SACGF / SACGF/variantgrid

HPO terms not pulling associated genes

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#1,862 1 comment 0 reactions 0 assignees View on GitHub
bug
Dominant language
Python
Stars
30
Forks
3
Avg merge
9h 28m
Merged PRs (30d)
42

Description

No genes associated with entered HPO terms are being found, so all variants are bypassing filtering at phenotype nodes when HPO field is used.

See: https://variantgrid.com/analysis/10038/ where the three phenotype nodes have HPO terms "acute leukaemia" and "acute myeloid leukaemia" with warning saing: "HPO terms: 'HP:0002488 Acute leukemia', 'HP:0004808 Acute myeloid leukemia' have no associated genes, and will not affect node filtering."

Contributor guide

No contributing guide indexed for this repository

Research direction

Reproduce the problem in analysis 10038 using phenotype nodes containing HP:0002488 and HP:0004808, then trace the HPO gene-association lookup and phenotype-node filtering path. Done means these terms resolve to associated genes and variants are no longer allowed through solely because the lookup reports no genes.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Active
Clarity
Mostly clear
Newbie friendliness
65/100

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