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Volumn 12, Issue , 2013, Pages 125-142

Novel integrative genomics approach for associating GWAS information with intrinsic subtypes of breast cancer

Author keywords

GWAS subtypes breast cancer

Indexed keywords

ARTICLE; BREAST CANCER; CANCER GENETICS; CANCER RISK; CONTROLLED STUDY; GENE IDENTIFICATION; GENE REGULATORY NETWORK; GENETIC ASSOCIATION; GENETIC RISK; GENETIC SCREENING; GENETIC VARIABILITY; GENOMICS; HUMAN GENOME; MEDICAL INFORMATION; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84877972217     PISSN: None     EISSN: 11769351     Source Type: Journal    
DOI: 10.4137/CIN.S11452     Document Type: Article
Times cited : (3)

References (52)
  • 1
    • 80053599055 scopus 로고    scopus 로고
    • An integrative genomics approach to biomarker discovery in breast cancer
    • Hicks C, Asfour R, Pannuti A, Miele L. An integrative genomics approach to biomarker discovery in breast cancer. Cancer Inform. 2011;10:185-204.
    • (2011) Cancer Inform , vol.10 , pp. 185-204
    • Hicks, C.1    Asfour, R.2    Pannuti, A.3    Miele, L.4
  • 2
    • 79955419172 scopus 로고    scopus 로고
    • Genetic variants associated with breast-cancer risk: Comprehensive research synopsis, meta-analysis, and epidemiological evidence
    • Zhang B, Beeghly-Fadiel A, Long J, Wei Z. Genetic variants associated with breast-cancer risk: comprehensive research synopsis, meta-analysis, and epidemiological evidence. Lancet. 2011;12:477-88.
    • (2011) Lancet , vol.12 , pp. 477-488
    • Zhang, B.1    Beeghly-Fadiel, A.2    Long, J.3    Wei, Z.4
  • 3
    • 0034680102 scopus 로고    scopus 로고
    • Molecular portraits of human breast tumours
    • Perou CM, Sorlie T, Eisen MB, et al. Molecular portraits of human breast tumours. Nature. 2000;406:747-52.
    • (2000) Nature , vol.406 , pp. 747-752
    • Perou, C.M.1    Sorlie, T.2    Eisen, M.B.3
  • 4
    • 9644310201 scopus 로고    scopus 로고
    • Molecular portraits of Breast cancer: Tumour subtypes as distinct disease entities
    • Sorlie T. Molecular portraits of Breast cancer: tumour subtypes as distinct disease entities. Eur J.Cancer. 2004;40:2667-75.
    • (2004) Eur J. Cancer , vol.40 , pp. 2667-2675
    • Sorlie, T.1
  • 6
    • 80053366674 scopus 로고    scopus 로고
    • Low penetrance breast cancer susceptibility loci are associated with specific breast tumor subtypes: Findings from the Breast Cancer Association Consortium
    • Broeks A, Schmidt MK, Sherman ME, et al. Low penetrance breast cancer susceptibility loci are associated with specific breast tumor subtypes: Findings from the Breast Cancer Association Consortium. Hum Mol Genet. 2011;20:1-15.
    • (2011) Hum Mol Genet , vol.20 , pp. 1-15
    • Broeks, A.1    Schmidt, M.K.2    Sherman, M.E.3
  • 7
    • 79551694006 scopus 로고    scopus 로고
    • Associations of breast cancer risk factors with tumor subtypes: A pooled analysis from the Breast Cancer Association Consortium studies
    • Yang XR, Chang-Claude J, Goode EL, et al. 2011. Associations of breast cancer risk factors with tumor subtypes: A pooled analysis from the Breast Cancer Association Consortium studies. J Natl Cancer Inst. 2011;103:250-63.
