This tutorial will take you through a sample workflow of using the tools on this website. If you have problems with the tutorial, please give the FAQ a look before contacting us.

In this scenario we are a researcher investigating the possible role of Allele-Specific Methylation (ASM) in YKL-40 Levels. We are interested in finding out whether: (A) Genotype → Methylation → Phenotype or if (B) Genotype → Phenotype → Methylation.

Our experiment will be to build a custom snp-chip that determines methylation levels of samples for which we already have genotype and phenotype information.

Thus, we are interested in finding out some SNP’s that could be candidates for ASM and involved in our phenotype, YKL-40 Levels. Let us pretend we are building a custom SNP-chip that can interrogate only a handful of SNP’s for the sake of the tutorial.

Currently, there is some information mapping Genotype → Phenotype in NHGRI’s Catalog of Published Genome-Wide Association Studies. We also have Genotype → Methylation data from the UBC Kobor methylation study of HapMap individuals. We can use this information to help us identify interesting ASM candidate SNP’s.

Our criteria for identifying these interesting ASM candidate SNP’s will be the following:

  • SNP is a candidate for ASM; specifically that it forms a CpG site
  • SNP is near GWAS hits in the literature for our phenotype
  • SNP is near SNP’s published as showing ASM in the literature
  • SNP shows correlation with methylation patterns from Kobor HapMap study stratifying by genotype

And our workflow will be to:

  1. Identify GWAS hits for our phenotype that are near ASM-known SNP’s
  2. Run regressions on these SNP’s to find out which show correlation with methylation patterns
  3. Find ASM candidates around SNP’s passing tests 1 and 2
  4. Pare down this list using some filters for Minor Allele Frequency and sample size
End Next