Single-nucleotide polymorphisms of HLA and Polygonum multiflorum-induced liver injury in the Han Chinese population

Table 1 Candidate single-nucleotide polymorphisms selected from whole-exome sequencing of 8 Polygonum multiflorum-induced liver injury patients and 8 healthy controls

SNP ID	Chromosome	Gene	Number of PM-DILI patients with candidate SNP	Number of healthy controls with candidate SNP
rs1042597	2	UGT1A8	6	0
rs37959583	2	DRC1	6	3
rs111686806	6	HLA-A	5	0
rs2231119	6	HLA-A	8	0
rs11369033	6	HLA-A	6	0
rs1156624013	6	HLA-A	6	0
rs1171629793	6	HLA-A	5	2
rs10595163	6	HLA-A	5	0
rs10503412	6	HLA-B	5	0
rs1055348	6	HLA-B	5	0
rs23086553	6	HLA-B	6	0
rs10504581	6	HLA-B	5	0
rs10514881	6	HLA-B	6	0
rs202047044	6	HLA-DRB1	4	0
rs111534875	6	HLA-DRB1	5	3
rs78246137	6	HLA-DRB1	7	0
rs23087683	6	HLA-DRB1	5	0
rs17999313	8	NAT2	4	0
rs5747933	22	PRODH	7	3

¹Single-nucleotide polymorphism (SNPs) detected in fewer than 95% of individuals (2 SNPs).

²SNPs with minor allele frequency < 5% (1 SNPs).

³SNPs with Hardy-Weinberg equilibrium test P values < 0.05 (8 SNPs). PM-DILI: Polygonum multiflorum-induced liver injury.

Table 2 Demographic and clinical features of Polygonum multiflorum-induced liver injury patients and other drug-induced liver injury patients

Characteristics	PM-DILI (n = 73)	Other-DILI (n = 118)	P
Mean age, yr	47.7 ± 15.8	52.3 ± 14.2	0.045
Female, n (%)	56 (76.7)	74 (62.7)	0.044
BMI	23.6 ± 3.2	24.0 ± 3.7	0.447
Medication time1, d	30 (45)	30 (60.8)	0.097
ALT (U/L)	1105.0 ± 679.9	626.3 ± 670.1	< 0.001
AST (U/L), n	797.7 ± 557.3 (65)	485.6 ± 596.5 (118)	0.001
ALP (U/L), n	148.5 ± 58.4 (59)	160.5 ± 212.3 (105)	0.673
TBil (mg/dL), n	112.9 ± 107.2 (61)	76.9 ± 92.5 (99)	0.026
Injury type	n = 59	n = 105	0.917
Hepatocellular	57	82
Cholestatic	1	12
Mixed	1	11
RUCAM score			0.319
3-5 (Possible)	7	20
6-8 (Probable)	53	82
≥ 9 (Highly probable)	13	16

¹A variable is expressed as the median (interquartile range). Other variables are expressed as the mean ± standard deviation (SD). BMI: Body mass index; ALT: Alanine aminotransferase; AST: Aspartate aminotransferase; ALP: Alkaline phosphatase; TBil: Total bilirubin level; RUCAM: Roussel Uclaf causality assessment method; Other-DILI: Other drug-induced liver injury; PM-DILI: Polygonum multiflorum-induced liver injury.

Table 3 Association between the 8 single-nucleotide polymorphisms and Polygonum multiflorum-induced liver injury

