Cell-type-specific enrichment of risk-associated regulatory elements at ovarian cancer susceptibility loci

Human Molecular Genetics

Volumn 24, Issue 13, 2015, Pages 3595-3607

  Coetzee, Simon G ^a,b   Shen, Howard C ^c   Hazelett, Dennis J ^c   Lawrenson, Kate ^c   Kuchenbaecker, Karoline ^d   Tyrer, Jonathan ^d   Rhie, Suhn K ^c   Levanon, Keren ^e   Karst, Alison ^f   Drapkin, Ronny ^g   Ramus, Susan J ^c   Couch, Fergus J ^g   Offit, Kenneth ^h   Chenevix Trench, Georgia ⁱ   Monteiro, Alvaro N A ^j   Antoniou, Antonis ^d   Freedman, Matthew ^f   Coetzee, Gerhard A ^c   Pharoah, Paul D P ^d   Noushmehr, Houtan ^a,b,k   Gayther, Simon A ^c   Anton Culver, Hoda ^k   Antonenkova, Natalia ^k   Baker, Helen ^k   Bandera, Elisa V ^k   Bean, Yukie ^k   Beckmann, Matthias W ^k   Berchuck, Andrew ^k   Bisogna, Maria ^k   Bjorge, Line ^k   Bogdanova, Natalia ^k   Brinton, Louise A ^k   Brooks Wilson, Angela ^k   Bruinsma, Fiona ^k   Butzow, Ralf ^k   Campbell, Ian G ^k   Carty, Karen ^k   Chang Claude, Jenny ^k   Chen, Ann ^k   Chen, Zhihua ^k   Cook, Linda S ^k   Cramer, Daniel W ^k   Cunningham, Julie M ^k   Cybulski, Cezary ^k   Dansonka Mieszkowska, Agnieszka ^k   Dennis, Joe ^k   Dicks, Ed ^k   Doherty, Jennifer A ^k   Dörk, Thilo ^k   Bois, Andreas du ^k   Dürst, Matthias ^k   Eccles, Diana ^k   Easton, Douglas F ^k   Edwards, Robert P ^k   Eilber, Ursula ^k   Ekici, Arif B ^k   Fasching, Peter A ^k   Fridley, Brooke L ^k   Gao, Yu Tang ^k   Gentry Maharaj, Aleksandra ^k   Giles, Graham G ^k   Glasspool, Rosalind ^k   Goode, Ellen L ^k   Goodman, Marc T ^k   Grownwald, Jacek ^k   Harrington, Patricia ^k   Harter, Philipp ^k   Hasmad, Hanis Nazihah ^k   Hein, Alexander ^k   Heitz, Florian ^k   Hildebrandt, Michelle A T ^k   Hillemanns, Peter ^k   Hogdall, Estrid ^k   Hogdall, Claus ^k   Hosono, Satoyo ^k   Iversen, Edwin S ^k   Jakubowska, Anna ^k   James, Paul ^k   Jensen, Allan ^k   Ji, Bu Tian ^k   Karlan, Beth Y ^k   Kjaer, Susanne Kruger ^k   Kelemen, Linda E ^k   Kellar, Melissa ^k   Kelley, Joseph L ^k   Kiemeney, Lambertus A ^k   Krakstad, Camilla ^k   Kupryjanczyk, Jolanta ^k   Lambrechts, Diether ^k   Lambrechts, Sandrina ^k   Le, Nhu D ^k   Lele, Shashi ^k   Leminen, Arto ^k   Lester, Jenny ^k   Levine, Douglas A ^k   Liang, Dong ^k   Lissowska, Jolanta ^k   Lu, Karen ^k   Lubinski, Jan ^k   Lundvall, Lene ^k   Massuger, Leon F A G ^k   Matsuo, Keitaro ^k   McGuire, Valerie ^k   McLaughlin, John R ^k   McNeish, Ian ^k   Menon, Usha ^k   Modugno, Francesmary ^k   Moysich, Kirsten B ^k   Narod, Steven A ^k   Nedergaard, Lotte ^k   Ness, Roberta B ^k   Azmi, Mat Adenan Noor ^k   Odunsi, Kunle ^k   Olson, Sara H ^k   Orlow, Irene ^k   Orsulic, Sandra ^k   Weber, Rachel Palmieri ^k   Pearce, Celeste L ^k   Pejovic, Tanja ^k   Pelttari, Liisa M ^k   Permuth Wey, Jennifer ^k   Phelan, Catherine M ^k   Pike, Malcolm C ^k   Poole, Elizabeth M ^k   Risch, Harvey A ^k   Rosen, Barry ^k   Rossing, Mary Anne ^k   Rothstein, Joseph H ^k   Rudolph, Anja ^k   Runnebaum, Ingo B ^k   Rzepecka, Iwona K ^k   Salvesen, Helga B ^k   Schildkraut, Joellen M ^k   Schwaab, Ira ^k   Sellers, Thomas A ^k   Shu, Xiao Ou ^k   Shvetsov, Yurii B ^k   Siddiqui, Nadeem ^k   Sieh, Weiva ^k   Song, Honglin ^k   Southey, Melissa C ^k   Sucheston, Lara ^k   Tangen, Ingvild L ^k   Teo, Soo Hwang ^k   Terry, Kathryn L ^k   Thompson, Pamela J ^k   Timorek, Agnieszka ^k   Tsai, Ya Yu ^k   Tworoger, Shelley S ^k   Van Altena, Anne M ^k   Van Nieuwenhuysen, Els ^k   Vergote, Ignace ^k   Vierkant, Robert A ^k   Wang Gohrke, Shan ^k   Walsh, Christine ^k   Wentzensen, Nicolas ^k   Whittemore, Alice S ^k   Wicklund, Kristine G ^k   Wilkens, Lynne R ^k   Woo, Yin Ling ^k   Wu, Xifeng ^k   Wu, Anna H ^k   Yang, Hannah ^k   Zheng, Wei ^k   Ziogas, Argyrios ^k   more..

