Table 3.

Mutation detection experiment with patient heterozygous for a variant not found in k control individuals (2k chromosomes)

A
Variant-specific θ for coding regions
Genome-wide average θ
Base conserved in mice
Base conserved in fugu
k
P-value if L = 10 kb
Max L (kb) for P < 0.05
P-value if L = 10 kb
Max L (kb) for P < 0.05
P-value if L = 10 kb
Max L (kb) for P < 0.05
10 0.44 0.7 0.27 1.4 0.23 1.8
20 0.28 1.3 0.16 2.7 0.13 3.4
50 0.14 3.2 0.07 6.5 0.06 8.2
100 0.08 6.4 0.04 12.9 0.03 16.3
200
0.04
12.8
0.02
25.8
0.02
32.4
B
C
k
Constant population
Expanding population
L (kb)
Minimum k
10 0.40 0.44 1 15
20 0.24 0.32 5 80
50 0.13 0.25 10 155
100 0.07 0.19 20 315
200
0.04
0.16
50
780

[i] A P-values, obtained using equation 2, for 10 kb of sequence examined and maximum length of sequence (kb) that may be examined to keep P-value under 0.05.

[ii] B P-values, obtained using simulation, for 10 kb of sequence examined for a population of constant size 10,000 and for a population that has expanded from 10,000 to 6 × 109 over the last 500 generations.

[iii] C Minimum number of control individuals (k), obtained using equation 2, that must be examined and found free of the variant of interest to obtain P-value close to 0.05, as a function of length of sequence examined (L). Genome-wide average θ of 8.25 × 10-4 was used.