Statistical method on nonrandom clustering with application to somatic mutations in cancer

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Ye, Jingjing ^a   Pavlicek, Adam ^a   Lunney, Elizabeth A ^a   Rejto, Paul A ^a   Teng, Chi Hse ^a,b  

^a PFIZER INC   (United States)

^b AMYLIN PHARMACEUTICALS INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC INSTABILITY; ORDER STATISTICS; PROBABILITY MODELING; PROTEIN SEQUENCES; SOMATIC MUTATION; STATISTICAL MEASURES; TUMOR SUPPRESSORS; UNIFORM DISTRIBUTION;

AMINO ACIDS; DIGITAL STORAGE; ONCOGENIC VIRUSES; PROBABILITY DISTRIBUTIONS; STATISTICAL METHODS; TUMORS;

DISEASES;

B RAF KINASE; BETA CATENIN; BRAF PROTEIN, HUMAN;

ARTICLE; CLUSTER ANALYSIS; GENETICS; HUMAN; HUMAN GENOME; MUTATION; NEOPLASM; ONCOGENE RAS; STATISTICAL MODEL;

BETA CATENIN; CLUSTER ANALYSIS; GENES, RAS; GENOME, HUMAN; HUMANS; MODELS, STATISTICAL; MUTATION; NEOPLASMS; PROTO-ONCOGENE PROTEINS B-RAF;

EID: 76949086002     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-11     Document Type: Article

References (47)