    • (2011) J Natl Cancer Inst , vol.103 , pp. 250-263
    • Yang, X.R.1    Chang-Claude, J.2    Goode, E.L.3
  • 8
    • 70249134919 scopus 로고    scopus 로고
    • Molecular networks as sensors and drivers of common human diseases
    • Schadt EE. Molecular networks as sensors and drivers of common human diseases. Nature. 2009;461:218-23.
    • (2009) Nature , vol.461 , pp. 218-223
    • Schadt, E.E.1
  • 9
    • 38949094880 scopus 로고    scopus 로고
    • Assessment of cumulative evidence on genetic associations: Interim guidelines
    • Ioannidis JP, Boffetta P, Little J, et al. Assessment of cumulative evidence on genetic associations: Interim guidelines. Int J Epidemiol. 2008;37:120-32.
    • (2008) Int J Epidemiol , vol.37 , pp. 120-132
    • Ioannidis, J.P.1    Boffetta, P.2    Little, J.3
  • 10
    • 67749106283 scopus 로고    scopus 로고
    • Genome-wide association studies, field synopses, and the development of the knowledge base on genetic variation in human diseases
    • Khoury MJ, Bertram I, Boffetta P, et al. Genome-wide association studies, field synopses, and the development of the knowledge base on genetic variation in human diseases. Am J Epidemiol. 2009;170:269-79.
    • (2009) Am J Epidemiol , vol.170 , pp. 269-279
    • Khoury, M.J.1    Bertram, I.2    Boffetta, P.3
  • 11
    • 63449095084 scopus 로고    scopus 로고
    • Systematic reviews of genetic association studies. Human Genome Epidemiology Network
    • Sagoo GS, Little J, Higgins JP. Systematic reviews of genetic association studies. Human Genome Epidemiology Network. PLoS Med. 2009;6:e28.
    • (2009) PLoS Med , vol.6
    • Sagoo, G.S.1    Little, J.2    Higgins, J.P.3
  • 12
    • 69149107165 scopus 로고    scopus 로고
    • Preferred reporting items for systematic reviews and meta-analyses: The PRISMA statement
    • Moher D, Liberati A, Tetzlaff J, Altman DG. Preferred reporting items for systematic reviews and meta-analyses: the PRISMA statement. Ann Intern Med. 2009;151:264-9.
    • (2009) Ann Intern Med , vol.151 , pp. 264-269
    • Moher, D.1    Liberati, A.2    Tetzlaff, J.3    Altman, D.G.4
  • 13
    • 68049137869 scopus 로고    scopus 로고
    • The PRISMA statement for reporting systematic reviews and meta-analyses studies that evaluate health care interventions: Explanation and elaboration
    • Liberati A, Altman DG, Tetzlaff J, et al. The PRISMA statement for reporting systematic reviews and meta-analyses studies that evaluate health care interventions: explanation and elaboration. PLoS Med. 2009;6(7):e1000100.
    • (2009) PLoS Med , vol.6 , Issue.7
    • Liberati, A.1    Altman, D.G.2    Tetzlaff, J.3
  • 14
    • 79959520764 scopus 로고    scopus 로고
    • Molecular stratification of triple-negative breast cancer
    • Perou CM. Molecular stratification of triple-negative breast cancer. Oncologist. 2011;16(Suppl 1):61-70.
    • (2011) Oncologist , vol.16 , Issue.1 SUPPL. , pp. 61-70
    • Perou, C.M.1
  • 15
    • 79960015997 scopus 로고    scopus 로고
    • Identification of triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies
    • Lehmann BD, Bauer JA, Chen X, et al. Identification of triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies. J Clin Invest. 2012;121:2750-67.
    • (2012) J Clin Invest , vol.121 , pp. 2750-2767
    • Lehmann, B.D.1    Bauer, J.A.2    Chen, X.3
  • 16
    • 0036081355 scopus 로고    scopus 로고
    • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    • Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucl Acids Res. 2002;30(1):207-10.
