Exploiting the noise: Improving biomarkers with ensembles of data analysis methodologies

Genome Medicine

Volumn 4, Issue 11, 2012, Pages

  Starmans, Maud H W ^a,b   Pintilie, Melania ^c   John, Thomas ^d   Der, Sandy D ^c   Shepherd, Frances A ^c   Jurisica, Igor ^c,e,f,g   Lambin, Philippe ^b   Tsao, Ming Sound ^c   Boutros, Paul C ^a,e  

^a ONTARIO INSTITUTE FOR CANCER RESEARCH   (Canada)

^b MAASTRICHT UNIVERSITY   (Netherlands)

^c PRINCESS MARGARET HOSPITAL   (Canada)

^d OLIVIA NEWTON JOHN CANCER RESEARCH INSTITUTE   (Australia)

^e UNIVERSITY OF TORONTO   (Canada)

^f UNIVERSITY HEALTH NETWORK   (Canada)

^g UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER;

ARTICLE; DATA ANALYSIS; LUNG NON SMALL CELL CANCER; PATIENT IDENTIFICATION; POWER ANALYSIS; PRIORITY JOURNAL; RANDOM ERROR; VALIDATION PROCESS;

EID: 84868647626     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/gm385     Document Type: Article

References (36)

1. Li D, Ambrogio L, Shimamura T, Kubo S, Takahashi M, Chirieac LR, Padera RF, Shapiro GI, Baum A, Himmelsbach F, Rettig WJ, Meyerson M, Solca F, Greulich H, Wong KK. BIBW2992, an irreversible EGFR/HER2 inhibitor highly effective in preclinical lung cancer models. Oncogene 2008, 27:4702-4711. 10.1038/onc.2008.109, 2748240, 18408761.
2. Holt SV, Logie A, Davies BR, Alferez D, Runswick S, Fenton S, Chresta CM, Gu Y, Zhang J, Wu YL, Wilkinson RW, Guichard SM, Smith PD. Enhanced apoptosis and tumor growth suppression elicited by combination of MEK (selumetinib) and mTOR kinase inhibitors (AZD8055). Cancer Res 2012, 72:1804-1813. 10.1158/0008-5472.CAN-11-1780, 22271687.
3. van't Veer LJ, Bernards R. Enabling personalized cancer medicine through analysis of gene-expression patterns. Nature 2008, 452:564-570. 10.1038/nature06915, 18385730.
4. Haferlach T, Kohlmann A, Wieczorek L, Basso G, Kronnie GT, Bene MC, De Vos J, Hernandez JM, Hofmann WK, Mills KI, Gilkes A, Chiaretti S, Shurtleff SA, Kipps TJ, Rassenti LZ, Yeoh AE, Papenhausen PR, Liu WM, Williams PM, Foa R. Clinical utility of microarray-based gene expression profiling in the diagnosis and subclassification of leukemia: report from the International Microarray Innovations in Leukemia Study Group. J Clin Oncol 2010, 28:2529-2537. 10.1200/JCO.2009.23.4732, 20406941.
5. Kratz JR, He J, Van Den Eeden SK, Zhu ZH, Gao W, Pham PT, Mulvihill MS, Ziaei F, Zhang H, Su B, Zhi X, Quesenberry CP, Habel LA, Deng Q, Wang Z, Zhou J, Li H, Huang MC, Yeh CC, Segal MR, Ray MR, Jones KD, Raz DJ, Xu Z, Jahan TM, Berryman D, He B, Mann MJ, Jablons DM. A practical molecular assay to predict survival in resected non-squamous, non-small-cell lung cancer: development and international validation studies. Lancet 2012, 379:823-832. 10.1016/S0140-6736(11)61941-7, 3294002, 22285053.
6. Zhu CQ, Ding K, Strumpf D, Weir BA, Meyerson M, Pennell N, Thomas RK, Naoki K, Ladd-Acosta C, Liu N, Printilie M, Der S, Seymour L, Jurisica L, Shepherd FA, Tsao MS. Prognostic and predictive gene signature for adjuvant chemotherapy in resected non-small-cell lung cancer. J Clin Oncol 2010, 28:4417-4424. 10.1200/JCO.2009.26.4325, 2988634, 20823422.
7. Baggerly KA, Coombes KR. Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducibility research in high-throughput biology. Ann Appl Stat 2009, 3:1309-1334.
