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. Author manuscript; available in PMC: 2015 Apr 7.
Published in final edited form as: Neuron. 2014 May 21;82(4):773–780. doi: 10.1016/j.neuron.2014.04.043

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.