Table 2. HLA stratified Transmission Disequilibrium Test (TDT).
| High Risk | Low risk | All | |||||||||||||||||||||||||
| Chr | SNP | gene(s) | BP | A1 | A2 | T | U | T/U | chisq | p-value | T | U | T/U | chisq | p-value | weighted chisq | T | U | T/U | chisq | P-value | ||||||
| 1 | rs12144971 | DUSP10 | 220099108 | C | T | 26 | 35 | 0.74 | 1.33 | 2.49E-01 | 87 | 28 | 3.11 | 30.27 | 3.76E-08 | 20.24 | 116 | 64 | 1.81 | 15.02 | 1.06E-04 | ||||||
| 1 | rs4240931 | DUSP10 | 220105678 | T | C | 26 | 35 | 0.74 | 1.33 | 2.49E-01 | 87 | 28 | 3.11 | 30.27 | 3.76E-08 | 20.24 | 116 | 64 | 1.81 | 15.02 | 1.06E-04 | ||||||
| 10 | rs1247697 | SVIL | 29901347 | C | A | 41 | 35 | 1.17 | 0.47 | 4.91E-01 | 22 | 69 | 0.32 | 24.27 | 8.35E-07 | 13.44 | 63 | 104 | 0.61 | 10.07 | 1.51E-03 | ||||||
| 1 | rs4846734 | DUSP10 | 220139621 | G | A | 20 | 25 | 0.80 | 0.55 | 4.56E-01 | 53 | 15 | 3.53 | 21.24 | 4.06E-06 | 13.00 | 76 | 41 | 1.85 | 10.47 | 1.21E-03 | ||||||
| 10 | rs7097380 | SORCS1 | 108671659 | A | G | 46 | 34 | 1.35 | 1.8 | 1.80E-01 | 72 | 26 | 2.77 | 21.59 | 3.37E-06 | 12.70 | 118 | 60 | 1.97 | 18.90 | 1.38E-05 | ||||||
| 2 | rs6755308 | PRKCE | 46083771 | A | G | 11 | 33 | 0.33 | 11 | 9.11E-04 | 32 | 8 | 4.00 | 14.40 | 1.48E-04 | 12.62 | 43 | 41 | 1.05 | 0.05 | 8.27E-01 | ||||||
| 1 | rs11811613 | DUSP10 | 220122026 | G | A | 19 | 25 | 0.76 | 0.82 | 3.66E-01 | 54 | 17 | 3.18 | 19.28 | 1.13E-05 | 12.22 | 76 | 43 | 1.77 | 9.15 | 2.49E-03 | ||||||
| 2 | rs13017044 | PRKCE | 46086853 | A | G | 12 | 39 | 0.31 | 14.29 | 1.56E-04 | 43 | 18 | 2.39 | 10.25 | 1.37E-03 | 12.09 | 55 | 57 | 0.96 | 0.04 | 8.50E-01 | ||||||
| 10 | rs11193120 | SORCS1 | 108678768 | G | A | 50 | 35 | 1.43 | 2.64 | 1.04E-01 | 70 | 26 | 2.69 | 20.17 | 7.10E-06 | 11.94 | 120 | 61 | 1.97 | 19.23 | 1.16E-05 | ||||||
| 1 | rs11102146 | KCNA3 | 111007559 | C | T | 13 | 17 | 0.76 | 0.53 | 4.65E-01 | 48 | 15 | 3.20 | 17.29 | 3.22E-05 | 11.88 | 61 | 34 | 1.79 | 7.67 | 5.60E-03 | ||||||
| 10 | rs4748417 | STAM TMEM236 | 17819812 | T | C | 2 | 0 | NA | 2 | 1.57E-01 | 18 | 2 | 9.00 | 12.80 | 3.47E-04 | 11.82 | 20 | 2 | 10.0 | 14.73 | 1.24E-04 | ||||||
| 2 | rs4972810 | DLX1 DLX2 PDK1 MAP1D ITGA6 | 172926135 | A | G | 15 | 11 | 1.36 | 0.61 | 4.33E-01 | 41 | 11 | 3.73 | 17.31 | 3.18E-05 | 11.74 | 56 | 22 | 2.55 | 14.82 | 1.18E-04 | ||||||
| 3 | rs1871352 | STAC | 36329541 | A | C | 15 | 25 | 0.60 | 2.5 | 1.14E-01 | 12 | 44 | 0.27 | 18.29 | 1.90E-05 | 11.71 | 27 | 69 | 0.39 | 18.38 | 1.81E-05 | ||||||
| 3 | rs1871350 | STAC | 36348769 | C | T | 15 | 25 | 0.60 | 2.5 | 1.14E-01 | 12 | 44 | 0.27 | 18.29 | 1.90E-05 | 11.71 | 27 | 69 | 0.39 | 18.38 | 1.81E-05 | ||||||
| 10 | rs10884387 | SORCS1 | 108682142 | T | C | 43 | 33 | 1.30 | 1.32 | 2.51E-01 | 71 | 27 | 2.63 | 19.76 | 8.80E-06 | 11.70 | 114 | 60 | 1.90 | 16.76 | 4.25E-05 | ||||||
| 3 | rs2046000 | STAC | 36327368 | A | C | 15 | 27 | 0.56 | 3.43 | 6.41E-02 | 13 | 45 | 0.29 | 17.66 | 2.65E-05 | 11.68 | 28 | 72 | 0.39 | 19.36 | 1.08E-05 | ||||||
| 1 | rs12734338 | PPP1R12B SYT2 UBE2T | 200736346 | C | T | 20 | 36 | 0.56 | 4.57 | 3.25E-02 | 18 | 53 | 0.34 | 17.25 | 3.27E-05 | 11.66 | 39 | 90 | 0.43 | 20.16 | 7.11E-06 | ||||||
| 22 | rs1296826 | BID BCL2L13 SLC25A18 ATP6V1E1 | 16459518 | C | T | 3 | 9 | 0.33 | 3 | 8.33E-02 | 3 | 23 | 0.13 | 15.38 | 8.77E-05 | 11.47 | 6 | 32 | 0.19 | 17.79 | 2.47E-05 | ||||||