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b Center for Cell Therapy and Regional Blood Center   (Brazil)

^c UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^d UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^e SHEBA MEDICAL CENTER   (Israel)

^f DANA FARBER CANCER INSTITUTE   (United States)

^g MAYO CLINIC   (United States)

^h MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

ⁱ QIMR BERGHOFER MEDICAL RESEARCH INSTITUTE   (Australia)

^j H LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE   (United States)

^k Center for Integrative Systems Biology CISBi NAP USP   (Brazil)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BREAST EPITHELIUM CELL; CANCER SUSCEPTIBILITY; CELLS BY BODY ANATOMY; CHROMATIN; CLEAR CELL CARCINOMA; CONTROLLED STUDY; CYTOARCHITECTURE; DEPLETION; DNA BINDING MOTIF; DNA RESPONSIVE ELEMENT; ENDOMETRIOSIS; ENHANCER REGION; EPITHELIUM CELL; EXON; FEMALE; GENE LOCUS; GENE SEQUENCE; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; HISTONE MODIFICATION; HUMAN; HUMAN CELL; IMMUNOPRECIPITATION; LNCAP CELL LINE; NUCLEOSOME; OVARY CANCER; OVARY CARCINOMA; OVARY CELL; POSITION WEIGHT MATRIX; PRIORITY JOURNAL; PROMOTER REGION; RNA SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM; STEM CELL; UNTRANSLATED REGION; UTERINE TUBE; ANTIBODY SPECIFICITY; GENETIC PREDISPOSITION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; METABOLISM; OVARY TUMOR; REGULATORY SEQUENCE;

CHROMATIN; HISTONE;

CHROMATIN; FEMALE; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HISTONES; HUMANS; ORGAN SPECIFICITY; OVARIAN NEOPLASMS; POLYMORPHISM, SINGLE NUCLEOTIDE; REGULATORY SEQUENCES, NUCLEIC ACID;

EID: 84936771937     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddv101     Document Type: Article

References (62)

