Table 1.
GCOD counts of significantly overtransmitted oligogenic pairs and genes, categorized by membership to the list of 744 curated human and mouse CHD genes (Richter et al. 2020)
| Tier | Disease status | No. of GCOD oligogenic pairs at FDR ≤ 0.01 | No. of unique genes in oligogenic pairs (no. of known CHD genes) | No. of (% of cohort) that carry at least one pair | No. of single TDT genes at raw P ≤ 0.01 (no. of known CHD genes) |
|---|---|---|---|---|---|
| Strict | Proband | 71 | 132 (23) | 134 (4.0%) | 31 (6) |
| Pseudosibling | 19 | 35 (3) | 42 (1.2%) | 4 (0) | |
| Base | Proband | 59 | 109 (20) | 110 (3.3%) | 31 (6) |
| Pseudosibling | 22 | 40 (3) | 46 (1.4%) | 3 (0) | |
| CADD-based | Proband | 94 | 165 (26) | 163 (4.8%) | 47 (5) |
| Pseudosibling | 67 | 124 (12) | 123 (3.6%) | 4 (0) | |
| Composite | Proband | 160 | 270 (41) | 266 (7.9%) | 77 (9) |
| Pseudosibling | 94 | 165 (15) | 159 (4.7%) | 8 (0) |
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Note that GCOD results use a cutoff of FDR ≤ 0.01; because no genes reached significance at that level using the rare variant TDT analysis, we report results at the level of unadjusted P-value ≤ 0.01 (McNemar's test).
