메뉴 건너뛰기




Volumn 7, Issue 1, 2015, Pages

The Sweden Cancerome Analysis Network - Breast (SCAN-B) Initiative: A large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine

Author keywords

[No Author keywords available]

Indexed keywords

EOSIN; HEMATOXYLIN; RNA; TRANSCRIPTOME;

EID: 84924342071     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/s13073-015-0131-9     Document Type: Article
Times cited : (144)

References (51)
  • 1
    • 77952874708 scopus 로고    scopus 로고
    • NORDCAN-a Nordic tool for cancer information, planning, quality control and research
    • Engholm G, Ferlay J, Christensen N, Bray F, Gjerstorff ML, Klint A, et al. NORDCAN-a Nordic tool for cancer information, planning, quality control and research. Acta Oncol. 2010;49:725-36.
    • (2010) Acta Oncol , vol.49 , pp. 725-736
    • Engholm, G.1    Ferlay, J.2    Christensen, N.3    Bray, F.4    Gjerstorff, M.L.5    Klint, A.6
  • 2
    • 79151478658 scopus 로고    scopus 로고
    • Cancer survival in Australia, Canada, Denmark, Norway, Sweden, and the UK, 1995-2007 (the International Cancer Benchmarking Partnership): an analysis of population-based cancer registry data
    • Coleman MP, Forman D, Bryant H, Butler J, Rachet B, Maringe C, et al. Cancer survival in Australia, Canada, Denmark, Norway, Sweden, and the UK, 1995-2007 (the International Cancer Benchmarking Partnership): an analysis of population-based cancer registry data. Lancet. 2011;377:127-38.
    • (2011) Lancet , vol.377 , pp. 127-138
    • Coleman, M.P.1    Forman, D.2    Bryant, H.3    Butler, J.4    Rachet, B.5    Maringe, C.6
  • 3
    • 0036843229 scopus 로고    scopus 로고
    • Very-long-term survival rates of patients with cancer
    • Brenner H, Hakulinen T. Very-long-term survival rates of patients with cancer. J Clin Oncol. 2002;20:4405-9.
    • (2002) J Clin Oncol , vol.20 , pp. 4405-4409
    • Brenner, H.1    Hakulinen, T.2
  • 4
    • 67651177577 scopus 로고    scopus 로고
    • Refining systemic therapy for early breast cancer: difficulties with subtraction
    • Dodwell D, Thorpe H, Coleman R. Refining systemic therapy for early breast cancer: difficulties with subtraction. Lancet Oncol. 2009;10:738-9.
    • (2009) Lancet Oncol , vol.10 , pp. 738-739
    • Dodwell, D.1    Thorpe, H.2    Coleman, R.3
  • 5
    • 37349021452 scopus 로고    scopus 로고
    • Exploring the economic impact of breast cancers during the 18 months following diagnosis
    • Gordon L, Scuffham P, Hayes S, Newman B. Exploring the economic impact of breast cancers during the 18 months following diagnosis. Psychooncology. 2007;16:1130-9.
    • (2007) Psychooncology , vol.16 , pp. 1130-1139
    • Gordon, L.1    Scuffham, P.2    Hayes, S.3    Newman, B.4
  • 6
    • 84858249883 scopus 로고    scopus 로고
    • Can genomics bend the cost curve?
    • Armstrong K. Can genomics bend the cost curve? JAMA. 2012;307:1031-2.
    • (2012) JAMA , vol.307 , pp. 1031-1032
    • Armstrong, K.1
  • 7
    • 77956838065 scopus 로고    scopus 로고
    • Advances in understanding cancer genomes through second-generation sequencing
    • Meyerson M, Gabriel S, Getz G. Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet. 2010;11:685-96.
    • (2010) Nat Rev Genet , vol.11 , pp. 685-696
    • Meyerson, M.1    Gabriel, S.2    Getz, G.3
  • 8
    • 18244409687 scopus 로고    scopus 로고
    • Gene expression profiling predicts clinical outcome of breast cancer
    • Van't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature. 2002;415:530-6.
    • (2002) Nature , vol.415 , pp. 530-536
    • Veer, L.J.1    Dai, H.2    Vijver, M.J.3    He, Y.D.4    Hart, A.A.5    Mao, M.6
  • 9
