-
1
-
-
84877579861
-
Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA
-
[1] Murtaza, M., Dawson, S.J., Tsui, D.W., Gale, D., Forshew, T., Piskorz, A.M., et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature 497 (2013), 108–112.
-
(2013)
Nature
, vol.497
, pp. 108-112
-
-
Murtaza, M.1
Dawson, S.J.2
Tsui, D.W.3
Gale, D.4
Forshew, T.5
Piskorz, A.M.6
-
2
-
-
84877865227
-
Complex tumor genomes inferred from single circulating tumor cells by array-CGH and next-generation sequencing
-
[2] Heitzer, E., Auer, M., Gasch, C., Pichler, M., Ulz, P., Hoffmann, E.M., et al. Complex tumor genomes inferred from single circulating tumor cells by array-CGH and next-generation sequencing. Cancer Res 73 (2013), 2965–2975.
-
(2013)
Cancer Res
, vol.73
, pp. 2965-2975
-
-
Heitzer, E.1
Auer, M.2
Gasch, C.3
Pichler, M.4
Ulz, P.5
Hoffmann, E.M.6
-
3
-
-
84887017686
-
Plasma is a better source of tumor-derived circulating cell-free DNA than serum for the detection of EGFR alterations in lung tumor patients
-
[3] Vallee, A., Marcq, M., Bizieux, A., Kouri, C.E., Lacroix, H., Bennouna, J., et al. Plasma is a better source of tumor-derived circulating cell-free DNA than serum for the detection of EGFR alterations in lung tumor patients. Lung Cancer 82 (2013), 373–374.
-
(2013)
Lung Cancer
, vol.82
, pp. 373-374
-
-
Vallee, A.1
Marcq, M.2
Bizieux, A.3
Kouri, C.E.4
Lacroix, H.5
Bennouna, J.6
-
4
-
-
84874309411
-
Isolation and retrieval of circulating tumor cells using centrifugal forces
-
[4] Hou, H.W., Warkiani, M.E., Khoo, B.L., Li, Z.R., Soo, R.A., Tan, D.S., et al. Isolation and retrieval of circulating tumor cells using centrifugal forces. Sci Rep, 3, 2013, 1259.
-
(2013)
Sci Rep
, vol.3
, pp. 1259
-
-
Hou, H.W.1
Warkiani, M.E.2
Khoo, B.L.3
Li, Z.R.4
Soo, R.A.5
Tan, D.S.6
-
5
-
-
84655167222
-
Epidermal growth factor receptor mutation status in circulating free DNA in serum: from IPASS, a phase III study of gefitinib or carboplatin/paclitaxel in non-small cell lung cancer
-
[5] Goto, K., Ichinose, Y., Ohe, Y., Yamamoto, N., Negoro, S., Nishio, K., et al. Epidermal growth factor receptor mutation status in circulating free DNA in serum: from IPASS, a phase III study of gefitinib or carboplatin/paclitaxel in non-small cell lung cancer. J Thorac Oncol 7 (2012), 115–121.
-
(2012)
J Thorac Oncol
, vol.7
, pp. 115-121
-
-
Goto, K.1
Ichinose, Y.2
Ohe, Y.3
Yamamoto, N.4
Negoro, S.5
Nishio, K.6
-
6
-
-
85015462482
-
-
Current challenges for detection of circulating tumor cells and cell-free circulating nucleic acids, and their characterization in non-small cell lung carcinoma patients. What is the best blood substrate for personalized medicine? Ann Transl Med
-
[6] Ilie M, Hofman V, Long E, Bordone O, Selva E, Washetine K, et al. Current challenges for detection of circulating tumor cells and cell-free circulating nucleic acids, and their characterization in non-small cell lung carcinoma patients. What is the best blood substrate for personalized medicine? Ann Transl Med 2014;2:107.
-
(2014)
, vol.2
, pp. 107
-
-
Ilie, M.1
Hofman, V.2
Long, E.3
Bordone, O.4
Selva, E.5
Washetine, K.6
-
7
-
-
84886379960
-
Going with the flow: from circulating tumor cells to DNA
-
ps14.
-
[7] Bidard FC, Weigelt B, Reis-Filho JS. Going with the flow: from circulating tumor cells to DNA. Sci Transl Med 2013;5:207ps14.
-
(2013)
Sci Transl Med
, vol.5
, pp. 207
-
-
Bidard, F.C.1
Weigelt, B.2
Reis-Filho, J.S.3
-
8
-
-
84952310964
-
SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution
-
[8] Miller, C.A., White, B.S., Dees, N.D., Griffith, M., Welch, J.S., Griffith, O.L., et al. SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution. PLoS Comput Biol, 10, 2014, e1003665.
