OncoRef 1.25.0: categorical protein decisions
698 CTA proteins, 600 Other, 18,031 Unsafe and 534 Unassessed. All 522 previous CTAs remain included. Unsafe membership is unchanged. CTA represents 741 member loci after identical selected reference protein sequences are collapsed.
Full report and funnel · PDF slides · Every change and individual evidence · Rules and API
| Category | 1.24.0 | 1.25.0 |
|---|---|---|
| CTA | 522 | 698 |
| Other (formerly Neither) | 20 | 600 |
| Unsafe | 18,031 | 18,031 |
| Unassessed | 1,290 | 534 |
What changed
Other now requires the complete normal screen to pass, without requiring cancer or Reproductive identity. Every Other protein receives a named category:
| Category | Proteins | Definition |
|---|---|---|
| Other:Diffuse | 8 | Complete HPA profile is dispersed (score >10% with a reference ≥2 nTPM), or the active concentration gate fails; no CTA route remains. |
| Other:Reproductive | 2 | Qualifying Reproductive evidence, but no qualifying cancer expression; the normal screen passes. |
| Other:Inducible | 5 | Cited expression in activated nonreproductive normal cells; a localized indirect atlas signal cannot establish Reproductive identity. |
| Other:Tumor-supported | 66 | Two distinct tumors ≥10 native TPM or reviewed reliable tumor protein, with low measured normal/developmental expression; not established tumor restriction. |
| Other:Disposable | 2 | Positive Disposable RNA/protein; measured RNA elsewhere below the descriptive 2-unit floor and no detected protein elsewhere, including low measured developmental RNA. |
| Other:Low | 254 | All measured normal RNA below the descriptive 2-unit floor and no detected normal protein. Cancer expression need not be low. |
| Other:Normal | 171 | Supported nonreproductive normal RNA reaches the descriptive 2-unit floor or reliable protein is detected; no preceding subtype or CTA definition qualifies. |
| Other:Weak | 92 | Reproductive signals are below admission requirements or lack support; no preceding subtype qualifies and no supported appreciable nonreproductive expression is established. |
The rules apply in table order. Normal describes supported normal expression below the safety ceilings; Weak describes signals insufficient for an earlier category. Low means low in measured normal panels, not never expressed. The 66 Tumor-supported proteins remain reconsideration leads, with rare normal-cell coverage tracked in #653.
Three admission repairs add 176 CTA proteins: reliable positive reproductive IHC again counts independently; the bulk maximum uses the full mapped Reproductive panel; and supported reproductive-cell RNA supplies a presence route. MAGEA11, FOXR2, CAGE1, PRDM9, SAGE1 and GAGE10 illustrate the corrections. The routes overlap, so their counts must not be added. MAGE-A4, NY-ESO-1, PRAME, CTAG2 and XAGE1A/B remain CTA.
Generic or immune cells sampled in reproductive tissue may supply indirect association if the same-source outside panel is complete and every outside cluster is below 5 nTPM. Published normal induction contradicts indirect-only localization: IFNA2/14 remain Other:Inducible. A sampling site does not establish the producing cell. All safety, normal coverage, cancer and measured concentration gates still apply.
Downstream contract
from oncoref import cta_selection
cta_selection.results(category="CTA")
cta_selection.results(category="Other", subtype="Low")
cta_selection.results()[["label", "classification", "reasons"]]
cta_selection.candidates() # CTA only
cta_selection.audit().explain("FOXR2")
classification is CTA, Unsafe, Other:category retains
CTA / Unsafe / Other / null, and subtype names each Other category. The deprecated
category="Neither" query returns Other and warns. No top-level Tumor-restricted
category is introduced. Missing normal coverage uses incomplete_evidence;
unresolved normal-screen holds use normal_evidence_hold.
Pin policy oncoref.cta-selection.2026-10-30.2 and the source snapshot. Dog and
mouse retain native nominations with Unassessed status; human decisions do not
transfer through orthology. The separately versioned legacy CTA and exact-protein
background APIs retain their own policies, including k-mer exclusion semantics.
These are research screening assignments, not demonstrated clinical safety or clearance of every epitope. The report retains source units, missing coverage, antibody concerns and exact clinical epitope/HLA/product limitations.