    • 19944422061 scopus 로고    scopus 로고
    • A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer
    • Paik S, Shak S, Tang G, Kim C, Baker J, Cronin M, et al. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med. 2004;351:2817-26.
    • (2004) N Engl J Med , vol.351 , pp. 2817-2826
    • Paik, S.1    Shak, S.2    Tang, G.3    Kim, C.4    Baker, J.5    Cronin, M.6
  • 10
    • 18944391930 scopus 로고    scopus 로고
    • Microarrays and breast cancer clinical studies: forgetting what we have not yet learnt
    • Ahmed AA, Brenton JD. Microarrays and breast cancer clinical studies: forgetting what we have not yet learnt. Breast Cancer Res. 2005;7:96-9.
    • (2005) Breast Cancer Res , vol.7 , pp. 96-99
    • Ahmed, A.A.1    Brenton, J.D.2
  • 11
    • 33644762282 scopus 로고    scopus 로고
    • The impact of expression profiling on prognostic and predictive testing in breast cancer
    • Reis-Filho JS, Westbury C, Pierga JY. The impact of expression profiling on prognostic and predictive testing in breast cancer. J Clin Pathol. 2006;59:225-31.
    • (2006) J Clin Pathol , vol.59 , pp. 225-231
    • Reis-Filho, J.S.1    Westbury, C.2    Pierga, J.Y.3
  • 13
    • 0035881617 scopus 로고    scopus 로고
    • Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns
    • Gruvberger S, Ringner M, Chen Y, Panavally S, Saal LH, Borg A, et al. Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns. Cancer Res. 2001;61:5979-84.
    • (2001) Cancer Res , vol.61 , pp. 5979-5984
    • Gruvberger, S.1    Ringner, M.2    Chen, Y.3    Panavally, S.4    Saal, L.H.5    Borg, A.6
  • 14
    • 34250687198 scopus 로고    scopus 로고
    • Poor prognosis in carcinoma is associated with a gene expression signature of aberrant PTEN tumor suppressor pathway activity
    • Saal LH, Johansson P, Holm K, Gruvberger-Saal SK, She QB, Maurer M, et al. Poor prognosis in carcinoma is associated with a gene expression signature of aberrant PTEN tumor suppressor pathway activity. Proc Natl Acad Sci U S A. 2007;104:7564-9.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 7564-7569
    • Saal, L.H.1    Johansson, P.2    Holm, K.3    Gruvberger-Saal, S.K.4    She, Q.B.5    Maurer, M.6
  • 15
    • 77951641554 scopus 로고    scopus 로고
    • Identification of subtypes in human epidermal growth factor receptor 2-positive breast cancer reveals a gene signature prognostic of outcome
    • Staaf J, Ringner M, Vallon-Christersson J, Jonsson G, Bendahl PO, Holm K, et al. Identification of subtypes in human epidermal growth factor receptor 2-positive breast cancer reveals a gene signature prognostic of outcome. J Clin Oncol. 2010;28:1813-20.
    • (2010) J Clin Oncol , vol.28 , pp. 1813-1820
    • Staaf, J.1    Ringner, M.2    Vallon-Christersson, J.3    Jonsson, G.4    Bendahl, P.O.5    Holm, K.6
  • 17
    • 84924312539 scopus 로고    scopus 로고
    • Sweden Cancerome Analysis Network - Breast
    • Sweden Cancerome Analysis Network - Breast. Available at: http://scan.bmc.lu.se/.
  • 18
    • 79954602547 scopus 로고    scopus 로고
    • Prediction of outcome after diagnosis of metachronous contralateral breast cancer
    • Alkner S, Bendahl PO, Ferno M, Manjer J, Ryden L. Prediction of outcome after diagnosis of metachronous contralateral breast cancer. BMC Cancer. 2011;11:114.
    • (2011) BMC Cancer , vol.11 , pp. 114
    • Alkner, S.1    Bendahl, P.O.2    Ferno, M.3    Manjer, J.4    Ryden, L.5
  • 20
    • 0037099005 scopus 로고    scopus 로고
    • BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data
    • SOFTWARE0003
    • Saal LH, Troein C, Vallon-Christersson J, Gruvberger S, Borg A, Peterson C. BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data. Genome Biol. 2002;3:SOFTWARE0003.