-
(2014)
PLoS Comput Biol
, vol.10
, pp. e1003665
-
-
Miller, C.A.1
White, B.S.2
Dees, N.D.3
Griffith, M.4
Welch, J.S.5
Griffith, O.L.6
-
9
-
-
84861550476
-
The life history of 21 breast cancers
-
[9] Nik-Zainal, S., Van Loo, P., Wedge, D.C., Alexandrov, L.B., Greenman, C.D., Lau, K.W., et al. The life history of 21 breast cancers. Cell 149 (2012), 994–1007.
-
(2012)
Cell
, vol.149
, pp. 994-1007
-
-
Nik-Zainal, S.1
Van Loo, P.2
Wedge, D.C.3
Alexandrov, L.B.4
Greenman, C.D.5
Lau, K.W.6
-
10
-
-
84860782006
-
Absolute quantification of somatic DNA alterations in human cancer
-
[10] Carter, S.L., Cibulskis, K., Helman, E., McKenna, A., Shen, H., Zack, T., et al. Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol 30 (2012), 413–421.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 413-421
-
-
Carter, S.L.1
Cibulskis, K.2
Helman, E.3
McKenna, A.4
Shen, H.5
Zack, T.6
-
11
-
-
48649093407
-
DNA amplification is a ubiquitous mechanism of oncogene activation in lung and other cancers
-
[11] Lockwood, W.W., Chari, R., Coe, B.P., Girard, L., Macaulay, C., Lam, S., et al. DNA amplification is a ubiquitous mechanism of oncogene activation in lung and other cancers. Oncogene 27 (2008), 4615–4624.
-
(2008)
Oncogene
, vol.27
, pp. 4615-4624
-
-
Lockwood, W.W.1
Chari, R.2
Coe, B.P.3
Girard, L.4
Macaulay, C.5
Lam, S.6
-
12
-
-
84885008220
-
Pan-cancer patterns of somatic copy number alteration
-
[12] Zack, T.I., Schumacher, S.E., Carter, S.L., Cherniack, A.D., Saksena, G., Tabak, B., et al. Pan-cancer patterns of somatic copy number alteration. Nat Genet 45 (2013), 1134–1140.
-
(2013)
Nat Genet
, vol.45
, pp. 1134-1140
-
-
Zack, T.I.1
Schumacher, S.E.2
Carter, S.L.3
Cherniack, A.D.4
Saksena, G.5
Tabak, B.6
-
13
-
-
84973467716
-
Identification and construction of combinatory cancer hallmark-based gene signature sets to predict recurrence and chemotherapy benefit in stage II colorectal cancer
-
[13] Gao, S., Tibiche, C., Zou, J., Zaman, N., Trifiro, M., O'Connor-McCourt, M., et al. Identification and construction of combinatory cancer hallmark-based gene signature sets to predict recurrence and chemotherapy benefit in stage II colorectal cancer. JAMA Oncol 2 (2016), 37–45.
-
(2016)
JAMA Oncol
, vol.2
, pp. 37-45
-
-
Gao, S.1
Tibiche, C.2
Zou, J.3
Zaman, N.4
Trifiro, M.5
O'Connor-McCourt, M.6
-
14
-
-
84870847298
-
Identification of high-quality cancer prognostic markers and metastasis network modules
-
[14] Li, J., Lenferink, A.E., Deng, Y., Collins, C., Cui, Q., Purisima, E.O., et al. Identification of high-quality cancer prognostic markers and metastasis network modules. Nat Commun, 1, 2010, 34.
-
(2010)
Nat Commun
, vol.1
, pp. 34
-
-
Li, J.1
Lenferink, A.E.2
Deng, Y.3
Collins, C.4
Cui, Q.5
Purisima, E.O.6
-
15
-
-
0035478854
-
Random forests
-
[15] Breiman, L., Random forests. Mach Learn 45 (2001), 5–32.
-
(2001)
Mach Learn
, vol.45
, pp. 5-32
-
-
Breiman, L.1
-
16
-
-
33750410937
-
Ada: an R package for stochastic boosting
-
[16] Culp, M., Johnson, K., Michailidis, G., Ada: an R package for stochastic boosting. Gen Inf 17 (2006), 1–27.
