Table 4.

GA analysis: chi-square test for detection of causal SNPs

Q1		Q2
Chromosome	p-value	Chromosome	p-value
1	6.2 × 10−2	2	3.4 × 10−1
4	0	3	0
5	0	6	0
6	9.3 × 10−2	7	2.8 × 10−3
13	0	8	0
14	0a	9	3.1 × 10−1
19	2.5 × 10−4	10	0
		12	5.2 × 10−2
		17	1.3 × 10−1

We report p-values resulting from a chi-square test for nonrandom association, across the 200 replicates of the GAW17 data, between those SNPs that were included in the best aggregation of SNPs found by our GA analysis and those that were actually causal (assessed by referencing the GAW17 answers). Analysis was performed after correction for population stratification using 10 PCs.

^a For the Q1–chromosome 14 combination, there was a significant tendency to miss the causal SNPs.