Genome-wide mutational spectra analysis reveals significant cancer-specific heterogeneity

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Tan, Hua ^a,b   Bao, Jiguang ^b   Zhou, Xiaobo ^a  

^a WAKE FOREST SCHOOL OF MEDICINE   (United States)

^b BEIJING NORMAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; GENETIC MARKER; TUMOR MARKER; TUMOR PROTEIN;

CHROMOSOMAL MAPPING; GENETIC DATABASE; GENETIC MARKER; GENETIC PREDISPOSITION; GENETICS; HUMAN; HUMAN GENOME; MUTATION; NEOPLASMS; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM; TUMOR GENE;

AMINO ACIDS; BIOMARKERS, TUMOR; CHROMOSOME MAPPING; DATABASES, GENETIC; GENES, NEOPLASM; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; HUMANS; MUTATION; NEOPLASM PROTEINS; NEOPLASMS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84938245424     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep12566     Document Type: Article

References (50)

1. Vogelstein, B. & Kinzler, K. W. Cancer genes and the pathways they control. Nat Med 10, 789-99 (2004).
2. Stratton, M. R., Campbell, P. J. & Futreal, P. A. The cancer genome. Nature 458, 719-724 (2009).
3. Weir, B., Zhao, X. & Meyerson, M. Somatic alterations in the human cancer genome. Cancer Cell 6, 433-8 (2004).
4. Michor, F., Iwasa, Y. & Nowak, M. A. Dynamics of cancer progression. Nat Rev Cancer 4, 197-205 (2004).
5. Hanahan, D. & Weinberg, R. A. Hallmarks of cancer: the next generation. Cell 144, 646-74 (2011).
6. Hanahan, D. & Weinberg, R. A. The hallmarks of cancer. Cell 100, 57-70 (2000).
7. Parsons, D. W. et al. An integrated genomic analysis of human glioblastoma multiforme. Science 321, 1807-12 (2008).
8. Jones, S. et al. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 321, 1801-6 (2008).
9. Wood, L. D. et al. The genomic landscapes of human breast and colorectal cancers. Science 318, 1108-13 (2007).
10. Cazier, J. B. et al. Whole-genome sequencing of bladder cancers reveals somatic CDKN1A mutations and clinicopathological associations with mutation burden. Nat Commun 5, 3756 (2014).
11. Huether, R. et al. The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes. Nat Commun 5, 3630 (2014).
12. India Project Team of the International Cancer Genome, C. Mutational landscape of gingivo-buccal oral squamous cell carcinoma reveals new recurrently-mutated genes and molecular subgroups. Nat Commun 4, 2873 (2013).
13. Pfeifer, G. P. & Besaratinia, A. Mutational spectra of human cancer. Human Genetics 125, 493-506 (2009).
14. Greenman, C. et al. Patterns of somatic mutation in human cancer genomes. Nature 446, 153-8 (2007).
15. Vogelstein, B. et al. Cancer genome landscapes. Science 339, 1546-58 (2013).
16. Futreal, P. A. et al. A census of human cancer genes. Nat Rev Cancer 4, 177-83 (2004).
17. Sintupisut, N., Liu, P. L. & Yeang, C. H. An integrative characterization of recurrent molecular aberrations in glioblastoma genomes. Nucleic Acids Res 41, 8803-21 (2013).
18. Pickering, C. R. et al. Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers. Cancer Discov 3, 770-81 (2013).
19. Lawrence, M. S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214-8 (2013).
20. Alexandrov, L. B., Nik-Zainal, S., Wedge, D. C., Campbell, P. J. & Stratton, M. R. Deciphering signatures of mutational processes operative in human cancer. Cell Rep 3, 246-59 (2013).
21. Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415-21 (2013).
22. Tan, H., Bao, J. & Zhou, X. A novel missense-mutation-related feature extraction scheme for 'driver' mutation identification. Bioinformatics 28, 2948-55 (2012).
23. Forbes, S. A. et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Research 39, D945-D950 (2011).
24. Ozel, A. B. et al. Genome-wide association study and meta-analysis of intraocular pressure. Hum Genet 133, 41-57 (2014).