    • (2002) Nucl Acids Res , vol.30 , Issue.1 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 17
    • 79958728723 scopus 로고    scopus 로고
    • A gene expression signature identifies two prognostic subgroups of basal breast cancer
    • Sabatier R, Finetti P, Cervera N, et al. A gene expression signature identifies two prognostic subgroups of basal breast cancer. Breast Cancer Res Treat. 2011;126:407-20.
    • (2011) Breast Cancer Res Treat , vol.126 , pp. 407-420
    • Sabatier, R.1    Finetti, P.2    Cervera, N.3
  • 18
    • 74849113364 scopus 로고    scopus 로고
    • Proliferative genes dominate malignancy-risk gene signature in histologically-normal breast tissue
    • Chen D, Nasir A, Culhane A, et al. Proliferative genes dominate malignancy-risk gene signature in histologically-normal breast tissue. Breast Cancer Res Treat. 2010;119(2):335-46.
    • (2010) Breast Cancer Res Treat , vol.119 , Issue.2 , pp. 335-346
    • Chen, D.1    Nasir, A.2    Culhane, A.3
  • 19
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J Royal Stat Soc Series B. 1995;57(1):289-300.
    • (1995) J Royal Stat Soc Series B , vol.57 , Issue.1 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 20
    • 0035991757 scopus 로고    scopus 로고
    • A paradigm for class prediction using gene expression profiles
    • RadMacher MD, McShane LM, Simon R. A paradigm for class prediction using gene expression profiles. J Comput Biol. 2002;9(3):505-11.
    • (2002) J Comput Biol , vol.9 , Issue.3 , pp. 505-511
    • Radmacher, M.D.1    McShane, L.M.2    Simon, R.3
  • 21
    • 67849097353 scopus 로고    scopus 로고
    • Pomello II: Finding differentially expressed genes
    • Morrissey ER, Diaz-Uriarte R. Pomello II: Finding differentially expressed genes. Nucleic Acids Res. 2009;37:W581-6.
    • (2009) Nucleic Acids Res , vol.37
    • Morrissey, E.R.1    Diaz-Uriarte, R.2
  • 24
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology. The Gene Ontolgy Consortium
    • Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. The Gene Ontolgy Consortium. Nat Genet. 2000;25(1):25-9.
    • (2000) Nat Genet , vol.25 , Issue.1 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3
  • 25
    • 85172046117 scopus 로고    scopus 로고
    • Ingenuity Pathways Analysis (IPA) system, California
    • Ingenuity Pathways Analysis (IPA) system. Ingenuity Incorporated, California.
    • Ingenuity Incorporated
  • 26
    • 80053375835 scopus 로고    scopus 로고
    • Common breast cancer susceptibility loci are associated with triple-negative breast cancer
    • Stevens KN, Vachon CM, Lee AM, et al. Common breast cancer susceptibility loci are associated with triple-negative breast cancer. Cancer Res. 2011;71(19):6240-9.
    • (2011) Cancer Res , vol.71 , Issue.19 , pp. 6240-6249
    • Stevens, K.N.1    Vachon, C.M.2    Lee, A.M.3
  • 27
    • 84859375225 scopus 로고    scopus 로고
    • 19p13.1 Is a triple-negative-specific breast cancer susceptibility locus
    • Stevens KN, Fredericksen Z, Vachon CM, et al. 19p13.1 Is a triple-negative-specific breast cancer susceptibility locus. Cancer Res. 2012;72(7): 1795-803.
    • (2012) Cancer Res , vol.72 , Issue.7 , pp. 1795-1803
    • Stevens, K.N.1    Fredericksen, Z.2    Vachon, C.M.3
  • 28
    • 58149331121 scopus 로고    scopus 로고
    • Genetic susceptibility loci for breast cancer by estrogen receptor (ER) status
    • Garcia-Closas M, Chanock S. Genetic susceptibility loci for breast cancer by estrogen receptor (ER) status. Cancer Res. 2008;14(24):8000-9.
