[iskandr]

Summary

• Double the approved absolute RNA ceilings: Vital 2/4/6/12, Protected 6/8/12/24, Manageable 10/20/30/60 nTPM. Keep reproductive admission >0, the approved selectivity percentages, coverage requirements and positive-IHC veto.
• Recompute all 20,097 human coding genes and the complete CTA intake. The current curated set retains 746 genes (98 gained, none lost); XAGE1A and XAGE1B both pass. Fixed/adaptive/zero-measured-outside-RNA comparisons retain 708/746/216.
• Replace report jargon with Clinical evidence / Result / Reason, add a searchable gene explorer, current publication counts, clinical evidence links, tissue measurements, comparison downloads, a funnel figure and navigation.
• Clarify GAGE2B's archived Ensembl ID versus its ambiguous current GAGE2A cross-reference. Preserve BAGE/GAGE2B as unassessed rather than borrowing paralog expression.
• Add disjoint gene and complete exact-protein partitions using all Ensembl 115 isoforms, full occurrence provenance and Normal > Unassessed > Reproductive > Other precedence. XAGE1A/B share 69- and 81-aa complete proteins in Reproductive. Partial translations keep their gene group; only Normal/Unassessed records enter additional background.
• Publish small report metadata in docs and place the 134 MiB of sequence tables/FASTA exports in v1.13.0 release assets. Historical reports remain immutable. Heavy DATA_VERSION remains 5.23.26.

Verification

• 117 policy/partition tests and 188 identity/clinical/source/manifest tests passed.
• Ruff lint/format and strict MkDocs build passed.
• Rechecked all 2,540 candidates' adaptive RNA/selectivity flags against raw pinned HPA v23; every decision matches the genome-wide report.
• Verified every new report input/output checksum, sequence disjointness, exact XAGE1A/B protein sharing, and partial-background routing.
• Executed the explorer JavaScript with a minimal DOM harness: initial render, pagination, clear, gene/alias search, inclusion/clinical filters and no-results behavior pass. All local report links resolve. Funnel figure visually inspected.
• Browser preview could not run: no browser provider was available and the native computer-use service failed to start. Responsive layout is implemented but has not received live browser visual QA.

Interpretation

These are user-approved research parameters, not validated clinical safety limits. Numerical passes do not erase measured trace expression. Positive normal IHC and the external MAGEA12 safety hold remain exclusions. Full-protein sets are disjoint; k-mers still require actual substring subtraction. Protein groups inherit gene-level expression and do not establish isoform-specific expression.