Multiple-criterion evaluation of reported mutations: A proposed scoring system for the intragenic somatic mutation literature

Cancer Biology and Therapy

Volumn 5, Issue 4, 2006, Pages 360-370

  Winter, Jordan M ^a   Brody, Jonathan R ^a   Kern, Scott E ^a,b  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b 451 CRB ^*  (United States)

Author keywords

Artifacts; Cancer; Cell lines; Mutations; Scoring system; Tissues

Indexed keywords

CANCER; CANCER SCINTISCANNING; CRITERION VARIABLE; EVALUATION RESEARCH; GENE MUTATION; GENE SEQUENCE; GENE TARGETING; HUMAN; MEDICAL LITERATURE; MISSENSE MUTATION; NEOPLASM; REVIEW; SCORING SYSTEM; SOMATIC MUTATION; TISSUE TYPES; VALIDATION PROCESS; VIGNETTE;

EID: 33646415964     PISSN: 15384047     EISSN: 15558576     Source Type: Journal    
DOI: 10.4161/cbt.5.4.2552     Document Type: Review

References (76)

1. Kern SE, Winter JM. Elegance, Silence, and Nonsense in the Mutations Literature for Solid Tumors. Cancer Biol Ther 2006.
2. Cotton RG, Horaitis O. Quality control in the discovery, reporting, and recording of genomic variation. Hum Mutat 2000; 15:16-21.
3. Wiley Interscience. Human Mutation, Instructions to Authors. In Cotton RGH, Kazazian HH, eds. Human Mutation, Vol. May 25, 2005. Hoboken: John Wiley & Sons, Inc., 2005-pp. Human Mutation Website.
4. Nowell PC, Hungerford DA. National Academy of Sciences. Abstracts of Papers Presented at the Autumn Meeting, 14-16 November 1960, Philadelphia, Pennsylvania. Science 1960; 132:1497.
5. Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, Rahman N, Stratton MR. A census of human cancer genes. Nat Rev Cancer 2004; 4:177-83.
6. Hempen PM, Zhang L, Bansal RK, Iacobuzio-Donahue CA, Murphy KM, Maitra A, Vogelstein B, Whitehead RH, Markowitz SD, Willson JK, Yeo CJ, Hruban RH, Kern SE. Evidence of selection for clones having genetic inactivation of the activin A type II receptor (ACVR2) gene in gastrointestinal cancers. Cancer Res 2003; 63:994-9.
7. Weber JL, David D, Heil J, Fan Y, Zhao C, Marth G. Human diallelic insertion/deletion polymorphisms. Am J Hum Genet 2002; 71:854-62.
8. Williams C, Ponten F, Moberg C, Soderkvist P, Uhlen M, Ponten J, Sitbon G, Lundeberg J. A high frequency of sequence alterations is due ro formalin fixation of archival specimens. Am J Pathol 1999; 155:1467-71.
9. Wong C, DiCioccio RA, Allen HJ, Werness BA, Piver MS. Mutations in BRCA1 from fixed, paraffin-embedded tissue can be artifacts ot preservation. Cancer Genet Cytogenet 1998; 107:21-7.
10. Hayashi K, Yandell DW. How sensitive is PCR-SSCP? Hum Mutat 1993; 2:338-46.
11. Wang TL, Rago C, Silliman N, Ptak J, Markowitz S, Willson JK, Parmigiani G, Kinzler KW, Vogelstein B, Velculescu VE. Prevalence of somatic alterations in the colorectal cancer cell genome. Proc Natl Acad Sci U S A 2002; 99:3076-80.
12. Capon DJ, Seeburg PH, McGrath JP, Hayflick JS, Edman U, Levinson AD, Goeddel DV. Activation of Ki-ras2 gene in human colon and lung carcinomas by two different point mutations. Nature 1983; 304:507-13.
