PGx: PharmVar genes (CYP1A2, CYP2A6, CYP2A13, CYP2C8, CYP3A4), CYP2A6 *4 from CN (PGX-001/006)
fetch_sources.sh downloads PharmVar per-gene zips; pgx db build adds core alleles for genes CPIC does not define (normalised against the FASTA, *1 = reference). Masks re-derived with the new variants. GeT-RM: CYP3A4 15/15, CYP2A6 7/9; all comparable genes 154/168 (CYP1A2/CYP2C8 definitions differ from GeT-RM's).
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@@ -41,7 +41,9 @@ Status: **implemented for CPIC star-allele genes, interim validation** (2026-09-
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| GSTM1 (CN: DEL/DEL vs present) | 9/9 | 9/9 |
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| GSTT1 (CN 0/1/2) | 7/9 | 7/9 |
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| UGT2B17 (CN) | 2/2 | 2/2 |
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| **total** | **132/144 (91.7 %)** | **135/144 (93.8 %)** |
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| CYP3A4 (PharmVar) | **15/15** | 15/15 |
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| CYP2A6 (PharmVar; *4 deletion from CN) | 7/9 | 8/9 |
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| **total** | **154/168 (91.7 %)** | **158/168 (94.0 %)** |
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PGX-032 target (≥ 90 % for CYP2D6/CYP2C19/CYP2C9 against truth): **42/45 = 93 %** (top solution), 45/45 within
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the array-equivalent feasible solutions.
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@@ -52,8 +54,10 @@ CYP2D6 structures (PGX-013) come from the three sub-region CNs (`simurg.pgx.star
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array cannot separate (both within the feasible set).
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Details and every discordant call: `V2_pgx_star_getrm16.json`.
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Not in the total (GeT-RM uses pre-2023 names the CPIC definitions no longer carry): UGT1A1 (GeT-RM `*60`;
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0/9 top) and SLCO1B1 (`*1B/*17/*21` vs CPIC `*37/*15/*20`; 9/15 top).
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Not in the total (GeT-RM uses older names or definitions than CPIC/PharmVar today): UGT1A1 (GeT-RM `*60`;
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0/9 top), SLCO1B1 (`*1B/*17/*21` vs CPIC `*37/*15/*20`; 9/15), CYP1A2 (lettered `*1F`; 0/9) and CYP2C8 (PharmVar now
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defines rs2071426 alone as `*19`; the array calls it concordantly with 1000G, GeT-RM reports those carriers as
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`*1`; 8/15).
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Remaining discordances: CYP2D6 *2 vs *1 where the array cannot separate them (prior picks *1), CYP2C19 *8, TPMT *21, CYP2B6 *27, CYP4F2 *2 — rare
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alleles whose defining variants are absent or masked on this array.
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@@ -84,5 +88,8 @@ so the per-call error is 1e-3 (GS ≥ 0.15) and errors are handled by the probe
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`Reference`, phenotype diplotype from the two lowest-activity carried variants), HLA-A/B tag variants (PGX-007,
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positions resolved from the manifest's probes, flag `tag_caveat`), and GSTM1/GSTT1/UGT2B17 `*0` genotypes from
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the targeted CN (PGX-006).
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* Not yet: PharmVar-only
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genes (CYP2A6, CYP3A4, CYP1A2, …); DPWG tables.
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* PharmVar genes without CPIC definitions (CYP1A2, CYP2A6, CYP2A13, CYP2C8, CYP3A4; PharmVar 6.2.29): core alleles
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from the GRCh38 haplotype VCFs, `*1` = reference, prior reference 0.8 (no population frequencies); genotype only
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(no CPIC phenotype). The probe mask was re-derived with these variants (one more record: CYP2A6 19:40843845 C>A,
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concordance 0.47, which had produced false *5 calls).
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* Not yet: DPWG tables.
