-
1
-
-
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
-
2
-
-
79953766940
-
Tumor evolution inferred by single-cell sequencing
-
Navin, N., et al. Tumor evolution inferred by single-cell sequencing. Nature 472, 90-94 (2011).
-
(2011)
Nature
, vol.472
, pp. 90-94
-
-
Navin, N.1
-
3
-
-
84874354257
-
The implications of clonal genome evolution for cancer medicine
-
Aparicio, S., Caldas, C. The implications of clonal genome evolution for cancer medicine. N. Engl. J. Med. 368, 842-851 (2013).
-
(2013)
N. Engl. J. Med.
, vol.368
, pp. 842-851
-
-
Aparicio, S.1
Caldas, C.2
-
4
-
-
84939165961
-
Intratumor genetic heterogeneity and alternative driver genetic alterations in breast cancers with heterogeneous HER2 gene amplification
-
Ng, C. K., et al. Intratumor genetic heterogeneity and alternative driver genetic alterations in breast cancers with heterogeneous HER2 gene amplification. Genome Biol. 16, 107 (2015).
-
(2015)
Genome Biol.
, vol.16
, pp. 107
-
-
Ng, C.K.1
-
5
-
-
84859637667
-
Genomic and mutational profiling of ductal carcinomas in situ and matched adjacent invasive breast cancers reveals intratumor genetic heterogeneity and clonal selection
-
Hernandez, L., et al. Genomic and mutational profiling of ductal carcinomas in situ and matched adjacent invasive breast cancers reveals intratumor genetic heterogeneity and clonal selection. J. Pathol. 227, 42-52 (2012).
-
(2012)
J. Pathol.
, vol.227
, pp. 42-52
-
-
Hernandez, L.1
-
6
-
-
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
-
7
-
-
84936890500
-
Subclonal diversification of primary breast cancer revealed by multi-region sequencing
-
Yates, L. R., et al. Subclonal diversification of primary breast cancer revealed by multi-region sequencing. Nat. Med. 21, 751-759 (2015).
-
(2015)
Nat. Med.
, vol.21
, pp. 751-759
-
-
Yates, L.R.1
-
8
-
-
84928421520
-
Breast cancer genomics from microarrays to massively parallel sequencing: Paradigms and new insights
-
Ng, C. K., Schultheis, A. M., Bidard, F. C., Weigelt, B., Reis-Filho, J. S. Breast cancer genomics from microarrays to massively parallel sequencing: paradigms and new insights. J. Natl. Cancer Inst. 107, 15 (2015).
-
(2015)
J. Natl. Cancer Inst.
, vol.107
, pp. 15
-
-
Ng, C.K.1
Schultheis, A.M.2
Bidard, F.C.3
Weigelt, B.4
Reis-Filho, J.S.5
-
9
-
-
84862776906
-
Clonal evolution in relapsed acute myeloid leukemia revealed by whole-genome sequencing
-
Ding, L., et al. Clonal evolution in relapsed acute myeloid leukemia revealed by whole-genome sequencing. Nature 481, 506-510 (2012).
-
(2012)
Nature
, vol.481
, pp. 506-510
-
-
Ding, L.1
-
10
-
-
84861550476
-
The life history of 21 breast cancers
-
Nik-Zainal, S., et al. The life history of 21 breast cancers. Cell 149, 994-1007 (2012).
-
(2012)
Cell
, vol.149
, pp. 994-1007
-
-
Nik-Zainal, S.1
-
11
-
-
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
-
12
-
-
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
-
13
-
-
84906238686
-
Clonal evolution in breast cancer revealed by single-nucleus genome sequencing
-
Wang, Y., et al. Clonal evolution in breast cancer revealed by single-nucleus genome sequencing. Nature 512, 155-160 (2014).
-
(2014)
Nature
, vol.512
, pp. 155-160
-
-
Wang, Y.1
-
14
-
-
84929658867
-
Optimizing sparse sequencing of single cells for highly multiplex copy-number profiling
-
Baslan, T., et al. Optimizing sparse sequencing of single cells for highly multiplex copy-number profiling. Genome Res. 25, 714-724 (2015).
-
(2015)
Genome Res.
