Table 4.
Summary of GWAS hits in leprosy phenotypes
| Referencesa | Population sample | Locus, candidate gene(s)b | Study statistical metrics/notesc,d |
|---|---|---|---|
| Zhang et al. (2009) | Chinese GWAS: 706 cases and 1225 controls. Rep: 2164 cases and 4373 controls (Chinese), 304 cases and 709 controls (Chinese), 786 cases and 873 controls (Chinese) | HLA-DR–DQ | rs602875, OR = 0.67 (0.62–0.72), p = 5.35 × 10−27 |
| RIPK2 | rs42490, OR = 0.76 (0.71–0.81), p = 1.38 × 10−16 | ||
| TNFSF15 | rs6478108, OR = 1.37 (1.28–1.46), p = 3.39 × 10−21 | ||
| LRRK2 | rs1873613, OR = 0.86 (0.80–0.92), p = 5.10 × 10−5 | ||
| CCDC122 | rs3088362, OR = 1.52 (1.41–1.63), p = 1.36 × 10−31 | ||
| LACC1 (C13orf31) | rs3764147, OR = 1.68 (1.57–1.80), p = 3.72 × 10−54 | ||
| NOD2 | rs9302752, OR = 1.59 (1.49–1.71), p = 3.77 × 10−40 | ||
| Zhang et al. (2011) | Chinese GWAS: 706 cases and 5581 controls. Rep: 2307 cases and 4585 controls (Chinese), 273 cases and 214 controls (Chinese), 721 cases and 500 controls (Chinese) | 1p31.3, IL23R | rs3762318, OR = 0.69 (0.62–0.77), p = 3.27 × 10−11 |
| 6q24.3, RAB32 | rs2275606, OR = 1.30 (1.21–1.39), p = 3.94 × 10−14 | ||
| Liu et al. (2015) | Chinese GWAS (I): 706 cases and 5587 controls. Chinese GWAS (II): 842 cases and 925 controls. Rep I: 2761 cases and 3038 controls (Chinese). Rep II: 4004 cases and 6467 controls (Chinese) | 1q32.3, BATF3 | rs2221593, OR = 1.15, p = 3.09 × 10−8 |
| 5p14.3, CDH18 | rs73058713, OR = 1.19, p = 9.54 × 10−9 | ||
| 9q32, DEC1 | rs10817758, OR = 1.13, p = 1.15 × 10−8 | ||
| 10q21.3, EGR2 | rs58600253, OR = 1.22, p = 3.02 × 10−12 | ||
| 11q13.1, CCDC88B | rs663743, OR = 1.24, p = 8.84 × 10−14 | ||
| 16p13.13, CIITA and SOCS1 | rs77061563, OR = 0.84, p = 6.23 × 10−15 | ||
| Wang et al. (2016) | Chinese GWAS (I): 706 cases and 1223 controls. Chinese GWAS (II): 840 cases and 924 controls. Chinese GWAS (III): 1197 cases and 1426 controls. Rep I: 1516 cases and 1512 controls. Rep II: 3897 cases and 10525 controls (Chinese) | 3p25.2, SYN2 | rs6807915, OR = 0.89, p = 1.94 × 10−8 |
| 7p14.3, BBS9 | rs4720118, OR = 1.16, p = 3.85 × 10−10 | ||
| 8p23.1, CTSB | rs55894533, OR = 1.15, p = 5.07 × 10−11 | ||
| 8q24.11, MED30 | rs10100465, OR = 0.85, p = 2.85 × 10−11 | ||
| Liu et al. (2017) | Chinese GWAS of protein-coding variants: 1648 cases and 2318 controls. Rep I: 3169 patients and 9814 controls (Chinese). Rep II: 2231 patients and 2266 controls (Chinese) | IL23R | rs76418789 (G149R), OR = 1.36 (1.24–1.49), p = 1.03 × 10−10 |
| FLG | rs146466242 (K4022*), OR = 1.45 (1.31–1.61), p* = 3.39 × 10−12 | ||
| NCKIPSD | rs145562243 (R176Q), OR = 4.35 (2.58–7.35), p = 1.44 × 10−8 (GWAS + Rep I). Meta-analysis p = 1.71 × 10−9 | ||
| CARD9 | rs149308743 (R494H), OR = 4.75 (2.87–7.86), p = 4.99 × 10−10 (GWAS + Rep I). Meta-analysis p = 2.09 × 10−8 | ||
| SLC29A3 | rs780668 (S158F), OR = 1.14 (1.09–1.19), p = 2.17 × 10−9 | ||
| IL27 | rs181206 (L119P), OR = 0.83 (0.78–0.89), p = 1.08 × 10−7 | ||
| TYK2 | rs55882956 (R703W), OR = 1.30 (1.17–1.45), p = 1.04 × 10−6 | ||
| Fava et al. (2017a) | Vietnamese GWAS in T1R: 221 families with 229 leprosy T1R-affected offspring and 209 families with 229 leprosy T1R-free offspring. Rep: 253 T1R cases and 563 T1R-free controls (Vietnamese). Validation: 471 T1R cases and 446 T1R-free controls (Brazilians) | 10p21.2, LOC105378318/ENSG00000235140 | T1R: rs1875147, OR = 1.54 (1.32–1.80), p = 4.5 × 10−8 |
OR odds ratio; Rep replication; T1R type 1 reaction
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 when available
dResults from meta-analysis or combined analysis with all population samples tested in the study are shown when available