13. Nakano H, Yamamoto F, Neville C, Evans D, Mizuno T, Perucho M. Isolation of transforming sequences of two human lung carcinomas: structural and functional analysis of the activated c-K-ras oncogenes. Proc Natl Acad Sci U S A 1984; 81:71-5.
14. Dunn JM, Phillips RA, Becker AJ, Gallie BL. Identification of germline and somatic mutations affecting the retinoblastoma gene. Science 1988; 241:1797-800.
15. Baker SJ, Fearon ER, Nigro JM, Hamilton SR, Pteisinger AC, Jessup JM, vanTuinen P, Ledbetter DH, Barker DF, Nakamura Y, White R, Vogelstein B. Chromosome 17 deletions and p53 gene mutations in colorectal carcinomas. Science 1989; 244:217-21.
16. Kinzler KW, Nilbert MC, Vogelstein B, Bryan TM, Levy DB, Smith KJ, Preisinger AC, Hamilton SR, Hedge P, Markham A, et al. Identification of a gene located at chromosome 5q21 that is mutated in colorectal cancers. Science 1991; 251:1366-70.
17. Nishisho I, Nakamura Y, Miyoshi Y, Miki Y, Ando H, Horii A, Koyama K, Utsunomiya J, Baba S, Hedge P. Mutations of chromosome 5q21 genes in FAP and colorectal cancer patients. Science 1991; 253:665-9.
18. Kamb A, Gruis NA, Weaver-Feldhaus J, Liu Q, Harshman K, Tavtigian SV, Stockert E, Day RS, 3rd, Johnson BE, Skolnick MH. A cell cycle regulator potentially involved in genesis of many tumor types. Science 1994; 264:436-40.
19. De Souza AT, Hankins GR, Washington MK, Orton TC, Jirtle RL. M6P/IGF2R gene is mutated in human hepatocellular carcinomas with loss of heterozygosity. Nat Genet 1995; 11:447-9.
20. Kawanishi J, Kato J, Sasaki K, Fujii S, Watanabe N, Niitsu Y. Loss of E-cadherin-dependent cell-cell adhesion due to mutation of the beta-catenin gene in a human cancer cell line, HSC-39. Mol Cell Biol 1995; 15:1175-81.
21. Hahn SA, Schutte M, Hoque AT, Moskaluk CA, da Costa LT, Rozenblum E, Weinstein CL, Fischer A, Yeo CJ, Hruban RH, Kern SE. DPC4, a candidate tumor suppressor gene at human chromosome 18q21.1. Science 1996; 271:350-3.
22. Riggins GJ, Thiagalingam S, Rozenblum E, Weinstein CL, Kern SE, Hamilton SR, Willson JK, Markowitz SD, Kinzler KW, Vogelstein B. Mad-related genes in the human. Nat Genet 1996; 13:347-9.
23. Li J, Yen C, Liaw D, Podsypanina K, Bose S, Wang SI, Puc J, Miliaresis C, Rodgers L, McCombie R, Bigner SH, Giovanella BC, Ittmann M, Tycko B, Hibshoosh H, Wigler MH, Parsons R. PTEN, a putative protein tyrosine phosphatase gene mutated in human brain, breast, and prostate cancer. Science 1997; 275:1943-7.
24. Steck PA, Pershouse MA, Jasser SA, Yung WK, Lin H, Ligon AH, Langford LA, Baumgard ML, Hattier T, Davis T, Frye C, Hu R, Swedlund B, Teng DH, Tavtigian SV. Identification of a candidate tumour suppressor gene, MMAC1, at chromosome 10q23.3 that is mutated in multiple advanced cancers. Nat Genet 1997; 15:356-62.
25. Wang SS, Esplin ED, Li JL, Huang L, Gazdar A, Minna J, Evans GA. Alterations of the PPP2R1B gene in human lung and colon cancer. Science 1998; 282:284-7.
