Integrated Bayesian analysis of rare exonic variants to identify risk genes for schizophrenia and neurodevelopmental disorders

Table 1 Estimated parameters of proportions of risk genes (pi) and mean relative risk (meanRR) for DN and CC SCZ data and four other NDDs: ID, EPI, ASD and DD

Parameter	Estimated	Lower credible	Upper credible
	mode	interval boundary	interval boundary
SCZ_pi (%)	8.01	4.59	12.9
SCZ_meanRR_silentFCPk_denovo	1.22	1.00	2.16
SCZ_meanRR_MiD_denovo	1.44	1.00	3.16
SCZ_meanRR_LoF_denovo	12.25	4.79	22.22
SCZ_meanRR_MiD+LoF_CCpop1	2.09	1.04	3.54
SCZ_meanRR_MiD+LoF_CCpop2	2.44	1.05	5.73
SCZ_meanRR_MiD+LoF_CCpop3	1.04	1	1.19
ASD_pi (%)	4.44	3.15	5.94
ASD_meanRR_MiDdenovo	3.71	2.06	8.71
ASD_meanRR_LoFdenovo	24.56	14.27	37.44
ASD_meanRR_LoFcc	4.04	2.08	8.24
ID_pi (%)	2.53	1.89	3.43
ID_meanRR_MiDdenovo	29.82	18.86	46.1
ID_meanRR_LoFdenovo	105.45	73.27	143.29
DD_pi (%)	2.84	2.29	3.45
DD_meanRR_MiDdenovo	23.42	13.97	33.97
DD_meanRR_LoFdenovo	88.32	67.54	115.09
EPI_pi (%)	1.14	0.52	2.1
EPI_meanRR_MiDdenovo	72.2	35.39	128.46
EPI_meanRR_LoFdenovo	89.71	45.31	169.43

These results were obtained by sampling three MCMC chains (20,000 times for each chain). These results are for three categories: loss of function (LoF) variants/mutations, missense damaging (MiD) variants/mutations, and silent within frontal cortex-derived DHS peaks (silentFCPk) variants.
ASD autism spectrum disorders, CC case–control, DD developmental disorder, DN de novo, EPI epilepsy, ID intellectual disability, LoF loss of function, MCMC Markov chain Monte Carlo, MiD missense damaging, NDD neurodevelopmental disorder, SCZ schizophrenia, silentFCPk silent within frontal cortex-derived DHS peaks