Bundled classifiers
Every classifier the package ships, one table per tumor type: rows are classifiers, columns are platforms, and a cell is the classifier's status. The tables are generated from sigma2.classifiers.cards() on the installed release (SigMA2 0.0.16-alpha.20, generated 2026-11-05) by scripts/sigma2/cards.py, never written by hand, and they carry no performance numbers; the status word states what a cell's calls support (Release status).
| Cell | Meaning |
|---|---|
| released | passed the release gate; a positive call at the stated operating point |
| released, weak evidence | released; a positive call raises the odds little, and call_evidence is weak |
| experimental | withheld by the gate; run() refuses it without force=True, and then gives scores, not calls |
| own model, pooled model | HRD: the tumor type has its own HRD model, or shares the pooled one |
| — | no classifier for the cell |
A signature cell reads "released before the gate" when its card records only the earlier release rule, a 10% false-positive rate on held-out simulated negatives, with no evidence grade (release status). An HRD cell names the model that scores the tumor type, its own or the pooled one, and the number of BRCA1/2-deficient tumors that model was trained with; HRD and MMRD/POLE models are cross-validated and shipped without a release gate. The SNV floor beside each tumor type is the floor its classifiers apply. sg2.describe() prints the same tables in the terminal, with glyphs: ● released, ◐ weak, ▲ experimental.
adrenalSNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 |
|---|---|---|---|---|---|
| HRD | pooled model, 6 BRCA1/2 | pooled model, 4 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped |
biliarySNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 |
|---|---|---|---|---|---|
| HRD | pooled model, 6 BRCA1/2 | pooled model, 4 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped |
bladderSNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 |
|---|---|---|---|---|---|
| HRD | own model, 11 BRCA1/2 | own model, 18 BRCA1/2 | own model, 11 BRCA1/2 | own model, 11 BRCA1/2 | own model, 11 BRCA1/2 |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped |
breastSNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 | wgs |
|---|---|---|---|---|---|---|
| SBS3 | released before the gate | released | released before the gate | released before the gate | released | released |
| SBS8 | released before the gate | released before the gate | released before the gate | released before the gate | released before the gate | released |
| SBS18 | released before the gate | released before the gate | released before the gate | released before the gate | released before the gate | released |
| APOBEC | released before the gate | released before the gate | released before the gate | released before the gate | released before the gate | released |
| HRD | own model, 63 BRCA1/2 | own model, 135 BRCA1/2 | own model, 63 BRCA1/2 | own model, 63 BRCA1/2 | own model, 63 BRCA1/2 | — |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped | — |
cervixSNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 |
|---|---|---|---|---|---|
| HRD | own model, 4 BRCA1/2 | own model, 6 BRCA1/2 | own model, 4 BRCA1/2 | own model, 4 BRCA1/2 | own model, 4 BRCA1/2 |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped |
crcSNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 |
|---|---|---|---|---|---|
| SBS8 | experimental | experimental | experimental | released | released |
| SBS18 | released, weak evidence | released, weak evidence | released, weak evidence | released | released |
| APOBEC | released, weak evidence | released, weak evidence | released, weak evidence | released | released |
| HRD | pooled model, 6 BRCA1/2 | own model, 5 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped |
esoSNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 | wgs |
|---|---|---|---|---|---|---|
| SBS28 | — | released | — | released | released | released |
| SBS36 | — | released, weak evidence | — | released, weak evidence | — | — |
| SBS93 | released, weak evidence | — | released, weak evidence | — | released, weak evidence | — |
| HRD | pooled model, 6 BRCA1/2 | pooled model, 4 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 | — |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped | — |
gliomaSNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 |
|---|---|---|---|---|---|
| HRD | pooled model, 6 BRCA1/2 | pooled model, 4 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped |
headSNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 |
|---|---|---|---|---|---|
| HRD | own model, 3 BRCA1/2 | own model, 5 BRCA1/2 | own model, 3 BRCA1/2 | own model, 3 BRCA1/2 | own model, 3 BRCA1/2 |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped |
kidneySNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 | wgs |
|---|---|---|---|---|---|---|
| SBS1 | — | released, weak evidence | — | released | released | released |
| SBS18 | — | — | — | — | released, weak evidence | — |
| SBS40 | — | released, weak evidence | — | — | — | released |
| APOBEC | — | released, weak evidence | — | released, weak evidence | released, weak evidence | — |
| HRD | pooled model, 6 BRCA1/2 | pooled model, 4 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 | — |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped | — |
leukSNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 |
|---|---|---|---|---|---|
| HRD | pooled model, 6 BRCA1/2 | pooled model, 4 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped |
lggSNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 | wgs |
|---|---|---|---|---|---|---|
| SBS18 | — | — | — | — | — | released |
| SBS30 | — | — | — | — | released, weak evidence | — |
| SBS37 | — | — | — | — | released, weak evidence | — |
| HRD | pooled model, 6 BRCA1/2 | pooled model, 4 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 | — |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped | — |
liverSNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 | wgs |
|---|---|---|---|---|---|---|
| SBS1 | — | released, weak evidence | — | released | released | released |
| SBS4 | released | released, weak evidence | released, weak evidence | released | released | released |
| SBS8 | released, weak evidence | released, weak evidence | released, weak evidence | — | — | — |
