Expanding the understanding of biases in development of clinical-grade molecular signatures: A case study in acute respiratory viral infections

PLoS ONE

Volumn 6, Issue 6, 2011, Pages

  Lytkin, Nikita I ^a   McVoy, Lauren ^a   Weitkamp, Jörn Hendrik ^b   Aliferis, Constantin F ^a,c   Statnikov, Alexander ^a  

^a NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b MONROE CARELL JR CHILDREN S HOSPITAL AT VANDERBILT   (United States)

^c VANDERBILT UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; CASE STUDY; CONTROLLED STUDY; DATA ANALYSIS; GENE EXPRESSION PROFILING; GENETIC DATABASE; INFORMATION PROCESSING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; REPRODUCIBILITY; RESPIRATORY TRACT INFECTION; RIBC2 GENE; SIMULATION; VALIDITY; VIRUS GENE; VIRUS INFECTION; ACUTE DISEASE; BIOLOGY; EPIDEMIOLOGY; GENETICS; HUMAN; METABOLISM; METHODOLOGY; STATISTICAL ANALYSIS; VIROLOGY;

BIOLOGICAL MARKER;

ACUTE DISEASE; BIAS (EPIDEMIOLOGY); BIOLOGICAL MARKERS; COMPUTATIONAL BIOLOGY; DATA INTERPRETATION, STATISTICAL; HUMANS; PHENOTYPE; RESPIRATORY TRACT INFECTIONS;

EID: 79957830827     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0020662     Document Type: Article

References (40)

