Design and Multiseries Validation of a Web-Based Gene Expression Assay for Predicting Breast Cancer Recurrence and Patient Survival

Journal of Molecular Diagnostics

Volumn 13, Issue 3, 2011, Pages 297-304

  Van Laar, Ryan K ^a  

^a ChipDX LLC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; BIOASSAY; BREAST CANCER; CANCER ADJUVANT THERAPY; CANCER DIAGNOSIS; CANCER SURVIVAL; DIAGNOSTIC TEST ACCURACY STUDY; FEMALE; GENE EXPRESSION; GENETIC ALGORITHM; GENETIC ASSOCIATION; HIGH RISK PATIENT; HUMAN; MAJOR CLINICAL STUDY; MULTIVARIATE ANALYSIS; OVERALL SURVIVAL; PREDICTIVE VALUE; PROGNOSIS; PROPORTIONAL HAZARDS MODEL; RECURRENT DISEASE; SENSITIVITY AND SPECIFICITY; VALIDATION PROCESS;

EID: 79954889005     PISSN: 15251578     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmoldx.2010.12.003     Document Type: Article

References (28)

1. Harris L, Fritsche H, Mennel R, Norton L, Ravdin P, Taube S, Somerfield MR, Hayes DF, Bast RC Jr: American Society of Clinical Oncology 2007 update of recommendations for the use of tumor markers in breast cancer. J Clin Oncol 2007, 25:5287-5312 (Pubitemid 350232263)
2. Paik S, Shak S, Tang G, Kim C, Baker J, Cronin M, Baehner FL, Walker MG, Watson D, Park T, Hiller W, Fisher ER, Wickerham DL, Bryant J, Wolmark N: A multigene assay to predict recurrence of tamoxifentreated, node-negative breast cancer. N Engl J Med 2004, 351:2817-2826 (Pubitemid 40051905)
3. van't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH: Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002, 415:530-536 (Pubitemid 34130608)
4. Wang Y, Klijn J, Zhang Y, Sieuwerts A, Look M, Yang F, Talantov D, Timmermans M, van Gelder M, Yu J, Jatkoe T, Berns E, Atkins D, Foekens J: Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet 2005, 365:671-679 (Pubitemid 40260888)
5. Ma XJ, Wang Z, Ryan PD, Isakoff SJ, Barmettler A, Fuller A, Muir B, Mohapatra G, Salunga R, Tuggle JT, Tran Y, Tran D, Tassin A, Amon P, Wang W, Enright E, Stecker K, Estepa-Sabal E, Smith B, Younger J, Balis U, Michaelson J, Bhan A, Habin K, Baer TM, Brugge J, Haber DA, Erlander MG, Sgroi DC: A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell 2004, 5:607-616 (Pubitemid 38748922)
6. Ein-Dor L, Kela I, Getz G, Givol D, Domany E: Outcome signature genes in breast cancer: is there a unique set? Bioinformatics 2005, 21:171-178 (Pubitemid 40202018)
7. Abraham G, Kowalczyk A, Loi S, Haviv I, Zobel J: Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context. BMC Bioinformatics 2010, 11:277
8. Haibe-Kains B, Desmedt C, Piette F, Buyse M, Cardoso F, van't Veer L, Piccart M, Bontempi G, Sotiriou C: Comparison of prognostic gene expression signatures for breast cancer. BMC Genomics 2008, 9:394
9. Cardoso F, Piccart-Gebhart M, Van't Veer L, Rutgers E: The MINDACT trial: the first prospective clinical validation of a genomic tool. Mol Oncol 2007, 1:246-251 (Pubitemid 350181650)
10. 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, 103:1852-1857
11. Loi S, Haibe-Kains B, Desmedt C, Lallemand F, Tutt AM, Gillet C, Ellis P, Harris A, Bergh J, Foekens JA, Klijn JGM, Larsimont D, Buyse M, Bontempi G, Delorenzi M, Piccart MJ, Sotiriou C: Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade. J Clin Oncol 2007, 25:1239-1246 (Pubitemid 46640570)
12. Ivshina AV, George J, Senko O, Mow B, Putti TC, Smeds J, Lindahl T, Pawitan Y, Hall P, Nordgren H, Wong JEL, Liu ET, Bergh J, Kuznetsov VA, Miller LD: Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer. Cancer Res 2006, 66:10292-10301 (Pubitemid 44799747)