| SBS12 | released, weak evidence | released, weak evidence | released, weak evidence | released | released | released |
| SBS16 | released, weak evidence | — | released, weak evidence | released | released | released |
| SBS18 | — | — | — | — | released, weak evidence | released |
| SBS22 | — | released, weak evidence | — | released | released, weak evidence | — |
| SBS30 | — | — | — | — | released, weak evidence | — |
| SBS36 | — | released, weak evidence | — | released, weak evidence | released, weak evidence | — |
| SBS85 | — | — | — | released, weak evidence | released, weak evidence | released |
| HRD | pooled model, 6 BRCA1/2 | pooled model, 4 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 | — |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped | — |
lungSNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 | wgs |
|---|---|---|---|---|---|---|
| SBS3 | released before the gate | experimental | released before the gate | released before the gate | released before the gate | released |
| SBS4 | released before the gate | released | released before the gate | released before the gate | released before the gate | released |
| SBS18 | released before the gate | experimental | released before the gate | released before the gate | released before the gate | released |
| APOBEC | released before the gate | released | released before the gate | released before the gate | released before the gate | released |
| HRD | own model, 17 BRCA1/2 | own model, 36 BRCA1/2 | own model, 17 BRCA1/2 | own model, 17 BRCA1/2 | own model, 17 BRCA1/2 | — |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped | — |
lymphSNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 | wgs |
|---|---|---|---|---|---|---|
| SBS9 | — | — | — | released | released | released |
| SBS17 | — | released | — | released | released | — |
| SBS30 | — | — | — | released, weak evidence | released, weak evidence | released |
| SBS34 | — | released | — | released | — | — |
| SBS36 | — | released | — | released, weak evidence | released | released |
| SBS84 | — | released | — | released | released | — |
| SBS85 | — | released, weak evidence | — | — | released | — |
| SBS89 | — | — | — | — | — | released |
| APOBEC | — | — | — | released, weak evidence | released, weak evidence | — |
| HRD | pooled model, 6 BRCA1/2 | pooled model, 4 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 | — |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped | — |
medulloSNV floor 5
| classifier | seqcap | tcga_mc3 | wgs |
|---|---|---|---|
| SBS3 | released | — | released |
| SBS8 | released | released, weak evidence | released |
mesoSNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 |
|---|---|---|---|---|---|
| HRD | pooled model, 6 BRCA1/2 | pooled model, 4 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped |
ovarySNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 |
|---|---|---|---|---|---|
| HRD | own model, 79 BRCA1/2 | own model, 164 BRCA1/2 | own model, 79 BRCA1/2 | own model, 79 BRCA1/2 | own model, 79 BRCA1/2 |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped |
panc_adSNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 | wgs |
|---|---|---|---|---|---|---|
| SBS3 | released | — | released | released | released | released |
| SBS9 | — | released, weak evidence | — | released, weak evidence | released, weak evidence | — |
| SBS17 | — | released, weak evidence | — | released, weak evidence | released, weak evidence | — |
| SBS18 | — | — | — | — | released, weak evidence | — |
| SBS30 | — | — | — | — | released | released |
| SBS36 | — | — | — | released, weak evidence | released, weak evidence | — |
| HRD | pooled model, 6 BRCA1/2 | own model, 11 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 | — |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped | — |
panc_enSNV floor 3
| classifier | msk | seqcap | tcga_mc3 | wgs |
|---|---|---|---|---|
| SBS18 | — | — | released | released |
| SBS30 | — | released | — | released |
| SBS36 | released, weak evidence | released | released | released |
| APOBEC | — | released, weak evidence | released, weak evidence | — |
prostSNV floor 4
| classifier | fo | msk | op | seqcap | tcga_mc3 | wgs |
|---|---|---|---|---|---|---|
| SBS3 | experimental | experimental | experimental | released | released | released |
| SBS8 | experimental | experimental | experimental | experimental | experimental | released |
| SBS18 | experimental | experimental | experimental | released | experimental | released |
| APOBEC | experimental | experimental | experimental | experimental | experimental | released |
| HRD | own model, 7 BRCA1/2 | own model, 83 BRCA1/2 | own model, 7 BRCA1/2 | own model, 7 BRCA1/2 | own model, 7 BRCA1/2 | — |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped | — |
skinSNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 | wgs |
|---|---|---|---|---|---|---|
| SBS7 | released before the gate | released before the gate | released before the gate | released before the gate | released before the gate | released |
| HRD | own model, 3 BRCA1/2 | own model, 4 BRCA1/2 | own model, 3 BRCA1/2 | own model, 3 BRCA1/2 | own model, 3 BRCA1/2 | — |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped | — |
stomachSNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 |
|---|---|---|---|---|---|
| SBS28 | — | released, weak evidence | — | released, weak evidence | released, weak evidence |
| SBS41 | — | released | released | — | — |
| HRD | own model, 5 BRCA1/2 | own model, 10 BRCA1/2 | own model, 5 BRCA1/2 | own model, 5 BRCA1/2 | own model, 5 BRCA1/2 |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped |
thyroidSNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 |
|---|---|---|---|---|---|
| HRD | pooled model, 6 BRCA1/2 | pooled model, 4 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 | pooled model, 6 BRCA1/2 |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped |
uterusSNV floor 5
| classifier | fo | msk | op | seqcap | tcga_mc3 |
|---|---|---|---|---|---|
| HRD | own model, 6 BRCA1/2 | own model, 11 BRCA1/2 | own model, 6 BRCA1/2 | own model, 6 BRCA1/2 | own model, 6 BRCA1/2 |
| MMRD/POLE | shipped | shipped | shipped | shipped | shipped |
HRD: tumor types a model refuses
An HRD model saw these tumor types in training but has no Signature 3 signature set for them, so run(soi="HRD") refuses them up front. Tumor types never in the HRD training are refused too. Detect HRD.
