Genomic landscape of metastatic colorectal cancer

Nature Communications

Volumn 5, Issue , 2014, Pages

  Haan, Josien C ^a   Labots, Mariette ^a   Rausch, Christian ^a   Koopman, Miriam ^b   Tol, Jolien ^c   Mekenkamp, Leonie J M ^c   Van De Wiel, Mark A ^a   Israeli, Danielle ^a   Van Essen, Hendrik F ^a   Van Grieken, Nicole C T ^a   Voorham, Quirinus J M ^a   Bosch, Linda J W ^a   Qu, Xueping ^d   Kabbarah, Omar ^d   Verheul, Henk M W ^a   Nagtegaal, Iris D ^c   Punt, Cornelis J A ^e   Ylstra, Bauke ^a   Meijer, Gerrit A ^a  

^a VU UNIVERSITY MEDICAL CENTER   (Netherlands)

^b UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^c RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^d GENENTECH INC   (United States)

^e ACADEMIC MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BEVACIZUMAB; CAPECITABINE; CETUXIMAB; FIRTECAN; IRINOTECAN; MESSENGER RNA; OXALIPLATIN; ANTINEOPLASTIC AGENT; CAMPTOTHECIN;

CANCER; CHROMOSOME; GENE EXPRESSION; GENOMICS; RNA;

ARTICLE; CANCER COMBINATION CHEMOTHERAPY; CANCER SURVIVAL; CHROMOSOME 13; CHROMOSOME 14; CHROMOSOME 15; CHROMOSOME 17P; CHROMOSOME 18; CHROMOSOME 18Q; CHROMOSOME 1P; CHROMOSOME 20; CHROMOSOME 4; CHROMOSOME 5; CHROMOSOME 7; CHROMOSOME 8P; CHROMOSOME 8Q; CONTROLLED STUDY; DRUG RESPONSE; DRUG SENSITIVITY; GENE DOSAGE; GENE EXPRESSION; GENE MUTATION; GENETIC ASSOCIATION; HUMAN; IN VITRO STUDY; MAJOR CLINICAL STUDY; METASTATIC COLORECTAL CANCER; MULTICENTER STUDY; PHASE 3 CLINICAL TRIAL; PROGRESSION FREE SURVIVAL; RANDOMIZED CONTROLLED TRIAL; TREATMENT RESPONSE; X CHROMOSOME; ANALOGS AND DERIVATIVES; BOOK; CHROMOSOME 6; CLINICAL TRIAL; COLORECTAL NEOPLASMS; COPY NUMBER VARIATION; DRUG RESISTANCE; GENETICS; HUMAN GENOME; MORTALITY; TREATMENT OUTCOME; TUMOR GENE;

ANTINEOPLASTIC AGENTS, PHYTOGENIC; ANTINEOPLASTIC COMBINED CHEMOTHERAPY PROTOCOLS; ATLASES AS TOPIC; CAMPTOTHECIN; CHROMOSOMES, HUMAN, PAIR 6; COLORECTAL NEOPLASMS; DNA COPY NUMBER VARIATIONS; DRUG RESISTANCE, NEOPLASM; GENES, NEOPLASM; GENOME, HUMAN; HUMANS; TREATMENT OUTCOME;

EID: 84923352670     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms6457     Document Type: Article

References (51)

