Extended Data Table 5. Comparison of genes hit by de novo mutations between this study and other disease studies and control individuals.
Each set of columns gives the number of mutations (either nonsynonymous (NS) or loss-of-function (LoF)) and enrichment p-value (as calculated by dnenrich, see Supplementary Text) in the set of genes hit by de novos in the study listed in the corresponding row. For example, the first two rows detail the significance of the overlap of the mutations from other studies of disease hitting the genes hit by mutations in this study. Nominally significant p-values (<0.05) are marked in bold. Disease sets and functional classes are as listed in Table 2.
| Mutations (N) | Current study | SZ (Gulsuner)14 | SZ (Xu)13 | ASD6-9 | ID10,11 | Controls7-10,13-14 | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NS (482) | LoF (64) | NS (68) | LoF (12) | NS (137) | LoF (20) | NS (789) | LoF (134) | NS (141) | LoF (34) | NS (434) | LoF (49) | ||||||||||||||
| Gene set | p | # mut | p | # mut | p | # mut | p | # mut | p | # mut | p | # mut | p | # mut | p | # mut | p | # mut | p | # mut | p | # mut | p | # mut | |
| Current study | NS (464) | - | 0.16 | 6 | 0.03 | 3 | 0.85 | 4 | 0.29 | 1 | 0.016 | 55 | 0.0066 | 15 | 0.044 | 13 | 0.26 | 3 | 0.61 | 21 | 0.72 | 2 | |||
| LoF (63) | 0.014 | 3 | 0.088 | 1 | 1 | 0 | 1 | 0 | 0.0023 | 14 | 0.00012 | 7 | 0.019 | 4 | 0.002 | 3 | 1 | 0 | 1 | 0 | |||||
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| SZ (Gulsuner)14 | NS (67) | 0.22 | 6 | 0.021 | 3 | - | 0.31 | 2 | 0.16 | 1 | 0.47 | 7 | 0.11 | 3 | 0.67 | 1 | 1 | 0 | 0.48 | 4 | 1 | 0 | |||
| LoF (12) | 0.051 | 3 | 0.11 | 1 | 0.21 | 1 | 1 | 0 | 0.15 | 3 | 0.21 | 1 | 0.21 | 1 | 1 | 0 | 1 | 0 | 1 | 0 | |||||
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| SZ (Xu)13 | NS (136) | 0.79 | 5 | 1 | 0 | 0.25 | 2 | 0.15 | 1 | - | 0.083 | 16 | 1 | 0 | 0.13 | 4 | 0.012 | 3 | 0.081 | 10 | 0.49 | 1 | |||
| LoF (20) | 0.24 | 2 | 1 | 0 | 0.13 | 1 | 1 | 0 | 1 | 0 | 1 | 0 | 0.0026 | 3 | 4.00E-05 | 3 | 0.21 | 2 | 1 | 0 | |||||
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| ASD6-9 | NS (743) | 0.14 | 45 | 0.023 | 9 | 0.49 | 6 | 0.13 | 3 | 0.32 | 14 | 1 | 0 | - | 6.00E-05 | 24 | 2.00E-05 | 12 | 0.26 | 38 | 0.64 | 4 | |||
| LoF (128) | 0.015 | 11 | 0.00072 | 4 | 0.11 | 2 | 0.17 | 1 | 1 | 0 | 1 | 0 | 2.00E-05 | 8 | 2.00E-05 | 5 | 0.36 | 8 | 0.52 | 1 | |||||
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| ID10,11 | NS (132) | 0.032 | 9 | 0.031 | 1 | 0.56 | 1 | 0.14 | 1 | 0.14 | 2 | 0.01 | 1 | 2.00E-05 | 24 | 2.00E-05 | 7 | - | 0.37 | 7 | 0.46 | 1 | |||
| LoF (30) | 0.27 | 1 | 0.019 | 1 | 1 | 0 | 1 | 0 | 0.046 | 1 | 0.0062 | 1 | 2.00E-05 | 15 | 2.00E-05 | 5 | 1 | 0 | 1 | 0 | |||||
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| Controls7-10,13-14 | NS (424) | 0.59 | 21 | 1 | 0 | 0.41 | 4 | 1 | 0 | 0.15 | 9 | 0.26 | 2 | 0.062 | 41 | 0.31 | 8 | 0.48 | 7 | 1 | 0 | - | |||
| LoF (49) | 0.6 | 2 | 1 | 0 | 1 | 0 | 1 | 0 | 0.44 | 1 | 1 | 0 | 0.42 | 4 | 0.45 | 1 | 0.45 | 1 | 1 | 0 | |||||