TABLE VIII.

Probability of a real gene given no-change/decrease in significance (any order of magnitude) of an associated 5-SNP haplotype after fine mapping, for a disease allele frequency of 0.2

Genetic model (H1)		Ten SNPs somewhere in the genome P(H1)=0.00167			One SNP somewhere under a 20Mb wide linkage peak P(H1)=0.025			One SNP immediately under the 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	0.00910	0.02190	−58	0.124	0.256	−52	0.917	0.964	−4.9
1.5	1.0	0.00237	0.00242	−2	0.035	0.036	−2	0.741	0.745	−0.5
1.5	1.25	0.00564	0.00889	−37	0.08	0.121	−34	0.872	0.915	−4.7
2.0	2.0	0.00906	0.03346	−73	0.123	0.347	−64	0.917	0.977	−6.1
2.0	1.0	0.00339	0.00399	−15	0.05	0.058	−14	0.803	0.828	−3.0
2.0	1.5	0.01073	0.02799	−62	0.143	0.307	−53	0.929	0.972	−4.4
3.0	3.0	0.00683	0.03458	−80	0.096	0.355	−73	0.892	0.977	−8.7
3.0	1.0	0.00526	0.00770	−32	0.075	0.107	−30	0.864	0.903	−4.3
3.0	2.0	0.00930	0.03432	−73	0.126	0.353	−64	0.919	0.977	−6.0

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).