RNA amplification for successful gene profiling analysis

Research output: Contribution to journalReview article

60 Citations (Scopus)

Abstract

The study of clinical samples is often limited by the amount of material available to study. While proteins cannot be multiplied in their natural form, DNA and RNA can be amplified from small specimens and used for high-throughput analyses. Therefore, genetic studies offer the best opportunity to screen for novel insights of human pathology when little material is available. Precise estimates of DNA copy numbers in a given specimen are necessary. However, most studies investigate static variables such as the genetic background of patients or mutations within pathological specimens without a need to assess proportionality of expression among different genes throughout the genome. Comparative genomic hybridization of DNA samples represents a crude exception to this rule since genomic amplification or deletion is compared among different specimens directly. For gene expression analysis, however, it is critical to accurately estimate the proportional expression of distinct RNA transcripts since such proportions directly govern cell function by modulating protein expression. Furthermore, comparative estimates of relative RNA expression at different time points portray the response of cells to environmental stimuli, indirectly informing about broader biological events affecting a particular tissue in physiological or pathological conditions. This cognitive reaction of cells is similar to the detection of electroencephalographic patterns which inform about the status of the brain in response to external stimuli. As our need to understand human pathophysiology at the global level increases, the development and refinement of technologies for high fidelity messenger RNA amplification have become the focus of increasing interest during the past decade. The need to increase the abundance of RNA has been met not only for gene specific amplification, but, most importantly for global transcriptome wide, unbiased amplification. Now gene-specific, unbiased transcriptome wide amplification accurately maintains proportionality among all RNA species within a given specimen. This allows the utilization of clinical, material obtained with minimally invasive methods such as fine needle aspirates (FNA) or cytological washings for high throughput functional genomics studies. This review provides a comprehensive and updated discussion of the literature in the subject and critically discusses the main approaches, the pitfalls and provides practical suggestions for successful unbiased amplification of the whole transcriptome in clinical samples.

Original languageEnglish
Article number28
JournalJournal of Translational Medicine
Volume3
DOIs
Publication statusPublished - 25 Jul 2005
Externally publishedYes

Fingerprint

Gene Amplification
Amplification
Genes
RNA
Transcriptome
DNA
Throughput
Comparative Genomic Hybridization
Genomics
Needles
Pathology
Proteins
Gene expression
Washing
Genome
Brain
Technology
Gene Expression
Messenger RNA
Mutation

Keywords

  • cDNA microarray
  • Gene profiling
  • High throughput analysis
  • Polymerase
  • RNA amplification

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

RNA amplification for successful gene profiling analysis. / Wang, Ena.

In: Journal of Translational Medicine, Vol. 3, 28, 25.07.2005.

Research output: Contribution to journalReview article

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