13. Desmedt C, Piette F, Loi S, Wang Y, Lallemand FO, Haibe-Kains B, Viale G, Delorenzi M, Zhang Y, d'Assignies MS, Bergh J, Lidereau R, Ellis P, Harris AL, Klijn JGM, Foekens JA, Cardoso F, Piccart MJ, Buyse M, Sotiriou C: Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series. Clin Cancer Res 2007, 13:3207-3214 (Pubitemid 46944903)
14. Schmidt M, Bohm D, von Torne C, Steiner E, Puhl A, Pilch H, Lehr H-A, Hengstler JG, Kolbl H, Gehrmann M: The humoral immune system has a key prognostic impact in node-negative breast cancer. Cancer Res 2008, 68:5405-5413
15. Pawitan Y, Bjohle J, Amler L, Borg AL, Egyhazi S, Hall P, Han X, Holmberg L, Huang F, Klaar S, Liu ET, Miller L, Nordgren H, Ploner A, Sandelin K, Shaw PM, Smeds J, Skoog L, Wedren S, Bergh J: Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast Cancer Res 2005, 7:R953-R964
16. van de Vijver MJ, He YD, van'T Veer LJ, Dai H, Hart AA, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, Marton MJ, Parrish M, Atsma D, Witteveen A, Glas A, Delahaye L, van der Velde T, Bartelink H, Rodenhuis S, Rutgers ET, Friend SH, Bernards R: A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002, 347:1999-2009 (Pubitemid 35461656)
17. Chowdary D, Lathrop J, Skelton J, Curtin K, Briggs T, Zhang Y, Yu J, Wang Y, Mazumder A: Prognostic gene expression signatures can be measured in tissues collected in RNAlater preservative. J Mol Diagn 2006, 8:31-39 (Pubitemid 43257432)
18. Bair E, Tibshirani R: Semi-supervised methods to predict patient survival from gene expression data. PLoS Biol 2004, doi: 10.1371/ journal.pbio.0020108
19. Simon R, Lam A, Li MC, Ngan M, Menenzes S, Zhao Y: Analysis of gene expression data using BRB-Array Tools. Cancer Inform 2007, 3:11-17 (Pubitemid 47075796)
20. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5:R80
21. Simon, R., A. Lam, Li M-C, Ngan M, Menenzes S, Zhao Y: Analysis of GeneExpression Data Using BRB-Array Tools. Cancer Inform 2007, 3:11-17 (Pubitemid 47075796)
22. Sørlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, Thorsen T, Quist H, Matese JC, Brown PO, Botstein D, Eystein Lønning P, Børresen-Dale AL: Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A 2001, 98:10869-10874
23. Shen R, Chinnaiyan AM, Ghosh D: Pathway analysis reveals functional convergence of gene expression profiles in breast cancer. BMC Med Genomics 2008, 1:28
24. Robbins P, Pinder S, Klerk ND, Dawkins H, Harvey J, Sterrett G, Ellis I, Elston C: Histological grading of breast carcinomas: a study of interobserver agreement. Human Pathol 1995, 26:873-879
25. Singletary SE, Allred C, Ashley P, Bassett LW, Berry D, Bland KI, Borgen PI, Clark G, Edge SB, Hayes DF, Hughes LL, Hutter RV, Morrow M, Page DL, Recht A, Theriault RL, Thor A, Weaver DL, Wieand HS, Greene FL: Revision of the American Joint Committee on Cancer staging system for breast cancer. J Clin Oncol 2002, 20: 3628-3636 (Pubitemid 34983222)
26. Trial watch: adaptive BATTLE trial uses biomarkers to guide lung cancer treatment. Nat Rev Drug Discov 2010, 9:423
27. Abdueva D, Wing M, Schaub B, Triche T, Davicioni E: Quantitative expression profiling in formalin-fixed paraffin-embedded samples by affymetrix microarrays. J Mol Diagn 2010, 12:409-417
28. Mutter G, Zahrieh D, Liu C, Neuberg D, Finkelstein D, Baker H, Warrington J: Comparison of frozen and RNALater solid tissue storage methods for use in RNA expression microarrays. BMC Genomics 2004, 5:8