Biological validation of differetially expressed genes in chronic lymphocytic leukemia identified by applying multiple statistical methods to oligonucleotide microarrays

Lynne V. Abruzzo, Jing Wang, Mini Kapoor, L. Jeffrey Medeiros, Michael J. Keating, W Edward Jr. Highsmith, Lynn L. Barron, Candy C. Cromwell, Kevin R. Coombes

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Oligonucleotide microarrays are a powerful tool for profiling the expression levels of thousands of genes. Different statistical methods for identifying differentially expressed genes can yield different results. To our knowledge, no experimental test has been performed to decide which method best identifies genes that are truly differentially expressed. We applied three statistical methods (dChip, t-test on log-transformed data, and Wilcoxon test) to identify differentially expressed genes in previously untreated patients with chronic lymphocytic leukemia (CLL). We used a training set of Affymetrix Hu133A microarray data from 11 patients with unmutated immunoglobulin (Ig) heavy chain variable region (VH) genes and 8 patients with mutated Ig VH genes. Differential expression was validated using semiquantitative real-time polymerase chain reaction assays and by validating models to predict the somatic mutation status of an independent test set of nine CLL samples. The methods identified 144 genes that were differentially expressed between cases of CLL with unmutated compared with mutated Ig VH genes. Eighty genes were identified by Wilcoxon test, 60 by t-test, and 65 by dChip, but only 11 were identified by all three methods. Greater agreement was found between the t-test and the Wilcoxon test. Differential expression was validated by semiquantitative real-time polymerase chain reaction assays for 83% of individual genes, regardless of the statistical method. However, the Wilcoxon test gave the most accurate predictions on new samples, and dChip, the least accurate. We found that all three methods were equally good for finding differentially expressed genes, but they found different genes. The genes selected by the nonparametric Wilcoxon test are the most robust for predicting the status of new cases. A comprehensive list of all differentially expressed genes can only be obtained by combining the results of multiple statistical tests.

Original languageEnglish (US)
Pages (from-to)337-345
Number of pages9
JournalJournal of Molecular Diagnostics
Volume7
Issue number3
StatePublished - Aug 2005

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B-Cell Chronic Lymphocytic Leukemia
Oligonucleotide Array Sequence Analysis
Genes
Immunoglobulin Genes
Real-Time Polymerase Chain Reaction
Immunoglobulin Heavy Chains

ASJC Scopus subject areas

  • Molecular Biology

Cite this

Abruzzo, L. V., Wang, J., Kapoor, M., Medeiros, L. J., Keating, M. J., Highsmith, W. E. J., ... Coombes, K. R. (2005). Biological validation of differetially expressed genes in chronic lymphocytic leukemia identified by applying multiple statistical methods to oligonucleotide microarrays. Journal of Molecular Diagnostics, 7(3), 337-345.

Biological validation of differetially expressed genes in chronic lymphocytic leukemia identified by applying multiple statistical methods to oligonucleotide microarrays. / Abruzzo, Lynne V.; Wang, Jing; Kapoor, Mini; Medeiros, L. Jeffrey; Keating, Michael J.; Highsmith, W Edward Jr.; Barron, Lynn L.; Cromwell, Candy C.; Coombes, Kevin R.

In: Journal of Molecular Diagnostics, Vol. 7, No. 3, 08.2005, p. 337-345.

Research output: Contribution to journalArticle

Abruzzo, LV, Wang, J, Kapoor, M, Medeiros, LJ, Keating, MJ, Highsmith, WEJ, Barron, LL, Cromwell, CC & Coombes, KR 2005, 'Biological validation of differetially expressed genes in chronic lymphocytic leukemia identified by applying multiple statistical methods to oligonucleotide microarrays', Journal of Molecular Diagnostics, vol. 7, no. 3, pp. 337-345.
Abruzzo, Lynne V. ; Wang, Jing ; Kapoor, Mini ; Medeiros, L. Jeffrey ; Keating, Michael J. ; Highsmith, W Edward Jr. ; Barron, Lynn L. ; Cromwell, Candy C. ; Coombes, Kevin R. / Biological validation of differetially expressed genes in chronic lymphocytic leukemia identified by applying multiple statistical methods to oligonucleotide microarrays. In: Journal of Molecular Diagnostics. 2005 ; Vol. 7, No. 3. pp. 337-345.
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