survey-cytogenetic-fish

Metadata

Status	done
Assigned	`agent-655`
Agent identity	`3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647`
Created	2026-05-05T04:15:44.670789677+00:00
Started	2026-05-05T04:18:40.454563496+00:00
Completed	2026-05-05T04:26:04.829924519+00:00
Tags	`paper-prep,survey,framing`, `eval-scheduled`
Eval score	0.92
└ blocking impact	0.95
└ completeness	0.95
└ coordination overhead	0.90
└ correctness	0.95
└ downstream usability	0.92
└ efficiency	0.85
└ intent fidelity	0.82
└ style adherence	0.90

Description

Locate any review/literature notes already in the repo that discuss subtelomeric FISH / flow-sorted-chromosome / cytogenetic exchange (search Synthesis/, Performance/, end-to-end-report/, *.md at root). Cite paths.
From end-to-end-report/report/12_literature.md, extract every reference to: cytogenetic, FISH, flow cytometry, Mefford, subtelomere review, Riethman, Stong, Linardopoulou. List concrete claims our work confirms / extends / overturns.
Synthesize a 1-2 page framing draft (introduction-flavored prose) that explains: (a) what cytogenetic-era studies could see, (b) what flow + FISH on a few samples revealed, (c) how our HPRC pangenome dataset shows the same patterns at scale, (d) what is therefore newly addressable.
List 6-10 high-priority citations to track down (Riethman, Mefford, Linardopoulou, Stong, Trask, Bailey, etc. — give author + topic + year if known). OUTPUT: paper_prep/surveys/SURVEY_FRAMING_cytogenetic_fish.md. ACCEPTANCE: File exists with the 4 numbered parts, concrete repo paths cited where prior text exists, named-author citation list at end.

CONTEXT: The Nature manuscript needs to position this work against deep prior literature on subtelomeric exchange that began in the cytogenetic era — flow cytometry and FISH studies that documented a tiny subset of the subtelomeric exchanges we now see across all 233 HPRC samples. The user explicitly highlighted: 'a review paper that was looking using flow cytometry and FISH, looking at the subtelomeres, a tiny subset of the subtelomeric exchanges we see, but we actually see the same patterns'.
TASK:
1. Locate any review/literature notes already in the repo that discuss subtelomeric FISH / flow-sorted-chromosome / cytogenetic exchange (search Synthesis/, Performance/, end-to-end-report/, *.md at root). Cite paths.
2. From end-to-end-report/report/12_literature.md, extract every reference to: cytogenetic, FISH, flow cytometry, Mefford, subtelomere review, Riethman, Stong, Linardopoulou. List concrete claims our work confirms / extends / overturns.
3. Synthesize a 1-2 page framing draft (introduction-flavored prose) that explains: (a) what cytogenetic-era studies could see, (b) what flow + FISH on a few samples revealed, (c) how our HPRC pangenome dataset shows the *same patterns* at scale, (d) what is therefore newly addressable.
4. List 6-10 high-priority citations to track down (Riethman, Mefford, Linardopoulou, Stong, Trask, Bailey, etc. — give author + topic + year if known).
OUTPUT: paper_prep/surveys/SURVEY_FRAMING_cytogenetic_fish.md.
ACCEPTANCE: File exists with the 4 numbered parts, concrete repo paths cited where prior text exists, named-author citation list at end.

Depends on

done .assign-survey-cytogenetic-fish

Required by

Log

2026-05-05T04:15:44.656453121+00:00 Task paused
2026-05-05T04:18:10.951038617+00:00 Task resumed
2026-05-05T04:18:37.488779058+00:00 Lightweight assignment: agent=random-agent-3577bc75 (3577bc75), exec_mode=full, context_scope=task, reason=Documenter role with verify-against-sources principle is ideal for literature survey synthesis; proven track record on documentation tasks.
2026-05-05T04:18:40.454567193+00:00 Spawned by coordinator --executor claude --model opus
2026-05-05T04:18:55.413563793+00:00 Starting: surveying repo for cytogenetic/FISH/flow cytometry framing references
2026-05-05T04:20:00.372583625+00:00 Have full context: framing_synthesis.md (PAR/PHR analogy), end-to-end-report/12_literature.md (claims), 13_appendix.md (refs), 01_pipeline.md f7501 FISH validation, 04_heterogeneity.md, subtelomeric_analysis_report.md (long-form refs). Drafting survey file now.
2026-05-05T04:23:05.916142111+00:00 Wrote SURVEY_FRAMING_cytogenetic_fish.md with 4 sections: (1) repo paths cited, (2) confirms/extends/overturns table, (3) 1-2 page framing prose with 4 sub-parts a-d, (4) 11 named-author citations covering Mefford/Flint/Linardopoulou/Stong/Trask/Bailey/Riethman/Ambrosini/van Deutekom/Stout/Rouyer.
2026-05-05T04:25:19.150690162+00:00 Committed: a9b61a3 — pushed to origin/wg/agent-655/survey-cytogenetic-fish
2026-05-05T04:25:59.109447534+00:00 Validated against acceptance criteria: file exists at paper_prep/surveys/SURVEY_FRAMING_cytogenetic_fish.md (114 lines); 4 numbered parts present; concrete repo paths cited (framing_synthesis.md, end-to-end-report/report/12_literature.md, 13_appendix.md, 01_pipeline.md, 04_heterogeneity.md, subtelomeric_analysis_report.md, SURVEY_01_pipeline.md, SURVEY_04_heterogeneity.md); named-author citation list at end (11 entries: Mefford & Trask, Flint, Linardopoulou (with Bailey), Ambrosini, Riethman, Stong, Bailey, Trask 1998, van Deutekom, Stout, Rouyer).
2026-05-05T04:26:04.829928307+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
2026-05-05T04:29:40.445667+00:00 PendingEval → Done (evaluator passed; downstream unblocks)