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Table 3 Significant associations between genomic variants and drug resistance phenotypes identified by variant-based GWAS

From: Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance

Variant Locus Variant Position Type Known Phenotype Association [13] Lineage Observed Phenotype Association (p-value) PhyC
rrs 1,473,246 inter STM, AG 2 CAP(2 × 10−31), KAN(1.1 × 10−37) 8
rrs 1,473,246 inter STM, AG 4 KAN(6.7 × 10−31) 15
rrs 1,473,246 inter STM, AG 2 + 4 AMK(2.4 × 10−39), CAP(3.9 × 10−48), KAN(6.5 × 10−69), XDRvMDR(5.3 × 10−27) 18
katG 2,155,168 NS INH 2 XDR(2.1 × 10− 42) 5
katG 2,155,168 NS INH 4 INH(6.1 × 10−65), MDR(6 × 10−45), XDR(1.5 × 10−29) 9
katG 2,155,168 NS INH 2 + 4 INH(4.4 × 10–56), MDR(7.4 × 10−25) 9
Rv0197 232,574 NS Novel 4 XDR(9.5 × 10−62) 0
Rv0197 232,574 NS Novel 2 + 4 XDR(232,574;3.8 × 10−51) 0
rpoB 761,155 NS RMP 2 XDR(3.5 × 10− 25) 4
rpoB 761,155 NS RMP 4 MDR(1.2 × 10−27), PZA(1.9 × 10−28), RMP(2.6 × 10− 42, 7.1 × 10−31, 761,139;3.4 × 10−23), XDR(3.8 × 10− 57) 7
rpoB 761,139 NS RMP 4 RMP(3.4 × 10−23) 3
rpoB 761,155 NS RMP 2 + 4 MDR(5 × 10−23), PZA(6 × 10−26), RMP(2 × 10−38), XDR(1.3 × 10− 27) 7
rpoB 761,139 NS RMP 2 + 4 PZA(4 × 10− 23), RMP(2.2 × 10−29), 7
recF 4047 S Novel 4 XDR(1.2 × 10− 52) 0
recF 4047 S Novel 2 + 4 XDR(8.6 × 10−41) 0
Rv1482c-fabG1 1,673,425 inter INH, ETH 4 INH(1.1 × 10−36) 3
Rv1482c-fabG1 1,673,425 inter INH, ETH 2 + 4 INH(1.1 × 10− 35) 14
rpsL 781,687 NS STM 2 STM(3 × 10−27) 4
rpsL 781,687 NS STM 2 + 4 STM(6.3 × 10−28) 6
argJ 1,867,614 S Novel 2 + 4 XDR(6.9 × 10−26) 0
gyrA 7570 NS FQ 4 XDR(8.6 × 10−23) 24
gyrA 7582 NS FQ 2 + 4 CIP(1.3 × 10−24), FQ(4.6 × 10−22) 44
  1. (p-values < 1E-22) NS = non-synonymous, S = synonymous, inter = intergenic region. Novel associations are given in bold. ‘PhyC’ column refers to the number of associations identified through PhyC analysis for the locus and lineage in question; AMK = Amikacin-resistance, AG = Aminoglycoside-resistance, CAP = Capreomycin-resistance, CIP = Ciprofloxacin-resistance, EMB = Ethambutol-resistance, ETH = Ethionamide-resistance, FQ = Fluoroquinolone-resistance, INH = Isoniazid-resistance, KAN = Kanamycin-resistance, MDR = Multidrug-resistant, OFL = Ofloxacin-resistance, PAN = pan-susceptible (no known drug-resistance), PZA = Pyrazinamide-resistance, RMP = Rifampicin-resistance, STM = Streptomycin-resistance, XDR = Extensively drug-resistant