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broadinstitute / regional_missense_constraint

Code to calculate regional missense constraint
BSD 3-Clause "New" or "Revised" License
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Inquiry on Availability of MPC Scores for Latest gnomAD Data #310

Closed gmerolli00 closed 2 months ago

gmerolli00 commented 2 months ago

Hello RMC Team,

I hope this message finds you well.

I am reaching out to inquire whether the MPC model has been run on the newest gnomAD data. The MPC scores are currently available on the gnomAD site for v2, but I don't see an equivalent tab for v4 (https://gnomad.broadinstitute.org/downloads#v2-regional-missense-constraint).

Could you please let me know if there are scores for the latest gnomAD data, and if so, whether the updated scores could be made available?

Thank you for your time and assistance. I look forward to hearing from you!

Best regards,
Giorgia

ch-kr commented 2 months ago

Hi Giorgia,

Thanks for reaching out and for your interest in MPC. Regional missense constraint and MPC are not available for v4 yet, and we don't have a timeline/ETA for when the metrics will be ready.

In case it is helpful, we have released a public gnomAD v2 MPC liftover resource (Google URL is gs://gcp-public-data--gnomad/release/2.1.1/regional_missense_constraint/gnomad_v2.1.1_mpc_liftover_GRCh38.ht). Note that this resource is not transcript-aware; it was created by lifting over loci from GRCh37 to GRCh38 and retaining the maximum MPC value per locus.

Best, Katherine

gmerolli00 commented 2 months ago

Hi Katherine,

Sounds great, thank you so much for your response! I hope you have a great day!

Sincerely, Giorgia