-
1
-
-
77952874708
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
12
-
-
0035931947
-
Gene-expression profiles in hereditary breast cancer
-
Hedenfalk I, Duggan D, Chen Y, Radmacher M, Bittner M, Simon R, et al. Gene-expression profiles in hereditary breast cancer. N Engl J Med. 2001;344:539-48.
-
(2001)
N Engl J Med
, vol.344
, pp. 539-548
-
-
Hedenfalk, I.1
Duggan, D.2
Chen, Y.3
Radmacher, M.4
Bittner, M.5
Simon, R.6
-
13
-
-
0035881617
-
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
-
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
-
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
-
16
-
-
84865146340
-
The retinoblastoma gene undergoes rearrangements in BRCA1-deficient basal-like breast cancer
-
Jonsson G, Staaf J, Vallon-Christersson J, Ringner M, Gruvberger-Saal SK, Saal LH, et al. The retinoblastoma gene undergoes rearrangements in BRCA1-deficient basal-like breast cancer. Cancer Res. 2012;72:4028-36.
-
(2012)
Cancer Res
, vol.72
, pp. 4028-4036
-
-
Jonsson, G.1
Staaf, J.2
Vallon-Christersson, J.3
Ringner, M.4
Gruvberger-Saal, S.K.5
Saal, L.H.6
-
17
-
-
84924312539
-
-
Sweden Cancerome Analysis Network - Breast
-
Sweden Cancerome Analysis Network - Breast. Available at: http://scan.bmc.lu.se/.
-
-
-
-
18
-
-
79954602547
-
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
-
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
-
23
-
-
70350653808
-
Transcriptome analysis by strand-specific sequencing of complementary DNA
-
Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, et al. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 2009;37:e123.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Parkhomchuk, D.1
Borodina, T.2
Amstislavskiy, V.3
Banaru, M.4
Hallen, L.5
Krobitsch, S.6
-
24
-
-
84875860000
-
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
-
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
-
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
-
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
-
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
-
-
Python script
-
Brueffer C. TopHat Recondition. Python script. Available at: https://github.com/cbrueffer/tophat-recondition.
-
TopHat Recondition
-
-
Brueffer, C.1
-
31
-
-
0037478605
-
Repeated observation of breast tumor subtypes in independent gene expression data sets
-
Sørlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, et al. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A. 2003;100:8418-23.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 8418-8423
-
-
Sørlie, T.1
Tibshirani, R.2
Parker, J.3
Hastie, T.4
Marron, J.S.5
Nobel, A.6
-
32
-
-
33646874546
-
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
-
33
-
-
62449131093
-
Supervised risk predictor of breast cancer based on intrinsic subtypes
-
Parker JS, Mullins M, Cheang MC, Leung S, Voduc D, Vickery T, et al. Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol. 2009;27:1160-7.
-
(2009)
J Clin Oncol
, vol.27
, pp. 1160-1167
-
-
Parker, J.S.1
Mullins, M.2
Cheang, M.C.3
Leung, S.4
Voduc, D.5
Vickery, T.6
-
34
-
-
84865766324
-
Probe mapping across multiple microarray platforms
-
Allen JD, Wang S, Chen M, Girard L, Minna JD, Xie Y, et al. Probe mapping across multiple microarray platforms. Brief Bioinform. 2012;13:547-54.
-
(2012)
Brief Bioinform
, vol.13
, pp. 547-554
-
-
Allen, J.D.1
Wang, S.2
Chen, M.3
Girard, L.4
Minna, J.D.5
Xie, Y.6
-
35
-
-
84877028141
-
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
-
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
-
37
-
-
1542515338
-
A census of human cancer genes
-
Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, et al. A census of human cancer genes. Nat Rev Cancer. 2004;4:177-83.
-
(2004)
Nat Rev Cancer
, vol.4
, pp. 177-183
-
-
Futreal, P.A.1
Coin, L.2
Marshall, M.3
Down, T.4
Hubbard, T.5
Wooster, R.6
-
38
-
-
84924312536
-
-
bam-readcount
-
bam-readcount. Available at: https://github.com/genome/bam-readcount/.
-
-
-
-
39
-
-
84863229597
-
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
-
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
-
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
-
-
The Cancer Genome Atlas
-
The Cancer Genome Atlas. Available at: https://tcga-data.nci.nih.gov/.
-
-
-
-
43
-
-
84924312534
-
-
Gene Expression Omnibus
-
Gene Expression Omnibus. Available at: http://www.ncbi.nlm.nih.gov/geo/.
-
-
-
-
44
-
-
20144387695
-
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
-
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
-
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
-
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
-
48
-
-
84867116994
-
Understanding the biology of triple-negative breast cancer
-
Criscitiello C, Azim Jr HA, Schouten PC, Linn SC, Sotiriou C. Understanding the biology of triple-negative breast cancer. Ann Oncol. 2012;23:vi13-18.
-
(2012)
Ann Oncol
, vol.23
, pp. vi13-18
-
-
Criscitiello, C.1
Azim, H.A.2
Schouten, P.C.3
Linn, S.C.4
Sotiriou, C.5
-
49
-
-
84862526929
-
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
-
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
-
51
-
-
84905581610
-
Integrated RNA and DNA sequencing improves mutation detection in low purity tumors
-
Wilkerson MD, Cabanski CR, Sun W, Hoadley KA, Walter V, Mose LE, et al. Integrated RNA and DNA sequencing improves mutation detection in low purity tumors. Nucleic Acids Res. 2014;42:e107.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Wilkerson, M.D.1
Cabanski, C.R.2
Sun, W.3
Hoadley, K.A.4
Walter, V.5
Mose, L.E.6
|