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phenopackets / phenopacket-schema

Repository for the GA4GH phenopacket schema
https://phenopacket-schema.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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AnVIL metadata #97

Closed julesjacobsen closed 3 years ago

julesjacobsen commented 5 years ago

As mentioned by Heidi Rehm during her talk at the recent Genomics of Rare Disease Conference, the AnVIL project is discussing a data model. How do we stack up to their requirements?

ANVIL Possible Metadata to Include for Rare Disease Cases

Demographic

Project ID Family ID/Individual ID/Paternal ID/Maternal ID PED file (relationships, affected status) Sex Ancestry Consanguinity Prior testing info (panel, WES, etc) Other Available Datasets (RNAseq, etc)

Phenotype Data

Affected Status Core Phenotype (OMIM, HPO) HPO Terms (present) HPO Terms (absent) Family history Age of onset Descriptive phenotype synopsis

Case Status and Included Genes/Variants

Solved state (Solved, Tier 1 Candidate, Tier 2 Candidate) Known/Published Gene Name and Variant Tier 1 Candidate Gene Name and Variant Tier 2 Candidate Gene Name and Variant

Flagged Variants - repeated if >1 variant

Chrom/Pos/Ref/Alt Gene/Transcript/hgvsc/hgvsp Zygosity Clinical significance (Pathogenic, LP, VUS, Other) Data Source Data type (WES/WGS/Array/RNAseq) Method details (WES capture, PCR-free WGS, etc) Date of data generation Tissue type

pnrobinson commented 5 years ago

@julesjacobsen Interesting -- I will send Heidi a mail and see if we can collaborate

julesjacobsen commented 5 years ago

Yes, unfortunately I didn't manage to talk to her about this.

@pnrobinson @mbrush note use of zygosity in the flagged variants section. Relevant to #90

mellybelly commented 5 years ago

some info relating to the ANVIL model, which is currently deriving from GDC, is here: https://docs.google.com/spreadsheets/d/1edxXULuJM5iHeL_mA4H21pgXmsbF08EsL1mUcNjbwZk/edit#gid=180970461

pnrobinson commented 3 years ago

@mellybelly I think the scope of ANVIL is not the same although there are overlaps. Do we have a concrete action item?

pnrobinson commented 3 years ago

@julesjacobsen @mellybelly I think the phenopackets cover all of these elements. I do not see an action item, can we close?

julesjacobsen commented 3 years ago

I think we can close.