    • (2008) Cancer Res , vol.14 , Issue.24 , pp. 8000-8009
    • Garcia-Closas, M.1    Chanock, S.2
  • 29
    • 67649584052 scopus 로고    scopus 로고
    • Gene ontology analysis of GWA study data sets provides insights into biology of bipolar disorder
    • Holmans P, Green EK, Pahwa JS, et al. Gene ontology analysis of GWA study data sets provides insights into biology of bipolar disorder. Am J Hum Genet. 2009;85:13-24.
    • (2009) Am J Hum Genet , vol.85 , pp. 13-24
    • Holmans, P.1    Green, E.K.2    Pahwa, J.S.3
  • 30
    • 67249117049 scopus 로고    scopus 로고
    • Potential etiologic and functional implications of genome-wide association loci of human diseases and traits
    • Hindorff LA, Sethupathy P, Junkins HA, et al. Potential etiologic and functional implications of genome-wide association loci of human diseases and traits. Proc Nat Acad Sci U S A. 2009;106:9362-7.
    • (2009) Proc Nat Acad Sci U S A , vol.106 , pp. 9362-9367
    • Hindorff, L.A.1    Sethupathy, P.2    Junkins, H.A.3
  • 31
    • 77954407332 scopus 로고    scopus 로고
    • Genomewide association studies and assessment of the risk of disease
    • Manolio TA. Genomewide association studies and assessment of the risk of disease. N Engl J Med. 2010;363:166-76.
    • (2010) N Engl J Med , vol.363 , pp. 166-176
    • Manolio, T.A.1
  • 32
    • 84862526929 scopus 로고    scopus 로고
    • The clonal and mutational evolution spectrum of primary triple-negative breast cancers
    • Shah SP, Roth A, Goya R, et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature. 2012;486:395-9.
    • (2012) Nature , vol.486 , pp. 395-399
    • Shah, S.P.1    Roth, A.2    Goya, R.3
  • 33
    • 2942572926 scopus 로고    scopus 로고
    • Quantifying the relationship between co-expression, co-regulation and gene function
    • Allocco DJ, Kohane IS, Butte AJ. Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinformatics. 2004; 5:18.
    • (2004) BMC Bioinformatics , vol.5 , pp. 18
    • Allocco, D.J.1    Kohane, I.S.2    Butte, A.J.3
  • 34
    • 42349112088 scopus 로고    scopus 로고
    • Genome-wide association studies for complex traits: Consensus, uncertainty and challenges
    • McCarthy MI, Abecasis GR, Cardon LR, et al. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet. 2008;9:356-69.
    • (2008) Nat Rev Genet , vol.9 , pp. 356-369
    • McCarthy, M.I.1    Abecasis, G.R.2    Cardon, L.R.3
  • 35
    • 42049122030 scopus 로고    scopus 로고
    • The DNA damage signalling kinase ATM is aberrantly reduced or lost in BRCA1/BRCA2-deficient and ER/PR/ERBB2-triple-negative breast cancer
    • Tommiska J, Bartkova J, Heinonen M, et al. The DNA damage signalling kinase ATM is aberrantly reduced or lost in BRCA1/BRCA2-deficient and ER/PR/ERBB2-triple-negative breast cancer. Oncogene. 2008;27(17):2501-6.
    • (2008) Oncogene , vol.27 , Issue.17 , pp. 2501-2506
    • Tommiska, J.1    Bartkova, J.2    Heinonen, M.3
  • 36
    • 0343618708 scopus 로고    scopus 로고
    • The ATM gene and breast cancer: Is it really a risk factor?
    • Angèle S, Hall J. The ATM gene and breast cancer: is it really a risk factor? Mutat Res. 2000;462(2-3):167-78.