-
(2006)
Gen Inf
, vol.17
, pp. 1-27
-
-
Culp, M.1
Johnson, K.2
Michailidis, G.3
-
17
-
-
79955166265
-
GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers
-
[17] Mermel, C.H., Schumacher, S.E., Hill, B., Meyerson, M.L., Beroukhim, R., Getz, G., GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol, 12, 2011, R41.
-
(2011)
Genome Biol
, vol.12
, pp. R41
-
-
Mermel, C.H.1
Schumacher, S.E.2
Hill, B.3
Meyerson, M.L.4
Beroukhim, R.5
Getz, G.6
-
18
-
-
33646361583
-
GenePattern 2.0
-
[18] Reich, M., Liefeld, T., Gould, J., Lerner, J., Tamayo, P., Mesirov, J.P., GenePattern 2.0. Nat Genet 38 (2006), 500–501.
-
(2006)
Nat Genet
, vol.38
, pp. 500-501
-
-
Reich, M.1
Liefeld, T.2
Gould, J.3
Lerner, J.4
Tamayo, P.5
Mesirov, J.P.6
-
19
-
-
84885845782
-
Signaling network assessment of mutations and copy number variations predict breast cancer subtype-specific drug targets
-
[19] Zaman, N., Li, L., Jaramillo, M.L., Sun, Z., Tibiche, C., Banville, M., et al. Signaling network assessment of mutations and copy number variations predict breast cancer subtype-specific drug targets. Cell Rep 5 (2013), 216–223.
-
(2013)
Cell Rep
, vol.5
, pp. 216-223
-
-
Zaman, N.1
Li, L.2
Jaramillo, M.L.3
Sun, Z.4
Tibiche, C.5
Banville, M.6
-
20
-
-
84946735654
-
Gene Ontology Consortium: going forward
-
[20] The Gene Ontology Consortium, Gene Ontology Consortium: going forward. Nucleic Acids Res 43 (2015), D1049–D1056.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. D1049-D1056
-
-
The Gene Ontology Consortium1
-
21
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
-
[21] Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25 (2000), 25–29.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
-
22
-
-
70449356774
-
QuickGO: a web-based tool for Gene Ontology searching
-
[22] Binns, D., Dimmer, E., Huntley, R., Barrell, D., O'Donovan, C., Apweiler, R., QuickGO: a web-based tool for Gene Ontology searching. Bioinformatics 25 (2009), 3045–3046.
-
(2009)
Bioinformatics
, vol.25
, pp. 3045-3046
-
-
Binns, D.1
Dimmer, E.2
Huntley, R.3
Barrell, D.4
O'Donovan, C.5
Apweiler, R.6
-
23
-
-
84919626787
-
Predictive genomics: a cancer hallmark network framework for predicting tumor clinical phenotypes using genome sequencing data
-
[23] Wang, E., Zaman, N., McGee, S., Milanese, J.S., Masoudi-Nejad, A., O'Connor-McCourt, M., Predictive genomics: a cancer hallmark network framework for predicting tumor clinical phenotypes using genome sequencing data. Semin Cancer Biol 30 (2015), 4–12.
-
(2015)
Semin Cancer Biol
, vol.30
, pp. 4-12
-
-
Wang, E.1
Zaman, N.2
McGee, S.3
Milanese, J.S.4
Masoudi-Nejad, A.5
O'Connor-McCourt, M.6
-
24
-
-
84887615010
-
Understanding genomic alterations in cancer genomes using an integrative network approach
-
[24] Wang, E., Understanding genomic alterations in cancer genomes using an integrative network approach. Cancer Lett 340 (2013), 261–269.
-
(2013)
Cancer Lett
, vol.340
, pp. 261-269
-
-
Wang, E.1
-
25
-
-
84995960806
-
Genomic copy number profiling using circulating free tumor DNA highlights heterogeneity in neuroblastoma
-
[25] Chicard, M., Boyault, S., Colmet Daage, L., Richer, W., Gentien, D., Pierron, G., et al. Genomic copy number profiling using circulating free tumor DNA highlights heterogeneity in neuroblastoma. Clin Cancer Res 22 (2016), 5564–5573.
-
(2016)
Clin Cancer Res
, vol.22
, pp. 5564-5573
-
-
Chicard, M.1
Boyault, S.2
Colmet Daage, L.3
Richer, W.4
Gentien, D.5
Pierron, G.6
-
26
-
-
84995592145
-
Usefulness of circulating free DNA for monitoring epidermal growth factor receptor mutations in advanced non-small cell lung cancer patients: a case report
-
[26] de Las Casas, C.M., Gonzalez-Cao, M., Ramirez, S.V., Ariza, N.J., Balada, A., Garzon, M., et al. Usefulness of circulating free DNA for monitoring epidermal growth factor receptor mutations in advanced non-small cell lung cancer patients: a case report. Transl Lung Cancer Res 5 (2016), 532–537.