    • (2002) Genome Biol , vol.3
    • Saal, L.H.1    Troein, C.2    Vallon-Christersson, J.3    Gruvberger, S.4    Borg, A.5    Peterson, C.6
  • 24
    • 84875860000 scopus 로고    scopus 로고
    • Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro
    • Nalpas NC, Park SD, Magee DA, Taraktsoglou M, Browne JA, Conlon KM, et al. Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro. BMC Genomics. 2013;14:230.
    • (2013) BMC Genomics , vol.14 , pp. 230
    • Nalpas, N.C.1    Park, S.D.2    Magee, D.A.3    Taraktsoglou, M.4    Browne, J.A.5    Conlon, K.M.6
  • 25
    • 79955691833 scopus 로고    scopus 로고
    • Large scale library generation for high throughput sequencing
    • Borgstrom E, Lundin S, Lundeberg J. Large scale library generation for high throughput sequencing. PLoS One. 2011;6:e19119.
    • (2011) PLoS One , vol.6
    • Borgstrom, E.1    Lundin, S.2    Lundeberg, J.3
  • 26
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357-9.
    • (2012) Nat Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 27
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14:R36.
    • (2013) Genome Biol , vol.14 , pp. R36
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5    Salzberg, S.L.6
  • 28
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    • Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7:562-78.
    • (2012) Nat Protoc , vol.7 , pp. 562-578
    • Trapnell, C.1    Roberts, A.2    Goff, L.3    Pertea, G.4    Kim, D.5    Kelley, D.R.6
  • 29
    • 84924312537 scopus 로고    scopus 로고
    • Python script
    • Brueffer C. TopHat Recondition. Python script. Available at: https://github.com/cbrueffer/tophat-recondition.
    • TopHat Recondition
    • Brueffer, C.1
  • 32
    • 33646874546 scopus 로고    scopus 로고
    • The molecular portraits of breast tumors are conserved across microarray platforms
    • Hu Z, Fan C, Oh DS, Marron JS, He X, Qaqish BF, et al. The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics. 2006;7:96.
    • (2006) BMC Genomics , vol.7 , pp. 96
    • Hu, Z.1    Fan, C.2    Oh, D.S.3    Marron, J.S.4    He, X.5    Qaqish, B.F.6
  • 35
    • 84877028141 scopus 로고    scopus 로고
    • Comprehensive molecular portraits of human breast tumours
    • Atlas TCG. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490:61-70.
    • (2012) Nature , vol.490 , pp. 61-70
    • Atlas, T.C.G.1
  • 36
    • 84861576201 scopus 로고    scopus 로고
    • The landscape of cancer genes and mutational processes in breast cancer
    • Stephens PJ, Tarpey PS, Davies H, Van Loo P, Greenman C, Wedge DC, et al. The landscape of cancer genes and mutational processes in breast cancer. Nature. 2012;486:400-4.
    • (2012) Nature , vol.486 , pp. 400-404
    • Stephens, P.J.1    Tarpey, P.S.2    Davies, H.3    Loo, P.4    Greenman, C.5    Wedge, D.C.6
  • 38
    • 84924312536 scopus 로고    scopus 로고
    • bam-readcount
    • bam-readcount. Available at: https://github.com/genome/bam-readcount/.
  • 39
    • 84863229597 scopus 로고    scopus 로고
    • VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing
    • Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012;22:568-76.
    • (2012) Genome Res , vol.22 , pp. 568-576
    • Koboldt, D.C.1    Zhang, Q.2    Larson, D.E.3    Shen, D.4    McLellan, M.D.5    Lin, L.6
  • 40
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: a flexible suite of utilities for comparing genomic features
    • Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841-2.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 41
    • 77956534324 scopus 로고    scopus 로고
    • ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
    • Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164.
    • (2010) Nucleic Acids Res , vol.38
    • Wang, K.1    Li, M.2    Hakonarson, H.3
  • 42
    • 84924312535 scopus 로고    scopus 로고
    • The Cancer Genome Atlas
    • The Cancer Genome Atlas. Available at: https://tcga-data.nci.nih.gov/.
  • 43
    • 84924312534 scopus 로고    scopus 로고
    • Gene Expression Omnibus
    • Gene Expression Omnibus. Available at: http://www.ncbi.nlm.nih.gov/geo/.
  • 44
    • 20144387695 scopus 로고    scopus 로고
    • PIK3CA mutations correlate with hormone receptors, node metastasis, and ERBB2, and are mutually exclusive with PTEN loss in human breast carcinoma
    • Saal LH, Holm K, Maurer M, Memeo L, Su T, Wang X, et al. PIK3CA mutations correlate with hormone receptors, node metastasis, and ERBB2, and are mutually exclusive with PTEN loss in human breast carcinoma. Cancer Res. 2005;65:2554-9.
    • (2005) Cancer Res , vol.65 , pp. 2554-2559
    • Saal, L.H.1    Holm, K.2    Maurer, M.3    Memeo, L.4    Su, T.5    Wang, X.6
  • 45
    • 33747029250 scopus 로고    scopus 로고
    • Prediction of venous metastases, recurrence, and prognosis in hepatocellular carcinoma based on a unique immune response signature of the liver microenvironment
    • Budhu A, Forgues M, Ye QH, Jia HL, He P, Zanetti KA, et al. Prediction of venous metastases, recurrence, and prognosis in hepatocellular carcinoma based on a unique immune response signature of the liver microenvironment. Cancer Cell. 2006;10:99-111.
    • (2006) Cancer Cell , vol.10 , pp. 99-111
    • Budhu, A.1    Forgues, M.2    Ye, Q.H.3    Jia, H.L.4    He, P.5    Zanetti, K.A.6
  • 46
    • 54049093957 scopus 로고    scopus 로고
    • The expression of 16 genes related to the cell of origin and immune response predicts survival in elderly patients with diffuse large B-cell lymphoma treated with CHOP and rituximab
    • Jais JP, Haioun C, Molina TJ, Rickman DS, de Reynies A, Berger F, et al. The expression of 16 genes related to the cell of origin and immune response predicts survival in elderly patients with diffuse large B-cell lymphoma treated with CHOP and rituximab. Leukemia. 2008;22:1917-24.
    • (2008) Leukemia , vol.22 , pp. 1917-1924
    • Jais, J.P.1    Haioun, C.2    Molina, T.J.3    Rickman, D.S.4    Reynies, A.5    Berger, F.6
  • 47
    • 58849167381 scopus 로고    scopus 로고
    • An immune response enriched 72-gene prognostic profile for early-stage non-small-cell lung cancer
    • Roepman P, Jassem J, Smit EF, Muley T, Niklinski J, van de Velde T, et al. An immune response enriched 72-gene prognostic profile for early-stage non-small-cell lung cancer. Clin Cancer Res. 2009;15:284-90.
    • (2009) Clin Cancer Res , vol.15 , pp. 284-290
    • Roepman, P.1    Jassem, J.2    Smit, E.F.3    Muley, T.4    Niklinski, J.5    Velde, T.6
  • 49
    • 84862526929 scopus 로고    scopus 로고
    • The clonal and mutational evolution spectrum of primary triple-negative breast cancers
    • Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, 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    Oloumi, A.4    Ha, G.5    Zhao, Y.6
  • 50
    • 84924312533 scopus 로고    scopus 로고
    • The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data
    • Tang X, Baheti S, Shameer K, Thompson KJ, Wills Q, Niu N, et al. The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data. Nucleic Acids Res. 2014;42:e172.
    • (2014) Nucleic Acids Res , vol.42
    • Tang, X.1    Baheti, S.2    Shameer, K.3    Thompson, K.J.4    Wills, Q.5    Niu, N.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.