, vol.25
, pp. 714-724
-
-
Baslan, T.1
-
15
-
-
84861033754
-
Genome-wide copy-number analysis of single cells
-
Baslan, T., et al. Genome-wide copy-number analysis of single cells. Nat. Protoc. 7, 1024-1041 (2012).
-
(2012)
Nat. Protoc.
, vol.7
, pp. 1024-1041
-
-
Baslan, T.1
-
16
-
-
84929686953
-
SNES: Single-nucleus exome sequencing
-
Leung, M. L., Wang, Y., Waters, J., Navin, N. E. SNES: single-nucleus exome sequencing. Genome Biol. 16, 55 (2015).
-
(2015)
Genome Biol.
, vol.16
, pp. 55
-
-
Leung, M.L.1
Wang, Y.2
Waters, J.3
Navin, N.E.4
-
17
-
-
84880213158
-
Single-cell paired-end genome sequencing reveals structural variation per cell cycle
-
Voet, T., et al. Single-cell paired-end genome sequencing reveals structural variation per cell cycle. Nucleic Acids Res. 41, 6119-6138 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 6119-6138
-
-
Voet, T.1
-
18
-
-
84933278862
-
Clinical management of breast cancer heterogeneity
-
Zardavas, D., Irrthum, A., Swanton, C., Piccart, M. Clinical management of breast cancer heterogeneity. Nat. Rev. Clin. Oncol. 12, 381-394 (2015).
-
(2015)
Nat. Rev. Clin. Oncol.
, vol.12
, pp. 381-394
-
-
Zardavas, D.1
Irrthum, A.2
Swanton, C.3
Piccart, M.4
-
19
-
-
77951631386
-
The isolation of nucleic acids from fixed, paraffin-embedded tissues-which methods are useful when
-
Gilbert, M. T., et al. The isolation of nucleic acids from fixed, paraffin-embedded tissues-which methods are useful when. PLoS One 2, e537 (2007).
-
(2007)
PLoS One
, vol.2
, pp. e537
-
-
Gilbert, M.T.1
-
20
-
-
84925582188
-
Anchored multiplex PCR for targeted next-generation sequencing
-
Zheng, Z., et al. Anchored multiplex PCR for targeted next-generation sequencing. Nat. Med. 20, 1479-1484 (2014).
-
(2014)
Nat. Med.
, vol.20
, pp. 1479-1484
-
-
Zheng, Z.1
-
21
-
-
84902148239
-
Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine
-
Van Allen, E. M., et al. Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine. Nat. Med. 20, 682-688 (2014).
-
(2014)
Nat. Med.
, vol.20
, pp. 682-688
-
-
Van Allen, E.M.1
-
22
-
-
0026099836
-
PCR amplification from paraffin-embedded tissues. Effects of fixative and fixation time
-
Greer, C. E., Peterson, S. L., Kiviat, N. B., Manos, M. M. PCR amplification from paraffin-embedded tissues. Effects of fixative and fixation time. Am. J. Clin. Pathol. 95, 117-124 (1991).
-
(1991)
Am. J. Clin. Pathol.
, vol.95
, pp. 117-124
-
-
Greer, C.E.1
Peterson, S.L.2
Kiviat, N.B.3
Manos, M.M.4
-
23
-
-
31444434447
-
A multiplex-PCR predictor for aCGH success of FFPE samples
-
van Beers, E. H., et al. A multiplex-PCR predictor for aCGH success of FFPE samples. Br. J. Cancer 94, 333-337 (2006).
-
(2006)
Br. J. Cancer
, vol.94
, pp. 333-337
-
-
Van Beers, E.H.1
-
24
-
-
84907198355
-
Prognostic value of tumor-infiltrating lymphocytes in triple-negative breast cancers from two phase 3 randomized adjuvant breast cancer trials: ECOG 2197 and ECOG 1199
-
Adams, S., et al. Prognostic value of tumor-infiltrating lymphocytes in triple-negative breast cancers from two phase 3 randomized adjuvant breast cancer trials: ECOG 2197 and ECOG 1199. J. Clin. Oncol. 32, 2959-2966 (2014).
