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PGx: PharmVar genes (CYP1A2, CYP2A6, CYP2A13, CYP2C8, CYP3A4), CYP2A6 *4 from CN (PGX-001/006)
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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).

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
This commit is contained in:
kemalandClaude Opus 5.5 committed 2026-09-29 16:50:27 +01:00
1 parent 1428535e91
commit 4176ef33de
9 files changed
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docs/validation/V2_pgx_star_getrm16.json
+151 -3
View File
@@ -1,6 +1,16 @@
{
"individuals": 30,
"genes": {
"CYP1A2": {
"n": 9,
"top": 0,
"equivalent": 0
},
"CYP2A6": {
"n": 9,
"top": 7,
"equivalent": 8
},
"CYP2B6": {
"n": 14,
"top": 12,
@@ -12,6 +22,11 @@
"top": 14,
"equivalent": 15
},
"CYP2C8": {
"n": 15,
"top": 8,
"equivalent": 9
},
"CYP2C9": {
"n": 15,
"top": 15,
@@ -22,6 +37,11 @@
"top": 13,
"equivalent": 15
},
"CYP3A4": {
"n": 15,
"top": 15,
"equivalent": 15
},
"CYP3A5": {
"n": 15,
"top": 15,
@@ -79,15 +99,31 @@
}
},
"legacy_nomenclature_genes": [
"CYP1A2",
"CYP2C8",
"SLCO1B1",
"UGT1A1"
],
"total": {
"n": 144,
"top": 132,
"equivalent": 135
"n": 168,
"top": 154,
"equivalent": 158
},
"discordant": [
{
"individual": "NA12156",
"gene": "CYP1A2",
"truth": "*1A/*1F",
"call": "*1/*15",
"within_equivalents": false
},
{
"individual": "NA12156",
"gene": "CYP2C8",
"truth": "*1/*15",
"call": "*1/*1",
"within_equivalents": true
},
{
"individual": "NA12156",
"gene": "CYP4F2",
@@ -116,6 +152,20 @@
"call": "*1/*1",
"within_equivalents": false
},
{
"individual": "NA07019",
"gene": "CYP1A2",
"truth": "*1A/*1F",
"call": "*1/*15",
"within_equivalents": false
},
{
"individual": "NA07019",
"gene": "CYP2C8",
"truth": "*1/*1",
"call": "*1/*19",
"within_equivalents": false
},
{
"individual": "NA07019",
"gene": "UGT1A1",
@@ -123,6 +173,13 @@
"call": "*1/*1",
"within_equivalents": false
},
{
"individual": "NA06991",
"gene": "CYP1A2",
"truth": "*1F/*1F",
"call": "*15/*24",
"within_equivalents": false
},
{
"individual": "NA06991",
"gene": "UGT1A1",
@@ -137,6 +194,13 @@
"call": "rs9923231 T/T",
"within_equivalents": false
},
{
"individual": "NA12878",
"gene": "CYP1A2",
"truth": "*1F/*1F",
"call": "*15/*24",
"within_equivalents": false
},
{
"individual": "NA12878",
"gene": "UGT1A1",
@@ -144,6 +208,20 @@
"call": "*28/*80",
"within_equivalents": false
},
{
"individual": "NA11993",
"gene": "CYP1A2",
"truth": "*1F/*1F",
"call": "*15/*24",
"within_equivalents": false
},
{
"individual": "NA11993",
"gene": "CYP2A6",
"truth": "*9/*17",
"call": "*15/*17",
"within_equivalents": true
},
{
"individual": "NA11993",
"gene": "SLCO1B1",
@@ -158,6 +236,20 @@
"call": "*28/*80",
"within_equivalents": false
},
{
"individual": "NA12003",
"gene": "CYP1A2",
"truth": "*1A/*1F",
"call": "*15/*24",
"within_equivalents": false
},
{
"individual": "NA12003",
"gene": "CYP2A6",
"truth": "*1/(*8)",
"call": "*1/*1",
"within_equivalents": false
},
{
"individual": "NA12003",
"gene": "UGT1A1",
@@ -179,6 +271,13 @@
"call": "*1/*0",
"within_equivalents": false
},
{
"individual": "NA07029",
"gene": "CYP1A2",
"truth": "*1A/*1F",
"call": "*1/*15",
"within_equivalents": false
},
{
"individual": "NA07029",
"gene": "CYP2B6",
@@ -193,6 +292,13 @@
"call": "*1/*17",
"within_equivalents": true
},
{
"individual": "NA07029",
"gene": "CYP2C8",
"truth": "*1/*3",
"call": "*19/*3",
"within_equivalents": false
},
{
"individual": "NA07029",
"gene": "UGT1A1",
@@ -207,6 +313,27 @@
"call": "*1/*5",
"within_equivalents": false
},
{
"individual": "NA10846",
"gene": "CYP2C8",
"truth": "*1/*1",
"call": "*1/*19",
"within_equivalents": false
},
{
"individual": "NA07000",
"gene": "CYP2C8",
"truth": "*1/*1",
"call": "*1/*19",
"within_equivalents": false
},
{
"individual": "NA11832",
"gene": "CYP1A2",
"truth": "*1F/*1F",
"call": "*15/*24",
"within_equivalents": false
},
{
"individual": "NA11832",
"gene": "NAT2",
@@ -242,6 +369,20 @@
"call": "*1/*14",
"within_equivalents": false
},
{
"individual": "NA12813",
"gene": "CYP1A2",
"truth": "*1F/*1L",
"call": "*15/*24",
"within_equivalents": false
},
{
"individual": "NA12813",
"gene": "CYP2C8",
"truth": "*1/*1",
"call": "*1/*19",
"within_equivalents": false
},
{
"individual": "NA12813",
"gene": "CYP2D6",
@@ -270,6 +411,13 @@
"call": "*1/*0",
"within_equivalents": false
},
{
"individual": "NA11881",
"gene": "CYP2C8",
"truth": "*1/*1",
"call": "*1/*19",
"within_equivalents": false
},
{
"individual": "NA11881",
"gene": "SLCO1B1",