26. Irby RB, Mao W, Coppola D, Kang J, Loubeau JM, Trudeau W, Karl R, Fujita DJ, Jove R, Yeatman TJ. Activating SRC mutation in a subset of advanced human colon cancers. Nat Genet 1999; 21:187-90.
27. Sarraf P, Mueller E, Smith WM, Wright HM, Kum JB, Aaltonen LA, de la Chapelle A, Spiegelman BM, Eng C. Loss-of-function mutations in PPAR gamma associated with human colon cancer. Mol Cell 1999; 3:799-804.
28. Gunduz M, Ouchida M, Fukushima K, Hanafusa H, Etani T, Nishioka S, Nishizaki K, Shimizu K. Genomic structure of the human ING1 gene and tumor-specific mutations detected in head and neck squamous cell carcinomas. Cancer Res 2000; 60:3143-6.
29. Wong AK, Shanahan F, Chen Y, Lian L, Ha P, Hendricks K, Ghaffari S, Iliev D, Penn B, Woodland AM, Smith R, Salada G, Carillo A, Laity K, Gupte J, Swedlund B, Tavtigian SV, Teng DH, Lees E. BRG1, a component of the SWI-SNF complex, is mutated in multiple human tumor cell lines. Cancer Res 2000; 60:6171-7.
30. Narla G, Heath KE, Reeves HL, Li D, Giono LE, Kimmelman AC, Glucksman MJ, Narla J, Eng FJ, Chan AM, Ferrari AC, Martignetti JA, Friedman SL. KLF6, a candidate tumor suppressor gene mutated in prostate cancer. Science 2001; 294:2563-6.
31. Popanda O, Flohr C, Dai JC, Hunzicker A, Thielmann HW. A mutation in subunit B of the DNA polymerase alpha-primase complex from Novikoff hepatoma cells concomitant with a conformational change and abnormal catalytic properties of the DNA polymerase alpha-primase complex. Mol Carcinog 2001; 31:171-83.
32. Zhao X, Li J, He Y, Lan F, Fu L, Guo J, Zhao R, Ye Y, He M, Chong W, Chen J, Zhang L, Yang N, Xu B, Wu M, Wan D, Gu J. A novel growth suppressor gene on chromosome 17p13.3 with a high frequency of mutation in human hepatocellular carcinoma. Cancer Res 2001; 61:7383-7.
33. Ruivenkamp CA, van Wezel T, Zanon C, Stassen AP, Vlcek C, Csikos T, Klous AM, Tripodis N, Perrakis A, Boerrigter L, Groot PC, Lindeman J, Mooi WJ, Meijjer GA, Scholten G, Dauwerse H, Paces V, van Zandwijk N, van Ommen GJ, Demant P. Ptprj is a candidate for the mouse colon-cancer susceptibility locus Scc1 and is frequently deleted in human cancers. Nat Genet 2002; 31:295-300.
34. Heinrich MC, Corless CL, Duensing A, McGreevey L, Chen CJ, Joseph N, Singer S, Griffith DJ, Haley A, Town A, Demetri GD, Fletcher CD, Fletcher JA. PDGFRA activating mutations in gastrointestinal stromal tumors. Science 2003; 299:708-10.
35. Baldinu P, Cossu A, Manca A, Satta MP, Sini MC, Rozzo C, Dessole S, Cherchi P, Gianfrancesco F, Pintus A, Carboni A, Deiana A, Tanda F, Palmieri G. Identification of a novel candidate gene, CASC2, in a region of common allelic loss at chromosome 10q26 in human endometrial cancer. Hum Mutat 2004; 23:318-26.
36. Kochevar GJ, Brody JR, Kadkol SS, Murphy KM, Pasternack GR. Identification of a functional mutation in pp32r1 (ANP32C). Hum Mutat 2004; 23:546-51.
37. Stephens P, Hunter C, Bignell G, Edkins S, Davies H, Teague J, Stevens C, O'Meara S, Smith R, Parker A, Barthorpe A, Blow M, Brackenbury L, Butler A, Clarke O, Cole J, Dicks E, Dike A, Drozd A, Edwards K, Forbes S, Foster R, Gray K, Greenman C, Halliday K, Hills K, Kosmidou V, Lugg R, Menzies A, Perry J, Petty R, Raine K, Ratford L, Shepherd R, Small A, Stephens Y, Tofts C, Varian J, West S, Widaa S, Yates A, Brasseur F, Cooper CS, Flanagan AM, Knowles M, Leung SY, Louis DN, Looijenga LH, Malkowicz B, Pierotti MA, Teh B, Chenevix-Trench G, Weber BL, Yuen ST, Harris G, Goldstraw P, Nicholson AG, Futreal PA, Wooster R, Stratton MR. Lung cancer: intragenic ERBB2 kinase mutations in tumours. Nature 2004; 431:525-6.
38. 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; 417:949-54.
39. Bos JL, Fearon ER, Hamilton SR, Verlaan-de Vries M, van Boom JH, van der Eb AJ, Vogelstein B. Prevalence of ras gene mutations in human colorectal cancers. Nature 1987; 327:293-7.
40. Dunn JM, Phillips RA, Zhu X, Becker A, Gallie BL. Mutations in the RB1 gene and their effects on transcription. Mol Cell Biol 1989; 9:4596-604.
41. Powell SM, Zilz N, Beazer-Barclay Y, Bryan TM, Hamilton SR, Thibodeau SN, Vogelstein B, Kinzler KW. APC mutations occur early during colorectal tumorigenesis. Nature 1992; 359:235-7.
42. Horii A, Nakatsuru S, Miyoshi Y, Ichii S, Nagase H, Ando H, Yanagisawa A, Tsuchiya E, Kato Y, Nakamura Y. Frequent somatic mutations of the APC gene in human pancreatic cancer. Cancer Res 1992; 52:6696-8.
43. Eppert K, Scherer SW, Ozcelik H, Pirone R, Hoodles P, Kim H, Tsui LC, Bapat B, Gallinger S, Andrulis IL, Thomsen GH, Wrana JL, Attisano L. MADR2 maps to 18q21 and encodes a TGFbeta-regulated MAD-related protein that is functionally mutated in colorectal carcinoma. Cell 1996; 86:543-52.
44. 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; 275:1787-90.
45. Yamada T, De Souza AT, Finkelstein S, Jirtle RL. Loss of the gene encoding mannose 6-phosphate/insulin-like growth factor II receptor is an early event in liver carcinogenesis. Proc Natl Acad Sci U S A 1997; 94:10351-5.
46. Park WS, Moon YW, Yang YM, Kim YS, Kim YD, Fuller BG, Vortmeyer AO, Fogt F, Lubensky IA, Zhuang Z. Mutations of the STK11 gene in sporadic gastric carcinoma. Int J Oncol 1998; 13:601-4.
47. Hirota S, Isozaki K, Moriyama Y, Hashimoto K, Nishida T, Ishiguro S, Kawano K, Hanada M, Kurata A, Takeda M, Muhammad Tunio G, Matsuzawa Y, Kanakura Y, Shinomura Y, Kitamura Y. Gain-of-function mutations of c-kit in human gastrointestinal stromal tumors. Science 1998; 279:577-80.
48. Su GH, Hruban RH, Bansal RK, Bova GS, Tang DJ, Shekher MC, Westerman AM, Entius MM, Goggins M, Yeo CJ, Kern SE. Germline and somatic mutations of the STKI1/LKB1 Peutz-Jeghers gene in pancreatic and biliary cancers. Am J Pathol 1999; 154:1835-40.
49. Dong SM, Kim KM, Kim SY, Shin MS, Na EY, Lee SH, Park WS, Yoo NJ, Jang JJ, Yoon CY, Kim JW, Kim SY, Yang YM, Kim SH, Kim CS, Lee JY. Frequent somatic mutations in serine/threonine kinase 11/Peutz-Jeghers syndrome gene in left-sided colon cancer. Cancer Res 1998; 58:3787-90.