1. Parker, S.C., Stitzel, M.L., Taylor, D.L., Orozco, J.M., Erdos, M.R., Akiyama, J.A., van Bueren, K.L., Chines, P.S., Narisu, N., Black, B.L. et al. (2013) Chromatin stretch enhancer states drive cellspecific gene regulation and harbor human disease risk variants. Proc. Natl Acad. Sci. USA, 110, 17921-17926.
2. Maurano, M.T., Humbert, R., Rynes, E., Thurman, R.E., Haugen, E., Wang, H., Reynolds, A.P., Sandstrom, R., Qu, H., Brody, J. et al. (2012) Systematic localization of common disease-associated variation in regulatory DNA. Science, 337, 1190-1195.
3. Network, C.G.A.R. (2011) Integrated genomic analyses of ovarian carcinoma. Nature, 474, 609-615.
4. Ahmed, A.A., Etemadmoghadam, D., Temple, J., Lynch, A.G., Riad, M., Sharma, R., Stewart, C., Fereday, S., Caldas, C., Defazio, A. et al. (2010) Driver mutations in TP53 are ubiquitous in high grade serous carcinoma of the ovary. J. Pathol., 221, 49-56.
5. Wiegand, K.C., Shah, S.P., Al-Agha, O.M., Zhao, Y., Tse, K., Zeng, T., Senz, J., McConechy, M.K., Anglesio, M.S., Kalloger, S.E. et al. (2010) ARID1A mutations in endometriosisassociated ovarian carcinomas. N. Engl. J. Med., 363, 1532-1543.
6. Rahman, M., Nakayama, K., Rahman, M.T., Nakayama, N., Ishikawa, M., Katagiri, A., Iida, K., Nakayama, S., Otsuki, Y., Shih, I.M. et al. (2012) Clinicopathologic and biological analysis of PIK3CA mutation in ovarian clear cell carcinoma. Hum. Pathol., 43, 2197-2206.
7. Auersperg, N. (2013) Ovarian surface epithelium as a source of ovarian cancers: unwarranted speculation or evidencebased hypothesis? Gynecol. Oncol., 130, 246-251.
8. Leeper, K., Garcia, R., Swisher, E., Goff, B., Greer, B. and Paley, P. (2002) Pathologic findings in prophylactic oophorectomy specimens in high-risk women. Gynecol. Oncol., 87, 52-56.
9. Crum, C.P., Herfs, M., Ning, G., Bijron, J.G., Howitt, B.E., Jimenez, C.A., Hanamornroongruang, S., McKeon, F.D. and Xian, W. (2013) Through the glass darkly: intraepithelial neoplasia, top-down differentiation, and the road to ovarian cancer. J. Pathol., 231, 402-412.
10. Sainz de la Cuesta, R., Eichhorn, J.H., Rice, L.W., Fuller, A.F., Nikrui, N. and Goff, B.A. (1996) Histologic transformation of benign endometriosis to early epithelial ovarian cancer. Gynecol. Oncol., 60, 238-244.
11. Foster, K.A., Harrington, P., Kerr, J., Russell, P., DiCioccio, R.A., Scott, I.V., Jacobs, I., Chenevix-Trench, G., Ponder, B.A. and Gayther, S.A. (1996) Somatic and germline mutations of the BRCA2 gene in sporadic ovarian cancer. Cancer Res., 56, 3622-3625.
12. Futreal, P.A., Liu, Q., Shattuck-Eidens, D., Cochran, C., Harshman, K., Tavtigian, S., Bennett, L.M., Haugen-Strano, A., Swensen, J. and Miki, Y. (1994) BRCA1 mutations in primary breast and ovarian carcinomas. Science, 266, 120-122.
13. Chui, M.H., Ryan, P., Radigan, J., Ferguson, S.E., Pollett, A., Aronson, M., Semotiuk, K., Holter, S., Sy, K., Kwon, J.S. et al. (2014) The histomorphology of Lynch syndrome-associated ovarian carcinomas: toward a subtype-specific screening strategy. Am. J. Surg. Pathol., 38, 1173-1181.
14. Song, H., Ramus, S.J., Tyrer, J., Bolton, K.L., Gentry-Maharaj, A., Wozniak, E., Anton-Culver, H., Chang-Claude, J., Cramer, D.W., DiCioccio, R. et al. (2009) A genome-wide association study identifies a new ovarian cancer susceptibility locus on 9p22.2. Nat. Genet., 41, 996-1000.
15. Bolton, K.L., Tyrer, J., Song, H., Ramus, S.J., Notaridou, M., Jones, C., Sher, T., Gentry-Maharaj, A., Wozniak, E., Tsai, Y.Y. et al. (2010) Common variants at 19p13 are associated with susceptibility to ovarian cancer. Nat. Genet., 42, 880-884.
