Question: Determine Sample Genotype Using Data From Illumina Methylation 450K Chip
gravatar for msbootwalla
7.4 years ago by
msbootwalla0 wrote:

I noticed that the Illumina HumanMethylation 450k array has 65 SNP probes on it. I would like to use the information provided by these probes to determine the genotype of the sample and compare it with genotype calls based on Affymetrix SNP6 data. Can anyone guide me as to how I can perform such an analysis?



methylation genotyping • 2.9k views
ADD COMMENTlink written 7.4 years ago by msbootwalla0

Did you mix up your samples in a paired SNP / methylation array experiment? You might consider looking for CpGs represented on the SNP array and when the CpG sites are polymorphic in a way that disrupts the CpG, look for corresponding lack of methylation on the methylation array. 65 SNPs may not be enough to determine identity by state of genotype.

ADD REPLYlink modified 7.4 years ago • written 7.4 years ago by Matt Shirley9.5k

What is the overlap between SNPs on the methylation array vs that on SNP6?

ADD REPLYlink written 7.4 years ago by Sean Davis26k
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