| 4 | rs7687176 | INTS12 GSTCD | 106746555 | T | C | 10 | 7 | 1.43 | 0.53 | 4.67E-01 | 2 | 24 | 0.08 | 18.62 | 1.60E-05 | 11.47 | 12 | 31 | 0.39 | 8.40 | 3.76E-03 | ||||||
| 2 | rs4972809 | DLX1 DLX2 PDK1 MAP1D ITGA6 | 172925337 | A | G | 16 | 12 | 1.33 | 0.57 | 4.50E-01 | 41 | 11 | 3.73 | 17.31 | 3.18E-05 | 11.45 | 57 | 23 | 2.48 | 14.45 | 1.44E-04 | ||||||
| 6 | rs13207543 | ELOVL4 SH3BGRL2 TTK | 80592601 | A | C | 13 | 26 | 0.50 | 4.33 | 3.74E-02 | 52 | 19 | 2.74 | 15.34 | 8.99E-05 | 11.44 | 65 | 45 | 1.44 | 3.64 | 5.65E-02 | ||||||
| 4 | rs1032355 | RG9MTD2 C4orf17 MTTP | 100758919 | C | T | 9 | 42 | 0.21 | 21.35 | 3.82E-06 | 24 | 37 | 0.65 | 2.77 | 9.60E-02 | 11.23 | 33 | 81 | 0.41 | 20.21 | 6.94E-06 | ||||||
| 5 | rs11952677 | SCAMP1 LHFPL2 | 77823690 | G | A | 27 | 34 | 0.79 | 0.80 | 3.70E-01 | 55 | 17 | 3.24 | 20.06 | 7.52E-06 | 11.23 | 84 | 51 | 1.65 | 8.07 | 4.51E-03 | ||||||
| 1 | rs12743521 | DUSP10 | 220167571 | A | G | 21 | 24 | 0.88 | 0.2 | 6.55E-01 | 50 | 15 | 3.33 | 18.85 | 1.42E-05 | 11.22 | 74 | 40 | 1.85 | 10.14 | 1.45E-03 | ||||||
| 12 | rs11068315 | FBXW8 HRK TESC RNFT2 | 115994935 | T | C | 8 | 6 | 1.33 | 0.28 | 5.93E-01 | 4 | 26 | 0.15 | 16.13 | 5.90E-05 | 11.09 | 12 | 32 | 0.38 | 9.09 | 2.57E-03 | ||||||
| 6 | rs7745052 | FBXL4 C6orf168 USP45 COQ3 POU3F2 SFRS18 | 99747331 | A | G | 54 | 17 | 3.18 | 19.28 | 1.13E-05 | 32 | 25 | 1.28 | 0.86 | 3.54E-01 | 11.08 | 86 | 42 | 2.05 | 15.12 | 1.01E-04 | ||||||
| 12 | rs17245501 | PPFIA2 | 80260470 | C | T | 17 | 18 | 0.94 | 0.028 | 8.66E-01 | 45 | 13 | 3.46 | 17.66 | 2.65E-05 | 11.02 | 62 | 31 | 2.00 | 10.33 | 1.31E-03 | ||||||
| 1 | rs7544501 | DUSP10 | 220168985 | T | C | 21 | 24 | 0.88 | 0.2 | 6.55E-01 | 51 | 16 | 3.19 | 18.28 | 1.90E-05 | 11.02 | 75 | 41 | 1.83 | 9.97 | 1.60E-03 | ||||||
| 1 | rs785627 | LPHN2 | 82521165 | T | C | 30 | 17 | 1.77 | 3.60 | 5.79E-02 | 25 | 61 | 0.41 | 15.07 | 1.04E-04 | 11.02 | 56 | 79 | 0.71 | 3.92 | 4.78E-02 | ||||||
| 8 | rs720131 | RAD21 | 117985196 | A | G | 35 | 40 | 0.88 | 0.33 | 5.64E-01 | 79 | 34 | 2.32 | 17.92 | 2.30E-05 | 10.90 | 115 | 75 | 1.53 | 8.42 | 3.71E-03 | ||||||
| 12 | rs11104365 | MGAT4C | 86164650 | C | T | 41 | 57 | 0.72 | 2.61 | 1.06E-01 | 34 | 79 | 0.43 | 17.92 | 2.30E-05 | 10.81 | 77 | 136 | 0.57 | 16.34 | 5.29E-05 | ||||||
| 14 | rs7144018 | NAT12 EXOC5 C14orf108 | 56676820 | C | T | 29 | 3 | 9.67 | 21.12 | 4.30E-06 | 14 | 20 | 0.70 | 1.06 | 3.04E-01 | 10.79 | 45 | 23 | 1.96 | 7.12 | 7.63E-03 | ||||||
The top 32 associated SNPs from the results of the HLA stratified analysis. Surrounding genes are defined by either Grail (www.broadinstitute.org/mpg/grail/) or the Genome Browser (http://genome.ucsc.edu/). The low risk group consists of 115 trios and the high risk group of 88 trios. Genotypes were imputed if any of the posterior probabilities were >0.95.
Chisq – the value of the TDT test statistic for the transmission counts.
Weighted Chisq – based on the transmission counts of the low and high-risk groups. This value is used for ranking the results.
T and U – the number of heterozygous parents who transmit the alleles A1 and A2, respectively. T/U – transmission odds based on the expected transmission counts.