Primer Extension Enrichment Reaction (PEER) and Other Methods for Difference Screening
Our knowledge on the subject of genetic divergence is ever expanding and encapsulates a wide spectrum of research areas from the study of single nucleotide polymorphism to examination of the complex differences of host–pathogen interactions. The understanding of genetic differences is essential to our ability to address adequately human health issues caused by mono allelic genetic disorders, altered gene expression in cancers, development of drug resistance and the variety of ways organisms respond to infections and the environment. Large number of hybridization-based applications has been developed to query and find such differences. This review introduces a new method for genetic difference screening — the primer extension enrichment reaction (PEER) — presented in the context of similar subtraction-based hybridization methods. PEER is a novel approach to difference screening and is not intended to replace the existing elegant hybridization methods but to expand their scope. PEER is tailored to find unknown targets present in very low copy numbers and in the context of an imperfect genomic match. The PEER method takes advantage of the greater hybridization specificity of shorter oligonucleotides coupled with enzymatic extension specificity.
KeywordsPrimary structure genetic differences gene expression sequencing-by-hybridization primer extension enrichment reaction (PEER) class II restriction endonuclease class IIS restriction endonuclease IIS enzyme spot hybridization enrichment enrichment value cost efficient subtractive cloning arbitrary primed PCR amplification fragment length polymorphism (AFLP) serial analysis of gene expression (SAGE) genomic signature tag (GST) serial analysis of binding elements (SABE) differential analysis of restriction fragments amplification (DARFA) ligation mediated enrichment selectively primed adaptive driver RDA enzymatic degrading subtraction (EDS) phenol linker capture subtraction (LCS) differential subtraction chain (DSC) cloning of deleted sequences (CODE) negative subtraction chain (NSC) SABRE DNA enrichment by allele-specific hybridization (DEASH)
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