    • (2000) Mutat Res , vol.462 , Issue.2-3 , pp. 167-178
    • Angèle, S.1    Hall, J.2
  • 37
    • 23844507598 scopus 로고    scopus 로고
    • The Ataxia-telangiectasia mutated gene and breast cancer: Gene expression profiles and sequence variants
    • Hall J. The Ataxia-telangiectasia mutated gene and breast cancer: gene expression profiles and sequence variants. Cancer Lett. 2005;227(2): 105-14.
    • (2005) Cancer Lett , vol.227 , Issue.2 , pp. 105-114
    • Hall, J.1
  • 38
    • 33749998118 scopus 로고    scopus 로고
    • Mutation analysis and characterization of ATR sequence variants in breast cancer cases from high-risk French Canadian breast/ovarian cancer families
    • Durocher F, Labrie Y, Soucy P, et al. Mutation analysis and characterization of ATR sequence variants in breast cancer cases from high-risk French Canadian breast/ovarian cancer families. BMC Cancer. 2006:29(6):230.
    • (2006) BMC Cancer , vol.29 , Issue.6 , pp. 230
    • Durocher, F.1    Labrie, Y.2    Soucy, P.3
  • 39
    • 84873448622 scopus 로고    scopus 로고
    • An integrative genomics approach for associating GWAS information with triple-negative breast cancer
    • Hicks C, Kumar R, Pannuti A, et al. An integrative genomics approach for associating GWAS information with triple-negative breast cancer. Cancer Inform. 2013;12:1-20.
    • (2013) Cancer Inform , vol.12 , pp. 1-20
    • Hicks, C.1    Kumar, R.2    Pannuti, A.3
  • 40
    • 84863626243 scopus 로고    scopus 로고
    • Low p53 binding protein 1 (53BP1) expression is associated with increased local recurrence in breast cancer patients treated with breast-conserving surgery and radiotherapy
    • Neboori HJ, Haffty BG, Wu H, et al. Low p53 binding protein 1 (53BP1) expression is associated with increased local recurrence in breast cancer patients treated with breast-conserving surgery and radiotherapy. Int J Radiat Oncol Biol Phys. 2012;83(5):e677-83.
    • (2012) Int J Radiat Oncol Biol Phys , vol.83 , Issue.5
    • Neboori, H.J.1    Haffty, B.G.2    Wu, H.3
  • 41
    • 77953291328 scopus 로고    scopus 로고
    • 53BP1 loss rescues BRCA1 deficiency and is associated with triple-negative and BRCA-mutated breast cancers
    • Bouwman P, Aly A, Escandell JM, et al. 53BP1 loss rescues BRCA1 deficiency and is associated with triple-negative and BRCA-mutated breast cancers. Nat Struct Mol Biol. 2010;17(6):688-95.
    • (2010) Nat Struct Mol Biol , vol.17 , Issue.6 , pp. 688-695
    • Bouwman, P.1    Aly, A.2    Escandell, J.M.3
  • 42
    • 56649086648 scopus 로고    scopus 로고
    • Aberrations of the MRE11-RAD50-NBS1 DNA damage sensor complex in human breast cancer: MRE11 as a candidate familial cancer-predisposing gene
    • Bartkova J, Tommiska J, Oplustilova L, et al. Aberrations of the MRE11-RAD50-NBS1 DNA damage sensor complex in human breast cancer: MRE11 as a candidate familial cancer-predisposing gene. Mol Oncol. 2008; 2(4):296-316.
    • (2008) Mol Oncol , vol.2 , Issue.4 , pp. 296-316
    • Bartkova, J.1    Tommiska, J.2    Oplustilova, L.3
  • 43
    • 44449112372 scopus 로고    scopus 로고
    • Therapeutic exploitation of tumor cell defects in homologous recombination
    • Powell SN, Kachnic LA. Therapeutic exploitation of tumor cell defects in homologous recombination. Anticancer Agents Med Chem. 2008;8(4): 448-60.
