TY - JOUR
T1 - The HELP assay.
AU - Oda, Mayumi
AU - Greally, John M.
PY - 2009
Y1 - 2009
N2 - Genomic representations using ligation-mediated PCR have been used successfully as the foundation for a number of high-throughput assays. HpaII tiny fragment enrichment by ligation-mediated PCR (HELP) is an example of the use of such representations to study cytosine methylation in the genome. The HELP assay differs from most other assays testing cytosine methylation because of its positive representation of hypomethylated DNA in the genome, whereas other assays infer the presence of hypomethylated sequences by the absence of signal, for which there can be confounding technical reasons. Hypomethylated sequences represent the minority of the genome and tend to be located at unique sequences with functionally interesting properties such as transcription start sites. By performing a comparative genomic hybridization using an MspI representation from the same DNA sample, we represent all potential loci that could be generated by HpaII in the situation of global hypomethylation; in practice, HpaII generates a subset of loci from this population, allowing us to discriminate hypomethylated loci (represented by both HpaII and MspI) from methylated loci (represented by MspI only).
AB - Genomic representations using ligation-mediated PCR have been used successfully as the foundation for a number of high-throughput assays. HpaII tiny fragment enrichment by ligation-mediated PCR (HELP) is an example of the use of such representations to study cytosine methylation in the genome. The HELP assay differs from most other assays testing cytosine methylation because of its positive representation of hypomethylated DNA in the genome, whereas other assays infer the presence of hypomethylated sequences by the absence of signal, for which there can be confounding technical reasons. Hypomethylated sequences represent the minority of the genome and tend to be located at unique sequences with functionally interesting properties such as transcription start sites. By performing a comparative genomic hybridization using an MspI representation from the same DNA sample, we represent all potential loci that could be generated by HpaII in the situation of global hypomethylation; in practice, HpaII generates a subset of loci from this population, allowing us to discriminate hypomethylated loci (represented by both HpaII and MspI) from methylated loci (represented by MspI only).
UR - http://www.scopus.com/inward/record.url?scp=61449396662&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=61449396662&partnerID=8YFLogxK
U2 - 10.1007/978-1-59745-522-0_7
DO - 10.1007/978-1-59745-522-0_7
M3 - Article
C2 - 18987808
AN - SCOPUS:61449396662
SN - 1064-3745
VL - 507
SP - 77
EP - 87
JO - Methods in molecular biology (Clifton, N.J.)
JF - Methods in molecular biology (Clifton, N.J.)
ER -