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@@ -1,6 +1,16 @@
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{
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"individuals": 30,
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"genes": {
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"CYP1A2": {
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"n": 9,
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"top": 0,
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"equivalent": 0
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},
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"CYP2A6": {
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"n": 9,
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"top": 7,
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"equivalent": 8
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},
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"CYP2B6": {
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"n": 14,
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"top": 12,
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@@ -12,6 +22,11 @@
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"top": 14,
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"equivalent": 15
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},
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"CYP2C8": {
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"n": 15,
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"top": 8,
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"equivalent": 9
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},
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"CYP2C9": {
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"n": 15,
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"top": 15,
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@@ -22,6 +37,11 @@
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"top": 13,
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"equivalent": 15
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},
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"CYP3A4": {
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"n": 15,
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"top": 15,
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"equivalent": 15
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},
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"CYP3A5": {
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"n": 15,
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"top": 15,
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@@ -79,15 +99,31 @@
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}
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},
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"legacy_nomenclature_genes": [
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"CYP1A2",
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"CYP2C8",
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"SLCO1B1",
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"UGT1A1"
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],
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"total": {
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"n": 144,
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"top": 132,
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"equivalent": 135
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"n": 168,
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"top": 154,
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"equivalent": 158
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},
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"discordant": [
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{
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"individual": "NA12156",
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"gene": "CYP1A2",
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"truth": "*1A/*1F",
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"call": "*1/*15",
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"within_equivalents": false
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},
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{
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"individual": "NA12156",
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"gene": "CYP2C8",
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"truth": "*1/*15",
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"call": "*1/*1",
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"within_equivalents": true
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},
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{
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"individual": "NA12156",
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"gene": "CYP4F2",
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@@ -116,6 +152,20 @@
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"call": "*1/*1",
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"within_equivalents": false
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},
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{
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"individual": "NA07019",
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"gene": "CYP1A2",
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"truth": "*1A/*1F",
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"call": "*1/*15",
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"within_equivalents": false
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},
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{
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"individual": "NA07019",
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"gene": "CYP2C8",
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"truth": "*1/*1",
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"call": "*1/*19",
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"within_equivalents": false
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},
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{
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"individual": "NA07019",
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"gene": "UGT1A1",
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@@ -123,6 +173,13 @@
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"call": "*1/*1",
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"within_equivalents": false
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},
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{
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"individual": "NA06991",
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"gene": "CYP1A2",
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"truth": "*1F/*1F",
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"call": "*15/*24",
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"within_equivalents": false
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},
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{
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"individual": "NA06991",
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"gene": "UGT1A1",
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@@ -137,6 +194,13 @@
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"call": "rs9923231 T/T",
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"within_equivalents": false
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},
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{
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"individual": "NA12878",
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"gene": "CYP1A2",
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"truth": "*1F/*1F",
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"call": "*15/*24",
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"within_equivalents": false
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},
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{
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"individual": "NA12878",
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"gene": "UGT1A1",
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@@ -144,6 +208,20 @@
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"call": "*28/*80",
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"within_equivalents": false
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},
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{
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"individual": "NA11993",
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"gene": "CYP1A2",
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"truth": "*1F/*1F",
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"call": "*15/*24",
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"within_equivalents": false
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},
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{
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"individual": "NA11993",
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"gene": "CYP2A6",
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"truth": "*9/*17",
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"call": "*15/*17",
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"within_equivalents": true
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},
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{
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"individual": "NA11993",
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"gene": "SLCO1B1",
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@@ -158,6 +236,20 @@
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"call": "*28/*80",
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"within_equivalents": false
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},
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{
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"individual": "NA12003",
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"gene": "CYP1A2",
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"truth": "*1A/*1F",
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"call": "*15/*24",
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"within_equivalents": false
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},
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{
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"individual": "NA12003",
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"gene": "CYP2A6",
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"truth": "*1/(*8)",
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"call": "*1/*1",
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"within_equivalents": false
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},
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{
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"individual": "NA12003",
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"gene": "UGT1A1",
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@@ -179,6 +271,13 @@
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"call": "*1/*0",
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"within_equivalents": false
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},
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{
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"individual": "NA07029",
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"gene": "CYP1A2",
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"truth": "*1A/*1F",
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"call": "*1/*15",
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"within_equivalents": false
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},
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{
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"individual": "NA07029",
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"gene": "CYP2B6",
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@@ -193,6 +292,13 @@
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"call": "*1/*17",
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"within_equivalents": true
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},
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{
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"individual": "NA07029",
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"gene": "CYP2C8",
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"truth": "*1/*3",
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"call": "*19/*3",
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"within_equivalents": false
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},
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{
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"individual": "NA07029",
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"gene": "UGT1A1",
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@@ -207,6 +313,27 @@
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"call": "*1/*5",
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"within_equivalents": false
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},
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{
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"individual": "NA10846",
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"gene": "CYP2C8",
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"truth": "*1/*1",
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"call": "*1/*19",
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"within_equivalents": false
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},
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{
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"individual": "NA07000",
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"gene": "CYP2C8",
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"truth": "*1/*1",
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"call": "*1/*19",
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"within_equivalents": false
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},
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{
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"individual": "NA11832",
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"gene": "CYP1A2",
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"truth": "*1F/*1F",
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"call": "*15/*24",
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"within_equivalents": false
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},
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{
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"individual": "NA11832",
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"gene": "NAT2",
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@@ -242,6 +369,20 @@
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"call": "*1/*14",
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"within_equivalents": false
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},
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{
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"individual": "NA12813",
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"gene": "CYP1A2",
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"truth": "*1F/*1L",
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"call": "*15/*24",
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"within_equivalents": false
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},
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{
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"individual": "NA12813",
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"gene": "CYP2C8",
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"truth": "*1/*1",
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"call": "*1/*19",
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"within_equivalents": false
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},
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{
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"individual": "NA12813",
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"gene": "CYP2D6",
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@@ -270,6 +411,13 @@
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"call": "*1/*0",
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"within_equivalents": false
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},
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{
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"individual": "NA11881",
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"gene": "CYP2C8",
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"truth": "*1/*1",
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"call": "*1/*19",
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"within_equivalents": false
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},
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{
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"individual": "NA11881",
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"gene": "SLCO1B1",
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