-
1
-
-
78049380554
-
The patterns and dynamics of genomic instability in metastatic pancreatic cancer
-
Campbell, P. J. et al. The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature 467, 1109-1113 (2010).
-
(2010)
Nature
, vol.467
, pp. 1109-1113
-
-
Campbell, P.J.1
-
2
-
-
78049398107
-
Distant metastasis occurs late during the genetic evolution of pancreatic cancer
-
Yachida, S. et al. Distant metastasis occurs late during the genetic evolution of pancreatic cancer. Nature 467, 1114-1117 (2010).
-
(2010)
Nature
, vol.467
, pp. 1114-1117
-
-
Yachida, S.1
-
3
-
-
84863393080
-
Intratumor heterogeneity and branched evolution revealed by multiregion sequencing
-
Gerlinger, M. et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N. Engl. J. Med. 366, 883-892 (2012).
-
(2012)
N. Engl. J. Med.
, vol.366
, pp. 883-892
-
-
Gerlinger, M.1
-
4
-
-
84885092663
-
Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling
-
Bashashati, A. et al. Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling. J. Pathol. 231, 21-34 (2013).
-
(2013)
J. Pathol.
, vol.231
, pp. 21-34
-
-
Bashashati, A.1
-
5
-
-
84924359778
-
Spatial and temporal heterogeneity in high-grade serous ovarian cancer: A phylogenetic analysis
-
Schwarz, R. F. et al. Spatial and temporal heterogeneity in high-grade serous ovarian cancer: a phylogenetic analysis. PLoS Med. 12, e1001789 (2015).
-
(2015)
PLoS Med.
, vol.12
, pp. e1001789
-
-
Schwarz, R.F.1
-
6
-
-
84968547900
-
Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer
-
McPherson, A. et al. Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer. Nat. Genet. 48, 758-767 (2016).
-
(2016)
Nat. Genet.
, vol.48
, pp. 758-767
-
-
McPherson, A.1
-
7
-
-
84926330368
-
Tracking the origins and drivers of subclonal metastatic expansion in prostate cancer
-
Hong, M. K. et al. Tracking the origins and drivers of subclonal metastatic expansion in prostate cancer. Nat. Commun. 6, 6605 (2015).
-
(2015)
Nat. Commun.
, vol.6
, pp. 6605
-
-
Hong, M.K.1
-
8
-
-
84928405167
-
The evolutionary history of lethal metastatic prostate cancer
-
Gundem, G. et al. The evolutionary history of lethal metastatic prostate cancer. Nature 520, 353-357 (2015).
-
(2015)
Nature
, vol.520
, pp. 353-357
-
-
Gundem, G.1
-
9
-
-
84907855592
-
Spatial and temporal diversity in genomic instability processes defines lung cancer evolution
-
de Bruin, E. C. et al. Spatial and temporal diversity in genomic instability processes defines lung cancer evolution. Science 346, 251-256 (2014).
-
(2014)
Science
, vol.346
, pp. 251-256
-
-
De Bruin, E.C.1
-
10
-
-
84895876130
-
Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing
-
Gerlinger, M. et al. Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing. Nat. Genet. 46, 225-233 (2014).
-
(2014)
Nat. Genet.
, vol.46
, pp. 225-233
-
-
Gerlinger, M.1
-
11
-
-
70349969478
-
Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution
-
Shah, S. P. et al. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature 461, 809-813 (2009).
-
(2009)
Nature
, vol.461
, pp. 809-813
-
-
Shah, S.P.1
-
12
-
-
77951139631
-
Genome remodelling in a basal-like breast cancer metastasis and xenograft
-
Ding, L. et al. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature 464, 999-1005 (2010).
-
(2010)
Nature
, vol.464
, pp. 999-1005
-
-
Ding, L.1
-
13
-
-
79953766940
-
Tumour evolution inferred by single-cell sequencing
-
Navin, N. et al. Tumour evolution inferred by single-cell sequencing. Nature 472, 90-94 (2011).