-
(2014)
J. Clin. Oncol.
, vol.32
, pp. 2959-2966
-
-
Adams, S.1
-
25
-
-
84878599846
-
Evaluating the repair of DNA derived from formalin-fixed paraffin-embedded tissues prior to genomic profiling by SNP-CGH analysis
-
Hosein, A. N., et al. Evaluating the repair of DNA derived from formalin-fixed paraffin-embedded tissues prior to genomic profiling by SNP-CGH analysis. Lab. Invest. 93, 701-710 (2013).
-
(2013)
Lab. Invest.
, vol.93
, pp. 701-710
-
-
Hosein, A.N.1
-
26
-
-
79958285669
-
Whole-genome amplification of DNA extracted from FFPE tissues
-
Bosso, M., Al-Mulla, F. Whole-genome amplification of DNA extracted from FFPE tissues. Methods Mol. Biol. 724, 161-180 (2011).
-
(2011)
Methods Mol. Biol.
, vol.724
, pp. 161-180
-
-
Bosso, M.1
Al-Mulla, F.2
-
27
-
-
18344396798
-
Comprehensive human genome amplification using multiple displacement amplification
-
Dean, F. B., et al. Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl. Acad. Sci. USA 99, 5261-5266 (2002).
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 5261-5266
-
-
Dean, F.B.1
-
28
-
-
84871461434
-
Genome-wide detection of single-nucleotide and copy-number variations of a single human cell
-
Zong, C., Lu, S., Chapman, A. R., Xie, X. S. Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science 338, 1622-1626 (2012).
-
(2012)
Science
, vol.338
, pp. 1622-1626
-
-
Zong, C.1
Lu, S.2
Chapman, A.R.3
Xie, X.S.4
-
29
-
-
84946488247
-
Interactive analysis and assessment of single-cell copy-number variations
-
Garvin, T., et al. Interactive analysis and assessment of single-cell copy-number variations. Nat. Methods 12, 1058-1060 (2015).
-
(2015)
Nat. Methods
, vol.12
, pp. 1058-1060
-
-
Garvin, T.1
-
30
-
-
84934775012
-
Whole-genome amplification with SurePlex results in better copy-number alteration detection using sequencing data compared to the MALBAC method
-
Deleye, L., et al. Whole-genome amplification with SurePlex results in better copy-number alteration detection using sequencing data compared to the MALBAC method. Sci. Rep. 5, 11711 (2015).
-
(2015)
Sci. Rep.
, vol.5
, pp. 11711
-
-
Deleye, L.1
-
31
-
-
84871357082
-
-
IARC
-
Lakhani, S. R., Ellis, I. O., Schnitt, S. J., Tan, P. H., van de Vijver, M. J. WHO Classification of Breast Tumors (IARC, 2012).
-
(2012)
WHO Classification of Breast Tumors
-
-
Lakhani, S.R.1
Ellis, I.O.2
Schnitt, S.J.3
Tan, P.H.4
Van De Vijver, M.J.5
-
32
-
-
84899752893
-
PI3K pathway activation in high-grade ductal carcinoma in situ-implications for progression to invasive breast carcinoma
-
Sakr, R. A., et al. PI3K pathway activation in high-grade ductal carcinoma in situ-implications for progression to invasive breast carcinoma. Clin. Cancer Res. 20, 2326-2337 (2014).
-
(2014)
Clin. Cancer Res.
, vol.20
, pp. 2326-2337
-
-
Sakr, R.A.1
-
33
-
-
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 (2013).
-
(2013)
J. Clin. Oncol.
, vol.31
, pp. 3997-4013
-
-
Wolff, A.C.1
-
34
-
-
77954526150
-
American Society of Clinical Oncology-College of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer
-
Hammond, M. E., et al. American Society of Clinical Oncology-College Of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer. J. Clin. Oncol. 28, 2784-2795 (2010).
-
(2010)
J. Clin. Oncol.
, vol.28
, pp. 2784-2795
-
-
Hammond, M.E.1
-
35
-
-
84956763981
-
Uterine adenosarcomas are mesenchymal neoplasms
-
Piscuoglio, S., et al. Uterine adenosarcomas are mesenchymal neoplasms. J. Pathol. 238, 381-388 (2016).