8. Dupuy A, Simon RM. Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting. J Natl Cancer Inst 2007, 99:147-157. 10.1093/jnci/djk018, 17227998.
9. Beer DG, Kardia SL, Huang CC, Giordano TJ, Levin AM, Misek DE, Lin L, Chen G, Gharib TG, Thomas DG, Lizyness ML, Kuick R, Hayasaka S, Taylor JM, Iannettoni MD, Orringer MB, Hanash S. Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med 2002, 8:816-824.
10. Raponi M, Zhang Y, Yu J, Chen G, Lee G, Taylor JM, Macdonald J, Thomas D, Moskaluk C, Wang Y, Beer DG. Gene expression signatures for predicting prognosis of squamous cell and adenocarcinomas of the lung. Cancer Res 2006, 66:7466-7472. 10.1158/0008-5472.CAN-06-1191, 16885343.
11. Guo L, Ma Y, Ward R, Castranova V, Shi X, Qian Y. Constructing molecular classifiers for the accurate prognosis of lung adenocarcinoma. Clin Cancer Res 2006, 12:3344-3354. 10.1158/1078-0432.CCR-05-2336, 16740756.
12. Subramanian J, Simon R. Gene expression-based prognostic signatures in lung cancer: ready for clinical use?. J Natl Cancer Inst 2010, 102:464-474. 10.1093/jnci/djq025, 2902824, 20233996.
13. Boutros PC, Lau SK, Pintilie M, Liu N, Shepherd FA, Der SD, Tsao MS, Penn LZ, Jurisica I. Prognostic gene signatures for non-small-cell lung cancer. Proc Natl Acad Sci USA 2009, 106:2824-2828. 10.1073/pnas.0809444106, 2636731, 19196983.
14. Ein-Dor L, Zuk O, Domany E. Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc Natl Acad Sci USA 2006, 103:5923-5928. 10.1073/pnas.0601231103, 1458674, 16585533.
15. Goldstraw P, Crowley J, Chansky K, Giroux DJ, Groome PA, Rami-Porta R, Postmus PE, Rusch V, Sobin L. The IASLC Lung Cancer Staging Project: proposals for the revision of the TNM stage groupings in the forthcoming (seventh) edition of the TNM Classification of malignant tumours. J Thorac Oncol 2007, 2:706-714. 10.1097/JTO.0b013e31812f3c1a, 17762336.
16. Pignon JP, Tribodet H, Scagliotti GV, Douillard JY, Shepherd FA, Stephens RJ, Dunant A, Torri V, Rosell R, Seymour L, Spiro SG, Rolland E, Fossati R, Aubert D, Ding K, Waller D, Le Chevalier T, . LACE Collaborative Group Lung adjuvant cisplatin evaluation: a pooled analysis by the LACE Collaborative Group. J Clin Oncol 2008, 26:3552-3559. 10.1200/JCO.2007.13.9030, 18506026, LACE Collaborative Group.
17. Jemal A, Thun MJ, Ries LA, Howe HL, Weir HK, Center MM, Ward E, Wu XC, Eheman C, Anderson R, Ajani UA, Kohler B, Edwards BK. Annual report to the nation on the status of cancer, 1975-2005, featuring trends in lung cancer, tobacco use, and tobacco control. J Natl Cancer Inst 2008, 100:1672-1694. 10.1093/jnci/djn389, 2639291, 19033571.
18. Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P, Ladd C, Beheshti J, Bueno R, Gillette M, Loda M, Weber G, Mark EJ, Lander ES, Wong W, Johnson BE, Golub TR, Sugarbaker DJ, Meyerson M. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci USA 2001, 98:13790-13795. 10.1073/pnas.191502998, 61120, 11707567.
19. Larsen JE, Pavey SJ, Passmore LH, Bowman RV, Hayward NK, Fong KM. Gene expression signature predicts recurrence in lung adenocarcinoma. Clin Cancer Res 2007, 13:2946-2954. 10.1158/1078-0432.CCR-06-2525, 17504995.
20. Lau SK, Boutros PC, Pintilie M, Blackhall FH, Zhu CQ, Strumpf D, Johnston MR, Darling G, Keshavjee S, Waddell TK, Liu N, Lau D, Penn LZ, Shepherd FA, Jurisica L, Der SD, Tsao MS. Three-gene prognostic classifier for early-stage non small-cell lung cancer. J Clin Oncol 2007, 25:5562-5569. 10.1200/JCO.2007.12.0352, 18065728.