-
(2011)
Nature
, vol.472
, pp. 90-94
-
-
Navin, N.1
-
14
-
-
84890054152
-
Metastatic progression of breast cancer: Insights from 50 years of autopsies
-
Cummings, M. C. et al. Metastatic progression of breast cancer: insights from 50 years of autopsies. J. Pathol. 232, 23-31 (2014).
-
(2014)
J. Pathol.
, vol.232
, pp. 23-31
-
-
Cummings, M.C.1
-
15
-
-
84925500147
-
Convergent loss of PTEN leads to clinical resistance to a PI(3)Ka inhibitor
-
Juric, D. et al. Convergent loss of PTEN leads to clinical resistance to a PI(3)Ka inhibitor. Nature 518, 240-244 (2015).
-
(2015)
Nature
, vol.518
, pp. 240-244
-
-
Juric, D.1
-
16
-
-
84946559772
-
Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer
-
Murtaza, M. et al. Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer. Nat. Commun. 6, 8760 (2015).
-
(2015)
Nat. Commun.
, vol.6
, pp. 8760
-
-
Murtaza, M.1
-
17
-
-
84946215072
-
Genomic characterization of brain metastases reveals branched evolution and potential therapeutic targets
-
Brastianos, P. K. et al. Genomic characterization of brain metastases reveals branched evolution and potential therapeutic targets. Cancer Discov. 5, 1164-1177 (2015).
-
(2015)
Cancer Discov.
, vol.5
, pp. 1164-1177
-
-
Brastianos, P.K.1
-
18
-
-
84959418842
-
Early and multiple origins of metastatic lineages within primary tumors
-
Zhao, Z. M. et al. Early and multiple origins of metastatic lineages within primary tumors. Proc. Natl Acad. Sci. USA 113, 2140-2145 (2016).
-
(2016)
Proc. Natl Acad. Sci. USA
, vol.113
, pp. 2140-2145
-
-
Zhao, Z.M.1
-
19
-
-
84936890500
-
Subclonal diversification of primary breast cancer revealed by multiregion sequencing
-
Yates, L. R. et al. Subclonal diversification of primary breast cancer revealed by multiregion sequencing. Nat. Med. 21, 751-759 (2015).
-
(2015)
Nat. Med.
, vol.21
, pp. 751-759
-
-
Yates, L.R.1
-
20
-
-
72249093615
-
Tumor self-seeding by circulating cancer cells
-
Kim, M. et al. Tumor self-seeding by circulating cancer cells. Cell 139, 1315-1326 (2009).
-
(2009)
Cell
, vol.139
, pp. 1315-1326
-
-
Kim, M.1
-
21
-
-
84860782006
-
Absolute quantification of somatic DNA alterations in human cancer
-
Carter, S. L. et al. Absolute quantification of somatic DNA alterations in human cancer. Nat. Biotechnol. 30, 413-421 (2012).
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 413-421
-
-
Carter, S.L.1
-
22
-
-
84938600532
-
Contralateral breast cancer can represent a metastatic spread of the first primary tumor: Determination of clonal relationship between contralateral breast cancers using next-generation whole genome sequencing
-
Alkner, S. et al. Contralateral breast cancer can represent a metastatic spread of the first primary tumor: determination of clonal relationship between contralateral breast cancers using next-generation whole genome sequencing. Breast Cancer Res. 17, 102 (2015).
-
(2015)
Breast Cancer Res.
, vol.17
, pp. 102
-
-
Alkner, S.1
-
23
-
-
84937758852
-
Exome sequencing of contralateral breast cancer identifies metastatic disease
-
Klevebring, D. et al. Exome sequencing of contralateral breast cancer identifies metastatic disease. Breast Cancer Res. Treat. 151, 319-324 (2015).
-
(2015)
Breast Cancer Res. Treat.