-
(2016)
J. Pathol.
, vol.238
, pp. 381-388
-
-
Piscuoglio, S.1
-
36
-
-
84879848702
-
PI3K pathway dependencies in endometrioid endometrial cancer cell lines
-
Weigelt, B., Warne, P. H., Lambros, M. B., Reis-Filho, J. S., Downward, J. PI3K pathway dependencies in endometrioid endometrial cancer cell lines. Clin. Cancer Res. 19, 3533-3544 (2013).
-
(2013)
Clin. Cancer Res.
, vol.19
, pp. 3533-3544
-
-
Weigelt, B.1
Warne, P.H.2
Lambros, M.B.3
Reis-Filho, J.S.4
Downward, J.5
-
37
-
-
84908867220
-
Hotspot-activating PRKD1 somatic mutations in polymorphous low-grade adenocarcinomas of the salivary glands
-
Weinreb, I., et al. Hotspot-activating PRKD1 somatic mutations in polymorphous low-grade adenocarcinomas of the salivary glands. Nat. Genet. 46, 1166-1169 (2014).
-
(2014)
Nat. Genet.
, vol.46
, pp. 1166-1169
-
-
Weinreb, I.1
-
38
-
-
0035888485
-
Doublet discrimination in DNA cell-cycle analysis
-
Wersto, R. P., et al. Doublet discrimination in DNA cell-cycle analysis. Cytometry 46, 296-306 (2001).
-
(2001)
Cytometry
, vol.46
, pp. 296-306
-
-
Wersto, R.P.1
-
39
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B., Trapnell, C., Pop, M., Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
-
(2009)
Genome Biol.
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
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
-
-
34147104969
-
A faster circular binary segmentation algorithm for the analysis of array CGH data
-
Venkatraman, E. S., Olshen, A. B. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23, 657-663 (2007).
-
(2007)
Bioinformatics
, vol.23
, pp. 657-663
-
-
Venkatraman, E.S.1
Olshen, A.B.2
-
42
-
-
84988924813
-
FACETS: Allele-specific copy-number and clonal heterogeneity analysis tool for high-throughput DNA sequencing
-
Shen, R., Seshan, V. E. FACETS: allele-specific copy-number and clonal heterogeneity analysis tool for high-throughput DNA sequencing. Nucleic Acids Res. 44, e131 (2016).
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. e131
-
-
Shen, R.1
Seshan, V.E.2
-
43
-
-
84861527388
-
The genomic and transcriptomic architecture of 2, 000 breast tumors reveals novel subgroups
-
Curtis, C., et al. The genomic and transcriptomic architecture of 2, 000 breast tumors reveals novel subgroups. Nature 486, 346-352 (2012).
-
(2012)
Nature
, vol.486
, pp. 346-352
-
-
Curtis, C.1
-
44
-
-
84874102335
-
Evolution and impact of subclonal mutations in chronic lymphocytic leukemia
-
Landau, D. A., et al. Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell 152, 714-726 (2013).
-
(2013)
Cell
, vol.152
, pp. 714-726
-
-
Landau, D.A.1
-
45
-
-
84977080556
-
Massively parallel sequencing-based clonality analysis of synchronous endometrioid endometrial and ovarian carcinomas
-
Schultheis, A. M., et al. Massively parallel sequencing-based clonality analysis of synchronous endometrioid endometrial and ovarian carcinomas. J. Natl. Cancer Inst. 108, 427 (2016).
-
(2016)
J. Natl. Cancer Inst.
, vol.108
, pp. 427
-
-
Schultheis, A.M.1
-
46
-
-
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
-
47
-
-
34250615012
-
CGHregions: Dimension reduction for array CGH data with minimal information loss
-
van de Wiel, M. A., Wieringen, W. N. CGHregions: dimension reduction for array CGH data with minimal information loss. Cancer Inform. 3, 55-63 (2007).
-
(2007)
Cancer Inform.
, vol.3
, pp. 55-63
-
-
Van De Wiel, M.A.1
Wieringen, W.N.2
-
48
-
-
84879288827
-
Target inference from collections of genomic intervals
-
Krasnitz, A., Sun, G., Andrews, P., Wigler, M. Target inference from collections of genomic intervals. Proc. Natl. Acad. Sci. USA 110, E2271-E2278 (2013).
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. E2271-E2278
-
-
Krasnitz, A.1
Sun, G.2
Andrews, P.3
Wigler, M.4
|