TABLE IV.

Probability of a real gene given an increase in significance (any order of magnitude) of an associated Five-SNP haplotype 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			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	0.03823	0.02190	75	0.379	0.256	48	0.979	0.964	1.6
1.5	1.0	0.00248	0.00242	3	0.037	0.036	3	0.749	0.745	0.6
1.5	1.25	0.01314	0.00889	48	0.170	0.121	40	0.941	0.915	2.8
2.0	2.0	0.06376	0.03346	91	0.512	0.347	47	0.988	0.977	1.2
2.0	1.0	0.00478	0.00399	20	0.069	0.058	19	0.852	0.828	2.9
2.0	1.5	0.04979	0.02799	78	0.446	0.307	45	0.984	0.972	1.3
3.0	3.0	0.06879	0.03458	99	0.532	0.355	50	0.989	0.977	1.2
3.0	1.0	0.01089	0.00770	41	0.145	0.107	36	0.930	0.903	2.9
3.0	2.0	0.06535	0.03432	90	0.518	0.353	47	0.988	0.977	1.1

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).