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PGx: CYP2D6 structures from sub-region CN — *68+*4, *36+*10, *13 (PGX-013/018)

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Sub-region CNs (p5, intron 2, exon 9) resolve full copies and *36/*68/*13 units; candidates carry the
tandem names, background alleles, and CPIC activity sums. GeT-RM: CYP2D6 13/15 top (NA12878 *3/*68+*4 and
NA11832 *1/*68+*4 exact), 15/15 within feasible; all genes 132/144.
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kemal committed 2026-09-29 16:29:54 +01:00
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docs/validation/V2_pgx_star.md
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@@ -30,7 +30,7 @@ Status: **implemented for CPIC star-allele genes, interim validation** (2026-09-
|---|---|---|
| CYP2C9 | **15/15** | 15/15 |
| CYP2C19 | **14/15** | 15/15 |
| CYP2D6 | **12/15** | 14/15 |
| CYP2D6 | **13/15** | **15/15** |
| CYP3A5 | 15/15 | 15/15 |
| TPMT | 15/16 | 15/16 |
| CYP2B6 | 12/14 | 12/14 |
@@ -41,16 +41,21 @@ Status: **implemented for CPIC star-allele genes, interim validation** (2026-09-
| GSTM1 (CN: DEL/DEL vs present) | 9/9 | 9/9 |
| GSTT1 (CN 0/1/2) | 7/9 | 7/9 |
| UGT2B17 (CN) | 2/2 | 2/2 |
| **total** | **131/144 (91.0 %)** | **134/144 (93.1 %)** |
| **total** | **132/144 (91.7 %)** | **135/144 (93.8 %)** |
PGX-032 target (≥ 90 % for CYP2D6/CYP2C19/CYP2C9 against truth): **41/45 = 91 %** (top solution).
PGX-032 target (≥ 90 % for CYP2D6/CYP2C19/CYP2C9 against truth): **42/45 = 93 %** (top solution), 45/45 within
the array-equivalent feasible solutions.
CYP2D6 structures (PGX-013) come from the three sub-region CNs (`simurg.pgx.star.cyp2d6_structure`): NA12878
`*3/*68+*4` and NA11832 `*1/*68+*4` are called exactly as GeT-RM reports them; one sample is called `*36+*10/*4`
(p5 = intron 2 = 3, exon 9 = 2; no GeT-RM truth). The two remaining top-solution misses are *1 vs *2, which this
array cannot separate (both within the feasible set).
Details and every discordant call: `V2_pgx_star_getrm16.json`.
Not in the total (GeT-RM uses pre-2023 names the CPIC definitions no longer carry): UGT1A1 (GeT-RM `*60`;
0/9 top) and SLCO1B1 (`*1B/*17/*21` vs CPIC `*37/*15/*20`; 9/15 top).
Remaining discordances: CYP2D6 `*3/(*68)+*4` (NA12878; *68 hybrids not modelled, *3 frameshift probe), CYP2D6 *2 vs
*1 where the array cannot separate them (prior picks *1), CYP2C19 *8, TPMT *21, CYP2B6 *27, CYP4F2 *2 — rare
Remaining discordances: CYP2D6 *2 vs *1 where the array cannot separate them (prior picks *1), CYP2C19 *8, TPMT *21, CYP2B6 *27, CYP4F2 *2 — rare
alleles whose defining variants are absent or masked on this array.
## Error model (K-029)
@@ -79,5 +84,5 @@ so the per-call error is 1e-3 (GS ≥ 0.15) and errors are handled by the probe
`Reference`, phenotype diplotype from the two lowest-activity carried variants), HLA-A/B tag variants (PGX-007,
positions resolved from the manifest's probes, flag `tag_caveat`), and GSTM1/GSTT1/UGT2B17 `*0` genotypes from
the targeted CN (PGX-006).
* Not yet: CYP2D6 hybrids (*13, *36, *68); PharmVar-only
* Not yet: PharmVar-only
genes (CYP2A6, CYP3A4, CYP1A2, …); DPWG tables.