Table 3 Allele frequencies and case–control association analysis of 49 variants in 37 selected candidate genes
Gene | HGVS | Number of Patients | Allele Frequency (%) | Odds Ratio (95% CI) | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
Cases | Controls | Our Study vs | dbGaP phs000822.v1.p1 vs | |||||||
Our Study | dbGaP phs000822.v1.p1 | gnomAD (EAS) | SG10K_Health | gnomAD (EAS) | SG10K_Health | gnomAD (EAS) | SG10K_Health | |||
KMT2C | NM_170606.3:c.C2689T | 7 | 1.21 | 0.11 | 0.02 | – | 72.88 (16.54–434.73***) p = 1.9e−08 | – | 6.40 (0.12–79.79) p = 0.21 | – |
KMT2C | NM_170606.3:c.C2710T | 28 | 4.83 | 2.37 | 0.20 | – | 25.25 (14.43–44.09***) p = 1.6e−23 | – | 12.07 (6.60–21.73***) p = 4.6e−14 | – |
RNF43 | NM_001305545.1:c.C311T | 7 | 1.21 | 17.81 | 0.06 | 1.64 | 19.99 (6.54–56.74***) p = 2.7e−06 | 0.73 (0.29–1.54) p = 0.58 | 351.43 (191.23–741.46***) p = 4.5e−206 | 12.99 (10.55–15.96***) p = 7e−100 |
RNF43 | NM_001305545.1:c.G1589C | 3 | 0.52 | – | 0.00 | 1.01 | Inf (14.25–Inf***) p = 5.3e−05 | 0.51 (0.10–1.52) p = 0.48 | – | – |
RNF43 | NM_001305545.1:c.G647A | 11 | 1.90 | 8.76 | 0.03 | 1.33 | 71.69 (21.14–308.16***) p = 2.3e−12 | 1.43 (0.70–2.63) p = 0.36 | 355.70 (132.69–1317.96***) p = 3.3e−93 | 7.11 (5.40–9.29***) p = 1.1e−34 |
GPRIN2 | NM_014696.4:c.C983G | 17 | 2.93 | 20.92 | 0.10 | – | 30.03 (14.69–60.72***) p = 5.4e−16 | – | 263.13 (165.05–446.60***) p = 1e−243 | – |
MUC4 | NM_018406.7:c.G8461A | 16 | 3.60 | – | 0.00 | 0.04 | Inf (112.61–Inf***) p = 1.7e−26 | 104.51 (37.90–359.64***) p = 3e−23 | – | – |
H3F3A | NM_002107.6:c.C344G | 14 | 2.41 | 0.65 | 0.71 | – | 3.47 (1.82–6.11***) p = 0.00027 | – | 0.91 (0.33–2.06) p = 1 | – |
AKAP9 | NM_005751.4:c.T3430C | 11 | 1.90 | – | 0.43 | 1.62 | 4.52 (2.16–8.56***) p = 0.00016 | 1.18 (0.58–2.15) p = 0.68 | – | – |
TPTE2 | NM_199254.2:c.483delT | 10 | 1.77 | – | 0.08 | 0.04 | 23.88 (9.05–62.22***) p = 7.5e−09 | 48.20 (15.81–161.69***) p = 1.1e−10 | – | – |
HLA-B | NM_005514.8:c.A161G | 9 | 1.55 | 5.71 | 0.30 | 1.05 | 5.32 (2.30–10.92***) p = 0.00023 | 1.49 (0.62–3.24) p = 0.37 | 20.43 (13.65–30.55***) p = 1e−40 | 5.71 (3.56–9.33***) p = 2.9e−14 |