21. Shedden K, Taylor JM, Enkemann SA, Tsao MS, Yeatman TJ, Gerald WL, Eschrich S, Jurisica I, Giordano TJ, Misek DE, Chang AC, Zhu CQ, Strumpf D, Hanash S, Shepherd FA, Ding K, Seymour L, Naoki K, Pennell N, Weir B, Verhaak R, Ladd-Acosta C, Golub T, Gruidl M, Sharma A, Szoke J, Zakowski M, Rusch V, Kris M, et al. Director's Challenge Consortium for the Molecular Classification of Lung Adenocarcinoma Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Nat Med 2008, 14:822-827. 10.1038/nm.1790, 2667337, 18641660, Director's Challenge Consortium for the Molecular Classification of Lung Adenocarcinoma.
22. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4:249-264. 10.1093/biostatistics/4.2.249, 12925520.
23. Schoenfeld DA. Sample-size formula for the proportional-hazards regression model. Biometrics 1983, 39:499-503. 10.2307/2531021, 6354290.
24. Wu Z, Irizarry RA, Gentleman R, Martinez-Murillo F, Spencer F. A model-based background adjustment for oligonucleotide expression arrays. J Am Stat Assoc 2004, 99:909-917.
25. Liu WM, Mei R, Di X, Ryder TB, Hubbell E, Dee S, Webster TA, Harrington CA, Ho MH, Baid J, Smeekens SP. Analysis of high density expression microarrays with signed-rank call algorithms. Bioinformatics 2002, 18:1593-1599. 10.1093/bioinformatics/18.12.1593, 12490443.
26. Hubbell E, Liu WM, Mei R. Robust estimators for expression analysis. Bioinformatics 2002, 18:1585-1592. 10.1093/bioinformatics/18.12.1585, 12490442.
27. Li C, Wong WH. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 2001, 98:31-36. 10.1073/pnas.98.1.31, 14539, 11134512.
28. Dai M, Wang P, Boyd AD, Kostov G, Athey B, Jones EG, Bunney WE, Myers RM, Speed TP, Akil H, Watson SJ, Meng F. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res 2005, 33:e175. 10.1093/nar/gni179, 1283542, 16284200.
29. Bild AH, Yao G, Chang JT, Wang Q, Potti A, Chasse D, Joshi MB, Harpole D, Lancaster JM, Berchuck A, Olson JA, Marks JR, Dressman HK, West M, Nevins JR. Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 2006, 439:353-357. 10.1038/nature04296, 16273092.
30. Ransohoff DF. Rules of evidence for cancer molecular-marker discovery and validation. Nat Rev Cancer 2004, 4:309-314. 10.1038/nrc1322, 15057290.
31. Coombes KR, Wang J, Baggerly KA. Microarrays: retracing steps. Nat Med 2007, 13:1276-1277. author reply 1277-1278.
32. Baggerly KA, Coombes KR, Neeley ES. Run batch effects potentially compromise the usefulness of genomic signatures for ovarian cancer. J Clin Oncol 2008, 26:1186-1187. author reply 1187-1188, 10.1200/JCO.2007.15.1951, 18309960.
33. Lim WK, Wang K, Lefebvre C, Califano A. Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. Bioinformatics 2007, 23:i282-288. 10.1093/bioinformatics/btm201, 17646307.
34. Hoffmann R, Seidl T, Dugas M. Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis. Genome Biol 2002, 3. RESEARCH0033.
35. Schmid R, Baum P, Ittrich C, Fundel-Clemens K, Huber W, Brors B, Eils R, Weith A, Mennerich D, Quast K. Comparison of normalization methods for Illumina BeadChip(R) HumanHT-12 v3. BMC Genomics 2010, 11:349. 10.1186/1471-2164-11-349, 3091625, 20525181.
36. Subramanian J, Simon R. Re: Gene expression-based prognostic signatures in lung cancer: ready for clinical use? - Author Reply. J Natl Cancer Inst 2010, 102:1678-1679.