ColoGuideEx: A robust gene classifier specific for stage II colorectal cancer prognosis

Gut

Volumn 61, Issue 11, 2012, Pages 1560-1567

  Ågesen, Trude H ^a,b   Sveen, Anita ^a,b   Merok, Marianne A ^a,b,c   Lind, Guro E ^a,b   Nesbakken, Arild ^b,c   Skotheim, Rolf I ^a,b   Lothe, Ragnhild A ^a,b  

^a OSLO UNIVERSITY HOSPITAL   (Norway)

^b UNIVERSITY OF OSLO   (Norway)

^c OSLO UNIVERSITY HOSPITAL   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA TUBULIN; ALPHA2 GLYCOPROTEIN; CXCL13 CHEMOKINE; DESMOCOLLIN; DESMOCOLLIN 3; ECTONUCLEOTIDE PYROPHOSPHATASE PHOSPHODIESTERASE 3; EPHRIN RECEPTOR A7; GAMMA INTERFERON INDUCIBLE PROTEIN 10; KALLIKREIN 6; PHOSPHODIESTERASE; PROTEIN BNIP3; SECRETORY COMPONENT; SEMAPHORIN 3A; STROMELYSIN; UNCLASSIFIED DRUG; ZINC BINDING PROTEIN;

ADULT; AGED; ARTICLE; AZGP1 GENE; CANCER CHEMOTHERAPY; CANCER PATIENT; CANCER PROGNOSIS; CANCER RECURRENCE; CANCER STAGING; CANCER SURVIVAL; CLASSIFIER; CLINICAL FEATURE; COLOGUIDEEX; COLORECTAL CANCER; CONTROLLED STUDY; CXCL10 GENE; CXCL13 GENE; DNIP3 GENE; DSC3 GENE; ENPP3 GENE; EPHA7 GENE; GENE EXPRESSION PROFILING; GENE SEQUENCE; GENE TECHNOLOGY; HUMAN; HUMAN TISSUE; KLK6 GENE; MAJOR CLINICAL STUDY; MMP3 GENE; NORWAY; NUCLEOTIDE SEQUENCE; ONCOGENE; PIGR GENE; PREDICTION; PREDICTIVE VALUE; PRIORITY JOURNAL; PROPORTIONAL HAZARDS MODEL; RISK ASSESSMENT; SEMA3A GENE; SESN1 GENE; TUBA1B GENE;

AGED; AGED, 80 AND OVER; ANALYSIS OF VARIANCE; COHORT STUDIES; COLORECTAL NEOPLASMS; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, NEOPLASM; HUMANS; KAPLAN-MEIER ESTIMATE; MALE; MIDDLE AGED; MULTIVARIATE ANALYSIS; NEOPLASM INVASIVENESS; NEOPLASM STAGING; NORWAY; PROGNOSIS; PROPORTIONAL HAZARDS MODELS; REPRODUCIBILITY OF RESULTS; RISK ASSESSMENT; RNA, NEOPLASM; SAMPLING STUDIES; SURVIVAL ANALYSIS;

EID: 84867019805     PISSN: 00175749     EISSN: 14683288     Source Type: Journal    
DOI: 10.1136/gutjnl-2011-301179     Document Type: Article

References (44)