NRG1 | NM_013962.2:c.G172A | 9 | 1.55 | 33.33 | 0.06 | 3.40 | 25.36 (3.50–1107.34***) p = 9.4e−05 | 0.45 (0.20–0.86*) p = 0.02 | 705.43 (31.16–4.50e15***) p = 4.6e−05 | 14.20 (1.28–99.40*) p = 0.02 |
ELN | NM_001278913.2:c.G1498C | 8 | 1.38 | 8.91 | 0.03 | 1.25 | 55.70 (16.02–218.37***) p = 3.1e−09 | 1.10 (0.47–2.23) p = 0.76 | 387.67 (159.04–1222.15***) p = 7.6e−106 | 7.72 (5.88–10.05***) p = 2.1e−38 |
ERBB3 | NM_001982.3:c.A3355T | 8 | 1.38 | 11.51 | 0.11 | 1.60 | 13.27 (5.06–31.33***) p = 3.4e−06 | 0.86 (0.37–1.73) p = 0.9 | 123.49 (76.10–207.51***) p = 3.4e−123 | 7.98 (6.26–10.10***) p = 1.3e−49 |
HLA-A | NM_001242758.1:c.268delA | 8 | 1.38 | 0.21 | 0.04 | 0.94 | 34.34 (11.19–105.30***) p = 2.4e–08 | 1.47 (0.61–3.07) p = 0.36 | 5.28 (0.55–26.52) p = 0.087 | 0.23 (0.03–0.85*) p = 0.028 |
HLA-A | NM_001242758.1:c.C791T | 8 | 1.38 | – | 0.13 | 1.95 | 10.66 (4.15–24.39***) p = 1.2e−05 | 0.70 (0.30–1.42) p = 0.53 | – | – |
HLA-A | NM_001242758.1:c.G1055T | 8 | 1.38 | 0.11 | 0.14 | 3.46 | 10.30 (4.03–23.44***) p = 1.5e−05 | 0.39 (0.17–0.79**) p = 0.0075 | 0.79 (0.02–4.81) p = 1 | 0.03 (0.00–0.17***) p = 3.5e−12 |
HLA-A | NM_001242758.1:c.G565A | 8 | 1.38 | 0.11 | 0.15 | 7.04 | 9.50 (3.74–21.43***) p = 2.2e−05 | 0.18 (0.08–0.37***) p = 1.9e−08 | 0.73 (0.02–4.41) p = 1 | 0.01 (0.00–0.08***) p = 3.1e−24 |
HLA-A | NM_001242758.1:c.G684A | 8 | 1.38 | – | 0.06 | 1.31 | 25.19 (8.76–69.03***) p = 1.2e−07 | 1.06 (0.45–2.15) p = 0.89 | – | – |
HLA-A | NM_001242758.1:c.T547C | 3 | 0.52 | 0.11 | 0.02 | 0.21 | 34.04 (4.55–254.09***) p = 0.00076 | 2.51 (0.39–12.93) p = 0.26 | 7.03 (0.13–87.78) p = 0.2 | 0.52 (0.01–4.64) p = 1 |
ROS1 | NM_002944.2:c.C3326T | 8 | 1.55 | 7.83 | 0.27 | 1.64 | 5.81 (2.51–11.93***) p = 0.00013 | 0.94 (0.43–1.83) p = 1 | 31.29 (21.55–45.61***) p = 2.4e−64 | 5.09 (3.85–6.65***) p = 9.5e−25 |
HLA-DRB1 | NM_002124.3:c.118_122del | 7 | 4.09 | 0.15 | 0.07 | 0.24 | 59.12 (19.62–213.94***) p = 1.5e−13 | 17.57 (7.84–38.33***) p = 5.7e−10 | 2.03 (0.04–18.14) p = 0.48 | 0.60 (0.01–3.82) p = 1 |
HLA-DRB1 | NM_002124.3:c.126_127insTTAAGTTT | 7 | 2.83 | – | 0.05 | 0.13 | 54.73 (16.83–230.03***) p = 1.4e−12 | 22.29 (9.16–55.30***) p = 1.9e−10 | – | – |
