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Table 3 Call concordance of PGx alleles using WGS and orthogonal methods in patient samples

From: Whole-genome sequencing as an investigational device for return of hereditary disease risk and pharmacogenomic results as part of the All of Us Research Program

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)  
  1. aBI Broad Institute, bWGS whole-genome sequencing, cBCM Baylor College of Medicine, dUW University of Washington, eColor Color Health, fCVL Clinical Validation Laboratory