Identifying common prognostic factors in genomic cancer studies: A novel index for censored outcomes

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Rouam, Sigrid ^a,b   Moreau, Thierry ^b,c   Broët, Philippe ^a,b  

^a GENOME INSTITUTE OF SINGAPORE   (Singapore)

^b UNIVERSITÉ PARIS SACLAY   (France)

^c INSERM   (France)

Author keywords

[No Author keywords available]

Indexed keywords

GENE EXPRESSION LEVELS; INDEPENDENT RESEARCH; LIKELIHOOD FUNCTIONS; OPERATING CHARACTERISTICS; PREDICTIVE ACCURACY; PROGNOSTIC FACTORS; PROPORTIONAL HAZARDS MODEL; PUBLIC REPOSITORIES;

DISEASES; GENE EXPRESSION; STATISTICAL TESTS;

SAMPLING;

ARTICLE; COMPUTER SIMULATION; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENETICS; HUMAN; HUMAN GENOME; METHODOLOGY; NEOPLASM; PROGNOSIS; SAMPLE SIZE; STATISTICAL MODEL;

COMPUTER SIMULATION; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENOME, HUMAN; HUMANS; LIKELIHOOD FUNCTIONS; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROGNOSIS; SAMPLE SIZE;

EID: 77952318977     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-150     Document Type: Article

References (43)

1. Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, Ledoux P, Rudnev D, Lash AE, Fujibuchi W, Edgar R. NCBI GEO: mining millions of expression profiles-database and tools. Nucleic Acids Research 2005, 33:D562-D566. 10.1093/nar/gki022, 539976, 15608262.
2. Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, Briggs BB, Barrette TR, Anstet MJ, Kincead-Beal C, Kulkarni P, Varambally S, Ghosh D, Chinnaiyan AM. Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia 2007, 9(2):166-180. 10.1593/neo.07112, 1813932, 17356713.
3. Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A. ArrayExpress update-from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Research 2009, 37:D868-D872. 10.1093/nar/gkn889, 2686529, 19015125.
4. Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM. Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proceedings of the National Academy of Sciences of the United States of America 2004, 101(25):9309-9314. 10.1073/pnas.0401994101, 438973, 15184677.
5. Basil CF, Zhao Y, Zavaglia K, Jin P, Panelli MC, Voiculescu S, Mandruzzato S, Lee HM, Seliger B, Freedman RS, Taylor PR, Hu N, Zanovello P, Marincola FM, Wang E. Common cancer biomarkers. Cancer Research 2006, 66(6):2953-2961. 10.1158/0008-5472.CAN-05-3433, 16540643.
6. Xu L, Geman D, Winslow RL. Large-scale integration of cancer microarray data identifies a robust common cancer signature. BMC Bioinformatics 2007, 8:275. 10.1186/1471-2105-8-275, 1950528, 17663766.
7. Lu Y, Yi Y, Liu P, Wen W, James M, Wang D, You M. Common human cancer genes discovered by integrated gene-expression analysis. PLoS One 2007, 2(11):e1149. 10.1371/journal.pone.0001149, 2065803, 17989776.
8. Kalbfleisch JD, Prentice RL. The statistical analysis of failure time data. Wiley series in Probability and Mathematical Statistics 2002, New York: Wiley.
9. Allison DB, Cui X, Page GP, Sabripour M. Microarray data analysis: from disarray to consolidation and consensus. Nature Review Genetics 2006, 7:55-65.
10. Harrell F, Califf R, Pryor D, Lee K, Rosati R. Evaluating the yield of medical tests. Journal of the American Medical Association 1982, 247(18):2543-2546. 10.1001/jama.247.18.2543, 7069920.
11. Antolini L, Boracchi P, Biganzoli E. A time-dependent discrimination index for survival data. Statistics in Medicine 2005, 24(24):3927-3944. 10.1002/sim.2427, 16320281.
12. Korn E, Simon R. Measures of explained variation for survival data. Statistics in Medicine 1990, 9(5):487-503. 10.1002/sim.4780090503, 2349402.
13. Schemper M. The explained variation in proportional hazards regression. Biometrika 1990, 77:216-218.
14. Schemper M, Henderson R. Predictive accuracy and explained variation in Cox regression. Biometrics 2000, 56:249-255. 10.1111/j.0006-341X.2000.00249.x, 10783803.
15. Schemper M, Stare J. Explained variation in survival analysis. Statistics in Medicine 1996, 15(19):1999-2012. 10.1002/(SICI)1097-0258(19961015)15:19<1999::AID-SIM353>3.0.CO;2-D, 8896135.
16. Allison PD. Survival Analysis Using SAS: A Practical Guide 1995, SAS Publishing.
17. Nagelkerke N. A note on a general definition of the coefficient of determination. Biometrika 1991, 78(3):691-692.
18. O'Quigley J, Xu R, Stare J. Explained randomness in proportional hazards models. Statistics in Medicine 2005, 24(3):479-489. 10.1002/sim.1946, 15532086.
19. Xu R, O'Quigley J. A R2 type measure of dependence for proportional hazards models. Journal of Nonparametric Statistics 1999, 12:83-107.
20. Bair E, Tibshirani R. Semi-supervised methods to predict patient survival from gene expression data. PLoS Biology 2004, 2(5):E108. 10.1371/journal.pbio.0020108, 387275, 15094809.
21. Dalmasso C, Broët P, Moreau T. A simple procedure for estimating the false discovery rate. Bioinformatics 2005, 21(5):660-668. 10.1093/bioinformatics/bti063, 15479710.
22. Qiu X, Klebanov L, Yakovlev A. Correlation between gene expression levels and limitations of the empirical bayes methodology for finding differentially expressed genes. Statistical Applications in Genetics and Molecular Biology 2005, 4. Article34, 10.2202/1544-6115.1157, 16646853.
23. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19(2):185-193. 10.1093/bioinformatics/19.2.185, 12538238.
24. Wang Y, Klijn JGM, Zhang Y, Sieuwerts AM, Look MP, Yang F, Talantov D, Timmermans M, Meijer-van Gelder ME, Yu J, Jatkoe T, Berns EMJJ, Atkins D, Foekens JA. Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet 2005, 365:671-679.
25. Pawitan Y, Bjöhle 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, Wedrén S, Bergh J. Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast Cancer Research 2005, 7(6):R953-R964. 10.1186/bcr1325, 1410752, 16280042.
26. Schmidt M, Böhm D, von Törne C, Steiner E, Puhl A, Pilch H, Lehr HA, Hengstler JG, Kölbl H, Gehrmann M. The humoral immune system has a key prognostic impact in node-negative breast cancer. Cancer Research 2008, 68(13):5405-5413. 10.1158/0008-5472.CAN-07-5206, 18593943.
27. Raponi M, Zhang Y, Yu J, Chen G, Lee G, Taylor JMG, 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 Research 2006, 66(15):7466-7472. 10.1158/0008-5472.CAN-06-1191, 16885343.
28. Als AB, Dyrskjot L, Maase H, Koed K, Mansilla F, Toldbod HE, Jensen JL, Ulhoi BP, Sengelov L, Jensen KME, Orntoft TF. Emmprin and survivin predict response and survival following cisplatin-containing chemotherapy in patients with advanced bladder cancer. Clinical Cancer Research 2007, 13(15):4407-4414. 10.1158/1078-0432.CCR-07-0109, 17671123.
29. Phillips HS, Kharbanda S, Chen R, Forrest WF, Soriano RH, Wu TD, Misra A, Nigro JM, Colman H, Soroceanu L, Williams PM, Modrusan Z, Feuerstein BG, Aldape K. Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis. Cancer Cell 2006, 9(3):157-173. 10.1016/j.ccr.2006.02.019, 16530701.
30. Freije WA, Castro-Vargas FE, Fang Z, Horvath S, Cloughesy T, Liau LM, Mischel PS, Nelson SF. Gene expression profiling of gliomas strongly predicts survival. Cancer Research 2004, 64(18):6503-6510. 10.1158/0008-5472.CAN-04-0452, 15374961.
31. Bogunovic D, O'Neill DW, Belitskaya-Levy I, Vacic V, Yu YL, Adams S, Darvishian F, Berman R, Shapiro R, Pavlick AC, Lonardi S, Zavadil J, Osman I, Bhardwaj N. Immune profile and mitotic index of metastatic melanoma lesions enhance clinical staging in predicting patient survival. Proceedings of the National Academy of Sciences of the United States of America 2009, 106(48):20429-20434. 10.1073/pnas.0905139106, 19915147.
32. Blangiardo M, Richardson S. Statistical tools for synthesizing lists of differentially expressed features in related experiments. Genome Biology 2007, 8(4):R54. 10.1186/gb-2007-8-4-r54, 1896017, 17428330.
33. Kato T, Sato N, Hayama S, Yamabuki T, Ito T, Miyamoto M, Kondo S, Nakamura Y, Daigo Y. Activation of Holliday junction recognizing protein involved in the chromosomal stability and immortality of cancer cells. Cancer Research 2007, 67(18):8544-8553. 10.1158/0008-5472.CAN-07-1307, 17823411.
34. Miller JK, Shattuck DL, Ingalla EQ, Yen L, Borowsky AD, Young LJT, Cardiff RD, Carraway KL, Sweeney C. Suppression of the negative regulator LRIG1 contributes to ErbB2 overexpression in breast cancer. Cancer Research 2008, 68(20):8286-8294. 10.1158/0008-5472.CAN-07-6316, 2597648, 18922900.
35. Wu G, Zhou L, Khidr L, Guo XE, Kim W, Lee YM, Krasieva T, Chen PL. A novel role of the chromokinesin Kif4A in DNA damage response. Cell Cycle 2008, 7(13):2013-2020.
36. Zhang N, Ge G, Meyer R, Sethi S, Basu D, Pradhan S, Zhao YJ, Li XN, Cai WW, El-Naggar AK, Baladandayuthapani V, Kittrell FS, Rao PH, Medina D, Pati D. Overexpression of Separase induces aneuploidy and mammary tumorigenesis. Proceedings of the National Academy of Sciences of the United States of America 2008, 105(35):13033-13038. 10.1073/pnas.0801610105, 2529090, 18728194.
37. Carter SL, Eklund AC, Kohane IS, Harris LN, Szallasi Z. A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nature Genetics 2006, 38(9):1043-1048. 10.1038/ng1861, 16921376.
38. Fleming TR, Harrington DP. Counting Processes and Survival Analysis 1991, Wiley.
39. Cox DR. Regression models and life-tables. Journal of the Royal Statistical Society Series B 1972, 34:187-220.
40. Breslow N, Crowley J. A Large Sample Study of the Life Table and Product Limit Estimates Under Random Censorship. Annals of Statistics 1974, 2(3):437-453.
41. Peto R. Contribution to the discussion of the paper by DR Cox. Journal of the Royal Statistical Society Series B 1972, 34:205-207.
42. Lin DY, Wei LJ. The robust inference for the Cox proportional hazards model. Journal of the American Statistical Association 1989, 84:1074-1078.
43. Lachin JM. Biostatistical Methods: The assessment of relative risks. Wiley series in Probability and Mathematical Statistics 2000, New York: Wiley.