Table 2.
Numbers of Transmitted and Untransmitted Alleles in Cases and Controls
Cohort | Transmitted | Untransmitted | T:U ratio | RTR (Case/Control) | p Value |
---|---|---|---|---|---|
Loss-of-Function Variants (Nonsense, Canonical Splice Site, and Frameshift Variants) | |||||
Private (hit once in parental population) | |||||
Cases | 1,682 | 1,945 | 0.86 | 1.49 | 0.0086 |
Controls | 159 | 274 | 0.58 | - | - |
Rare (nonprivate and frequency ≤ 0.05) | |||||
Cases | 5,948 | 7,168 | 0.83 | 1.31 | 0.0051 |
Controls | 902 | 1,425 | 0.63 | - | - |
Common (frequency > 0.05) | |||||
Cases | 26,350 | 27,724 | 0.95 | 1.08 | 0.037 |
Controls | 3,732 | 4,231 | 0.88 | - | - |
MODERATE-Effect Variants | |||||
Private | |||||
Cases | 26,558 | 25,250 | 1.05 | 0.99 | 0.607 |
Controls | 2,286 | 2,155 | 1.06 | - | - |
Rare | |||||
Cases | 146,052 | 158,361 | 0.92 | 1.10 | 0.022 |
Controls | 20,603 | 24,663 | 0.84 | - | - |
Common | |||||
Cases | 920,641 | 958,085 | 0.96 | 1.02 | 0.023 |
Controls | 127,551 | 135,706 | 0.94 | - | - |
LOW-Effect Variants | |||||
Private | |||||
Cases | 16,622 | 15,249 | 1.09 | 0.99 | 0.361 |
Controls | 1,464 | 1,335 | 1.10 | - | - |
Rare | |||||
Cases | 129,196 | 136,780 | 0.94 | 1.05 | 0.176 |
Controls | 17,610 | 19,562 | 0.90 | - | - |
Common | |||||
Cases | 1,148,993 | 1,177,446 | 0.98 | 1.01 | 0.058 |
Controls | 159,769 | 165,749 | 0.96 | - | - |
T:U ratio, transmitted to untransmitted ratio; RTR, relative transmission ratio (T:U ratio in cases/T:U ratio in controls). Detailed definition for MODERATE-and LOW-effect variants are described in the Supplemental Experimental Procedures. p values were calculated by one-sided permutations.