, vol.151
, pp. 319-324
-
-
Klevebring, D.1
-
24
-
-
84882837534
-
Signatures of mutational processes in human cancer
-
Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415-421 (2013).
-
(2013)
Nature
, vol.500
, pp. 415-421
-
-
Alexandrov, L.B.1
-
25
-
-
84952871468
-
Locoregional treatment versus no treatment of the primary tumour in metastatic breast cancer: An open-label randomised controlled trial
-
Badwe, R. et al. Locoregional treatment versus no treatment of the primary tumour in metastatic breast cancer: an open-label randomised controlled trial. Lancet Oncol. 16, 1380-1388 (2015).
-
(2015)
Lancet Oncol.
, vol.16
, pp. 1380-1388
-
-
Badwe, R.1
-
26
-
-
85013851211
-
A randomized controlled trial evaluating resection of the primary breast tumor in women presenting with de novo stage IV breast cancer: Turkish study (Protocol MF07-01)
-
abstr 1005
-
Soran, A. et al. A randomized controlled trial evaluating resection of the primary breast tumor in women presenting with de novo stage IV breast cancer: turkish study (Protocol MF07-01). J. Clin. Oncol. 34, abstr 1005 (2016).
-
(2016)
J. Clin. Oncol.
, vol.34
-
-
Soran, A.1
-
27
-
-
33646546374
-
Effect of primary tumor extirpation in breast cancer patients who present with stage IV disease and an intact primary tumor
-
Babiera, G. V. et al. Effect of primary tumor extirpation in breast cancer patients who present with stage IV disease and an intact primary tumor. Ann. Surg. Oncol. 13, 776-782 (2006).
-
(2006)
Ann. Surg. Oncol.
, vol.13
, pp. 776-782
-
-
Babiera, G.V.1
-
28
-
-
0024556568
-
Presence of a growthstimulating factor in serum following primary tumor removal in mice
-
Fisher, B., Gunduz, N., Coyle, J., Rudock, C. & Saffer, E. Presence of a growthstimulating factor in serum following primary tumor removal in mice. Cancer Res. 49, 1996-2001 (1989).
-
(1989)
Cancer Res.
, vol.49
, pp. 1996-2001
-
-
Fisher, B.1
Gunduz, N.2
Coyle, J.3
Rudock, C.4
Saffer, E.5
-
29
-
-
77149153719
-
Stage IV breast cancer in the era of targeted therapy: Does surgery of the primary tumor matter?
-
Neuman, H. B. et al. Stage IV breast cancer in the era of targeted therapy: does surgery of the primary tumor matter? Cancer 116, 1226-1233 (2010).
-
(2010)
Cancer
, vol.116
, pp. 1226-1233
-
-
Neuman, H.B.1
-
30
-
-
84888381937
-
Activating ESR1 mutations in hormone-resistant metastatic breast cancer
-
Robinson, D. R. et al. Activating ESR1 mutations in hormone-resistant metastatic breast cancer. Nat. Genet. 45, 1446-1451 (2013).
-
(2013)
Nat. Genet.
, vol.45
, pp. 1446-1451
-
-
Robinson, D.R.1
-
31
-
-
84862584058
-
Whole-genome analysis informs breast cancer response to aromatase inhibition
-
Ellis, M. J. et al. Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature 486, 353-360 (2012).
-
(2012)
Nature
, vol.486
, pp. 353-360
-
-
Ellis, M.J.1
-
32
-
-
84947967799
-
Analysis of ESR1 mutation in circulating tumor DNA demonstrates evolution during therapy for metastatic breast cancer
-
Schiavon, G. et al. Analysis of ESR1 mutation in circulating tumor DNA demonstrates evolution during therapy for metastatic breast cancer. Sci. Transl. Med. 7, 313ra182 (2015).
-
(2015)
Sci. Transl. Med.