HLA-DRB1 | NM_002124.3:c.C301T | 4 | 0.99 | 0.00 | 0.00 | 0.06 | Inf (12.54–Inf***) p = 5e−06 | 16.51 (3.79–72.00***) p = 0.00023 | 0.00 (0.00–Inf) p = 1 | 0.00 (0.00–14.41) p = 1 |
NTRK1 | NM_001012331.1:c.C1792T | 6 | 1.03 | 6.01 | 0.03 | 1.16 | 34.72 (9.25–130.03***) p = 1.8e−06 | 0.89 (0.32–1.98) p = 1 | 212.31 (91.71–602.69***) p = 1.3e−68 | 5.43 (3.94–7.38***) p = 1.5e−20 |
NTRK1 | NM_001012331.1:c.G1820T | 5 | 0.86 | 6.02 | 0.03 | 1.13 | 28.88 (6.95–113.95***) p = 2.2e−05 | 0.76 (0.24–1.81) p = 0.76 | 212.73 (91.75–603.88***) p = 1.3e−68 | 5.58 (4.05–7.59***) p = 5.2e−21 |
CHIC2 | NM_012110.4:c.G36T | 5 | 0.86 | – | 0.03 | 0.37 | 28.44 (6.85–112.29***) p = 2.2e−05 | 2.33 (0.73–5.74) p = 0.11 | – | – |
CNTRL | NM_001330762.2:c.G1009A | 5 | 0.86 | 5.52 | 0.02 | 0.82 | 57.55 (11.17–368.15***) p = 3.4e−06 | 1.05 (0.34–2.53) p = 0.86 | 385.11 (124.23–2015.72***) p = 2.9e−65 | 7.08 (5.02–9.85***) p = 4.2e−23 |
ISX | NM_001303508.2:c.G248A | 5 | 0.86 | 5.15 | 0.04 | 1.41 | 21.66 (5.56–75.41***) p = 4.9e−05 | 0.61 (0.20–1.45) p = 0.46 | 135.30 (63.17–330.64***) p = 1.9e−56 | 3.81 (2.72–5.24***) p = 6.8e−13 |
MYO5A | NM_000259.3:c.A3960T | 5 | 0.86 | – | 0.01 | 0.19 | 84.79 (13.85–894.94***) p = 1.8e−06 | 4.64 (1.42–11.92*) p = 0.01 | – | – |
TET2 | NM_001127208.2:c.C1088T | 5 | 1.03 | 4.94 | 0.04 | 0.82 | 29.69 (8.22–103.70***) p = 2.9e−06 | 1.26 (0.45–2.82) p = 0.57 | 147.52 (65.91–392.69***) p = 1.2e−54 | 6.26 (4.38–8.81***) p = 3e−19 |
BRD7 | NM_001173984.3:c.A44C | 4 | 0.80 | – | – | – | – | – | – | – |
CBFA2T3 | NM_005187.6:c.G308C | 4 | 0.69 | 9.55 | 0.01 | 0.53 | 69.07 (9.88–783.26***) p = 2.5e−05 | 1.31 (0.35–3.49) p = 0.62 | 1036.93 (280.67–8192.00***) p = 6.9e−118 | 19.97 (14.70–27.09***) p = 1.8e−66 |
DCC | NM_005215.4:c.A3578G | 4 | 0.69 | – | 0.10 | 0.65 | 7.08 (1.74–21.57**) p = 0.0065 | 1.06 (0.28–2.80) p = 0.85 | – | – |
PTPRB | NM_001206971.3:c.C3412T | 4 | 0.69 | 2.15 | 0.01 | 0.44 | 67.61 (9.67–732.95***) p = 2.6e−05 | 1.58 (0.42–4.23) p = 0.42 | 214.17 (51.95–1908.91***) p = 5.6e−25 | 5.01 (2.90–8.29***) p = 6.8e−08 |
RNF213 | NM_001256071.3:c.C12847A | 3 | 0.52 | 6.55 | 0.00 | 0.39 | Inf (14.24–Inf***) p = 5.3e−05 | 1.32 (0.27–4.04) p = 0.58 | Inf (366.99–Inf***) p = 4.5e−83 | 17.80 (12.36–25.52***) p = 3.4e−44 |
