HELP assay

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

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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].