, vol.7
, pp. 313ra182
-
-
Schiavon, G.1
-
33
-
-
84884559238
-
Endocrine-therapy-resistant ESR1 variants revealed by genomic characterization of breast-cancer-derived xenografts
-
Li, S. et al. Endocrine-therapy-resistant ESR1 variants revealed by genomic characterization of breast-cancer-derived xenografts. Cell Rep. 4, 1116-1130 (2013).
-
(2013)
Cell Rep.
, vol.4
, pp. 1116-1130
-
-
Li, S.1
-
34
-
-
84983543658
-
Plasma ESR1 mutations and the treatment of estrogen receptor-positive advanced breast cancer
-
Fribbens, C. et al. Plasma ESR1 mutations and the treatment of estrogen receptor-positive advanced breast cancer. J. Clin. Oncol. 34, 2961-2968 (2016).
-
(2016)
J. Clin. Oncol.
, vol.34
, pp. 2961-2968
-
-
Fribbens, C.1
-
35
-
-
84890252506
-
D538G mutation in estrogen receptor-alpha: A novel mechanism for acquired endocrine resistance in breast cancer
-
Merenbakh-Lamin, K. et al. D538G mutation in estrogen receptor-alpha: a novel mechanism for acquired endocrine resistance in breast cancer. Cancer Res. 73, 6856-6864 (2013).
-
(2013)
Cancer Res.
, vol.73
, pp. 6856-6864
-
-
Merenbakh-Lamin, K.1
-
36
-
-
84979639070
-
Heterogeneity and clinical significance of ESR1 mutations in ER-positive metastatic breast cancer patients receiving fulvestrant
-
Spoerke, J. M. et al. Heterogeneity and clinical significance of ESR1 mutations in ER-positive metastatic breast cancer patients receiving fulvestrant. Nat. Commun. 7, 11579 (2016).
-
(2016)
Nat. Commun.
, vol.7
, pp. 11579
-
-
Spoerke, J.M.1
-
37
-
-
84888391516
-
ESR1 ligand-binding domain mutations in hormone-resistant breast cancer
-
Toy, W. et al. ESR1 ligand-binding domain mutations in hormone-resistant breast cancer. Nat. Genet. 45, 1439-1445 (2013).
-
(2013)
Nat. Genet.
, vol.45
, pp. 1439-1445
-
-
Toy, W.1
-
38
-
-
84940416459
-
Mutation tracking in circulating tumor DNA predicts relapse in early breast cancer
-
Garcia-Murillas, I. et al. Mutation tracking in circulating tumor DNA predicts relapse in early breast cancer. Sci. Transl. Med. 7, 302ra133 (2015).
-
(2015)
Sci. Transl. Med.
, vol.7
, pp. 302ra133
-
-
Garcia-Murillas, I.1
-
39
-
-
84890254448
-
Recommendations for human epidermal growth factor receptor 2 testing in breast cancer: American Society of Clinical Oncology/ College of American Pathologists clinical practice guideline update
-
Wolff, A. C. et al. Recommendations for human epidermal growth factor receptor 2 testing in breast cancer: American Society of Clinical Oncology/ College of American Pathologists clinical practice guideline update. J. Clin. Oncol. 31, 3997-4013 (2007).
-
(2007)
J. Clin. Oncol.
, vol.31
, pp. 3997-4013
-
-
Wolff, A.C.1
-
40
-
-
67649884743
-
Fast and accurate short read alignment with Burrows- Wheeler transform
-
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
41
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
-
42
-
-
77956295988
-
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
-
McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 1297-1303
-
-
McKenna, A.1
-
43
-
-
79957932376
-
Dindel: Accurate indel calls from short-read data
-
Albers, C. A. et al. Dindel: accurate indel calls from short-read data. Genome Res. 21, 961-973 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 961-973
-
-
Albers, C.A.1
-
44
-
-
84975795680
-
An integrated map of genetic variation from 1, 092 human genomes
-
Abecasis, G. R. et al. An integrated map of genetic variation from 1, 092 human genomes. Nature 491, 56-65 (2012).
