TABLE III.

Probability of a real gene given an increase in significance (any order of magnitude) of an associated single SNP following fine mapping, for a disease allele frequency of 0.2

Genetic model (H1)		Ten SNPs somewhere in the genome P(H1)=0.00166			One SNP somewhere under a 20-Mb wide linkage peak P(H1)=0.025			One SNP immediately under a linkage peak P(H1)=0.667
GRRhom	GRRhet	P(H1|i,s)	P(H1|s)	PC (%)	P(H1|I,s)	P(H1|s)	PC (%)	P(H1|i,s)	P(H1|s)	PC (%)
1.5	1.5	0.02662	0.01379	93	0.296	0.177	67	0.970	0.944	2.8
1.5	1.0	0.00234	0.00198	18	0.035	0.030	18	0.738	0.704	4.8
1.5	1.25	0.01161	0.00699	66	0.153	0.098	57	0.934	0.894	4.4
2.0	2.0	0.04306	0.01959	120	0.409	0.235	74	0.982	0.960	2.3
2.0	1.0	0.00444	0.00310	43	0.064	0.046	41	0.843	0.789	6.8
2.0	1.5	0.03469	0.01706	103	0.356	0.211	69	0.977	0.954	2.4
3.0	3.0	0.04460	0.02039	119	0.418	0.243	72	0.982	0.962	2.2
3.0	1.0	0.00905	0.00574	58	0.123	0.082	51	0.917	0.874	4.9
3.0	2.0	0.04233	0.01994	112	0.405	0.238	70	0.982	0.961	2.2

P(H₁) – prior probability of a genetic effect.

P(H₁|i,s) – posterior probability of a genetic effect given a significant primary analysis signal increasing in significance following fine-mapping.

P(H₁|s) – posterior probability of a genetic effect given a significant primary analysis signal.

PC (%) – proportional change in posterior probability of a genetic effect, given by 100[P(H₁|i, s)–P(H₁|s)]/P(H₁|s).