TABLE V.

Probability of a real gene given an increase in significance (at least one 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 20Mb wide linkage peak P(H1)=0.025
GRRhom	GRRhet	P(H1|i,s)	P(H1|s)	PC (%)	P(H1|i,s)	P(H1|s)	PC (%)
1.5	1.5	0.14744	0.01379	969	0.727	0.177	310
1.5	1.0	0.00234	0.00198	18	0.035	0.030	18
1.5	1.25	0.03341	0.00699	378	0.347	0.098	255
2.0	2.0	0.41587	0.01959	2023	0.916	0.235	290
2.0	1.0	0.00730	0.00310	135	0.102	0.046	122
2.0	1.5	0.24350	0.01706	1327	0.832	0.211	295
3.0	3.0	0.48161	0.02039	2262	0.935	0.243	285
3.0	1.0	0.02359	0.00574	311	0.271	0.082	232
3.0	2.0	0.42342	0.01994	2023	0.919	0.238	285

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).