1. Jemal, A. et al. Global cancer statistics. CA Cancer J. Clin. 61, 69-90 (2011).
2. Fearon, E. R. & Vogelstein, B. A genetic model for colorectal tumorigenesis. Cell 61, 759-767 (1990).
3. Lievre, A. et al. KRAS mutations as an independent prognostic factor in patients with advanced colorectal cancer treated with cetuximab. J. Clin. Oncol. 26, 374-379 (2008).
4. Koopman, M. et al. Predictive and prognostic markers for the outcome of chemotherapy in advanced colorectal cancer, a retrospective analysis of the phase III randomised CAIRO study. Eur. J. Cancer 45, 1999-2006 (2009).
5. Tol, J. et al. Markers for EGFR pathway activation as predictor of outcome in metastatic colorectal cancer patients treated with or without cetuximab. Eur. J. Cancer 46, 1997-2009 (2010).
6. Perez, E. A. et al. HER2 and chromosome 17 effect on patient outcome in the N9831 adjuvant trastuzumab trial. J. Clin. Oncol. 28, 4307-4315 (2010).
7. Greshock, J. et al. Genome-wide DNA copy number predictors of lapatinib sensitivity in tumor-derived cell lines. Mol. Cancer Ther. 7, 935-943 (2008).
8. Climent, J. et al. Deletion of chromosome 11q predicts response to anthracycline-based chemotherapy in early breast cancer. Cancer Res. 67, 818-826 (2007).
9. Osterberg, L. et al. High-resolution genomic profiling of carboplatin resistance in early-stage epithelial ovarian carcinoma. Cytogenet. Genome Res. 125, 8-18 (2009).
10. Postma, C. et al. DNA copy number profiles of primary tumors as predictors of response to chemotherapy in advanced colorectal cancer. Ann. Oncol. 20, 1048-1056 (2009).
11. Futreal, P. A. et al. A census of human cancer genes. Nat. Rev. Cancer 4, 177-183 (2004).
12. Wood, L. D. et al. The genomic landscapes of human breast and colorectal cancers. Science 318, 1108-1113 (2007).
13. Leary, R. J. et al. Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers. Proc. Natl Acad. Sci. USA 105, 16224-16229 (2008).
14. Beroukhim, R. et al. The landscape of somatic copy-number alteration across human cancers. Nature 463, 899-905 (2010).
15. Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330-337 (2012).
16. Xie, T. et al. A comprehensive characterization of genome-wide copy number aberrations in colorectal cancer reveals novel oncogenes and patterns of alterations. PLoS One 7, e42001 (2012).
17. Koopman, M. et al. Sequential versus combination chemotherapy with capecitabine, irinotecan, and oxaliplatin in advanced colorectal cancer (CAIRO): a phase III randomised controlled trial. Lancet 370, 135-142 (2007).
18. Tol, J. et al. Chemotherapy, bevacizumab, and cetuximab in metastatic colorectal cancer. N. Engl. J. Med. 360, 563-572 (2009).
19. Hermsen, M. et al. Colorectal adenoma to carcinoma progression follows multiple pathways of chromosomal instability. Gastroenterology 123, 1109-1119 (2002).
20. Brosens, R. P. et al. Candidate driver genes in focal chromosomal aberrations of stage II colon cancer. J. Pathol. 221, 411-424 (2010).
21. Forbes, S. A. et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 39, D945-D950 (2011).
22. Yang, W. et al. Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells. Nucleic Acids Res. 41, D955-D961 (2013).
23. McDonagh, E. M., Whirl-Carrillo, M., Garten, Y., Altman, R. B. & Klein, T. E. From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource. Biomark. Med. 5, 795-806 (2011).
24. Hudson, T. J. et al. International network of cancer genome projects. Nature 464, 993-998 (2010).
25. Baylin, S. B. et al. Aberrant patterns of DNA methylation, chromatin formation and gene expression in cancer. Hum. Mol. Genet. 10, 687-692 (2001).
26. Esteller, M., Corn, P. G., Baylin, S. B. & Herman, J. G. A gene hypermethylation profile of human cancer. Cancer Res. 61, 3225-3229 (2001).
27. Krijgsman, O. et al. CGH arrays compared for DNA isolated from formalin-fixed, paraffin-embedded material. Genes Chromosomes. Cancer 51, 344-352 (2012).
28. Casparie, M. et al. Pathology databanking and biobanking in The Netherlands, a central role for PALGA, the nationwide histopathology and cytopathology data network and archive. Cell Oncol. 29, 19-24 (2007).
29. Grothey, A. et al. Regorafenib monotherapy for previously treated metastatic colorectal cancer (CORRECT): an international, multicentre, randomised, placebo-controlled, phase 3 trial. Lancet 381, 303-312 (2013).
30. Mekenkamp, L. J. et al. Chromosomal copy number aberrations in colorectal metastases resemble their primary counterparts and differences are typically non-recurrent. PLoS One 9, e86833 (2014).
31. Knijn, N. et al. KRAS mutation analysis: a comparison between primary tumours and matched liver metastases in 305 colorectal cancer patients. Br. J. Cancer 104, 1020-1026 (2011).
32. Meijer, G. A. What makes CRCs metastasise? Gut 59, 1164-1165 (2010).
33. van Essen, H. F. & Ylstra, B. High-resolution copy number profiling by array CGH using DNA isolated from formalin-fixed, paraffin-embedded tissues. Methods Mol. Biol. 838, 329-341 (2012).
34. Buffart, T. E. et al. DNA quality assessment for array CGH by isothermal whole genome amplification. Cell Oncol. 29, 351-359 (2007).
35. Buffart, T. E. et al. Across array comparative genomic hybridization: a strategy to reduce reference channel hybridizations. Genes Chromosomes. Cancer 47, 994-1004 (2008).
36. Edgar, R., Domrachev, M. & Lash, A. E. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30, 207-210 (2002).
37. van de Wiel, M. A. et al. Smoothing waves in array CGH tumor profiles. Bioinformatics 25, 1099-1104 (2009).
38. Olshen, A. B., Venkatraman, E. S., Lucito, R. & Wigler, M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5, 557-572 (2004).
39. van de Wiel, M. A. et al. CGHcall: calling aberrations for array CGH tumor profiles. Bioinformatics 23, 892-894 (2007).
40. van de Wiel, M. A. & van Wieringen, W. N. CGHregions: dimension reduction for array cgh data with minimal information loss. Cancer Inform. 2, 55-63 (2007).
41. van Wieringen, W. N., van de Wiel, M. A. & Ylstra, B. Weighted clustering of called array CGH data. Biostatistics 9, 484-500 (2008).
42. Smeets, S. J. et al. Genetic classification of oral and oropharyngeal carcinomas identifies subgroups with a different prognosis. Cell Oncol. 31, 291-300 (2009).
43. Koopman, M. et al. Deficient mismatch repair system in patients with sporadic advanced colorectal cancer. Br. J. Cancer 100, 266-273 (2009).
44. van de Wiel, M. A., Smeets, S. J., Brakenhoff, R. H. & Ylstra, B. CGHMultiArray: exact P-values for multi-array comparative genomic hybridization data. Bioinformatics 21, 3193-3194 (2005).
45. Kent, W. J. et al. The human genome browser at UCSC. Genome Res. 12, 996-1006 (2002).
46. Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061-1068 (2008).
47. Whirl-Carrillo, M. et al. Pharmacogenomics knowledge for personalized medicine. Clin. Pharmacol. Ther. 92, 414-417 (2012).
48. Thorn, C. F. et al. PharmGKB summary: fluoropyrimidine pathways. Pharmacogenet. Genomics 21, 237-242 (2011).
49. Marsh, S. et al. Platinum pathway. Pharmacogenet. Genomics 19, 563-564 (2009).
50. Maitland, M. L. et al. Vascular endothelial growth factor pathway. Pharmacogenet. Genomics 20, 346-349 (2010).
51. Greenman, C. D. et al. PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data. Biostatistics 11, 164-175 (2010).