HELP assay

From Wikipedia, the free encyclopedia

The introduction to this article provides insufficient context for those unfamiliar with the subject. Please help improve the article with a good introductory style.

This article is orphaned as few or no other articles link to it. Please help introduce links in articles on related topics. (January 2007)

Please help improve this article or section by expanding it. Further information might be found on the talk page or at requests for expansion. (January 2007)

The HELP Assay is HpaII-tiny fragment Enrichment by Ligation-mediated PCR.

To study cytosine methylation throughout the genome, techniques usually involve the use of restriction enzymes or proteins with affinity for 5-methylcytosine.

The HELP assay [1] compares representations generated by HpaII and by MspI digestion of the genome followed by ligation-mediated PCR. As HpaII only digests 5'-CCGG-3' sites when the cytosine in the central CG dinucleotide is unmethylated, the HpaII representation is enriched for the hypomethylated fraction of the genome. The MspI representation is a control for copy number changes and PCR amplification difficulties.

It was recently shown [2] that cytosine methylation patterns tend to be concordant over short (~1 kb) regions. The patterns represented by the HpaII sites therefore tend to be representative of other CG dinucleotides locally.

The protocol for the HELP assay is available from [3].

The analysis of HELP data involves quality analysis and normalization. An analytical pipeline written in the R programming language was recently published [4] to allow HELP data to be processed.