Table 2.
Genotype frequencies of NUDT15 and TPMT variants in available patients with AZA‐induced leukopenia and general population controls in retrospective cohort study
| Gene | Chr. (location) | Fun. | WES/WGS in Chinese population | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Minor allele | MAF | OR (95% CI) | P value | Pc value | HWE | ||||
| Cases, N = 40 | Ctrls, N = 507 | ||||||||
| SNP | |||||||||
| NUDT15 | |||||||||
| rs116855232 | 13 (48045719) | NSV | T | 0.714 | 0.111 | 21.7 (12.1–38.8) | 3.7 × 10 −25 | 6.5 × 10 −19 | 0.303 |
| rs186364861 | 13 (48037798) | NSV | A | 0 | 0.022 | 0.0 (0.0–2.4) | 0.998 | – | 0.311 |
| rs746071566 a | 13 (48037783‐48037801) | Indel | GGAGTCGGAGTCG | 0.288 | 0.069 | 7.1 (3.7–13.7) | 4.2 × 10−9 | 0.007 | 0.020 |
|
TPMT rs1142345 |
6 (18130687) | NSV | C | 0 | 0.015 | 0.40 (0.0–6.8) | 0.999 | – | 0.965 |
P values were calculated with the use of logistic‐regression model adjusted by sex and age. Pc values were calculated by Bonferroni correction for the multiple comparisons (0.05/1,745,379). Bold values represent the significant P values for comprasion.
95% CI, 95% confidence interval; AZA, azathioprine; Chr., chromosome; Ctrls, population controls; Fun., functional variant type; HWE, Hardy–Weinberg equilibrium P values for 507 controls from the Chinese general population of Taiwan; Indel, insertion and deletion; MAF, minor allele frequency; NUDT15, nudix hydrolase 15; NSV, nonsynonymous; OR, odds ratio; SNP, single‐nucleotide polymorphism; TPMT, Thiopurine methyltransferase or thiopurine S‐methyltransferase; WES, whole exome sequencing; WGS, whole genome sequencing.
The rs554405994 was merged into rs869320766 which was further merged into rs746071566 on October 12, 2018 (based on the build 155 of NCBI dbSNP website; https://www.ncbi.nlm.nih.gov/snp/rs746071566?horizontal_tab=true). The rs746071566 belongs to inframe deletion variant.