1. Ferlay J, Shin HR, Bray F, et al. Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int J Cancer 2010;127:2893-917.
2. O'Connell JB, Maggard MA, Ko CY. Colon cancer survival rates with the new American Joint Committee on Cancer sixth edition staging. J Natl Cancer Inst 2004;96:1420-5. (Pubitemid 39429665)
3. NIH Consensus Conference. Adjuvant therapy for patients with colon and rectal cancer. JAMA 1990;264:1444-50.
4. Figueredo A, Coombes ME, Mukherjee S. Adjuvant therapy for completely resected stage II colon cancer. Cochrane Database Syst Rev 2008; (3):CD005390.
5. Benson AB III, Schrag D, Somerfield MR, et al. American Society of Clinical Oncology recommendations on adjuvant chemotherapy for stage II colon cancer. J Clin Oncol 2004;22:3408-19. (Pubitemid 41103700)
6. Gray R, Barnwell J, McConkey C, et al. Adjuvant chemotherapy versus observation in patients with colorectal cancer: a randomised study. Lancet 2007;370:2020-9.
7. Farina-Sarasqueta A, van LG, Moerland E, et al. The BRAF V600E mutation is an independent prognostic factor for survival in stage II and stage III colon cancer patients. Ann Oncol 2010;21:2396-402.
8. Roth AD, Tejpar S, Delorenzi M, et al. Prognostic role of KRAS and BRAF in stage II and III resected colon cancer: results of the translational study on the PETACC-3, EORTC 40993, SAKK 60-00 trial. J Clin Oncol 2010;28:466-74.
9. Walther A, Houlston R, Tomlinson I. Association between chromosomal instability and prognosis in colorectal cancer: a meta-analysis. Gut 2008;57:941-50. (Pubitemid 351919529)
10. Popat S, Hubner R, Houlston RS. Systematic review of microsatellite instability and colorectal cancer prognosis. J Clin Oncol 2005;23:609-18. (Pubitemid 46224239)
11. Locker GY, Hamilton S, Harris J, et al. ASCO 2006 update of recommendations for the use of tumor markers in gastrointestinal cancer. J Clin Oncol 2006;24:5313-27. (Pubitemid 46631379)
12. Van SS, Allen WL, Turkington RC, et al. Implementing prognostic and predictive biomarkers in CRC clinical trials. Nat Rev Clin Oncol 2011;8:222-32.
13. Jorissen RN, Gibbs P, Christie M, et al. Metastasis-Associated gene expression changes predict poor outcomes in patients with Dukes stage B and C colorectal cancer. Clin Cancer Res 2009;15:7642-51.
14. Van Laar RK. An online gene expression assay for determining adjuvant therapy eligibility in patients with stage 2 or 3 colon cancer. Br J Cancer 2010;103:1852-7.
15. Jiang Y, Casey G, Lavery IC, et al. Development of a clinically feasible molecular assay to predict recurrence of stage II colon cancer. J Mol Diagn 2008;10:346-54. (Pubitemid 352019121)
16. Bertucci F, Salas S, Eysteries S, et al. Gene expression profiling of colon cancer by DNA microarrays and correlation with histoclinical parameters. Oncogene 2004;23:1377-91. (Pubitemid 38406833)
17. Salazar R, Roepman P, Capella G, et al. Gene expression signature to improve prognosis prediction of stage II and III colorectal cancer. J Clin Oncol 2011;29:17-24.
18. Smith JJ, Deane NG, Wu F, et al. Experimentally derived metastasis gene expression profile predicts recurrence and death in patients with colon cancer. Gastroenterology 2010;138:958-68.
19. Wang Y, Jatkoe T, Zhang Y, et al. Gene expression profiles and molecular markers to predict recurrence of Dukes' B colon cancer. J Clin Oncol 2004;22 :1564-71. (Pubitemid 41079793)
20. Berg M, Danielsen SA, Ahlquist T, et al. DNA sequence profiles of the colorectal cancer critical gene set KRAS-BRAF-PIK3CA-PTEN-TP53 related to age at disease onset. PLoS One 2010;5:e13978.
21. Diep CB, Thorstensen L, Meling GI, et al. Genetic tumor markers with prognostic impact in Dukes' stages B and C colorectal cancer patients. J Clin Oncol 2003;21:820-9. (Pubitemid 46606441)
22. Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 2008;9:559.
23. Langfelder P, Horvath S. Package 'WGCNA'. 2011. http://cran.r-project. org/web/packages/WGCNA/WGCNA.pdf
24. Smyth GK, Ritchie M, Thorne N, et al. Limma: Linear Models for Microarray Data User's Guide. 2010. http://www.bioconductor.org/packages/2.6/bioc/ vignettes/limma/inst/doc/usersguide.pdf
25. Goeman JJ. L1 penalized estimation in the Cox proportional hazards model. Biom J 2010;52:70-84.
26. Goeman JJ. Package 'Penalized'. 2011. http://cran.r-project.org/web/ packages/penalized/penalized.pdf
27. Huang daW Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009;4:44-57.
28. Quackenbush J. Microarray analysis and tumor classification. N Engl J Med 2006;354:2463-72. (Pubitemid 43855049)
29. Tibshirani R. The lasso method for variable selection in the Cox model. Stat Med 1997;16 :385-95. (Pubitemid 27073009)
30. Tibshirani R. Regression shrinkage and selection via the LASSO. J R Stat Soc 1996;58 :267-88.
31. Agendia Inc. ColoPrint . 2011. http://www.agendia.com/pages/coloprint/ 173.php
32. Genomic Health Inc. Oncotype DX Colon Cancer Assay. 2011. http://www.oncotypedx.com/en-US/Colon.aspx
33. O'Connell MJ, Lavery I, Yothers G, et al. Relationship between tumor gene expression and recurrence in four independent studies of patients with stage II/III colon cancer treated with surgery alone or surgery plus adjuvant fluorouracil plus leucovorin. J Clin Oncol 2010;28:3937-44.
34. PARSC study (NCT00903565): A Prospective Study for the Assessment of Recurrence Risk in Stage II Colon Cancer Patients Using ColoPrint (PARSC) . 2011. http://clinicaltrials.gov/ct2/show/NCT00903565
35. Clark-Langone KM, Wu JY, Sangli C, et al. Biomarker discovery for colon cancer using a 761 gene RT-PCR assay. BMC Genomics 2007;8 :279.
36. Webber EM, Lin JS, Evelyn PW. Oncotype DX tumor gene expression profiling in stage II colon cancer. Application: prognostic, risk prediction. PLoS Curr 2010;2:RRN1177.
37. Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell 2011;144:646-74.
38. Agesen TH, Berg M, Clancy T, et al. CLC and IFNAR1 are differentially expressed and a global immunity score is distinct between early- and late-onset colorectal cancer. Genes Immun 2011;12:653-62.
39. Traicoff JL, De ML, Ginsburg BL, et al. Characterization of the human polymeric immunoglobulin receptor (PIGR) 3'UTR and differential expression of PIGR mRNA during colon tumorigenesis. J Biomed Sci 2003;10:792-804. (Pubitemid 38032496)
40. Moran A, Iniesta P, de JC, et al. Stromelysin-1 promoter mutations impair gelatinase B activation in high microsatellite instability sporadic colorectal tumors. Cancer Res 2002;62:3855-60. (Pubitemid 34728872)
41. Yazdani U, Terman JR. The semaphorins. Genome Biol 2006;7:211.
42. Gaur P, Bielenberg DR, Samuel S, et al. Role of class 3 semaphorins and their receptors in tumor growth and angiogenesis. Clin Cancer Res 2009;15:6763-70.
43. Muller MW, Giese NA, Swiercz JM, et al. Association of axon guidance factor semaphorin 3A with poor outcome in pancreatic cancer. Int J Cancer 2007;121:2421-33. (Pubitemid 350022411)
44. Kim JT, Song EY, Chung KS, et al . Up-regulation and clinical significance of serine protease kallikrein 6 in colon cancer. Cancer 2011;117:2608-19.