Obtaining Infinium Methylation450K manifest for hg38
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6 weeks ago
elisheva ▴ 120

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 • 303 views
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6 weeks ago
marco.barr ▴ 150

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


Entering edit mode

Since you are getting data from the GDC, analysis-related reference/annotations can be found in the GDC reference page here https://gdc.cancer.gov/about-data/gdc-data-processing/gdc-reference-files

But also second what is said above, Wanding (https://zwdzwd.github.io/InfiniumAnnotation) helped us generating these methylation array annotation files.


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