Abstract
As interest in studying allele-specific methylation (ASM) grows, there is a need for a resource that stores and catalogs SNPs and regions that demonstrate allele specific methylation, analogous to dbSNP. We have created a new web resource called dbASM, hosted on the Genapha web server (www.genapha.ca),in order to help fulfill this need. The aim of dbASM is twofold: 1. Curate from the literature a publicly-accessible database of known sites of ASM. 2. Provide a web-based platform of tools for exploring ASM and determining regions of interest. These regions of interest can then be assayed for methylation status using small, custom arrays that are currently cheaper than using whole-genome approaches such as the Illumina 450K or bisulphite sequencing. We present the dbASM resource including details on the underlying database construction and datasets, in addition to the web tools and example workflows. The web tools that are currently available are: GWAS Catalog SNP Search, ASM SNP Search, SNP Counter, Methylation Plots Generation, and Sequence Viewer. GWAS Catalog SNP Search allows browsing through NHGRI's Catalog of Published Genome-Wide Association Studies by phenotype and filtering SNPs based on their relation to suspected sites of ASM. ASM SNP Search supports finding SNPs based on: ASM status or interrogability; location compared to genes, a chromosomal region, or other SNP's; and filtering by population minor allele frequencies and sample size. Methylation Plots Generation calculates SNP correlation stratifying by genotype with CpG site methlyation patterns from the HapMap population. These tools are all freely available for use at: http://genapha.icapture.ubc.ca/asm/.
- © 2014 ERS