Expectations, validity, and reality in gene expression profiling

Abstract

Objective: To provide a critical overview of gene expression profiling methodology and discuss areas of future development.Results: Gene expression profiling has been used extensively in biological research and has resulted in significant advances in the understanding of the molecular mechanisms of complex disorders, including cancer, heart disease, and metabolic disorders. However, translating this technology into genomic medicine for use in diagnosis and prognosis faces many challenges. In addition, gene expression profile analysis is frequently controversial, because its conclusions often lack reproducibility and claims of effective dissemination into translational medicine have, in some cases, been remarkably unjustified. In the last decade, a large number of methodological and technical solutions have been offered to overcome the challenges. Study Design and Setting:We consider the strengths, limitations, and appropriate applications of gene expression profiling techniques, with particular reference to the clinical relevance. Conclusion:Some studies have demonstrated the ability and clinical utility of gene expression profiling for use as diagnostic, prognostic, and predictive molecular markers. The challenges of gene expression profiling lie with the standardization of analytic approaches and the evaluation of the clinical merit in broader heterogeneous populations by prospective clinical trials.

A Five-Gene Hedgehog Signature Developed as a Patient Preselection Tool for Hedgehog Inhibitor Therapy in Medulloblastoma

“…Recent genomic-based molecular subclassification of medulloblastoma suggests that identification of an Hh gene signature through gene expression profiling could be used for treatment decisions (18). However, the current expression profiling methods require a large quantity of tumor and are time intensive, both of which are not amenable for translation to the clinic (18).…”

Genomic Expression Profiles: From Molecular Signatures to Clinical Oncology Translation

“…However, the expression of traditionally used controls such as ribosomal RNA genes, also changes across different tissues and experimental conditions making it difficult to select "gold standards" (150). Sampling issues such as biopsy method (151), contamination from neighboring tissues may seriously affect in different expression profiles as microarray technology is very sensitive to such variations (152). RNA quality is a critical issue in genome-wide analysis of gene expression.…”

“…Nevertheless, the results from comparison across different platforms can be misleading and should be interpreted with great caution (156). Technicalities of the microarray platforms deals with binding efficiency of labeled target to the respective probe as well as technical variation during experiments also may affect the reproducibility of the gene expression profiles (152). With regards to prospective experiments, the uniformity of experimental conduct will help to minimize potential bias and thus improve the validity of a study.…”

“…Another issue of classification is "overfitting", which occurs when a classifier is made to perfectly fit a set of data that was used in the model development, but has no discriminatory power so that the results cannot be reproduced in a set of completely independent samples (161). This may lead to insufficient evidence of accuracy and reproducibility of multigene signature from gene expression profiles for clinical use, although it showed initial promising and reproducible results in class discovery studies and preclinical analysis (162). An adequate sample size is essential for any cross-validation technique to be effective.…”

Comparison of whole genome expression profile between preterm and full-term newborns

“…Introduction of the microarray techniques to clinical studies was one of the most important turning points resulting in a dramatic progress in the field of human genetics during the last decade [9]. RNA-microarray allows analyzing the expression of all human genes.…”