    • (2008) Anticancer Agents Med Chem , vol.8 , Issue.4 , pp. 448-460
    • Powell, S.N.1    Kachnic, L.A.2
  • 44
    • 0035963435 scopus 로고    scopus 로고
    • Specific protection against breast cancers by cyclin D1 ablation
    • Yu Q, Geng Y, Sicinski P. Specific protection against breast cancers by cyclin D1 ablation. Nature. 2001;411(6841):1017-21.
    • (2001) Nature , vol.411 , Issue.6841 , pp. 1017-1021
    • Yu, Q.1    Geng, Y.2    Sicinski, P.3
  • 45
    • 0033564697 scopus 로고    scopus 로고
    • CDK inhibitors: Positive and negative regulators of G1-phase progression
    • Sherr CJ, Roberts JM. CDK inhibitors: positive and negative regulators of G1-phase progression. Genes Dev. 1999;13(12):1501-12.
    • (1999) Genes Dev , vol.13 , Issue.12 , pp. 1501-1512
    • Sherr, C.J.1    Roberts, J.M.2
  • 46
    • 37549056200 scopus 로고    scopus 로고
    • The emerging landscape of breast cancer susceptibility
    • Stratton MS, Rahman N. The emerging landscape of breast cancer susceptibility. Nat Genet. 2008;40(1):17-22.
    • (2008) Nat Genet , vol.40 , Issue.1 , pp. 17-22
    • Stratton, M.S.1    Rahman, N.2
  • 47
    • 77953151341 scopus 로고    scopus 로고
    • Pathway analysis of breast cancer genome-wide association study highlights three pathways and one canonical signaling cascade
    • Menashe I, Maeder D, Garcia-Closas M, et al. Pathway analysis of breast cancer genome-wide association study highlights three pathways and one canonical signaling cascade. Cancer Res. 2010;70(11):4453-9.
    • (2010) Cancer Res , vol.70 , Issue.11 , pp. 4453-4459
    • Menashe, I.1    Maeder, D.2    Garcia-Closas, M.3
  • 48
    • 40549116980 scopus 로고    scopus 로고
    • Comprehensive association testing of common genetic variation in DNA repair pathways genes in relationship with breast cancer risk in multiple populations
    • Haiman CA, Hsu C, de Bakker PI, et al. Comprehensive association testing of common genetic variation in DNA repair pathways genes in relationship with breast cancer risk in multiple populations. Hum Mol Genet. 2008; 17(6):825-34.
    • (2008) Hum Mol Genet , vol.17 , Issue.6 , pp. 825-834
    • Haiman, C.A.1    Hsu, C.2    de Bakker, P.I.3
  • 50
    • 5444256188 scopus 로고    scopus 로고
    • Allele-specific gene expression differences in humans
    • Buckland PR. Allele-specific gene expression differences in humans. Hum Mol Genet. 2004;13(2):R255-60.
    • (2004) Hum Mol Genet , vol.13 , Issue.2
    • Buckland, P.R.1
  • 51
    • 58349092614 scopus 로고    scopus 로고
    • Allelle-specific gene expression is widespread across the genome and biological processes
    • Paracios R, Gazave E, Goni J, et al. Allelle-specific gene expression is widespread across the genome and biological processes. PLoS One. 2009;4(1): e4150.
    • (2009) PLoS One , vol.4 , Issue.1
    • Paracios, R.1    Gazave, E.2    Goni, J.3
  • 52
    • 45149099137 scopus 로고    scopus 로고
    • Allele-specific up-regulation of FGFR2 increases susceptibility to breast cancer
    • Meyer KB, Maja A-T, O'Reilly M, et al. Allele-specific up-regulation of FGFR2 increases susceptibility to breast cancer. PLoS Biol. 2008;6(5): e108.
    • (2008) PLoS Biol , vol.6 , Issue.5
    • Meyer, K.B.1    Maja, A.-T.2    O'Reilly, M.3


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