feat: redesign around phenotype-driven triage, not variant filtering
A table with filters made the user do the work. Rare disease triage is a different task:
which few variants could explain *this* patient's phenotype, and why. The app now answers
that, and lets a reviewer act on the answer.
Domain
- a case is a proband: a VCF plus the HPO terms observed in the patient (samples -> cases)
- HPO's gene-to-phenotype annotations are loaded as reference data (scripts/load-hpo.py)
- each candidate can be shortlisted or dismissed with a reason and a note
Ranking (app/services/triage.py, 21 tests)
- weighted sum of phenotype match, rarity, consequence severity and the model's score,
with every component shown next to the candidate
- rarity and consequence filter; phenotype only ranks, because a real diagnosis can sit in
a gene nobody has annotated yet and filtering on it would hide exactly that case
- ClinVar is deliberately not an input: it appears beside the result as independent
confirmation, so nothing ranks highly merely because ClinVar already said pathogenic
UI
- the funnel is the headline: variants called -> rare -> coding candidates -> phenotype-matched
- ranked candidates with evidence chips, not a grid of everything; filters are demoted
- a variant panel showing the score breakdown, the matched HPO terms, the raw VEP record and
links out to Ensembl/gnomAD/ClinVar, with the decision controls
- a printable case report: phenotype, funnel, shortlisted variants with reasons, provenance
API: /cases with phenotypes, /cases/{id}/candidates (funnel + ranked + weights),
/variants/{id}, /variants/{id}/decision, /cases/{id}/report, /phenotypes for the picker.
Scoring moved under the case and now answers 503 with the reason when no model registry is
reachable, instead of a 500.
Verified end to end on a simulated proband (scripts/make-demo-case.sh: real GIAB HG002
background + one real ClinVar 2-star pathogenic NF2 variant). 13 variants called -> 1 coding
candidate, and the planted variant ranks first at 0.80 on phenotype 1.00, rarity 1.00 and
consequence 1.00, with ClinVar agreeing afterwards.
Tests: api 75, ml 18, loader 16, web 27; ruff, mypy, svelte-check, terraform validate, both
kustomize overlays and the Nextflow stub run all clean.
This commit is contained in:
@@ -1,4 +1,4 @@
|
||||
.PHONY: up down clean migrate test lint data loader pipeline annotate images kind serverless-deploy serverless-destroy gcp-configure gcp-secrets
|
||||
.PHONY: up down clean migrate test lint data hpo demo-case loader pipeline annotate images kind serverless-deploy serverless-destroy gcp-configure gcp-secrets
|
||||
|
||||
VCF ?= data/example.vcf.gz
|
||||
TAG ?= latest
|
||||
@@ -30,6 +30,12 @@ lint:
|
||||
data: ## download the public demo slice: GIAB HG002 + ClinVar, chr22 (see docs/data.md)
|
||||
scripts/fetch-demo-data.sh
|
||||
|
||||
hpo: ## load HPO gene-to-phenotype annotations, which the ranking matches against
|
||||
scripts/load-hpo.py
|
||||
|
||||
demo-case: ## build the simulated proband: GIAB background + one ClinVar pathogenic variant
|
||||
scripts/make-demo-case.sh
|
||||
|
||||
loader:
|
||||
docker build -t rarelens/loader:dev -f pipeline/loader.Dockerfile pipeline
|
||||
|
||||
|
||||
Reference in New Issue
Block a user