title: An analytical pipeline for genomic representations used for cytosine methylation studies.
abstract: Representations of the genome can be generated by the selection of a subpopulation of restriction fragments using ligation-mediated PCR. Such representations form the basis for a number of high-throughput assays, including the HELP assay to study cytosine methylation. We find that HELP data analysis is complicated not only by PCR amplification heterogeneity but also by a complex and variable distribution of cytosine methylation. To address this, we created an analytical pipeline and novel normalization approach that improves concordance between microarray-derived data and single locus validation results, demonstrating the value of the analytical approach. A major influence on the PCR amplification is the size of the restriction fragment, requiring a quantile normalization approach that reduces the influence of fragment length on signal intensity. Here we describe all of the components of the pipeline, which can also be applied to data derived from other assays based on genomic representations.
authors: Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
authors: Reid F
authors: RF
authors: Thompson
authors: Mark
authors: M
authors: Reimers
authors: Batbayar
authors: B
authors: Khulan
authors: Mathieu
authors: M
authors: Gissot
authors: Todd A
authors: TA
authors: Richmond
authors: Quan
authors: Q
authors: Chen
authors: Xin
authors: X
authors: Zheng
authors: Kami
authors: K
authors: Kim
authors: John M
authors: JM
authors: Greally
mesh_terms: D016477:Artifacts; D002874:Chromosome Mapping / Q000379:methods*; D003596:Cytosine; D019175:DNA Methylation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D003596:Cytosine