50. Avizienyte E, Roth S, Loukola A, Hemminki A, Lothe RA, Stenwig AE, Fossa SD, Salovaara R, Aaltonen LA. Somatic mutations in LKB1 are rare in sporadic colorectal and testicular tumors. Cancer Res 1998; 58:2087-90.
51. Oka Y, Waterland RA, Killian JK, Nolan CM, Jang HS, Tohara K, Sakaguchi S, Yao T, Iwashita A, Yata Y, Takahara T, Sato S, Suzuki K, Masuda T, Jirtle RL. M6P/IGF2R tumor suppressor gene mutated in hepatocellular carcinomas in Japan. Hepatology 2002; 35:1153-63.
52. Moore PS, Missiaglia E, Antonello D, Zamo A, Zamboni G, Corleto V, Falconi M, Scarpa A. Role of disease-causing genes in sporadic pancreatic endocrine tumors: MEN1 and VHL. Genes Chromosomes Cancer 2001; 32:177-81.
53. Kurose K, Gilley K, Matsumoto S, Watson PH, Zhou XP, Eng C. Frequent somatic mutations in PTEN and TP53 are mutually exclusive in the stroma of breast carcinomas. Nat Genet 2002; 32:355-7.
54. Chen L, Matsubara N, Yoshino T, Nagasaka T, Hoshizima N, Shirakawa Y, Naomoto Y, Isozaki H, Riabowol K, Tanaka N. Genetic alterations of candidate tumor suppressor ING1 in human esophageal squamous cell cancer. Cancer Res 2001; 61:4345-9.
55. Sanchez-Cespedes M, Parrella P, Esteller M, Nomoto S, Trink B, Engles JM, Westra WH, Herman JG, Sidransky D. Inactivation of LKB1/STK11 is a common event in adenocarcinomas of the lung. Cancer Res 2002; 62:3659-62.
56. Park WS, Lee JH, Shin MS, Park JY, Kim HS, Lee JH, Kim YS, Lee SN, Xiao W, Park CH, Lee SH, Yoo NJ, Lee JY. Inactivating mutations of the caspase-10 gene in gastric cancer. Oncogene 2002; 21:2919-25.
57. van der Heijden MS, Yeo CJ, Hruban RH, Kern SE. Fanconi anemia gene mutations in young-onset pancreatic cancer. Cancer Res 2003; 63:2585-8.
58. Medina PP, Carretero J, Fraga MF, Esteller M, Sidransky D, Sanchez-Cespedes M. Genetic and epigenetic screening for gene alterations of the chromatin-remodeling factor, SMARCA4/BRG1, in lung tumors. Genes Chromosomes Cancer 2004; 41:170-7.
59. Chen C, Hyytinen ER, Sun X, Helin HJ, Koivisto PA, Frierson HF, Jr., Vessella RL, Dong JT. Deletion, mutation, and loss of expression of KLF6 in human prostate cancer. Am J Pathol 2003; 162:1349-54.
60. Bentires-Alj M, Paez JG, David FS, Keilhack H, Halmos B, Naoki K, Maris JM, Richardson A, Baidelli A, Sugarbaker DJ, Richards WG, Du J, Girard L, Minna JD, Loh ML, Fisher DE, Velculescu VE, Vogelstein B, Meyerson M, Sellers WR, Neel BG. Activating mutations of the noonan syndrome-associated SHP2/PTPN11 gene in human solid tumors and adult acute myelogenous leukemia. Cancer Res 2004; 64:8816-20.
61. Tan YX, Wang HT, Zhang P, Yan ZH, Dai GL, Wu MC, Wang HY. c-src activating mutation analysis in Chinese patients with colorectal cancer. World J Gastroenterol 2005; 11:2351-3.
