Cancer and Reproductive Antigens

CTA = Cancer Antigens ∩ Reproductive Antigens.
Target candidates = Cancer Antigens ∪ Reproductive Antigens.

Rebuilt catalog: oncoref.target-selection.2026-11-10.1. 626 CTA, 245 Cancer Antigen only, 31 Reproductive Antigen only, 750 Other, 18,241 Unsafe. Filterable protein table, measurements and category changes. The released 1.36.0 catalog remains a separate snapshot under its earlier policy.

One shared eligibility screen

Accepted normal-tissue or applicable clinical exclusion → Unsafe. Required coverage, identity, translation or unresolved evidence → Other:Review. Nested or Unsafe-contained sequence → Other:Sequence. Target maximum or Disposable cap failure → Other:Expression. The remaining proteins enter the two independent association checks.

Rare normal-cell RNA

Each adult donor is assessed separately in each named Vital or Protected cell population. A count matrix cannot show where a read aligned: one mis-assigned read per cell from a paralog, pseudogene or overlapping gene looks like sparse expression. Cells with a single molecule therefore never change a category.

Question	Requirement
Is there a signal?	>= 1% of a donor's cells and >= 10 cells carry >= 2 molecules.
Is it replicated?	The signal in >= 2 independent studies of the same organ, which agree on a cell type or include >= 3 donors. Donors of one study share its libraries and reference; one donor in each of two studies, in different cell types, agrees on nothing but the organ. Without replication, a signal counts only when >= 5% of a donor's cells carry multiple molecules.
Could the reads belong elsewhere?	Shared transcript sequence with another locus, or an exon inside another same-strand gene. Counts for a flagged gene cannot be attributed to it.
Does another assay agree?	Bulk RNA >= 1 native TPM in the same organ in both the HPA and GTEx sample sets, a different assay with its own read assignment.

Outcome	Rule
Established	A replicated signal at a locus without mapping risk, or any signal with bulk confirmation. Unsafe.
Dismissed	A signal that is neither: counts at a flagged locus, or from one study, that no other assay confirms. Recorded with its reason; no category effect.
Below the screen	No replicated or frequent multi-molecule signal. No finding; not evidence of absence or safety.

Protected populations need 2 times these frequencies. Where a reviewed publication reports the gene in the same organ by a gene-specific assay, 1% detection in one donor is established, single molecules included: two assay types then agree. Published protein in a Vital or Protected tissue excludes through the knowledge layer without any counts. 1%, 2% and 5% detection remain reported comparison metrics. There is no review state. Donor-level evidence · Literature review.

Cancer evidence

Let N be the highest qualified nonexempt normal measurement in a complete, compatible comparison panel. Two independent patients each need T ≥1 and T >N; alternatively, one tumor needs T ≥10 × max(N, 1). Sample quality and exact protein identity must pass. The highest tumor, reproductive or developmental value must also exceed every measured nonreproductive normal and Disposable value, and Disposable expression must stay at or below 32 TPM and 32 nTPM, each on its own scale.

Normal maximum N	Two independent tumors	One tumor
0	≥1 each	≥10
0.4	≥1 each	≥10
1	>1 each	≥10
3	>3 each	≥30
8	>8 each	≥80

Do not divide tumor TPM by an unrelated normal nTPM or CP10K maximum. Record the comparison methods, normal contexts, source statistics and sample identities. Missing required normal data leave the comparison unassessed. All other normal panels continue to enforce their exclusions. Wang et al., 2018.

Reviewed reliable tumor protein is a separate positive evidence route. Qualitative staining does not supply an RNA fold change. A high tumor value never cancels a normal exclusion.

Reproductive and developmental evidence

Adult reproductive, placental, extraembryonic, embryonic and fetal associations count. Use ≥1 native TPM/nTPM with the existing cell/read support, or reliable mapped protein evidence. Record the actual branch and stage. The old adult reproductive concentration score becomes descriptive; it is not an admission gate.

The 1-unit detection convention is distinct from protein production or antigen presentation. HPA methods.

Published target support

A curated target nomination adds supporting evidence. Preserve the exact protein–paper link and what it establishes: nomination, biology, tumor expression, protein identity, immune recognition, or normal-tissue counterevidence. Source-wide roles do not turn every gene in a paper into a target.

Core papers cover the catalog efficiently; supplementary papers retain independent experiments, identity limits and counterevidence. Both remain available through cta_literature.attestations(), including links attached to Other and Unsafe proteins.

Read the decision precisely

“Cancer Antigen only” and “Reproductive Antigen only” describe membership in one qualified set. They do not establish absence everywhere else. Unassessed associations stay visible. Target candidates is the union's name; it does not assert clinical safety.

Full definitions and API · Machine-readable contract