Table 2.
Summary of GWAS hits in PTB
| Referencesa | Population sample | Locus, candidate gene(s)b | Study statistical metrics/notesc,d |
|---|---|---|---|
| Thye et al. (2010) | Ghanaian GWAS: 921 cases and 1740 controls. Gambian GWAS: 1316 cases and 1382 controls. Rep I: 1076 cases and 1611 controls (Ghanaian). Rep II: 150 cases and 2214 controls (Ghanaian), 236 cases 779 controls (Malawian) | 18q11.2 | rs4331426, OR = 1.19 (1.12–1.26), p = 6.8 × 10−9 |
| Thye et al. (2012) | Ghanaian GWAS: 1329 cases and 1847 controls. Rep I: 817 cases and 3805 controls (Ghanaian). Rep II: 1207 cases and 1349 controls (Gambian), 1025 cases and 983 controls (Indonesian), 4441 cases and 5874 controls (Russian) | 11p13, WT1 | rs2057178, OR = 0.77 (0.71–0.84), p = 2.63 × 10−9 (GWAS + Rep 1). Meta-analysis p = 2.57 × 10−11 |
| Png et al. 2012 | Indonesian GWAS: 108 cases and 115 controls. Rep I: 600 cases and 540 controls (Indonesian). Rep II: 1837 cases and 1779 controls (Russian) | TMEFF2 | rs10497744, OR = 0.87 (0.80–0.95), p = 0.0014 |
| EBF1 | rs10515787, OR = 0.79 (0.68–0.91), p = 0.001 | ||
| HAUS6 | rs10245298, OR = 1.23 (1.06–1.41), p = 0.005 | ||
| PENK | rs6985962, OR = 1.17 (1.05–1.31), p = 0.006 | ||
| TXNDC4 | rs1418267, OR = 1.13 (1.03–1.23), p = 0.007 | ||
| CCL17 | rs188872, OR = 0.87 (0.80–0.95), p = 0.002 | ||
| DYNLRB2 | rs4461087, OR = 1.18 (1.07–1.30), p = 0.001 | ||
| JAG1 | rs2273061, OR = 1.16 (1.07–1.26), p = 0.0004 | ||
| Mahasirimongkol et al. (2012) | Thai GWAS: 433 cases and 295 controls. Japanese GWAS: 188 cases and 934 controls. Rep: 369 cases and 439 controls (Thai), 112 cases and 1089 controls (Japanese) | 20q12, HSPEP1 and MAFB | TB cases with age-at-onset < 45 years: rs6071980, OR = 1.73 (1.42–2.11), p = 6.69 × 10−8 |
| Chimusa et al. (2014) | South African Colored GWAS: 642 cases and 91 controls | 20 loci | 24 SNPs in 20 loci with suggestive p-value (≤ 10−6), including 2 SNPs in WT1 [rs2057178, OR = 0.62 (0.50–0.75), p = 2.71 × 10−6] |
| Curtis et al. (2015) | Russian GWAS: 5530 cases and 5607 controls. Rep: 1085 cases and 2865 controls (Russian) | 8q24, ASAP1 | rs4733781, OR = 0.84 (0.80–0.88), p = 2.6 × 10−11 |
| Grant et al. (2016) | Family-based Moroccan GWAS: 252 parents and 306 offspring (239 affected and 67 unaffected). Rep: 317 cases and 657 controls (Morocco) | AGMO | TB cases with age-at-onset < 25 years: rs9169432, OR = 2.73 (1.78–4.18), p = 2.0 × 10−6 |
| WNT5A | rs358793, OR = 0.68 (0.57–0.82), p = 4.0 × 10−5 | ||
| FOXP1 | rs6786408, OR = 1.47 (1.23–1.79), p = 1.9 × 10−5 | ||
| PCDH10 | rs17590261, OR = 6.24 (2.38–16.33), p = 2.2 × 10−5 | ||
| Sveinbjornsson et al. (2016) | Icelanders GWAS: 3686 PTB cases, 8162 clinical TB cases, 14,723 Mtb-infected cases and > 277,643 controls. Rep: 5530 PTB cases and 5607 controls (Russian), 438 PTB cases and 1009 controls (Croatian) | 6p21, HLA-DQA1 and HLA-DRB1 | rs557011, OR = 1.18 (1.13–1.23), p = 2.0 × 10−15; rs9271378, OR = 0.85 (0.82–0.89), p = 3.2 × 10−15; rs9272785 (HLA-DQA1 p.Ala210Thr), OR = 1.18 (1.12–1.25), p = 1.9 × 10−9 |
| Sobota et al. (2016) | Ugandans and Tanzanians GWAS in HIV + individuals: 267 TB cases and 314 controls | 5q33.3, IL12B | rs4921437, OR = 0.37 (0.27–0.53), p = 2.11 × 10−8 |
| Omae et al. (2017) | Thai GWAS data set: 263 cases and 282 controls. Rep: 423 cases and 489 (Thai) | 1p13, CD53 and LRIF1 | TB cases with age-at-onset > 45 years and non-Beijing lineages of Mtb: rs1418425, OR = 1.74 (1.43–2.12), p = 2.54 × 10−8 |
GWAS genome-wide association study; HIV human immunodeficiency virus; Mtb Mycobacterium tuberculosis; OR Odds ratio; PTB Pulmonary tuberculosis; Rep replication; TB tuberculosis
aFollow-up association analysis in independent studies are not included in this table
bFor studies in which the population sample consists of an extension of a previous published GWAS, only the new findings from the extended population analysis are shown
cResults for the SNP with the strongest association, showing OR (95% confidence interval) and p value
dResults from meta-analysis or combined analysis with all population samples tested in the study are shown when available