16. Goode, E.L., Chenevix-Trench, G., Song, H., Ramus, S.J., Notaridou, M., Lawrenson, K., Widschwendter, M., Vierkant, R.A., Larson, M.C., Kjaer, S.K. et al. (2010) A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24. Nat. Genet., 42, 874-879.
17. Bojesen, S.E., Pooley, K.A., Johnatty, S.E., Beesley, J., Michailidou, K., Tyrer, J.P., Edwards, S.L., Pickett, H.A., Shen, H.C., Smart, C.E. et al. (2013) Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer. Nat. Genet., 45, 371-384, 384e371-372.
18. Pharoah, P.D., Tsai, Y.Y., Ramus, S.J., Phelan, C.M., Goode, E.L., Lawrenson, K., Buckley, M., Fridley, B.L., Tyrer, J.P., Shen, H. et al. (2013) GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer. Nat. Genet., 45, 362-370, 370e361-362.
19. Shen, H., Fridley, B.L., Song, H., Lawrenson, K., Cunningham, J.M., Ramus, S.J., Cicek, M.S., Tyrer, J., Stram, D., Larson, M.C. et al. (2013) Epigenetic analysis leads to identification of HNF1B as a subtype-specific susceptibility gene for ovarian cancer. Nat. Commun., 4, 1628.
20. Chen, K., Ma, H., Li, L., Zang, R., Wang, C., Song, F., Shi, T., Yu, D., Yang, M., Xue, W. et al. (2014) Genome-wide association study identifies new susceptibility loci for epithelial ovarian cancer in Han Chinese women. Nat. Commun., 5, 4682.
21. Kuchenbaecker, K.B., Ramus, S.J., Tyrer, J., Lee, A., Shen, H.C., Beesley, J., Lawrenson, K., McGuffog, L., Healey, S., Lee, J.M. et al. (2015) Identification of six new susceptibility loci for invasive epithelial ovarian cancer. Nat. Genet., 47, 164-171.
22. Lawrenson, K., Sproul, D., Grun, B., Notaridou, M., Benjamin, E., Jacobs, I.J., Dafou, D., Sims, A.H. and Gayther, S.A. (2011) Modelling genetic and clinical heterogeneity in epithelial ovarian cancers. Carcinogenesis, 32, 1540-1549.
23. Lawrenson, K., Grun, B., Benjamin, E., Jacobs, I.J., Dafou, D. and Gayther, S.A. (2010) Senescent fibroblasts promote neoplastic transformation of partially transformed ovarian epithelial cells in a three-dimensional model of early stage ovarian cancer. Neoplasia, 12, 317-325.
24. Karst, A.M., Levanon, K. and Drapkin, R. (2011) Modeling highgrade serous ovarian carcinogenesis from the fallopian tube. Proc. Natl Acad. Sci. USA, 108, 7547-7552.
25. Karst, A.M. and Drapkin, R. (2012) Primary culture and immortalization of human fallopian tube secretory epithelial cells. Nat. Protoc., 7, 1755-1764.
26. Brueggmann, D., Templeman, C., Starzinski-Powitz, A., Rao, N.P., Gayther, S.A. and Lawrenson, K. (2014) Novel threedimensional in vitro models of ovarian endometriosis. J. Ovarian Res., 7, 17.
27. Rhie, S.K., Hazelett, D.J., Coetzee, S.G., Yan, C., Noushmehr, H. and Coetzee, G.A. (2014) Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells. BMC Genomics, 15, 331.
28. Abecasis, G.R., Auton, A., Brooks, L.D., DePristo, M.A., Durbin, R.M., Handsaker, R.E., Kang, H.M., Marth, G.T., McVean, G.A. and Consortium, G.P. (2012) An integrated map of genetic variation from 1, 092 human genomes. Nature, 491, 56-65.
29. Kurman, R.J. and Shih, I.M. (2010) The origin and pathogenesis of epithelial ovarian cancer: a proposed unifying theory. Am. J. Surg. Pathol., 34, 433-443.
30. Pearce, C.L., Templeman, C., Rossing, M.A., Lee, A., Near, A.M., Webb, P.M., Nagle, C.M., Doherty, J.A., Cushing-Haugen, K.L., Wicklund, K.G. et al. (2012) Association between endometriosis and risk of histological subtypes of ovarian cancer: a pooled analysis of case-control studies. Lancet Oncol., 13, 385-394.
