Table 7.
CHD-associated gene regions significantly enriched with large, rare CNVs
| Gains, % |
Losses, % |
Enriched For |
||||||
|---|---|---|---|---|---|---|---|---|
| Gene | CHD | CHOP | MFHS | CHD | CHOP | MFHS | Gains | Losses |
| PRKAB2 | 0.4 | 0.1 | 0.0 | 0.2 | 0.1 | 0.2 | √ | |
| FMO5 | 0.4 | 0.1 | 0.0 | 0.2 | 0.1 | 0.2 | √ | |
| CHD1L | 0.4 | 0.1 | 0.0 | 0.2 | 0.1 | 0.2 | √ | |
| BCL9 | 0.3 | 0.1 | 0.0 | 0.2 | 0.1 | 0.2 | √ | |
| ACP6 | 0.3 | 0.1 | 0.0 | 0.2 | 0.1 | 0.2 | √ | |
| GJA5 | 0.3 | 0.1 | 0.0 | 0.2 | 0.1 | 0.2 | √ | |
| FKBP6 | 0.3 | 0.1 | 0.3 | 0.3 | 0.0 | 0.0 | √ | |
| ELN | 0.0 | 0.0 | 0.0 | 0.3 | 0.0 | 0.0 | √ | |
| GTF2IRD1 | 0.0 | 0.0 | 0.0 | 0.3 | 0.0 | 0.0 | √ | |
| GATA4 | 0.1 | 0.0 | 0.0 | 0.3 | 0.0 | 0.0 | √ | |
| HRAS | 0.3 | 0.0 | 0.0 | 0.0 | 0.1 | 0.0 | √ | |
| GATA6 | 0.3 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | √ | |
| RUNX1 | 8.5 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | √ | |
| CRKL | 0.4 | 0.0 | 0.3 | 4.2 | 0.1 | 0.0 | √ | |
| TBX1 | 0.2 | 0.0 | 0.2 | 4.4 | 0.1 | 0.0 | √ | |
| ATRX | 0.2 | 0.0 | 0.0 | 1.9 | 0.0 | 0.0 | √ | |
| GPC3 | 0.2 | 0.0 | 0.0 | 1.9 | 0.0 | 0.0 | √ | |
| BCOR | 0.2 | 0.0 | 0.0 | 1.9 | 0.0 | 0.3 | √ | |
| ZIC3 | 0.2 | 0.1 | 0.0 | 1.9 | 0.0 | 0.0 | √ | |
| FLNA | 0.2 | 0.1 | 0.0 | 1.9 | 0.0 | 0.0 | √ | |
| MID1 | 0.2 | 0.0 | 0.3 | 2.1 | 0.0 | 0.3 | √ | |
The statistical test applied was the Barnard's exact test. Of our 100 candidate genes, 21 were found to be significantly enriched for CNVs (null hypothesis rejected P ≤ 0.05 in both cohorts: CHD vs. CHOP and CHD vs. MFHS, see boldface). We used the full cohorts for genes in autosomal chromosomes, and only the female portion for any genes on chromosomes (Chr.) X or Y. This leaves 322/880 for MFHS, 416/945 for CHD, and an estimated 1,013/2,026 for CHOP, usable for testing on the Chr. X genes.