1. Sparano JA, Paik S, (2008) Development of the 21-gene assay and its application in clinical practice and clinical trials. J Clin Oncol 26: 721-728.
2. Glas AM, Floore A, Delahaye LJ, Witteveen AT, Pover RC, et al. (2006) Converting a breast cancer microarray signature into a high-throughput diagnostic test. BMC Genomics 7: 278.
3. Baggerly KA, Morris JS, Coombes KR, (2004) Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. Bioinformatics 20: 777-785.
4. Simon R, Radmacher MD, Dobbin K, McShane LM, (2003) Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification. J Natl Cancer Inst 95: 14-18.
5. Ambroise C, McLachlan GJ, (2002) Selection bias in gene extraction on the basis of microarray gene-expression data. Proc Natl Acad Sci U S A 99: 6562-6566.
6. Statnikov A, Li C, Aliferis CF, (2007) Effects of Environment, Genetics and Data Analysis Pitfalls in an Esophageal Cancer Genome-Wide Association Study. PLoS ONE 2: e958.
7. Aliferis CF, Statnikov A, Tsamardinos I, Schildcrout JS, Shepherd BE, et al. (2009) Factors Influencing the Statistical Power of Complex Data Analysis Protocols for Molecular Signature Development from Microarray Data. PLoS ONE 4: e4922.
8. Statnikov A, Lytkin N, McVoy L, Weitkamp J, Aliferis C, (2010) Using gene expression profiles from peripheral blood to identify asymptomatic responses to acute respiratory viral infections. BMC Research Notes 3: 264.
9. Zaas AK, Chen M, Varkey J, Veldman T, Hero AO III, et al. (2009) Gene expression signatures diagnose influenza and other symptomatic respiratory viral infections in humans. Cell Host Microbe 6: 207-217.
10. Statnikov A, McVoy L, Lytkin N, Aliferis CF, (2010) Improving development of the molecular signature for diagnosis of acute respiratory viral infections. Cell Host Microbe 7: 100-101.
11. Zaas AK, Aziz H, Lucas J, Perfect JR, Ginsburg GS, (2010) Blood gene expression signatures predict invasive candidiasis. Sci Transl Med 2: 21ra17.
12. Ramilo O, Allman W, Chung W, Mejias A, Ardura M, et al. (2007) Gene expression patterns in blood leukocytes discriminate patients with acute infections. Blood 109: 2066-2077.
13. Jackson GG, Dowling HF, Spiesman IG, Boand AV, (1958) Transmission of the common cold to volunteers under controlled conditions. I. The common cold as a clinical entity. AMA Arch Intern Med 101: 267-278.
14. Statnikov A, Aliferis CF, (2010) TIED: An Artificially Simulated Dataset with Multiple Markov Boundaries. Journal of Machine Learning Research Workshop and Conference Proceedings, Volume 6: Causality: Objectives and Assessment (NIPS 2008) 6: 249-256.
15. Statnikov A, Aliferis CF, (2010) Analysis and Computational Dissection of Molecular Signature Multiplicity. PLoS Computational Biology 6: e1000790.
16. Guyon I, Janzing D, Schölkopf B, (2010) Causality: Objectives and Assessment. Journal of Machine Learning Research Workshop and Conference Proceedings, Volume 6: Causality: Objectives and Assessment (NIPS 2008) 6: 1-42.
17. Azuaje F, Dopazo J, (2005) Data analysis and visualization in genomics and proteomics Hoboken, NJ John Wiley.
18. Somorjai RL, Dolenko B, Baumgartner R, (2003) Class prediction and discovery using gene microarray and proteomics mass spectroscopy data: curses, caveats, cautions. Bioinformatics 19: 1484-1491.
19. Pearl J, (1988) Probabilistic reasoning in intelligent systems: networks of plausible inference San Mateo, California Morgan Kaufmann Publishers.
20. Pearl J, (2000) Causality: models, reasoning, and inference Cambridge, U.K Cambridge University Press.
21. Tsamardinos I, Aliferis CF, (2003) Towards principled feature selection: relevancy, filters and wrappers. Proceedings of the Ninth International Workshop on Artificial Intelligence and Statistics (AI & Stats).
22. Guyon I, Aliferis CF, Elisseeff A, (2007) Causal Feature Selection. In: Liu H, Motoda H, editors. Computational Methods of Feature Selection Chapman and Hall.
23. Aliferis CF, Statnikov A, Tsamardinos I, Mani S, Koutsoukos XD, (2010) Local Causal and Markov Blanket Induction for Causal Discovery and Feature Selection for Classification. Part II: Analysis and Extensions. Journal of Machine Learning Research 11: 235-284.
24. Aliferis CF, Statnikov A, Tsamardinos I, Mani S, Koutsoukos XD, (2010) Local Causal and Markov Blanket Induction for Causal Discovery and Feature Selection for Classification. Part I: Algorithms and Empirical Evaluation. Journal of Machine Learning Research 11: 171-234.
25. Vapnik VN, (1998) Statistical learning theory New York Wiley.
26. Kohavi R, John GH, (1997) Wrappers for feature subset selection. Artificial Intelligence 97: 273-324.
27. Anderson TW, (2003) An introduction to multivariate statistical analysis Hoboken, N.J Wiley-Interscience.
28. DeLong ER, DeLong DM, Clarke-Pearson DL, (1988) Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach. Biometrics 44: 837-845.
29. Braga-Neto UM, Dougherty ER, (2004) Is cross-validation valid for small-sample microarray classification? Bioinformatics 20: 374-380.
30. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.
31. Irizarry RA, Wu Z, Jaffee HA, (2006) Comparison of Affymetrix GeneChip expression measures. Bioinformatics 22: 789-794.
32. Benjamini Y, Hochberg Y, (1995) Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B (Methodological) 57: 289-300.
33. Benjamini Y, Yekutieli D, (2001) The control of the false discovery rate in multiple testing under dependency. Ann Statist 29: 1165-1188.
34. Johnson WE, Li C, Rabinovic A, (2007) Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8: 118-127 kxj037 [pii];10.1093/biostatistics/kxj037 [doi].
35. Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, et al. (2010) Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet 11: 733-739 nrg2825 [pii];10.1038/nrg2825 [doi].
36. Cope LM, Irizarry RA, Jaffee HA, Wu Z, Speed TP, (2004) A benchmark for Affymetrix GeneChip expression measures. Bioinformatics 20: 323-331 10.1093/bioinformatics/btg410 [doi];20/3/323 [pii].
37. Gonzalez FJ, Yu AM, (2006) Cytochrome P450 and xenobiotic receptor humanized mice. Annu Rev Pharmacol Toxicol 46: 41-64 10.1146/annurev.pharmtox.45.120403.100007 [doi].
38. Liu Z, Maas K, Aune TM, (2004) Comparison of differentially expressed genes in T lymphocytes between human autoimmune disease and murine models of autoimmune disease. Clin Immunol 112: 225-230 10.1016/j.clim.2004.03.017 [doi];S1521661604001081 [pii].
39. Rangarajan A, Weinberg RA, (2003) Opinion: Comparative biology of mouse versus human cells: modelling human cancer in mice. Nat Rev Cancer 3: 952-959 10.1038/nrc1235 [doi];nrc1235 [pii].
40. Ntzani EE, Ioannidis JP, (2003) Predictive ability of DNA microarrays for cancer outcomes and correlates: an empirical assessment. Lancet 362: 1439-1444.