1. Vogelstein B, Kinzler KW. Cancer genes and the pathways they control. Nat Med 2004, 10:789-799. 10.1038/nm1087, 15286780.
2. Weinstein IB, Joe AK. Mechanisms of disease: Oncogene addiction--a rationale for molecular targeting in cancer therapy. Nat Clin Pract Oncol 2006, 3:448-457. 10.1038/ncponc0558, 16894390.
3. Cahill DP, Kinzler KW, Vogelstein B, Lengauer C. Genetic instability and darwinian selection in tumours. Trends Cell Biol 1999, 9:M57-60. 10.1016/S0962-8924(99)01661-X, 10611684.
4. Wang TL, Rago C, Silliman N, Ptak J, Markowitz S, Willson JKV, Parmigiani G, Kinzler KW, Vogelstein B, Velculescu VE. Prevalence of somatic alterations in the colorectal cancer cell genome. PNAS 2002, 99:3076-3080. 10.1073/pnas.261714699, 122475, 11867767.
5. Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, Greulich H, Muzny DM, Morgan MB, Fulton L, Fulton RS, Zhang Q, Wendl MC, Lawrence MS, Larson DE, Chen K, Dooling DJ, Sabo A, Hawes AC, Shen H, Jhangiani SN, Lewis LR, Hall O, Zhu Y, Mathew T, Ren Y, Yao J, Scherer SE, Clerc K, Metcalf GA, Ng B, Milosavljevic A, Gonzalez-Garay ML, Osborne JR, Meyer R, Shi X, Tang Y, Koboldt DC, Lin L, Abbott R, Miner TL, Pohl C, Fewell G, Haipek C, Schmidt H, Dunford-Shore BH, Kraja A, Crosby SD, Sawyer CS, Vickery T, Sander S, Robinson J, Winckler W, Baldwin J, Chirieac LR, Dutt A, Fennell T, Hanna M, Johnson BE, Onofrio RC, Thomas RK, Tonon G, Weir BA, Zhao X, Ziaugra L, Zody MC, Giordano T, Orringer MB, Roth JA, Spitz MR, Wistuba II, Ozenberger B, Good PJ, Chang AC, Beer DG, Watson MA, Ladanyi M, Broderick S, Yoshizawa A, Travis WD, Pao W, Province MA, Weinstock GM, Varmus HE, Gabriel SB, Lander ES, Gibbs RA, Meyerson M, Wilson RK. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 2008, 455:1069-1075. 10.1038/nature07423, 2694412, 18948947.
6. Bardelli A, Parsons DW, Silliman N, Ptak J, Szabo S, Saha S, Markowitz S, Willson JKV, Parmigiani G, Kinzler KW, Vogelstein B, Velculescul VE. Mutational analysis of the tyrosine kinome in colorectal cancers. Science 2003, 300:949. 10.1126/science.1082596, 12738854.
7. Yang Z, Ro S, Rannala B. Likelihood models of somatic mutation and codon substitution in cancer genes. Genetics 2003, 165:695-705. 1462779, 14573481.
8. Samuels Y, Wang Z, Bardelli A, Silliman N, Ptak J, Szabo S, Yan H, Gazdar A, Powell SM, Riggins GJ, Willson JKV, Markowitz S, Kinzler KW, Vogelstein B, Velculescu1 VE. High frequency of mutations of the PIK3CA gene in human cancers. Science 2004, 304:554. 10.1126/science.1096502, 15016963.
9. Davies H, Hunter C, Smith R, Stephens P, Greenman C, Bignell G, Teague J, Butler A, Edkins S, Stevens C, Parker A, O'Meara S, Avis T, Barthorpe S, Brackenbury L, Buck G, Clements J, Cole J, Dicks E, Edwards K, Forbes S, Gorton M, Gray K, Halliday K, Harrison R, Hills K, Hinton J, Jones D, Kosmidou V, Laman R, Lugg R, Menzies A, Perry J, Petty R, Raine K, Shepherd R, Small A, Solomon H, Stephens Y, Tofts C, Varian J, Webb A, West S, Widaa S, Yates A, Brasseur F, Cooper CS, Flanagan AM, Green A, Knowles M, Leung SY, Looijenga LHJ, Malkowicz B, Pierotti MA, Teh BT, Yuen ST, Lakhani SR, Easton DF, Weber BL, Goldstraw P, Nicholson AG, Wooster R, Stratton MR, Futreal PA. Somatic mutations of the protein kinase gene family in human lung cancer. Cancer Res 2005, 65:7591-7595.
10. Greenman C, Wooster R, Futreal PA, Stratton MR, Easton DF. Statistical analysis of pathogenicity of somatic mutations in cancer. Genetics 2006, 173:2187-2198. 10.1534/genetics.105.044677, 1569711, 16783027.
11. Sjöblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, Mandelker D, Leary RJ, Ptak J, Silliman N, Szabo S, Buckhaults P, Farrell C, Meeh P, Markowitz SD, Willis J, Dawson D, Willson JKV, Gazdar AF, Hartigan J, Wu L, Liu C, Parmigiani G, Park BH, Bachman KE, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE. The consensus coding sequences of human breast and colorectal cancers. Science 2006, 314:268-274. 10.1126/science.1133427, 16959974.
12. Kaminker JS, Zhang Y, Waugh A, Haverty PM, Peters B, Sebisanovic D, Stinson J, Forrest WF, Bazan JF, Seshagiri S, Zhang Z. Distinguishing cancer-associated missense mutations from common polymorphisms. Cancer Res 2007, 67:465-473. 10.1158/0008-5472.CAN-06-1736, 17234753.
13. Yip YL, Zoete V, Scheib H, Michielin O. Structural assessment of single amino acid mutations: application to TP53 function. Hum Mutat 2006, 27:926-937. 10.1002/humu.20379, 16917930.
14. Graur D, Li W-H. Dynamics of Genes in Population. Fundamentals of Molecular Evolution 2000, 39-65. Sinauer Associates, 2.
15. Torkamani A, Schork NJ. Prediction of cancer driver mutations in protein kinases. Cancer Res 2008, 68:1675-1682. 10.1158/0008-5472.CAN-07-5283, 18339846.
16. Naus JI. The distribution of the size of the maximum cluster of points on a line. JASA 1965, 60(310):532-538.
17. Naus JI. A power comparison of two tests of non-random clustering. Technometrics 1966, 8:493-517.
18. Balakrishnan N, Koutras MV. Runs and scans with applications. 2002, Wiley, New York.
19. Glaz J, Zhang Z. Maximum scan score-type statistics. Statistics and Probability Letters 2006, 76:1316-1322.
20. Forbes SA, Bhamra G, Bamford S, Dawson E, Kok C, Clements J, Menzies A, Teague JW, Futreal PA, Stratton MR. The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr Protoc Hum Genet 2008, Chapter 10(Unit 10):11. 2705836, 18428421.
21. Davies H, Bignell GR, Cox C, Stephens P, Edkins S, Clegg S, Teague J, Woffendin H, Garnett MJ, Bottomley W, Davis N, Dicks E, Ewing R, Floyd Y, Gray K, Hall S, Hawes R, Hughes J, Kosmidou V, Menzies A, Mould C, Parker A, Stevens C, Watt S, Hooper S, Wilson R, Jayatilake H, Gusterson BA, Cooper C, Shipley J, Hargrave D, Pritchard-Jones K, Maitland N, Chenevix-Trench G, Riggins GJ, Bigner DD, Palmieri G, Cossu A, Flanagan A, Nicholson A, Ho JW, Leung SY, Yuen ST, Weber BL, Seigler HF, Darrow TL, Paterson H, Marais R, Marshall CJ, Wooster R, Stratton MR, Futreal PA. Mutations of the BRAF gene in human cancer. Nature 2002, 417:949-954. 10.1038/nature00766, 12068308.
22. Bos JL. The ras gene family and human carcinogenesis. Mutat Res 1988, 195:255-271.
23. Hagen T, Vidal-Puig A. Characterisation of the phosphorylation of β-catenin at the GSK-3 priming site Ser45. Biochem Biophys Res Comm 2002, 294(2):324-328. 10.1016/S0006-291X(02)00485-0, 12051714.
24. Morin PJ, Sparks AB, Korinek V, Barker N, Clevers H, Vogelstein B, Kinzler KW. Activation of beta-catenin-Tcf signaling in colon cancer by mutations in beta-catenin or APC. Science 1997, 275:1787-1790. 10.1126/science.275.5307.1787, 9065402.
25. Fan Y-X, Wong L, Ding J, Spiridonov NA, Johnson RC, Johnson GR. Mutational activation of ErbB2 reveals a new protein kinase autoinhibition mechanism. J Biol Chem 2008, 283(3):1588-1596. 10.1074/jbc.M708116200, 18039657.
26. Mata IF, Wedemeyer WJ, Farrer MJ, Taylor JP, Gallo KA. LRRK2 in Parkinson's disease: protein domains and functional insights. Trends Neurosci 2006, 29:286-293. 10.1016/j.tins.2006.03.006, 16616379.
27. Inzelberg R, Jankovic J. Are Parkinson disease patients protected from some but not all cancers?. Neurology 2007, 69:1542-1550. and discussion., 10.1212/01.wnl.0000277638.63767.b8, 17699801.
28. Strongosky AJ, Jankovic J. Are Parkinson disease patients protected from some but not all cancers?. Neurology 2008, 71:1650. 10.1212/01.wnl.0000339367.54460.8c, 19001259.