25. Brophy, P. D. et al. Genome-wide copy number variation analysis of a Branchio-oto-renal syndrome cohort identifies a recombination hotspot and implicates new candidate genes. Hum Genet 132, 1339-50 (2013).
26. Gonzalez-Aguilera, C. et al. Genome-wide analysis links emerin to neuromuscular junction activity in Caenorhabditis elegans. Genome Biol 15, R21 (2014).
27. Duitama, J. et al. Large-scale analysis of tandem repeat variability in the human genome. Nucleic Acids Res 42, 5728-41 (2014).
28. Yeang, C. H., McCormick, F. & Levine, A. Combinatorial patterns of somatic gene mutations in cancer. Faseb Journal 22, 2605-2622 (2008).
29. Vandin, F., Upfal, E. & Raphael, B. J. De novo discovery of mutated driver pathways in cancer. Genome Res 22, 375-85 (2012).
30. Ciriello, G., Cerami, E., Sander, C. & Schultz, N. Mutual exclusivity analysis identifies oncogenic network modules. Genome Res 22, 398-406 (2012).
31. Hussain, S. P. & Harris, C. C. Molecular epidemiology of human cancer: contribution of mutation spectra studies of tumor suppressor genes. Cancer Res 58, 4023-37 (1998).
32. Davies, H. et al. Mutations of the BRAF gene in human cancer. Nature 417, 949-54 (2002).
33. Fodde, R. The APC gene in colorectal cancer. Eur J Cancer 38, 867-71 (2002).
34. Smit, V. T. H. B. M. et al. KRAS codon 12 mutations occur very frequently in pancreatic adenocarcinomas. Nucleic Acids Research 16, 7773-7782 (1988).
35. Tornesello, M. L. et al. Mutations in TP53, CTNNB1 and PIK3CA genes in hepatocellular carcinoma associated with hepatitis B and hepatitis C virus infections. Genomics 102, 74-83 (2013).
36. Li, M. et al. Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma. Nat Genet 43, 828-9 (2011).
37. Brugarolas, J. PBRM 1 and BAP1 as novel targets for renal cell carcinoma. Cancer J 19, 324-32 (2013).
38. Shugay, M., Ortiz de Mendibil, I., Vizmanos, J. L. & Novo, F. J. Oncofuse: a computational framework for the prediction of the oncogenic potential of gene fusions. Bioinformatics 29, 2539-46 (2013).
39. Kalari, S. & Pfeifer, G. P. Identification of driver and passenger DNA methylation in cancer by epigenomic analysis. Adv Genet 70, 277-308 (2010).
40. Witte, M. B. & Barbul, A. Arginine physiology and its implication for wound healing. Wound Repair Regen 11, 419-23 (2003).
41. Tomasetti, C., Vogelstein, B. & Parmigiani, G. Half or more of the somatic mutations in cancers of self-renewing tissues originate prior to tumor initiation. Proc Natl Acad Sci U S A 110, 1999-2004 (2013).
42. Sherr, C. J. The Pezcoller lecture: cancer cell cycles revisited. Cancer Res 60, 3689-95 (2000).
43. Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P. L. & Ideker, T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27, 431-2 (2011).
44. Rajagopalan, H. et al. Tumorigenesis: RAF/RAS oncogenes and mismatch-repair status. Nature 418, 934 (2002).
45. Kosaka, T. et al. Mutations of the epidermal growth factor receptor gene in lung cancer: biological and clinical implications. Cancer Res 64, 8919-23 (2004).
46. Sparks, A. B., Morin, P. J., Vogelstein, B. & Kinzler, K. W. Mutational analysis of the APC/beta-catenin/Tcf pathway in colorectal cancer. Cancer Res 58, 1130-4 (1998).
47. Forbes, S. A. et al. COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res 43, D805-11 (2015).
48. Sprouffske, K., Pepper, J. W. & Maley, C. C. Accurate reconstruction of the temporal order of mutations in neoplastic progression. Cancer Prev Res (Phila) 4, 1135-44 (2011).
49. Attolini, C. S. O. et al. A mathematical framework to determine the temporal sequence of somatic genetic events in cancer. Proc Natl Acad Sci USA 107, 17604-17609 (2010).
50. Dempster, A. P., Laird, N. M. & Rubin, D. B. Maximum Likelihood from Incomplete Data Via Em Algorithm. J Roy Stat Soc B Met 39, 1-38 (1977).