Scope

Every candidate on this page is a hypothesis, not a target. The release ships scored candidate parquets + manifest + validation panel for downstream wet-lab pre-selection; it has not been validated prospectively. Selecting a row from the released candidates for therapeutic application requires running the full freeze-and-validate pipeline documented at the framework repository.

v0.5 release tag + manifest

GitHub release tag

atlas-tcga-lihc-v0.5.0-wg-sigmoid ↗

Manifest sha256

2ae90a7a48f3…

Reference assembly

hg19 (GRCh37)

Probe array

Illumina HM450 (GPL13534)

Catalog size

19,787,820 sites

Cohort

TCGA-LIHC patient tissue

Reviewer-access caveat: the sigaihealth/atlas repository is currently restricted to organization members; unauthenticated requests return HTTP 404. Public-read access is a held GigaScience submission gate. The release URL above resolves once the repo flips to public.

Tier breakdown (v0.5)

Tier classifications follow the v0.5 schema (Tier A–E). Tier A is reserved for the future v1 layer set (guide feasibility + off-target methylation + normal-tissue protection); v0.5 populates Tier B–E from the layers it currently audits. LIHC's Tier B count (149,099) is ~2.3× COAD's and ~7× LUAD's — the largest under v0.5.

Tier	candidates	shape
A	—	reserved (pending v1 guide-feasibility layer)
B	149,099	tissue-driven; EXACT evidence share 9.89%
C	3,673,584	trust-floor candidates
D	4,730,058	decoy archetypes
E	11,235,079	no-evidence remainder
total	19,787,820	matches HM450 catalog size

`panel_layer` normal-tissue coverage

83.77%

panel_layer.status: available

covered: 16,576,426 / 19,787,820 HM450 catalog sites

uncovered: 3,211,394 sites

envelope: 10 tissues × 687 samples (broad-normal v0.2 panel)

panel sha256: 773a9369…d3d7cb (shared across the three TCGA HM450 releases)

Validation panel composition

The TCGA-LIHC v0.5 validation panel is 18 rows × 3 selection classes (6 rows per class), uniform with the COAD and LUAD patient-cohort panels.

selection class	rows
`always_unmethylated_decoy`	6
`target_side_methylated_negative`	6
`feature_matched_control`	6
total	18

The full per-row schema (candidate coordinates, PAM family, score, off-target detail, feature class) lives in the release artifact atlas_validation_panel_liver.tsv under the release tag above.

Cross-cancer context

LIHC's Tier B candidate set shares a 3-way intersection with COAD and LUAD of 6,441 candidates / 1,378 probe loci / 1,635 nearest-gene symbols — same loci, different signal strength across cancers. Pairwise Tier B shared counts: COAD ∩ LIHC = 26,969; LUAD ∩ LIHC = 10,796.

The BRCA EPIC-v2 / hg38 release does not intersect with this HM450 / hg19 release at the candidate-id level (different probe space + different reference assembly). For BRCA cross-comparison, work at the nearest-gene-symbol level and treat the cell-line cohort separately from the TCGA patient-cohort releases.

Cite or reproduce

v0.5 release manifest + scored parquet + validation panel — atlas-tcga-lihc-v0.5.0-wg-sigmoid (sha256 2ae90a7a48f3…).
Coordinated release-set overview — /atlas/ § v0.5 Posture B.
Methods framework — PAPER.pdf at tag paper-5-10j.
Roth et al., Nature 2026 — DOI 10.1038/s41586-026-10384-z.