ContrastRank: A new method for ranking putative cancer driver genes and classification of tumor samples

Bioinformatics

Volumn 30, Issue 17, 2014, Pages

  Tian, Rui ^a   Basu, Malay K ^a,b   Capriotti, Emidio ^a,b,c  

^a Division of Informatics Department of Pathology   (United States)

^b UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^c 803 Shelby Interdisciplinary Biomedical Research Building   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOCARCINOMA; CLASSIFICATION; GENETIC VARIABILITY; GENETICS; GENOMICS; GENOTYPE; HUMAN; NEOPLASM; PROCEDURES; STATISTICAL ANALYSIS; TUMOR GENE;

ADENOCARCINOMA; DATA INTERPRETATION, STATISTICAL; GENES, NEOPLASM; GENETIC VARIATION; GENOMICS; GENOTYPE; HUMANS; NEOPLASMS;

EID: 84907022277     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu466     Document Type: Article

References (31)

1. 1000 Genomes Project Consortium. (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061-1073.
2. 1000 Genomes Project Consortium et al. (2012) An integrated map of genetic variation from 1, 092 human genomes. Nature, 491, 56-65.
3. Alexandrov, L.B. et al. (2013) Signatures of mutational processes in human cancer. Nature, 500, 415-421.
4. Bamshad, M.J. et al. (2011) Exome sequencing as a tool for Mendelian disease gene discovery. Nat. Rev. Genet., 12, 745-755.
5. Bushman, F. (2013) Cancer gene listhttp://www.bushmanlab.org/links/ genelists.
6. Cancer Genome Atlas Research Network. (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455, 1061-1068.
7. Capriotti, E. and Altman, R.B. (2011) A new disease-specific machine learning approach for the prediction of cancer-causing missense variants. Genomics, 98, 310-317.
8. Capriotti, E. et al. (2012) Bioinformatics for personal genome interpretation. Brief. Bioinform., 13, 495-512.
9. Carter, H. et al. (2009) Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. Cancer Res., 69, 6660-6667.
10. Cerami, E. et al. (2012) The cBio cancer genomics portal: An open platform for exploring multidimensional cancer genomics data. Cancer Discov., 2, 401-404.
11. Cheng, W.C. et al. (2014) DriverDB: An exome sequencing database for cancer driver gene identification. Nucleic Acids Res., 42, D1048-D1054.
12. Dees, N.D. et al. (2012) MuSiC: identifying mutational significance in cancer genomes. Genome Res., 22, 1589-1598.
13. Fernald, G.H. et al. (2011) Bioinformatics challenges for personalized medicine. Bioinformatics, 27, 1741-1748.
14. Forbes, S.A. et al. (2011) COSMIC: Mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res., 39, D945-D950.
15. Futreal, P.A. et al. (2004) A census of human cancer genes. Nat. Rev. Cancer, 4, 177-183.
16. Garraway, L.A. and Lander, E.S. (2013) Lessons from the cancer genome. Cell, 153, 17-37.
17. Gonzalez-Perez, A. and Lopez-Bigas, N. (2012) Functional impact bias reveals cancer drivers. Nucleic Acids Res., 40, e169.
18. Imielinski, M. et al. (2012) Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell, 150, 1107-1120.
19. Kaminker, J.S. et al. (2007) Distinguishing cancer-Associated missense mutations from common polymorphisms. Cancer Res., 67, 465-473.
20. Kandoth, C. et al. (2013) Mutational landscape and significance across 12 major cancer types. Nature, 502, 333-339.
21. Khurana, E. et al. (2013) Integrative annotation of variants from 1092 humans: Application to cancer genomics. Science, 342, 1235587.
22. Lawrence, M.S. et al. (2013) Mutational heterogeneity in cancer and the search for new cancer-Associated genes. Nature, 499, 214-218.
23. Lawrence, M.S. et al. (2014) Discovery and saturation analysis of cancer genes across 21 tumour types. Nature, 505, 495-501.
24. Meyerson, M. et al. (2010) Advances in understanding cancer genomes through second-generation sequencing. Nat. Rev. Genet., 11, 685-696.
25. Sherry, S.T. et al. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res., 29, 308-311.
26. Stratton, M.R. et al. (2009) The cancer genome. Nature, 458, 719-724.
27. Tamborero, D. et al. (2013) Comprehensive identification of mutational cancer driver genes across 12 tumor types. Sci. Rep., 3, 2650.
28. Vogelstein, B. et al. (2013) Cancer genome landscapes. Science, 339, 1546-1558.
29. Wang, K. et al. (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res., 38, e164.
30. Watson, I.R. et al. (2013) Emerging patterns of somatic mutations in cancer. Nat. Rev. Genet., 14, 703-718.
31. Youn, A. and Simon, R. (2011) Identifying cancer driver genes in tumor genome sequencing studies. Bioinformatics, 27, 175-181.