Kemal Yaylali
07a01715fd
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.
36 lines
1.1 KiB
Python
36 lines
1.1 KiB
Python
from contextlib import asynccontextmanager
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from fastapi import APIRouter, FastAPI
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from fastapi.middleware.cors import CORSMiddleware
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from app.config import settings
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from app.routers import cases, jobs, phenotypes, variants
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@asynccontextmanager
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async def lifespan(app: FastAPI):
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# Warm the model cache here once ml/ is wired in.
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yield
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app = FastAPI(title="rarelens API", version="0.1.0", lifespan=lifespan)
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app.add_middleware(
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CORSMiddleware,
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allow_origins=settings.cors_origins,
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allow_methods=["GET", "POST"],
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allow_headers=["content-type"],
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)
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# The ingress forwards /api/* to this service unchanged, and local dev uses the same prefix.
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api = APIRouter(prefix="/api")
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api.include_router(cases.router, prefix="/cases", tags=["cases"])
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api.include_router(jobs.router, prefix="/jobs", tags=["jobs"])
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api.include_router(variants.router, prefix="/variants", tags=["variants"])
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api.include_router(phenotypes.router, prefix="/phenotypes", tags=["phenotypes"])
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app.include_router(api)
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@app.get("/health", tags=["ops"])
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async def health() -> dict[str, str]:
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return {"status": "ok"}
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