Table 1.

The frequencies of predicted functional variants in 12 pharmacogenes (including HLA) identified in sequencing data and frequencies of detected copy-number variants in CYP2D6

Variation in 11 pharmacogenes detected by sequencing
	n	%
Loss-of-function and missense	198	n/a
Missense	188	94.95
Loss-of-function	10	5.05
Known variants	96	48.48
Novel variants	102	51.52
MAF >5%	21	10.61
1% ≤ MAF <5%	11	5.56
0.1% ≤ MAF <1%	34	17.17
MAF <0.1%	132	66.67
HLA alleles of high-risk phenotypes a detected by genome sequencing data	n	%
Individuals with data of typing HLA alleles	2243	100
Individuals with presence of at least one HLA-B*57:01 allele	105	4.68
Individuals with presence of at least one HLA-B*58:01 allele	32	1.43
Individuals with presence of at least one HLA-B*15:02 allele	0	0
Individuals with presence of at least one HLA-A*31:01 allele	109	4.86
CYP2D6  copy-number variants detected by genome sequencing and microarray data	n	%
Number of individuals	32,369	n/a
Individuals with CYP2D6 deletion	1073	3.31
Individuals with CYP2D6 duplication	257	0.79

MAF minor allele frequency.

^aFour high-risk phenotypes of the HLA region covered with Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines.