Table 1. Odds ratio of functional classes of DNMs in coding region.
| Group | Trios | VS Control | Total DNM | De novo SNVs | De novo InDels | Extreme mutations | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
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| Total SNVs | Damaging SNVs | Tolerant missense | Synonymous | Total | Frameshift | Non- frameshift | |||||
| ASD | 1038 | DNMs | 1040 | 967 | 329 | 394 | 244 | 73 | 63 | 10 | 364 |
| OR | 1.36 | 1.31 | 2.03 | 1.18 | 1.21 | 2.66 | 3.31 | 1.18 | 1.80 | ||
| 95% Cl | 1.24-1.50 | 1.19-1.45 | 1.67-2.48 | 1.02-1.38 | 1.00-1.47 | 1.68-4.33 | 1.94-5.94 | 0.42-3.45 | 1.51-2.16 | ||
| P-value | 1.34E-10 | 3.27E-08 | 6.69E-14 | 0.027 | 0.055 | 7.12E-06 | 1.76E-06 | 0.82 | 1.49E-11 | ||
| Pcorrected | 5.36E-10 | 1.31E-07 | 2.67E-13 | 0.11 | 0.22 | 2.85E-05 | 7.02E-06 | 1 | 5.96E-11 | ||
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| EE | 291 | DNMs | 327 | 303 | 124 | 123 | 56 | 24 | 21 | 3 | 144 |
| OR | 1.52 | 1.47 | 2.73 | 1.32 | 0.99 | 3.11 | 3.94 | 1.26 | 2.54 | ||
| 95% Cl | 1.34-1.74 | 1.28-1.68 | 2.14-3.49 | 1.06-1.63 | 0.72-1.34 | 1.71-5.64 | 2.00-7.84 | 0.22-5.27 | 2.03-3.18 | ||
| P-value | 7.11E-10 | 5.30E-08 | 1.13E-15 | 0.01 | 1 | 0.000121 | 2.65E-05 | 0.722003 | 4.74E-16 | ||
| Pcorrected | 2.84E-09 | 2.12E-07 | 4.54E-15 | 0.042 | 1 | 0.00048 | 0.0001 | 1 | 1.89E-15 | ||
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| ID | 220 | DNMs | 259 | 229 | 108 | 78 | 43 | 30 | 26 | 4 | 130 |
| OR | 1.60 | 1.47 | 3.15 | 1.10 | 1.00 | 5.15 | 6.45 | 2.23 | 3.03 | ||
| 95% Cl | 1.38-1.85 | 1.26-1.71 | 2.44-4.06 | 0.85-1.42 | 0.70-1.41 | 2.94-9.07 | 3.40-12.48 | 0.49-8.33 | 2.41-3.82 | ||
| P-value | 3.81E-10 | 1.16E-06 | 4.97E-18 | 0.433678 | 1 | 3.19E-09 | 2.12E-09 | 0.25 | 3.24E-20 | ||
| Pcorrected | 1.52E-09 | 4.64E-06 | 1.99E-17 | 1 | 1 | 1.28E-08 | 8.49E-09 | 1 | 1.30E-19 | ||
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| SCZ | 1024 | DNMs | 986 | 917 | 275 | 416 | 226 | 69 | 54 | 15 | 299 |
| OR | 1.31 | 1.26 | 1.72 | 1.27 | 1.13 | 2.54 | 2.88 | 1.79 | 1.50 | ||
| 95% Cl | 1.19-1.44 | 1.14-1.40 | 1.41-2.11 | 1.09-1.47 | 0.93-1.38 | 1.60-4.16 | 1.66-5.21 | 0.72-4.90 | 1.25-1.81 | ||
| P-value | 3.29E-08 | 3.14E-06 | 4.00E-08 | 0.0016 | 0.20 | 2.09E-05 | 4.53E-05 | 0.21 | 1.10E-05 | ||
| Pcorrected | 1.31E-07 | 1.26E-05 | 1.60E-07 | 0.0066 | 0.81232 | 8.36E-05 | 0.00018 | 0.85 | 4.40E-05 | ||
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| Control | 982 | DNMs | 722 | 696 | 153 | 315 | 191 | 26 | 18 | 8 | 191 |
In total, we collected 3,334 exonic DNMs from 3,555 trios, including 1040 DNMs from1038 ASD trios, 327 DNMs from 291 EE trios, 259 DNMs from 220 ID trios, 986 DNMs from 1,024 SCZ trios and 722 DNMs from 982 trios of control. In each group, exonic DNMs were classified into different functional classes. Compared to control group, P-values were calculated on the basis of two-sample Poisson rate test (Supplementary Materials and Methods). Bonferroni correction was used to counteract the problem of multiple comparisons. We referred to LoF/deleterious SNVs as damaging SNVs. The rare LoF/deleterious SNVs and rare frame-shift indels, which were regarded as as extreme mutations. P values below 0.005 are highlighted in bold.