NEOPLASMS; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, PAIR 16; FEMALE; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 77955297273     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddq122     Document Type: Article

References (25)

1. Easton, D.F., Pooley, K.A., Dunning, A.M., Pharoah, P.D., Thompson, D., Ballinger, D.G., Struewing, J.P., Morrison, J., Field, H., Luben, R. et al. (2007) Genome-wide association study identifies novel breast cancer susceptibility loci. Nature, 447, 1087-1093.
2. Stacey, S.N., Manolescu, A., Sulem, P., Rafnar, T., Gudmundsson, J., Gudjonsson, S.A., Masson, G., Jakobsdottir, M., Thorlacius, S., Helgason, A. et al. (2007) Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer. Nat. Genet., 39, 865-869.
3. Yuan, S.H., Qiu, Z. and Ghosh, A. (2009) TOX3 regulates calciumdependent transcription in neurons. Proc. Natl. Acad. Sci. USA, 106, 2909-2914.
4. Smid, M., Wang, Y., Klijn, J.G., Sieuwerts, A.M., Zhang, Y., Atkins, D., Martens, J.W. and Foekens, J.A. (2006) Genes associated with breast cancer metastatic to bone. J. Clin. Oncol., 24, 2261-2267.
5. Rakha, E.A., Green, A.R., Powe, D.G., Roylance, R. and Ellis, I.O. (2006) Chromosome 16 tumor-suppressor genes in breast cancer. Genes Chromosomes Cancer, 45, 527-535.
6. (2003) The International HapMap Project. Nature, 426, 789-796.
7. Barrett, J.C., Fry, B., Maller, J. and Daly, M.J. (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21, 263-265.
8. Stranger, B.E., Forrest, M.S., Clark, A.G., Minichiello, M.J., Deutsch, S., Lyle, R., Hunt, S., Kahl, B., Antonarakis, S.E., Tavare, S. et al. (2005) Genome-wide associations of gene expression variation in humans. PLoS Genet., 1, e78.
9. Dixon, A.L., Liang, L., Moffatt, M.F., Chen, W., Heath, S., Wong, K.C., Taylor, J., Burnett, E., Gut, I., Farrall, M. et al. (2007) A genome-wide association study of global gene expression. Nat. Genet., 39, 1202-1207.
10. Mayol, X., Grana, X., Baldi, A., Sang, N., Hu, Q. and Giordano, A. (1993) Cloning of a new member of the retinoblastoma gene family (pRb2) which binds to the E1A transforming domain. Oncogene, 8, 2561-2566.
11. Naylor, T.L., Greshock, J., Wang, Y., Colligon, T., Yu, Q.C., Clemmer, V., Zaks, T.Z. and Weber, B.L. (2005) High resolution genomic analysis of sporadic breast cancer using array-based comparative genomic hybridization. Breast Cancer Res., 7, R1186-R1198.
12. Lesueur, F., Pharoah, P.D., Laing, S., Ahmed, S., Jordan, C., Smith, P.L., Luben, R., Wareham, N.J., Easton, D.F., Dunning, A.M. et al. (2005) Allelic association of the human homologue of the mouse modifier Ptprj with breast cancer. Hum. Mol. Genet., 14, 2349-2356.
13. Follows, G.A., Janes, M.E., Vallier, L., Green, A.R. and Gottgens, B. (2007) Real-time PCR mapping of DNaseI-hypersensitive sites using a novel ligation-mediated amplification technique. Nucleic Acids Res., 35, e56.
14. Udler, M.S., Meyer, K.B., Pooley, K.A., Karlins, E., Struewing, J.P., Zhang, J., Doody, D.R., MacArthur, S., Tyrer, J., Pharoah, P.D. et al. (2009) FGFR2 variants and breast cancer risk: fine-scale mapping using African American studies and analysis of chromatin conformation. Hum. Mol. Genet., 18, 1692-1703.
15. Scacheri, P.C., Crawford, G.E. and Davis, S. (2006) Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays. Methods Enzymol., 411, 270-282.
16. Grabe, N. (2002) AliBaba2: context specific identification of transcription factor binding sites. In Silico Biol., 2, S1-S15.
17. Heinemeyer, T., Wingender, E., Reuter, I., Hermjakob, H., Kel, A.E., Kel, O.V., Ignatieva, E.V., Ananko, E.A., Podkolodnaya, O.A., Kolpakov, F.A. et al. (1998) Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucleic Acids Res., 26, 362-367.
18. Cartharius, K., Frech, K., Grote, K., Klocke, B., Haltmeier, M., Klingenhoff, A., Frisch, M., Bayerlein, M. and Werner, T. (2005) MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics, 21, 2933-2942.
19. Blanchette, M., Bataille, A.R., Chen, X., Poitras, C., Laganiere, J., Lefebvre, C., Deblois, G., Giguere, V., Ferretti, V., Bergeron, D. et al. (2006) Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res., 16, 656-668.
20. Ferretti, V., Poitras, C., Bergeron, D., Coulombe, B., Robert, F. and Blanchette, M. (2007) PReMod: a database of genome-wide mammalian cis-regulatory module predictions. Nucleic Acids Res., 35, D122-D126.
21. Chin, S.F., Teschendorff, A.E., Marioni, J.C., Wang, Y., Barbosa-Morais, N.L., Thorne, N.P., Costa, J.L., Pinder, S.E., van de Wiel, M.A., Green, A.R. et al. (2007) High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biol., 8, R215.
22. Blenkiron, C., Goldstein, L.D., Thorne, N.P., Spiteri, I., Chin, S.F., Dunning, M.J., Barbosa-Morais, N.L., Teschendorff, A.E., Green, A.R., Ellis, I.O. et al. (2007) MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biol., 8, R214.
23. Malone, K.E., Daling, J.R., Doody, D.R., Hsu, L., Bernstein, L., Coates, R.J., Marchbanks, P.A., Simon, M.S., McDonald, J.A., Norman, S.A. et al. (2006) Prevalence and predictors of BRCA1 and BRCA2 mutations in a population-based study of breast cancer in white and black American women ages 35 to 64 years. Cancer Res., 66, 8297-8308.
24. Schaid, D.J., Rowland, C.M., Tines, D.E., Jacobson, R.M. and Poland, G.A. (2002) Score tests for association between traits and haplotypes when linkage phase is ambiguous. Am. J. Hum. Genet., 70, 425-434.
25. Stram, D.O., Haiman, C.A., Hirschhorn, J.N., Altshuler, D., Kolonel, L.N., Henderson, B.E. and Pike, M.C. (2003) Choosing haplotype-tagging SNPS based on unphased genotype data using a preliminary sample of unrelated subjects with an example from the Multiethnic Cohort Study. Hum. Hered., 55, 27-36.