| platform | refused tumor types |
|---|---|
| fo | paraganglioma, sarc, testicular, thymoma, uveal |
| msk | sarc |
| op | paraganglioma, sarc, testicular, thymoma, uveal |
| seqcap | paraganglioma, sarc, testicular, thymoma, uveal |
| tcga_mc3 | paraganglioma, sarc, testicular, thymoma, uveal |
SigMA v1 classifiers (model="legacy")
SigMA v1's Signature 3 classifiers, ported, by platform, with the features the port passes to each as missing (R computes them, so those classifiers' scores can differ from R's). The msk cells have msk_cf variants (wcf=True), and SigMA v1's MMRD/POLE classifiers exist for msk and tcga_mc3 (predict_mmrd_ppd(model="legacy")). Reproduce SigMA v1.
| platform | reads every feature | a feature passed as missing | does not run |
|---|---|---|---|
| msk | bladder, breast, eso, ovary, prost, stomach | crc (APOBEC_c1, rat_sig3), osteo (clock_c1, clock_c2, clock_c3), panc_ad (APOBEC_c1), panc_en (APOBEC_c1), uterus (APOBEC_c1, APOBEC_c2) | none |
| msk_cf | bladder, breast, eso, ovary, panc_ad, panc_en, prost, stomach | osteo (clock_c1, clock_c2, clock_c3), uterus (APOBEC_c1) | none |
| seqcap | bladder, breast, eso, ewing, ovary, panc_ad, stomach | medullo (rat_sig3), osteo (APOBEC_c1), panc_en (APOBEC_c1), prost (rat_sig3), uterus (APOBEC_c1) | none |
| seqcap_probe | bladder, eso, ewing, ovary, panc_ad, prost, stomach | breast (APOBEC_c1, APOBEC_c2), medullo (rat_sig3), osteo (APOBEC_c1), panc_en (APOBEC_c1), uterus (APOBEC_c1) | none |
| tcga_mc3 | ovary | adrenal (rat_sig3), biliary (APOBEC_c1, rat_sig3), bladder (APOBEC_c2, rat_sig3), breast (APOBEC_c1), cervix (APOBEC_c3, rat_sig3), crc (APOBEC_c1, rat_sig3), eso (APOBEC_c1, APOBEC_c2, rat_sig3), glioma (rat_sig3), head (APOBEC_c1, rat_sig3), kidney (rat_sig3), lgg (rat_sig3), liver (rat_sig3), lung (rat_sig3), lymph (rat_sig3), meso (rat_sig3), panc_ad (rat_sig3), prost (rat_sig3), skin (APOBEC_c1, oxi_c1, rat_sig3), stomach (rat_sig3), uterus (APOBEC_c1, APOBEC_c2, rat_sig3) | none |
| wgs | none | biliary (rat_sig3), bladder (rat_sig3), bone_other (rat_sig3), breast (rat_sig3), cervix (rat_sig3), crc (rat_sig3), eso (APOBEC_c2, rat_sig3), ewing (rat_sig3), lms (rat_sig3), lung (APOBEC_c3, rat_sig3), medullo (rat_sig3), osteo (rat_sig3), ovary (rat_sig3), panc_ad (rat_sig3), panc_en (rat_sig3), prost (rat_sig3), skin (rat_sig3), stomach (rat_sig3), uterus (APOBEC_c1, rat_sig3) | kidney |
| wgs_pancan | breast | none | generic |
Regenerating these tables
Template — Terminalbash
SIGMA2_DATA_DIR=$(mktemp -d) python scripts/sigma2/cards.py
SIGMA2_DATA_DIR=$(mktemp -d) python scripts/sigma2/legacy_features.py
The empty data directory keeps a user's own store out of the listing. The scripts write config/sigma2-classifiers.json, with the release and date they ran on, and config/sigma2-legacy-features.json, from one run of each SigMA v1 classifier; these pages render the two files.