Table 2. Burden analysis for (a) ‘rare and novel' CNVs and deletions; (b) duplications in independent cases compared with population controls.
| No. of CNVs | Average no. of CNVs per individual | Proportion of sample with one or more CNV | Average total length of CNVs spanned per individual (kb) | Average CNV size (kb) | Average no. of genes spanned by CNVs per individual | Proportion of CNVs containing at least one gene | Average no. of genes per total CNV (kb) | |
|---|---|---|---|---|---|---|---|---|
| Total burden | ||||||||
| All CNVs in independent cases vs controls | ||||||||
| Cases | 131 | 1.03 | 0.58 | 102.4 | 55.42 | 2 | 0.41 | 0.05 |
| Controls | 275 | 1.02 | 0.63 | 77.56 | 47.4 | 0.99 | 0.41 | 0.07 |
| Empirical P-value | — | 0.47 | 0.85 | 0.08 | 0.13 | 0.08 | 0.54 | 0.59 |
| Deletions | ||||||||
| Deletions in independent cases vs controls | ||||||||
| Cases | 61 | 0.48 | 0.38 | 42.47 | 33.31 | 0.46 | 0.24 | 0.07 |
| Controls | 177 | 0.66 | 0.46 | 62.6 | 46.36 | 0.52 | 0.26 | 0.05 |
| Empirical P-value | — | 0.98 | 0.96 | 0.98 | 0.95 | 0.7 | 0.74 | 0.21 |
| Duplications | ||||||||
| Independent cases vs controls | ||||||||
| Cases | 67 | 0.53 | 0.29 | 142 | 88.12 | 1.5 | 0.22 | 0.03 |
| Controls | 97 | 0.36 | 0.3 | 65.95 | 53.72 | 0.45 | 0.18 | 0.11 |
| Empirical P-value | — | 0.14 | 0.59 | 0.004 | 0.006 | 0.06 | 0.2 | 0.86 |
| All SLIC family members and population controls | ||||||||
| Family members | 98 | 92.23 | 76.44 | |||||
| Controls | 97 | 65.95 | 53.72 | |||||
| Empirical P-value | 0.03 | 0.02 | ||||||
| Affected SLIC family members and population controls | ||||||||
| Family members | 22 | 95.71 | 89.66 | |||||
| Controls | 97 | 65.95 | 53.72 | |||||
| Empirical P-value | 0.12 | 0.08 | ||||||
| Unaffected SLIC family members and population controls | ||||||||
| Family members | 18 | 92.32 | 67.32 | |||||
| Controls | 97 | 65.95 | 53.72 | |||||
| Empirical P-value | 0.15 | 0.22 | ||||||
Abbreviations: CNV, copy number variant; SLIC, specific language impairment Consortium.
As no significant differences were found for the total burden and deletion burden of ‘rare and novel' CNVs, only independent cases vs controls are shown in this table.
Those metrics which differed significantly between independent cases and population controls were then examined further in affected first-degree relatives, unaffected first-degree relatives and all first-degree relatives compared with population controls. Categories in bold had a P-value <0.05. Although the affected- and unaffected-only family members did not reach significance, similar trends were seen within these smaller groups.