This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Obtaining Infinium Methylation450K manifest for hg38

Hello everyone,

I'm currently working with VCF files of mutations from the TCGA dataset using the hg38 assembly.
To further my analysis, I'm interested in comparing mutation rates with the methylation status for each cancer type. However, I've encountered a challenge in locating the genomic coordinates of the Illumina Methylation450K array for hg38 assembly.

While I'm aware that I can liftover the coordinates from hg37 to hg38, I was wondering if there is an official version available for hg38. Since the TCGA data I'm utilizing is based on hg38, I'd prefer to align with the same standard.

Does anyone know where I can find the official version, if it exists? or suggest other solutions?

Thank you in advance for your assistance

tcga hg38 methylation illumina
• 2,033 views • link
updated by Zhenyu Zhang Zhenyu Zhang • written by elisheva elisheva

1 answer

Hi, you can check it from github here: https://zwdzwd.github.io/InfiniumAnnotation.

I don't know if this is what you are looking for your Chip. In any case, there are pipelines and R package to do liftover , such as mLiftOver or ELMER to identify tumor-specific changes in DNA methylation.

Hope this can help you

Marco

• 0 views • link
written by marco.barr • marco.barr

Log in to answer this question.

More posts like this