HELP assay
Encyclopedia
The HELP Assay is an abbreviation for HpaII tiny fragment Enrichment by Ligation-mediated PCR
Polymerase chain reaction
The polymerase chain reaction is a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence....

. It is one of several techniques used for determining whether DNA has been methylated. The technique can be adapted to examine DNA methylation within and around individual genes
Gênes
Gênes is the name of a département of the First French Empire in present Italy, named after the city of Genoa. It was formed in 1805, when Napoleon Bonaparte occupied the Republic of Genoa. Its capital was Genoa, and it was divided in the arrondissements of Genoa, Bobbio, Novi Ligure, Tortona and...

, or it can be expanded to examine methylation in an entire genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....

.

The technique relies upon the properties of two restriction enzymes: HpaII and MspI. The HELP assay compares representations generated by HpaII and by MspI digestion of the genome followed by ligation-mediated PCR. 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 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 analysis of HELP data involves quality analysis and normalization. An analytical pipeline written in the R programming language was recently published to allow HELP data processing.

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