Identification of Constrained Cancer Driver Genes Based on Mutation Timing

PLoS Computational Biology

Volumn 11, Issue 1, 2015, Pages

  Sakoparnig, Thomas ^a,b   Fried, Patrick ^a,b   Beerenwinkel, Niko ^a,b  

^a ETH ZURICH   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

DIGITAL STORAGE; DISEASES; TIMING CIRCUITS; TUMORS;

COPY-NUMBER ALTERATIONS; FUNCTION STRUCTURES; GENE FUNCTION; GENE NETWORKS; GENOMIC ALTERATIONS; LOWER FREQUENCIES; OR-NETWORKS; SINGLE NUCLEOTIDES; TUMOR SAMPLES; VERY LOW FREQUENCY;

GENES;

ARTICLE; BREAST TUMOR; CANCER DRIVER GENE; CARCINOGENESIS; COLORECTAL CANCER; COPY NUMBER VARIATION; CROSS-SECTIONAL STUDY; GENE FREQUENCY; GENE IDENTIFICATION; GENE MUTATION; GENETIC VARIABILITY; GENOME; GENOMICS; OVARY CANCER; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; TUMOR GENE; TUMOR GROWTH; BIOLOGY; GENETIC DATABASE; GENETICS; HUMAN; MUTATION; NEOPLASM; ONCOGENE; PROCEDURES; TIME;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; HUMANS; MUTATION; NEOPLASMS; ONCOGENES; POLYMORPHISM, SINGLE NUCLEOTIDE; TIME FACTORS;

EID: 84922226043     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1004027     Document Type: Article

References (40)