62. Soung YH, Lee JW, Kim SY, Park WS, Nam SW, Lee JY, Yoo NJ, Lee SH. Somatic mutations of CASP3 gene in human cancers. Hum Genet 2004; 115:112-5.
63. Shigematsu H, Takahashi T, Nomura M, Majmudar K, Suzuki M, Lee H, Wistuba, II, Fong KM, Toyooka S, Shimizu N, Fujisawa T, Minna JD, Gazdar AF. Somatic mutations of the HER2 kinase domain in lung adenocarcinomas. Cancer Res 2005; 65:1642-6.
64. Paez JG, Janne PA, Lee JC, Tracy S, Greulich H, Gabriel S, Herman P, Kaye FJ, Lindeman N, Boggon TJ, Naoki K, Sasaki H, Fujii Y, Eck MJ, Sellers WR, Johnson BE, Meyerson M. EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science 2004; 304:1497-500.
65. Lynch TJ, Bell DW, Sordella R, Gurubhagavatula S, Okimoto RA, Brannigan BW, Harris PL, Haserlat SM, Supko JG, Haluska FG, Louis DN, Christiani DC, Settleman J, Haber DA. Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N EngJ J Med 2004; 350:2129-39.
66. Carretero J, Medina PP, Pio R, Montuenga LM, Sanchez-Cespedes M. Novel and natural knockout lung cancer cell lines for the LKB1/STK11 tumor suppressor gene. Oncogene 2004; 23:4037-40.
67. Muhlbauer KR, Grone HJ, Ernst T, Grone E, Tschada R, Hergenhahn M, Hollstein M. Analysis of human prostate cancers and cell lines for mutations in the TP53 and KLF6 tumour suppressor genes. Br J Cancer 2003; 89:687-90.
68. Koivisto PA, Hyytinen ER, Matikainen M, Tammela TL, Ikonen T, Schleutker J. Kruppel-like factor 6 germ-line mutations are infrequent in Finnish hereditary prostate cancer. J Urol 2004; 172:506-7.
69. Koivisto PA, Zhang X, Sallinen SL, Sallinen P, Helin HJ, Dong JT, Van Meir EG, Haapasalo H, Hyytinen ER. Absence of KLF6 gene mutations in human astrocytic tumors and cell lines. Int J Cancer 2004; 111:642-3.
70. Jeng YM, Hsu HC. KLF6, a putative tumor suppressor gene, is mutated in astrocytic gliomas. Int J Cancer 2003; 105:625-9.
71. Sugimura M, Kobayashi K, Sagae S, Nishioka Y, Ishioka S, Terasawa K, Tokino T, Kudo R. Mutation of the SRC gene in endometrial carcinoma. Jpn J Cancer Res 2000; 91:395-8.
72. Wang P, Fromowitz F, Koslow M, Hagag N, Johnson B, Viola M. c-src structure in human cancers with elevated pp60c-src activity. Br J Cancer 1991; 64:531-3.
73. Nilbert M, Fernebro E. Lack of activating c-SRC mutations at codon 531 in rectal cancer. Cancer Genet Cytogenet 2000; 121:94-5.
74. Laghi L, Bianchi P, Orbetegli O, Gennari L, Roncalli M, Malesci A. Lack of mutation at codon 531 of SRC in advanced colorectal cancers from Italian patients. Br J Cancer 2001; 84:196-8.
75. Daigo Y, Furukawa Y, Kawasoe T, Ishiguro H, Fujita M, Sugai S, Nakamori S, Liefers GJ, Tollenaar RA, van de Velde CT, Nakamura Y. Absence of genetic alteration at codon 531 of the human c-src gene in 479 advanced colorectal cancers from Japanese and Caucasian patients. Cancer Res 1999; 59:4222-4.
76. Garber K. Human Cancer Genome Project moving forward despite some doubts in community. J Natl Cancer Inst 2005; 97:1322-4.