31. Dzatic-Smiljkovic, O., Vasiljevic, M., Djukic, M., Vugdelic, R. and Vugdelic, J. (2011) Frequency of ovarian endometriosis in epithelial ovarian cancer patients. Clin. Exp. Obstet. Gynecol., 38, 394-398.
32. Yamamoto, S., Tsuda, H., Takano, M., Tamai, S. and Matsubara, O. (2012) PIK3CA mutations and loss of ARID1A protein expression are early events in the development of cystic ovarian clear cell adenocarcinoma. Virchows Arch., 460, 77-87.
33. Yamamoto, S., Tsuda, H., Takano, M., Iwaya, K., Tamai, S. and Matsubara, O. (2011) PIK3CA mutation is an early event in the development of endometriosis-associated ovarian clear cell adenocarcinoma. J. Pathol., 225, 189-194.
34. Bernstein, B.E., Birney, E., Dunham, I., Green, E.D., Gunter, C., Snyder, M. and Consortium, E.P. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
35. Dunham, I., Kundaje, A., Aldred, S.F., Collins, P.J., Davis, C.A., Doyle, F., Epstein, C.B., Frietze, S., Harrow, J., Kaul, R. et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
36. Reade, C.J., McVey, R.M., Tone, A.A., Finlayson, S.J., McAlpine, J.N., Fung-Kee-Fung, M. and Ferguson, S.E. (2014) The fallopian tube as the origin of high grade serous ovarian cancer: review of a paradigm shift. J. Obstet. Gynaecol. Can., 36, 133-140.
37. Lee, Y., Miron, A., Drapkin, R., Nucci, M.R., Medeiros, F., Saleemuddin, A., Garber, J., Birch, C., Mou, H., Gordon, R.W. et al. (2007) A candidate precursor to serous carcinoma that originates in the distal fallopian tube. J. Pathol., 211, 26-35.
38. Dubeau, L. and Drapkin, R. (2013) Coming into focus: the nonovarian origins of ovarian cancer. Ann. Oncol., 24(Suppl. 8), viii28-viii35.
39. Medeiros, F., Muto, M.G., Lee, Y., Elvin, J.A., Callahan, M.J., Feltmate, C., Garber, J.E., Cramer, D.W. and Crum, C.P. (2006) The tubal fimbria is a preferred site for early adenocarcinoma in women with familial ovarian cancer syndrome. Am. J. Surg. Pathol., 30, 230-236.
40. Perets, R., Wyant, G.A., Muto, K.W., Bijron, J.G., Poole, B.B., Chin, K.T., Chen, J.Y., Ohman, A.W., Stepule, C.D., Kwak, S. et al. (2013) Transformation of the fallopian tube secretory epithelium leads to high-grade serous ovarian cancer in brca;tp53;pten models. Cancer Cell, 24, 751-765.
41. Sherman-Baust, C.A., Kuhn, E., Valle, B.L., Shih, I.M., Kurman, R.J., Wang, T.L., Amano, T., Ko, M.S., Miyoshi, I., Araki, Y. et al. (2014) A genetically engineered ovarian cancer mouse model based on fallopian tube transformation mimics human highgrade serous carcinoma development. J. Pathol., 233, 228-237.
42. Howell, V.M. (2014) Genetically engineered mouse models for epithelial ovarian cancer: are we there yet? Semin. Cell Dev. Biol., 27, 106-117.
43. Antoniou, A.C., Wang, X., Fredericksen, Z.S., McGuffog, L., Tarrell, R., Sinilnikova, O.M., Healey, S., Morrison, J., Kartsonaki, C., Lesnick, T. et al. (2010) A locus on 19p13 modifies risk of breast cancer in BRCA1 mutation carriers and is associated with hormone receptor-negative breast cancer in the general population. Nat. Genet., 42, 885-892.
44. Turnbull, C., Ahmed, S., Morrison, J., Pernet, D., Renwick, A., Maranian, M., Seal, S., Ghoussaini, M., Hines, S., Healey, C.S. et al. (2010) Genome-wide association study identifies five new breast cancer susceptibility loci. Nat. Genet., 42, 504-507.
45. Hazelett, D.J., Rhie, S.K., Gaddis, M., Yan, C., Lakeland, D.L., Coetzee, S.G., Henderson, B.E., Noushmehr, H., Cozen, W., Kote-Jarai, Z. et al. (2014) Comprehensive functional annotation of 77 prostate cancer risk loci. PLoS Genet., 10, e1004102.