-
(2016)
Transl Lung Cancer Res
, vol.5
, pp. 532-537
-
-
de Las Casas, C.M.1
Gonzalez-Cao, M.2
Ramirez, S.V.3
Ariza, N.J.4
Balada, A.5
Garzon, M.6
-
27
-
-
84999048325
-
+ circulating tumor cells as a biomarker of treatment selection and liver metastasis in patients with colorectal cancer
-
+ circulating tumor cells as a biomarker of treatment selection and liver metastasis in patients with colorectal cancer. Oncotarget 7 (2016), 77389–77403.
-
(2016)
Oncotarget
, vol.7
, pp. 77389-77403
-
-
Fang, C.1
Fan, C.2
Wang, C.3
Huang, Q.4
Meng, W.5
Yu, Y.6
-
28
-
-
84971592187
-
Diagnostic and prognostic relevance of circulating exosomal miR-373, miR-200a, miR-200b and miR-200c in patients with epithelial ovarian cancer
-
[28] Meng, X., Muller, V., Milde-Langosch, K., Trillsch, F., Pantel, K., Schwarzenbach, H., Diagnostic and prognostic relevance of circulating exosomal miR-373, miR-200a, miR-200b and miR-200c in patients with epithelial ovarian cancer. Oncotarget 7 (2016), 16923–16935.
-
(2016)
Oncotarget
, vol.7
, pp. 16923-16935
-
-
Meng, X.1
Muller, V.2
Milde-Langosch, K.3
Trillsch, F.4
Pantel, K.5
Schwarzenbach, H.6
-
29
-
-
84990922467
-
Concentration and methylation of cell-free DNA from blood plasma as diagnostic markers of renal cancer
-
[29] Skrypkina, I., Tsyba, L., Onyshchenko, K., Morderer, D., Kashparova, O., Nikolaienko, O., et al. Concentration and methylation of cell-free DNA from blood plasma as diagnostic markers of renal cancer. Dis Markers, 2016, 2016, 3693096.
-
(2016)
Dis Markers
, vol.2016
, pp. 3693096
-
-
Skrypkina, I.1
Tsyba, L.2
Onyshchenko, K.3
Morderer, D.4
Kashparova, O.5
Nikolaienko, O.6
-
30
-
-
85015353456
-
Genetic alteration and mutation profiling of circulating cell-free tumor DNA (cfDNA) for diagnosis and targeted therapy of gastrointestinal stromal tumors
-
[30] Yan, W., Zhang, A., Powell, M.J., Genetic alteration and mutation profiling of circulating cell-free tumor DNA (cfDNA) for diagnosis and targeted therapy of gastrointestinal stromal tumors. Chin J Cancer, 35, 2016, 68.
-
(2016)
Chin J Cancer
, vol.35
, pp. 68
-
-
Yan, W.1
Zhang, A.2
Powell, M.J.3
-
31
-
-
84881088550
-
Cancer systems biology in the genome sequencing era: part 2, evolutionary dynamics of tumor clonal networks and drug resistance
-
[31] Wang, E., Zou, J., Zaman, N., Beitel, L.K., Trifiro, M., Paliouras, M., Cancer systems biology in the genome sequencing era: part 2, evolutionary dynamics of tumor clonal networks and drug resistance. Semin Cancer Biol 23 (2013), 286–292.
-
(2013)
Semin Cancer Biol
, vol.23
, pp. 286-292
-
-
Wang, E.1
Zou, J.2
Zaman, N.3
Beitel, L.K.4
Trifiro, M.5
Paliouras, M.6
-
32
-
-
84881110695
-
Cancer systems biology in the genome sequencing era: part 1, dissecting and modeling of tumor clones and their networks
-
[32] Wang, E., Zou, J., Zaman, N., Beitel, L.K., Trifiro, M., Paliouras, M., Cancer systems biology in the genome sequencing era: part 1, dissecting and modeling of tumor clones and their networks. Semin Cancer Biol 23 (2013), 279–285.
-
(2013)
Semin Cancer Biol
, vol.23
, pp. 279-285
-
-
Wang, E.1
Zou, J.2
Zaman, N.3
Beitel, L.K.4
Trifiro, M.5
Paliouras, M.6
-
33
-
-
84885092663
-
Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling
-
[33] Bashashati, A., Ha, G., Tone, A., Ding, J., Prentice, L.M., Roth, A., et al. Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling. J Pathol 231 (2013), 21–34.
