Good practice guidelines for biomarker discovery from array data: A case study for breast cancer prognosis

BMC Systems Biology

Volumn 7, Issue SUPPL4, 2013, Pages

  Cheng, Jie ^a   Greshock, Joel ^a   Shi, Leming ^b   Zheng, Shu ^c   Menius, Alan ^a   Lee, Kwan ^a  

^a GLAXOSMITHKLINE   (United States)

^b NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH   (United States)

^c ZHEJIANG UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

TUMOR MARKER;

ARTICLE; BIOLOGY; BREAST TUMOR; DNA MICROARRAY; FEMALE; GENETIC DATABASE; GENETICS; HUMAN; METHODOLOGY; MIDDLE AGED; PRACTICE GUIDELINE; PROGNOSIS; RECURRENT DISEASE;

BREAST NEOPLASMS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; FEMALE; HUMANS; MIDDLE AGED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROGNOSIS; RECURRENCE; TUMOR MARKERS, BIOLOGICAL;

EID: 84886619948     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-7-S4-S2     Document Type: Article

References (15)

1. Subramanian J, Simon R. Gene expression-based prognostic signatures in lung cancer: ready for clinical use?. J Natl Cancer Inst 2010, 102:464-74. 10.1093/jnci/djq025, 2902824, 20233996.
2. Simon R. Roadmap for developing and validating therapeutically relevant genomic classifi-ers. J Clin Oncol 2005, 23:7332-41. 10.1200/JCO.2005.02.8712, 16145063.
3. Dudoit R, Fridly J, Speed TP. Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data. JAMA 2002, 97-457:77-87.
4. Cheng J, Greshock J, Shi L, Painter J, Lin X, Lee K, Zheng S, Wooster R, Pusztai L, Menius A. An adaptive feature selection method for microarray data analysis. Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference on: 4-7 October 2012 2012, 1-6.
5. Greshock J, Cheng J, Rusnak D, Martin AM, Wooster R, Gilmer T, Lee K, Weber BL, Zaks T. Genome-wide DNA copy number predictors of lapatinib sensitivity in tumor-derived cell lines. Mol Cancer Ther 2008, 7:935-943. 10.1158/1535-7163.MCT-07-2072, 18413807.
6. MAQC consortium. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation. Nat Biotechnol 2010, 28:827-838. 10.1038/nbt.1665, 3315840, 20676074.
7. 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. 10.1056/NEJMoa021967, 12490681.
8. Buyse M, Loi S, van't Veer L, Viale G, Delorenzi M, Glas AM, d'Assignies MS, Bergh J, Lidereau R, Ellis P, Harris A, Bogaerts J, Therasse P, Floore A, Amakrane M, Piette F, Rutgers E, Sotiriou C, Cardoso F, Piccart MJ. Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer. J Natl Cancer Inst 2006, 98:1183-92. 10.1093/jnci/djj329, 16954471.
9. 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. 10.1038/415530a, 11823860.
10. Haybittle JL, Blamey RW, Elston CW, Johnson J, Doyle PJ, Campbell FC, Nicholson RI, Griffiths K. A prognostic index in primary breast cancer. British journal of cancer 1982, 45(3):361-6. 10.1038/bjc.1982.62, 2010939, 7073932.
11. Ravdin PM, Siminoff LA, Davis GJ, Mercer MB, Hewlett J, Gerson N, Parker HL. Computer program to assist in making decisions about adjuvant therapy for women with early breast cancer. J Clin Oncol 2001, 19:980-91.
12. Esteva FJ, Sahin AA, Cristofanilli M, Coombes K, Lee SJ, Baker J, Cronin M, Walker M, Watson D, Shak S, Hortobagyi GN. Prognostic role of a multigene reverse transcriptase-PCR assay in patients with node-negative breast cancer not receiving adjuvant systemic therapy. Clin Cancer Res 2005, 11:3315-3319. 10.1158/1078-0432.CCR-04-1707, 15867229.
13. Wang Y, Klijn JG, Zhang Y, Sieuwerts AM, Look MP, Yang F, Talantov D, Timmermans M, Meijer-van Gelder ME, Yu J, Jatkoe T, Berns EM, Atkins D, Foekens JA. Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet 2005, 365(9460):671-9.
14. Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, Sun XW, Varambally S, Cao X, Tchinda J, Kuefer R, Lee C, Montie JE, Shah RB, Pienta KJ, Rubin MA, Chinnaiyan AM. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 2005, 310:644-8. 10.1126/science.1117679, 16254181.
15. Tibshirani R, Hastie T. Outlier sums for differential gene expression analysis. Biostatistics 2007, 8:2-8. 10.1093/biostatistics/kxl005, 16702229.