RNF213 | NM_001256071.3:c.C13945G | 4 | 0.69 | 8.37 | 0.00 | 0.53 | Inf (22.77–Inf***) p = 2.7e−06 | 1.31 (0.35–3.48) p = 0.62 | Inf (481.56–Inf***) p = 2.7e−106 | 17.22 (12.54–23.59***) p = 2.5e−55 |
CLIP1 | NM_001247997.1:c.C80T | 3 | 0.52 | 1.29 | 0.00 | 0.04 | Inf (14.10–Inf***) p = 5.3e−05 | 14.11 (2.35–62.12**) p = 0.0043 | Inf (59.62–Inf***) p = 1.1e−16 | 35.48 (12.85–106.41***) p = 5.3e−12 |
CUX1 | NM_001202543.2:c.C3317T | 3 | 0.52 | – | 0.01 | 0.09 | 51.86 (5.92–612.07***) p = 0.00038 | 5.75 (1.08–19.95*) p = 0.03 | – | – |
FBLN2 | NM_001998.3:c.G2569T | 3 | 0.52 | 0.22 | 0.00 | 1.34 | Inf (12.79–Inf***) p = 6.5e−05 | 0.38 (0.08–1.14) p = 0.13 | Inf (3.62–Inf**) p = 0.0031 | 0.16 (0.02–0.58**) p = 0.0011 |
GNAS | NM_016592.4:c.A266G | 3 | 0.52 | – | 0.00 | 0.03 | Inf (13.11–Inf***) p = 6.2e−05 | 16.06 (2.59–75.51**) p = 0.0034 | – | – |
MAF | NM_001031804.3:c.G655T | 3 | 4.81 | – | 0.00 | – | Inf (13.95–Inf***) p = 3.4e−06 | – | – | – |
MGA | NM_001080541.2:c.C1883A | 3 | 0.52 | 1.54 | 0.00 | 0.08 | Inf (12.57–Inf***) p = 6.7e−05 | 6.19 (1.15–21.71*) p = 0.026 | Inf (64.84–Inf***) p = 7.9e−19 | 18.55 (8.36–40.72***) p = 1.6e−11 |
MLLT1 | NM_005934.4:c.G889A | 3 | 0.52 | 3.00 | 0.03 | 0.20 | 17.85 (2.77–91.79**) p = 0.0029 | 2.54 (0.48–8.66) p = 0.19 | 106.35 (40.38–354.94***) p = 2.6e−31 | 15.11 (8.10–28.74***) p = 1.1e−17 |
NBEA | NM_015678.4:c.C2317A | 3 | 0.99 | – | – | – | – | – | – | – |
NUP214 | NM_001318324.2:c.A2263G | 3 | 0.52 | 1.29 | 0.02 | 1.01 | 34.26 (4.58–255.75***) p = 0.00076 | 0.51 (0.10–1.51) p = 0.48 | 85.96 (23.16–475.65***) p = 4e−14 | 1.28 (0.65–2.29) p = 0.46 |
PDGFRB | NM_001355016.2:c.G1261A | 3 | 0.52 | 3.54 | 0.00 | 0.18 | Inf (14.24–Inf***) p = 5.3e−05 | 2.84 (0.56–9.04) p = 0.14 | Inf (186.85–Inf***) p = 5.1e−45 | 20.03 (12.01–33.36***) p = 7.7e−26 |
RABEP1 | NM_001291581.2:c.G1755C | 3 | 0.52 | 4.51 | 0.00 | 0.36 | Inf (13.90–Inf***) p = 5.3e−05 | 1.46 (0.29–4.47) p = 0.56 | Inf (236.36–Inf***) p = 8.9e−57 | 13.22 (8.71–19.86***) p = 2.5e−27 |
ZNF479 | NM_001370129.1:c.T1421C | 3 | 0.52 | 2.58 | 0.00 | 0.54 | Inf (13.94–Inf***) p = 5.3e−05 | 0.96 (0.19–2.90) p = 1 | Inf (128.88–Inf***) p = 1.2e−32 | 4.89 (2.98–7.73***) p = 5.3e−09 |