SNP ID	Chromose (Gene)	Minor allele	Minor allele frequency (%)			PM-DILI vs control		PM-DILI vs Other-DILI
			PM-DILI (n = 73)	Other-DILI (n = 118)	Control (n = 191)	P value	OR (95%CI)	P value	OR (95%CI)
rs1055348	6 (HLA-B)	G	42.5%	13.6%	8.6%	1.72 × 10-19a	13.62 (7.16-25.9)	1.84 × 10-10a	10.06 (5.06-20)
rs202047044	6 (HLA-DRB1)	C	22.9%	17.5%	8.1%	4.64 × 10-6a	4.1 (2.25-7.47)	0.212	1.53 (0.84-2.76)
rs111686806	6 (HLA-A)	T	27.2%	27.6%	11.6%	1.72 × 10-5a	3.96 (2.21-7.1)	0.937	0.97 (0.53-1.77)
rs2231119	6 (HLA-A)	A	26.0%	24.4%	36.8%	0.020	0.57 (0.36-0.90)	0.714	1.11 (0.66-1.85)
rs111534875	6 (HLA-DRB1)	A	29.6%	32.0%	20.1%	0.022	1.64 (1.06-2.55)	0.622	0.89 (0.57-1.40)
rs1042597	2 (UGT1A8)	G	42.1%	44.0%	51.0%	0.071	0.71 (0.48-1.04)	0.723	0.93 (0.61-1.41)
rs78246137	6 (HLA-DRB1)	T	29.5%	31.6%	22.5%	0.095	1.45 (0.94-2.25)	0.656	0.9 (0.57-1.43)
rs5747933	22 (PRODH)	T	13.6%	16.7%	10.2%	0.279	1.35 (0.77-2.39)	0.424	0.8 (0.45-1.42)

^aP value that reached the threshold of P < 6.25 × 10^-3 by Bonferroni correction. Other-DILI: Other drug-induced liver injury; SNP: Single-nucleotide polymorphisms; PM-DILI: Polygonum multiflorum-induced liver injury; OR: Odd ratio; CI: Confidence interval.

Table 4 Biochemical characteristics between patients with the rs1055348 G allele and those without the rs1055348 G allele

Variables	PM-DILI				Other-DILI
	With the rs1055348 G allele (n = 58)	Without the rs1055348 G allele (n = 15)		P value	With the rs1055348 G allele (n = 32)	Without the rs1055348 G allele (n = 86)	P value
Age, mean ± SD, yr	46.7 ± 15.1	51.2 ± 16.2	0.317		49.2 ± 14.4	53.4 ± 14.0	0.152
Female, n (%)	42 (72.4)	14 (93.3)	0.167		22 (68.8)	52 (60.5)	0.408
BMI	23.7 ± 2.9	23.0 ± 3.0	0.407		23.8 ± 3.0	24.0 ± 3.9	0.774
Medication time1, d	30 (40.8)	30 (22)	0.533		46.5 (63.5)	30 (54)	0.269
ALT (U/L)	1234.8 ± 609.5	603.2 ± 517.0	< 0.0001		936.7 ± 866.7	510.8 ± 532.7	0.013
AST (U/L), n	876.9 ± 537.8 (51)	509.2 ± 507.6 (14)	0.025		712.8 ± 691.5 (32)	401.0 ± 513.4 (86)	0.009
ALP (U/L), n	155.8 ± 59.8 (48)	116.7 ± 40.0 (11)	0.044		140.3 ± 99.4 (28)	167.8 ± 240.8 (77)	0.559
TBil (mg/dL), n	123.9 ± 110.5 (48)	70.7 ± 84.9 (13)	0.113		85.7 ± 104.8 (29)	73.3 ± 87.4 (70)	0.547

¹A variable is expressed as the median (interquartile range). Variables are expressed as the mean ± SD. PM-DILI: Polygonum multiflorum-induced liver injury; Other-DILI: Other drug-induced liver injury; BMI: Body mass index; ALT: Alanine aminotransferase; AST: Aspartate aminotransferase; ALP: Alkaline phosphatase; Tbil: Total bilirubin level.

Table 5 Performance of the rs1055348 G allele for HLA-B*35:01 in the Polygonum multiflorum-induced liver injury group (n = 73) and the other drug-induced liver injury group (n = 78)

Group	TP	TN	FP	FN	Sensitivity (95%CI)	Specificity (95%CI)	PPV (95%CI)	NPV (95%CI)	κ (95%CI)
PM-DILI	60	84	2	0	100.0 (94.0-100.0)	97.7 (91.9-99.7)	96.8 (88.8-99.6)	100.0 (95.7-100.0)	0.959 (0.879-1.000)
Other-DILI	28	204	4	0	100.0 (87.7-100.0)	98.1 (95.1-99.5)	87.5 (71.0-96.5)	100.0 (98.2-100.0)	0.911 (0.825-0.996)

TP: True positive; TN: True negative; FP: False positive; FN: False negative; PPV: Positive predictive value; NPV: Negative predictive value; Other-DILI: Other drug-induced liver injury; PM-DILI: Polygonum multiflorum-induced liver injury; CI: Confidence interval.