deep-research-or4f — workgraph

Metadata

Status	done
Assigned	`agent-453`
Agent identity	`3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3`
Created	2026-04-02T03:35:34.025741928+00:00
Started	2026-04-02T03:36:47.346300720+00:00
Completed	2026-04-02T03:39:05.105016610+00:00
Tags	`research,deep,fan-out`, `eval-scheduled`
Eval score	0.52
└ blocking impact	0.50
└ completeness	0.35
└ coordination overhead	0.65
└ correctness	0.45
└ downstream usability	0.55
└ efficiency	0.75
└ intent fidelity	0.82
└ style adherence	0.60

Description

Goal

Deep literature research on the olfactory receptor genes enriched in PHRs (OR4F29, OR4F3, OR4F5, OR4F17) — 58 copies, 598-fold enrichment in copy-aware analysis.

Questions

What is known about OR4F specifically? Are OR4F29/3/5/17 functionally characterized? Do they have known ligands? Are they expressed, or are they pseudogenes despite being annotated as protein-coding?
Subtelomeric OR gene biology literature: What do Trask et al. (1998), Niimura (2012), and others say about why OR genes cluster at chromosome ends? What is the evolutionary mechanism?
Copy number variation: Is OR4F copy number known to vary between individuals or populations? Is there CNV data from 1000 Genomes, gnomAD, or HPRC?
Functional significance of multi-copy ORs: Does having 20 copies of OR4F17 across chromosome arms mean anything functionally? Can multiple copies be expressed? Or are most copies silenced/pseudogenized?
Disease associations: Any links between OR4F CNV and anosmia, neurodegenerative disease, or other conditions?
Connection to PHR biology: Has anyone previously noted that OR genes in subtelomeric PHRs are part of inter-chromosomal sharing? Does the HPRC or T2T literature discuss this?

Output

Log a detailed research summary with citations/references where possible. Save as deep_research_olfactory_receptors.md.

Validation

Each question is addressed with specific evidence or 'not known'
Literature references are cited
Connection to our specific findings (58 copies, 4 families, C3/C11 communities) is made

## Goal
Deep literature research on the olfactory receptor genes enriched in PHRs (OR4F29, OR4F3, OR4F5, OR4F17) — 58 copies, 598-fold enrichment in copy-aware analysis.

## Questions
1. **What is known about OR4F specifically?** Are OR4F29/3/5/17 functionally characterized? Do they have known ligands? Are they expressed, or are they pseudogenes despite being annotated as protein-coding?
2. **Subtelomeric OR gene biology literature**: What do Trask et al. (1998), Niimura (2012), and others say about why OR genes cluster at chromosome ends? What is the evolutionary mechanism?
3. **Copy number variation**: Is OR4F copy number known to vary between individuals or populations? Is there CNV data from 1000 Genomes, gnomAD, or HPRC?
4. **Functional significance of multi-copy ORs**: Does having 20 copies of OR4F17 across chromosome arms mean anything functionally? Can multiple copies be expressed? Or are most copies silenced/pseudogenized?
5. **Disease associations**: Any links between OR4F CNV and anosmia, neurodegenerative disease, or other conditions?
6. **Connection to PHR biology**: Has anyone previously noted that OR genes in subtelomeric PHRs are part of inter-chromosomal sharing? Does the HPRC or T2T literature discuss this?

## Output
Log a detailed research summary with citations/references where possible. Save as `deep_research_olfactory_receptors.md`.

## Validation
- Each question is addressed with specific evidence or 'not known'
- Literature references are cited
- Connection to our specific findings (58 copies, 4 families, C3/C11 communities) is made

Depends on

done .assign-deep-research-or4f

Required by

Log

2026-04-02T03:35:34.016787251+00:00 Task paused
2026-04-02T03:36:25.076509390+00:00 Task published
2026-04-02T03:36:47.346301983+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
2026-04-02T03:37:02.490643244+00:00 Starting deep research on OR4F olfactory receptors in subtelomeric PHRs
2026-04-02T03:37:38.480246967+00:00 Found context: OR4F families (OR4F17, OR4F3, OR4F5, OR4F29) with 72 total copies showing 598-fold enrichment. Beginning systematic research on 6 key questions.
2026-04-02T03:38:57.019371732+00:00 Decomposed research into 6 parallel subtasks using fan-out pattern: OR4F functional characterization, subtelomeric OR biology literature, OR4F CNV, multi-copy OR significance, disease associations, and PHR-OR connections. Created synthesis task to integrate findings.
2026-04-02T03:39:05.105020086+00:00 Task marked as done