File containing binned methylation level of SNVs

General
1

Greetings!
Is there any .ht table for GRCh38, containing binned methylation info (1, 2 or 3 values) for trinucleotide context of the SNV?

I need it for MAPS or CAPS estimation, but the only table I found is gs://gcp-public-data–gnomad/papers/2019-flagship-lof/v1.0/context//Homo_sapiens_assembly19.fasta.snps_only.vep_20181129.ht.

Thanks for any help!

2

Hi!

Yes, there are Hail Tables (HT) containing methylation information for GRCh38, which might be useful for you. The determination of the methylation scores is described in Chen et al: https://www.biorxiv.org/content/10.1101/2022.03.20.485034v2.full. You can access the methylation data here:

  • For autosomes (methylation scores ranging from 0 to 15):
    gs://gcp-public-data--gnomad/resources/grch38/methylation_sites/methylation.ht
  • For chromosome X (methylation scores ranging from 0 to 12):
    gs://gcp-public-data--gnomad/resources/grch38/methylation_sites/methylation_chrX.ht
  • They can be annotated onto the all SNV context Hail Table:
    gs://gcp-public-data--gnomad/resources/context/grch38_context_vep_annotated.v105.ht

Keep in mind that although both tables provide methylation scores, are not directly comparable. They were analyzed separately, and the levels are relative to their specific analyses. However, you can bin the scores into 0, 1, or 2 levels for both. For autosomes, the proposed cutoffs are:

  • 0 (unmethylated),
  • 1-5 (partially methylated),
  • 6+ (methylated).

For chromosome X:

  • 0 (unmethylated),
  • 1-3 (partially methylated),
  • 4+ (methylated).

You can also check out the gnomad_methods resources related to these methylation files here, and where we annotate them onto the context Hail Table in our constraint pipeline here.

1 Like
3

it helped a lot, thank you!

4

By the way, if the methylation data isn’t identified for the position of interest, should one consider it as “0”?