-
(2012)
Nature
, vol.491
, pp. 56-65
-
-
Abecasis, G.R.1
-
45
-
-
0035173378
-
DbSNP: The NCBI database of genetic variation
-
Sherry, S. T. et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308-311 (2001).
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 308-311
-
-
Sherry, S.T.1
-
46
-
-
84875634162
-
Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration
-
Thorvaldsdottir, H., Robinson, J. T. & Mesirov, J. P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 14, 178-192 (2013).
-
(2013)
Brief Bioinform.
, vol.14
, pp. 178-192
-
-
Thorvaldsdottir, H.1
Robinson, J.T.2
Mesirov, J.P.3
-
47
-
-
84873813238
-
Copynumber: Efficient algorithms for single- and multi-track copy number segmentation
-
Nilsen, G. et al. Copynumber: efficient algorithms for single- and multi-track copy number segmentation. BMC Genomics 13, 591 (2012).
-
(2012)
BMC Genomics
, vol.13
, pp. 591
-
-
Nilsen, G.1
-
48
-
-
76249097734
-
Genome Alteration Print (GAP): A tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays
-
Popova, T. et al. Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays. Genome Biol. 10, R128 (2009).
-
(2009)
Genome Biol.
, vol.10
, pp. R128
-
-
Popova, T.1
-
49
-
-
78049248432
-
Allele-specific copy number analysis of tumors
-
Van Loo, P. et al. Allele-specific copy number analysis of tumors. Proc. Natl Acad. Sci. USA 107, 16910-16915 (2010).
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 16910-16915
-
-
Van Loo, P.1
-
50
-
-
84900374826
-
Methods and challenges in timing chromosomal abnormalities within cancer samples
-
Purdom, E. et al. Methods and challenges in timing chromosomal abnormalities within cancer samples. Bioinformatics 29, 3113-3120 (2013).
-
(2013)
Bioinformatics
, vol.29
, pp. 3113-3120
-
-
Purdom, E.1
-
51
-
-
84897954204
-
PyClone: Statistical inference of clonal population structure in cancer
-
Roth, A. et al. PyClone: statistical inference of clonal population structure in cancer. Nat. Methods 11, 396-398 (2014).
-
(2014)
Nat. Methods
, vol.11
, pp. 396-398
-
-
Roth, A.1
-
52
-
-
0003991673
-
-
Felsenstein Sinauer Associates Inc.
-
Felsenstein. Inferring Phylogenies (Sinauer Associates Inc., 2004).
-
(2004)
Inferring Phylogenies
-
-
-
53
-
-
1042304216
-
APE: Analyses of Phylogenetics and Evolution in R language
-
Paradis, E., Claude, J. & Strimmer, K. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 20, 289-290 (2004).
-
(2004)
Bioinformatics
, vol.20
, pp. 289-290
-
-
Paradis, E.1
Claude, J.2
Strimmer, K.3
-
54
-
-
0000142497
-
Reconstructing ancestral character states under Wagner parsimony
-
Swofford, D. L. & Maddison, W. P. Reconstructing ancestral character states under Wagner parsimony. Math. Biosci. 87, 199-229 (1987).
-
(1987)
Math. Biosci.
, vol.87
, pp. 199-229
-
-
Swofford, D.L.1
Maddison, W.P.2
-
56
-
-
79951548848
-
Phangorn: Phylogenetic analysis in R
-
Schliep, K. P. phangorn: phylogenetic analysis in R. Bioinformatics 27, 592-593 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 592-593
-
-
Schliep, K.P.1
-
57
-
-
84901318643
-
Phylogenetic quantification of intra-tumour heterogeneity
-
Schwarz, R. F. et al. Phylogenetic quantification of intra-tumour heterogeneity. PLoS Comput. Biol. 10, e1003535 (2014).
-
(2014)
PLoS Comput. Biol.
, vol.10
, pp. e1003535
-
-
Schwarz, R.F.1
|