-
(2013)
J Pathol
, vol.231
, pp. 21-34
-
-
Bashashati, A.1
Ha, G.2
Tone, A.3
Ding, J.4
Prentice, L.M.5
Roth, A.6
-
34
-
-
84926157747
-
Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes
-
[34] Leiserson, M.D., Vandin, F., Wu, H.T., Dobson, J.R., Eldridge, J.V., Thomas, J.L., et al. Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes. Nat Genet 47 (2015), 106–114.
-
(2015)
Nat Genet
, vol.47
, pp. 106-114
-
-
Leiserson, M.D.1
Vandin, F.2
Wu, H.T.3
Dobson, J.R.4
Eldridge, J.V.5
Thomas, J.L.6
-
35
-
-
84945925969
-
Detection of clonal and subclonal copy-number variants in cell-free DNA from patients with breast cancer using a massively multiplexed PCR methodology
-
[35] Kirkizlar, E., Zimmermann, B., Constantin, T., Swenerton, R., Hoang, B., Wayham, N., et al. Detection of clonal and subclonal copy-number variants in cell-free DNA from patients with breast cancer using a massively multiplexed PCR methodology. Transl Oncol 8 (2015), 407–416.
-
(2015)
Transl Oncol
, vol.8
, pp. 407-416
-
-
Kirkizlar, E.1
Zimmermann, B.2
Constantin, T.3
Swenerton, R.4
Hoang, B.5
Wayham, N.6
-
36
-
-
84859413615
-
High-resolution analyses of copy number changes in disseminated tumor cells of patients with breast cancer
-
[36] Mathiesen, R.R., Fjelldal, R., Liestol, K., Due, E.U., Geigl, J.B., Riethdorf, S., et al. High-resolution analyses of copy number changes in disseminated tumor cells of patients with breast cancer. Int J Cancer 131 (2012), E405–E415.
-
(2012)
Int J Cancer
, vol.131
, pp. E405-E415
-
-
Mathiesen, R.R.1
Fjelldal, R.2
Liestol, K.3
Due, E.U.4
Geigl, J.B.5
Riethdorf, S.6
-
37
-
-
84896371874
-
Detection of circulating tumor DNA in early- and late-stage human malignancies
-
[37] Bettegowda, C., Sausen, M., Leary, R.J., Kinde, I., Wang, Y., Agrawal, N., et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med, 6, 2014, 22ra24.
-
(2014)
Sci Transl Med
, vol.6
, pp. 22ra24
-
-
Bettegowda, C.1
Sausen, M.2
Leary, R.J.3
Kinde, I.4
Wang, Y.5
Agrawal, N.6
-
38
-
-
84903218109
-
An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage
-
[38] Newman, A.M., Bratman, S.V., To, J., Wynne, J.F., Eclov, N.C., Modlin, L.A., et al. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat Med 20 (2014), 548–554.
-
(2014)
Nat Med
, vol.20
, pp. 548-554
-
-
Newman, A.M.1
Bratman, S.V.2
To, J.3
Wynne, J.F.4
Eclov, N.C.5
Modlin, L.A.6
-
39
-
-
84900333051
-
Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer
-
[39] Lohr, J.G., Adalsteinsson, V.A., Cibulskis, K., Choudhury, A.D., Rosenberg, M., Cruz-Gordillo, P., et al. Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer. Nat Biotechnol 32 (2014), 479–484.
-
(2014)
Nat Biotechnol
, vol.32
, pp. 479-484
-
-
Lohr, J.G.1
Adalsteinsson, V.A.2
Cibulskis, K.3
Choudhury, A.D.4
Rosenberg, M.5
Cruz-Gordillo, P.6
-
40
-
-
84931052979
-
Gene expression profiles of circulating tumor cells versus primary tumors in metastatic breast cancer
-
[40] Onstenk, W., Sieuwerts, A.M., Weekhout, M., Mostert, B., Reijm, E.A., van Deurzen, C.H., et al. Gene expression profiles of circulating tumor cells versus primary tumors in metastatic breast cancer. Cancer Lett 362 (2015), 36–44.
-
(2015)
Cancer Lett
, vol.362
, pp. 36-44
-
-
Onstenk, W.1
Sieuwerts, A.M.2
Weekhout, M.3
Mostert, B.4
Reijm, E.A.5
van Deurzen, C.H.6
|