29. Nigro JM, Baker SJ, Preisinger AC, Jessup JM, Hosteller R, Cleary K, Signer SH, Davidson N, Baylin S, Devilee P, Glover T, Collins FS, Weslon A, Modali R, Harris CC, Vogelstein B. Mutations in the p53 gene occur in diverse human tumour types. Nature 1989, 342:705-708. 10.1038/342705a0, 2531845.
30. Hollstein M, Sidransky D, Vogelstein B, Harris CC. p53 mutations in human cancers. Science 1991, 253:49-53. 10.1126/science.1905840, 1905840.
31. Song H, Hollstein M, Xu Y. p53 gain-of-function cancer mutants induce genetic instability by inactivating ATM. Nat Cell Biol 2007, 9:573-580. 10.1038/ncb1571, 17417627.
32. Tolkacheva T, Chan AM. Inhibition of H-Ras transformation by the PTEN/MMAC1/TEP1 tumor suppressor gene. Oncogene 2000, 19:680-689. 10.1038/sj.onc.1203331, 10698513.
33. Yu WP, Pallen CJ, Tay A, Jirik FR, Brenner S, Tan YH, Venkatesh B. Conserved synteny between the fugu and human PTEN locus and the evolutionary conservation of vertebrate PTEN function. Oncogene 2001, 20:5554-5561. 10.1038/sj.onc.1204679, 11571655.
34. Wagner A. Rapid detection of positive selection in genes and genomes through variation clusters. Genetics 2007, 176:2451-2463. 10.1534/genetics.107.074732, 1950645, 17603100.
35. Jones S, Zhang X, Parsons DW, Lin JC-H, Leary RJ, Angenendt P, Mankoo P, Carter H, Kamiyama H, Jimeno A, Hong S-M, Fu B, Lin M-T, Calhoun ES, Kamiyama M, Walter K, Nikolskaya T, Nikolsky Y, Hartigan J, Smith DR, Hidalgo M, Leach SD, Klein AP, Jaffee EM, Goggins M, Maitra A, Iacobuzio-Donahue C, Eshleman JR, Kern SE, Hruban RH, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 2008, 321:1801-1806. 10.1126/science.1164368, 18772397.
36. Parsons DW, Jones S, Zhang X, Lin JC-H, Leary RJ, Angenendt P, Mankoo P, Carter H, Siu I-M, Gallia GL, Olivi A, McLendon R, Rasheed BA, Keir S, Nikolskaya T, Nikolsky Y, Busam DA, Tekleab H, Diaz LA, Hartigan J, Smith DR, Strausberg RL, Marie SKN, Shinjo SMO, Yan H, Riggins GJ, Bigner DD, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW. An integrated genomic analysis of human glioblastoma multiforme. Science 2008, 321:807-812.
37. Cancer Genome Atlas Research Network Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008, 455:1061-1068. 10.1038/nature07385, 2671642, 18772890, Cancer Genome Atlas Research Network.
38. Sved J, Bird A. The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model. PNAS 1990, 87:4692-4696. 10.1073/pnas.87.12.4692, 54183, 2352943.
39. Jones PA, Rideout WM, Shen JC, Spruck CH, Tsai YC. Methylation, mutation and cancer. Bioessays 1992, 14:33-36. 10.1002/bies.950140107, 1546979.
40. Burr IW. Calculation of exact sampling distribution of ranges from a discrete population. The Annals of Mathematical Statistics 1955, 26:530-532.
41. Evans DL, Leemis LM, Drew JH. The distribution of order statistics for discrete random variables with applications to bootstrapping. INFORMS Journal on Computing 2006, 18(1):19-30.
42. Johnson NL, Kotz S, Balakrishnan N. Continuous Univariate Distributions. 1995, 2:280-281. Wiley-Interscience, 2.
43. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. JRSS, Series B 1995, 57(1):289-300.
44. Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Annals of Stat 2001, 29(4):1165-1188.
45. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Research 2000, 28:235-242. 10.1093/nar/28.1.235, 102472, 10592235.
46. Huang CH, Mandelker D, Schmidt-Kittler O, Samuels Y, Velculescu VE, Kinzler KW, Vogelstein B, Gabelli SB, Amzel LM. The structure of a human p110alpha/p85alpha complex elucidates the effects of oncogenic PI3Kalpha mutations. Science 2007, 318:1744-1748. 10.1126/science.1150799, 18079394.
47. Wang Y, Rosengarth A, Luecke H. Structure of the human p53 core domain in the absence of DNA. Acta Crystallogr, Sect D 2007, 63:276-281.