46. Petersen, G.M., Amundadottir, L., Fuchs, C.S., Kraft, P., Stolzenberg-Solomon, R.Z., Jacobs, K.B., Arslan, A.A., Buenode-Mesquita, H.B., Gallinger, S., Gross, M. et al. (2010) A genome-wide association study identifies pancreatic cancer susceptibility loci on chromosomes 13q22.1, 1q32.1 and 5p15.33. Nat. Genet., 42, 224-228.
47. Turnbull, C., Rapley, E.A., Seal, S., Pernet, D., Renwick, A., Hughes, D., Ricketts, M., Linger, R., Nsengimana, J., Deloukas, P. et al. (2010) Variants near DMRT1, TERT and ATF7IP are associated with testicular germ cell cancer. Nat. Genet., 42, 604-607.
48. Stacey, S.N., Sulem, P., Masson, G., Gudjonsson, S.A., Thorleifsson, G., Jakobsdottir, M., Sigurdsson, A., Gudbjartsson, D.F., Sigurgeirsson, B., Benediktsdottir, K.R. et al. (2009) New common variants affecting susceptibility to basal cell carcinoma. Nat. Genet., 41, 909-914.
49. Li, Q., Seo, J.H., Stranger, B., McKenna, A., Pe'er, I., Laframboise, T., Brown, M., Tyekucheva, S. and Freedman, M.L. (2013) Integrative eQTL-based analyses reveal the biology of breast cancer risk loci. Cell, 152, 633-641.
50. Li, N.F., Wilbanks, G., Balkwill, F., Jacobs, I.J., Dafou, D. and Gayther, S.A. (2004) A modified medium that significantly improves the growth of human normal ovarian surface epithelial (OSE) cells in vitro. Lab. Invest., 84, 923-931.
51. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
52. Ross-Innes, C.S., Stark, R., Teschendorff, A.E., Holmes, K.A., Ali, H.R., Dunning, M.J., Brown, G.D., Gojis, O., Ellis, I.O., Green, A.R. et al. (2012) Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature, 481, 389-393.
53. Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y.C., Laslo, P., Cheng, J.X., Murre, C., Singh, H. and Glass, C.K. (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell, 38, 576-589.
54. Permuth-Wey, J., Kim, D., Tsai, Y.Y., Lin, H.Y., Chen, Y.A., Barnholtz-Sloan, J., Birrer, M.J., Bloom, G., Chanock, S.J., Chen, Z. et al. (2011) LIN28B polymorphisms influence susceptibility to epithelial ovarian cancer. Cancer Res., 71, 3896-3903.
55. Gaudet, M.M., Kuchenbaecker, K.B., Vijai, J., Klein, R.J., Kirchhoff, T., McGuffog, L., Barrowdale, D., Dunning, A.M., Lee, A., Dennis, J. et al. (2013) Identification of a BRCA2-specific modifier locus at 6p24 related to breast cancer risk. PLoS Genet., 9, e1003173.
56. Couch, F.J., Wang, X., McGuffog, L., Lee, A., Olswold, C., Kuchenbaecker, K.B., Soucy, P., Fredericksen, Z., Barrowdale, D., Dennis, J. et al. (2013) Genome-wide association study in BRCA1 mutation carriers identifies novel loci associated with breast and ovarian cancer risk. PLoS Genet., 9, e1003212.
57. Quinlan, A.R. and Hall, I.M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-842.
58. Jeggari, A., Marks, D.S. and Larsson, E. (2012) miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Bioinformatics, 28, 2062-2063.
59. Wang, J., Zhuang, J., Iyer, S., Lin, X., Whitfield, T.W., Greven, M.C., Pierce, B.G., Dong, X., Kundaje, A., Cheng, Y. et al. (2012) Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res., 22, 1798-1812.
60. Kulakovskiy, I.V., Medvedeva, Y.A., Schaefer, U., Kasianov, A.S., Vorontsov, I.E., Bajic, V.B. and Makeev, V.J. (2013) HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. Nucleic Acids Res., 41, D195-D202.
61. Suzuki, R. and Shimodaira, H. (2006) Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics, 22, 1540-1542.
62. Shimodaira, H. (2002) An approximately unbiased test of phylogenetic tree selection. Syst. Biol., 51, 492-508.