1. Hanahan D, Weinberg Ra, (2011) Hallmarks of cancer: the next generation. Cell 144: 646–74.
2. Fearon E, Vogelstein B, (1990) A genetic model for colorectal tumorigenesis. Cell 61: 759–767.
3. McLendon R, Friedman A, Bigner D, (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455: 1061–1068.
4. Bell D, Berchuck A, Birrer M, Chien J, Cramer DW, et al. (2011) Integrated genomic analyses of ovarian carcinoma. Nature 474: 609–615.
5. Bozic I, Antal T, Ohtsuki H, Carter H, Kim D, et al. (2010) Accumulation of driver and passenger mutations during tumor progression. Proceedings of the National Academy of Sciences of the United States of America 107: 18545–18550.
6. Beroukhim R, Getz G, Nghiemphu L, Barretina J, Hsueh T, et al. (2007) Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proceedings of the National Academy of Sciences of the United States of America 104: 20007–12.
7. Carter H, Chen S, Isik L, Tyekucheva S, Velculescu VE, et al. (2009) Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. Cancer research 69: 6660–6667.
8. Youn A, Simon R, (2011) Identifying cancer driver genes in tumor genome sequencing studies. Bioinformatics (Oxford, England) 27: 175–81.
9. Miller Ca, Settle SH, Sulman EP, Aldape KD, Milosavljevic A, (2011) Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors. BMC medical genomics 4: 34.
10. Vandin F, Upfal E, Raphael B, (2012) De novo discovery of mutated driver pathways in cancer. Genome research 22: 375–385.
11. Szczurek E, Beerenwinkel N, (2014) Modeling mutual exclusivity of cancer mutations. PLoS computational biology 10: e1003503.
12. Ciriello G, Cerami E, Sander C, Schultz N, (2012) Mutual exclusivity analysis identifies oncogenic network modules. Genome research 22: 398–406.
13. Tamborero D, Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Kandoth C, et al. (2013) Comprehensive identification of mutational cancer driver genes across 12 tumor types. Scientific reports 3: 2650.
14. Eifert C, Powers RS, (2012) From cancer genomes to oncogenic drivers, tumour dependencies and therapeutic targets. Nature reviews Cancer 12: 572–578.
15. Beerenwinkel N, Eriksson N, Sturmfels B, (2007) Conjunctive Bayesian networks. Bernoulli 13: 893–909.
16. Gao J, Aksoy B, Dogrusoz U, (2013) Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal. Science signaling 6: pl1.
17. Mermel CH, Schumacher SE, Hill B, Meyerson ML, Beroukhim R, et al. (2011) GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome biology 12: R41.
18. John K, Alla V, Meier C, Pützer BM, (2011) GRAMD4 mimics p53 and mediates the apoptotic function of p73 at mitochondria. Cell death and differentiation 18: 874–886.
19. Ohashi Y, Kaneko SJ, Cupples TE, Young SR, (2004) Ubiquinol cytochrome c reductase (UQCRFS1) gene amplification in primary breast cancer core biopsy samples. Gynecologic oncology 93: 54–58.
20. Theurillat JP, Metzler SC, Henzi N, Djouder N, Helbling M, et al. (2011) URI is an oncogene amplified in ovarian cancer cells and is required for their survival. Cancer cell 19: 317–332.
21. Sugimoto T, Seki N, (2009) The galanin signaling cascade is a candidate pathway regulating oncogenesis in human squamous cell carcinoma. Genes, Chromosomes and Cancer 142: 132–142.
22. Chen CF, Hsu EC, Lin KT, Tu PH, Chang HW, et al. (2010) Overlapping high-resolution copy number alterations in cancer genomes identified putative cancer genes in hepatocellular carcinoma. Hepatology 52: 1690–1701.
23. Liu L, Wang YD, Wu J, Cui J, Chen T, (2012) Carnitine palmitoyltransferase 1A (CPT1A): a transcriptional target of PAX3-FKHR and mediates PAX3-FKHR-dependent motility in alveolar rhabdomyosarcoma cells. BMC cancer 12: 154.
24. Huang QM, Tomida S, Masuda Y, Arima C, Cao K, et al. (2010) Regulation of DNA polymerase POLD4 influences genomic instability in lung cancer. Cancer research 70: 8407–8416.
25. Frescas D, Guardavaccaro D, Kuchay SM, Kato H, Poleshko A, et al. (2008) KDM1A represses transcription of centromeric satellite repeats and maintains the heterochromatic state. Cell Cycle 7: 3539–3547.
26. Stephens PJ, Tarpey PS, Davies H, Van Loo P, Greenman C, et al. (2012) The landscape of cancer genes and mutational processes in breast cancer. Nature 486: 400–404.
27. Carpten JD, Faber AL, Horn C, Donoho GP, Briggs SL, et al. (2007) A transforming mutation in the pleckstrin homology domain of AKT1 in cancer. Nature 448: 439–444.
28. King MC, Marks JH, Mandell JB, (2003) Breast and ovarian cancer risks due to inherited mutations in BRCA1 and BRCA2. Science 302: 643–646.
29. Tomasetti C, Vogelstein B, Parmigiani G, (2013) Half or more of the somatic mutations in cancers of self-renewing tissues originate prior to tumor initiation. Proceedings of the National Academy of Sciences of the United States of America 110: 1999–2004.
30. Fodde R, Smits R, Clevers H, (2001) APC, signal transduction and genetic instability in colorectal cancer. Nature reviews Cancer 1: 55–67.
31. Irahara N, Baba Y, Nosho K, (2010) NRAS mutations are rare in colorectal cancer. Diagnostic Molecular Pathology 19: 157–163.
32. Liao X, Lochhead P, Nishihara R, Morikawa T, Kuchiba A, et al. (2012) Aspirin use, tumor PIK3CA mutation, and colorectal-cancer survival. The New England journal of medicine 367: 1596–606.
33. Szabo A, Boucher K, (2002) Estimating an oncogenetic tree when false negatives and positives are present. Mathematical biosciences 176: 219–236.
34. Desper R, Jiang F, Kallioniemi OP, Moch H, Papadimitriou CH, et al. (1999) Inferring tree models for oncogenesis from comparative genome hybridization data. Journal of Computational Biology 6: 37–51.
35. Gerstung M, Baudis M, Moch H, Beerenwinkel N, (2009) Quantifying cancer progression with conjunctive Bayesian networks. Bioinformatics 25: 2809–2815.
36. Sakoparnig T, Beerenwinkel N, (2012) Efficient sampling for Bayesian inference of conjunctive Bayesian networks. Bioinformatics 28: 2318–2324.
37. Cheng YK, Beroukhim R, Levine RL, Mellinghoff IK, Holland EC, et al. (2012) A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis. PLoS computational biology 8: e1002337.
38. Akavia UD, Litvin O, Kim J, Sanchez-Garcia F, Kotliar D, et al. (2010) An integrated approach to uncover drivers of cancer. Cell 143: 1005–1017.
39. Schuster-Böckler B, Lehner B, (2012) Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature 488: 504–507.
40. R Core Team (2013) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.