Table 3.
Call concordance of PGx alleles using WGS and orthogonal methods in patient samples
| Gene and star allele | Number of clinical samples | Correct calls | Incorrect calls | Correct calls | Incorrect calls | Correct calls | Incorrect calls | Correct calls | Incorrect calls | Correct calls | Incorrect calls | Correct calls | Incorrect calls | Correct calls | Incorrect calls | Overall concordance |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CYP2C19*10 | 1 | 1/1 | 0 | - | - | - | - | 1/1 | 0 | - | - | - | - | - | - | 2/2 |
| CYP2C19*17 | 40 | 25/25 | 0 | 15/15 | 0 | - | - | 25/25 | 0 | 15/15 | 0 | - | - | - | - | 80/80 |
| CYP2C19*17/*17 | 1 | 1/1 | - | - | - | - | - | 1/1 | - | - | - | - | - | - | - | 2/2 |
| CYP2C19*2 | 48 | 33/33 | 0 | - | - | 15/15 | 0 | 33/33 | - | - | - | - | - | 15/15 | 0 | 96/96 |
| CYP2C19*2/*2 | 3 | 3/3 | 0 | - | - | - | - | 3/3 | - | - | - | - | - | - | - | 3/3 |
| CYP2C19*22 | 1 | - | - | 1/1 | 0 | - | - | - | - | 1/1 | 0 | - | - | - | - | 2/2 |
| CYP2C19*3 | 3 | 3/3 | 0 | - | - | - | - | 3/3 | - | - | - | - | - | - | - | 3/3 |
| CYP2C19*35 | 1 | 1/1 | 0 | - | - | - | - | 1/1 | - | - | - | - | - | - | - | 1/1 |
| CYP2C19*4 | 6 | 3/3 | 0 | 3/3 | 0 | - | - | 3/3 | 0 | 3/3 | 0 | - | - | - | - | 12/12 |
| CYP2C19*8 | 1 | - | - | - | - | 1/1 | 0 | - | - | - | - | - | - | 1/1 | 0 | 2/2 |
| CYP2C19*9 | 2 | - | - | 2/2 | 0 | - | - | - | - | 2/2 | 0 | - | - | - | - | 4/4 |
| DPYD c.1129-5923C>G | 2 | 2/2 | 0 | 2/2 | - | - | - | - | - | - | - | 4/4 | ||||
| DPYD c.1679T>G (*13) | 3 | 3/3 | 0 | 3/3 | - | - | - | - | - | - | - | 6/6 | ||||
| DPYD c.2846A>T | 2 | - | - | 2/2 | 0 | - | - | - | - | 2/2 | 0 | - | - | - | - | 4/4 |
| DPYD*2 (c.1905+1G>A) | 2 | - | - | 2/2 | 0 | - | - | - | - | 2/2 | 0 | - | - | - | - | 4/4 |
| G6PD A-202A_376G | 3 | 3/3 | 0 | - | - | - | - | 3/3 | 0 | - | - | - | - | - | - | 6/6 |
| G6PD Canton, Taiwan-Hakka, Gifu-like, Agrigento-like | 1 | 1/1 | 0 | - | - | - | - | 1/1 | 0 | - | - | - | - | - | - | 2/2 |
| G6PD Ilesha | 2 | 2/2 | 0 | - | - | - | - | 2/2 | 0 | - | - | - | - | - | - | 4/4 |
| G6PD Mediterranean, Dallas, Panama, Sassari, Cagliari, Birmingham | 5 | 5/5 | 0 | - | - | - | - | 5/5 | 0 | - | - | - | - | - | - | 10/10 |
| G6PD Seattle, Lodi, Modena, Ferrara II, Athens-like | 1 | 1/1 | 0 | - | - | - | - | 1/1 | 0 | - | - | - | - | - | - | 2/2 |
| G6PD Union, Maewo, Chinese-2, Kalo | 2 | 2/2 | 0 | - | - | - | - | 2/2 | 0 | - | - | - | - | - | - | 4/4 |
| NUDT15*2 | 2 | 2/2 | 0 | - | - | - | - | 2/2 | 0 | - | - | - | - | - | - | 4/4 |
| NUDT15*3 | 9 | 8/8 | 0 | - | - | 1/1 | 0 | 8/8 | 0 | - | - | - | - | 1/1 | 0 | 18/18 |
| SLCO1B1*15 | 28 | 22/22 | 0 | - | - | 6/6 | 0 | 22/22 | 0 | - | - | - | - | 6/6 | 0 | 56/56 |
| SLCO1B1*15/*15 | 4 | 4/4 | 0 | - | - | 4/4 | 0 | - | - | - | - | - | - | 8/8 | ||
| SLCO1B1*17 | 3 | - | - | - | - | 3/3 | 0 | - | - | - | - | - | - | 3/3 | 0 | 6/6 |
| SLCO1B1*5 | 8 | 7/7 | 0 | - | - | 1/1 | 0 | 7/7 | 0 | - | - | - | - | 1/1 | 0 | 16/16 |
| TPMT*2 | 6 | 5/5 | 0 | 1/1 | 0 | - | - | 5/5 | 0 | 1/1 | 0 | - | - | - | - | 12/12 |
| TPMT*3A | 9 | 9/9 | 0 | - | - | - | - | 9/9 | 0 | - | - | - | - | - | - | 18/18 |
| TPMT*3C | 5 | 5/5 | 0 | - | - | - | - | 5/5 | 0 | - | - | - | - | - | - | 10/10 |
| UGT1A1*27 | 3 | 3/3 | 0 | - | - | - | - | 3/3 | 0 | - | - | - | - | - | - | 6/6 |
| UGT1A1*28 | 70 | 37/37 | 0 | 33/33 | 0 | - | - | 37/37 | 0 | 33/33 | 0 | - | - | - | - | 140/140 |
| UGT1A1*36 | 12 | 4/4 | 0 | 8/8 | 0 | - | - | 4/4 | 0 | 8/8 | 0 | - | - | - | - | 24/24 |
| UGT1A1*36/*36 | 1 | 1/1 | 0 | - | - | - | - | 1/1 | 0 | - | - | - | - | - | - | 2/2 |
| UGT1A1*37 | 3 | 2/2 | 0 | - | - | 1/1 | 0 | 2/2 | 0 | - | - | 1/1 | 0 | - | - | 6/6 |
| UGT1A1*6 | 8 | 3/3 | 0 | 5/5 | 0 | - | - | 3/3 | 0 | 5/5 | 0 | - | - | - | - | 16/16 |
| Broada (WGSb) | BCMc (WGS) | UWd (WGS) | Colore CVLf (Panel) | BCM CVL (Sanger) | UW CVL (Panel) | UW CVL (Array) | ||||||||||
aBI Broad Institute, bWGS whole-genome sequencing, cBCM Baylor College of Medicine, dUW University of Washington, eColor Color Health, fCVL Clinical Validation Laboratory