Datasets:

lighteternal
/

psychiatric-mr-evidence-atlas

exposure large_stringclasses 7 values	outcome large_stringclasses 11 values	n_instruments int64 3 76	n_instruments_after_presso int64 3 74	f_stat_mean float64 34.4 43.3	presso_global_pval float64 0 1	presso_outliers_removed int64 0 26	steiger_correct_direction bool 1 class	steiger_z2_ratio float64 6.69 155	rucker_recommended large_stringclasses 2 values	fdr_qval float64 0 0.93 ⌀	overall_pass bool 2 classes	method large_stringclasses 3 values	beta float64 -1.12 0.76	se float64 0.01 0.74	pval float64 0 0.99	ci_lower float64 -3.85 0.54	ci_upper float64 -0.82 4.52	heterogeneity_q float64 0 203 ⌀	heterogeneity_pval float64 0 1 ⌀	egger_intercept float64 -0.03 0.01 ⌀	egger_intercept_pval float64 0 0.98 ⌀
adhd	anxiety	24	20	38.87	0	4	true	7.615	IVW	0	true	IVW	-0.160618	0.022196	0	-0.204123	-0.117113	26.884666	0.107368	null	null
adhd	anxiety	24	20	38.87	0	4	true	7.615	IVW	null	false	MR-Egger	-0.16217	0.021803	0.000001	-0.207976	-0.116365	null	null	-0.001825	0.202491
adhd	anxiety	24	20	38.87	0	4	true	7.615	IVW	null	false	Weighted-Median	-0.182992	0.042128	0.000014	-0.265564	-0.100421	null	null	null	null
adhd	autism	24	20	38.87	0	4	true	12.272	IVW	0.167315	false	IVW	-0.165987	0.091714	0.070321	-0.345745	0.013772	54.721634	0.000026	null	null
adhd	autism	24	20	38.87	0	4	true	12.272	IVW	null	false	MR-Egger	-0.167903	0.093924	0.090683	-0.36523	0.029425	null	null	0.002381	0.691487
adhd	autism	24	20	38.87	0	4	true	12.272	IVW	null	false	Weighted-Median	-0.257668	0.107863	0.016901	-0.46908	-0.046257	null	null	null	null
adhd	bipolar	24	21	38.87	0	3	true	36.267	IVW	0.000007	true	IVW	0.202846	0.042031	0.000001	0.120465	0.285227	29.445183	0.079356	null	null
adhd	bipolar	24	21	38.87	0	3	true	36.267	IVW	null	false	MR-Egger	0.204235	0.043333	0.000151	0.113538	0.294933	null	null	0.000772	0.786419
adhd	bipolar	24	21	38.87	0	3	true	36.267	IVW	null	false	Weighted-Median	0.176104	0.093305	0.059107	-0.006775	0.358982	null	null	null	null
adhd	bpd	22	17	37.24	0	5	true	11.781	MR-Egger	0.389242	false	IVW	0.173467	0.150227	0.248212	-0.120977	0.467911	68.584907	0	null	null
adhd	bpd	22	17	37.24	0	5	true	11.781	MR-Egger	null	false	MR-Egger	0.186917	0.149324	0.229826	-0.131358	0.505193	null	null	0.010141	0.272782
adhd	bpd	22	17	37.24	0	5	true	11.781	MR-Egger	null	false	Weighted-Median	0.241177	0.279873	0.388833	-0.307375	0.789729	null	null	null	null
adhd	eating_disorders	24	23	38.87	0.0005	1	true	64.682	IVW	0.177762	false	IVW	-0.186143	0.106278	0.079864	-0.394447	0.022161	23.635721	0.36661	null	null
adhd	eating_disorders	24	23	38.87	0.0005	1	true	64.682	IVW	null	false	MR-Egger	-0.197803	0.105849	0.075675	-0.417928	0.022323	null	null	-0.007971	0.253942
adhd	eating_disorders	24	23	38.87	0.0005	1	true	64.682	IVW	null	false	Weighted-Median	-0.195401	0.094488	0.03864	-0.380596	-0.010205	null	null	null	null
adhd	mdd	24	20	38.87	0	4	true	14.847	IVW	0.000007	true	IVW	-0.192378	0.039391	0.000001	-0.269584	-0.115172	30.829798	0.042143	null	null
adhd	mdd	24	20	38.87	0	4	true	14.847	IVW	null	false	MR-Egger	-0.191491	0.041026	0.000192	-0.277684	-0.105299	null	null	0.000346	0.89832
adhd	mdd	24	20	38.87	0	4	true	14.847	IVW	null	false	Weighted-Median	-0.237716	0.054512	0.000013	-0.34456	-0.130872	null	null	null	null
adhd	ocd	24	23	38.87	0.0001	1	true	28.85	IVW	0.367793	false	IVW	-0.064453	0.052991	0.223874	-0.168315	0.03941	36.278411	0.028344	null	null
adhd	ocd	24	23	38.87	0.0001	1	true	28.85	IVW	null	false	MR-Egger	-0.056685	0.052415	0.291752	-0.165688	0.052318	null	null	0.004523	0.197776
adhd	ocd	24	23	38.87	0.0001	1	true	28.85	IVW	null	false	Weighted-Median	-0.021113	0.092902	0.820222	-0.203201	0.160975	null	null	null	null
adhd	ptsd	24	23	38.87	0	1	true	12.775	IVW	0.122507	false	IVW	-0.195433	0.099587	0.049713	-0.390623	-0.000242	60.148895	0.000021	null	null
adhd	ptsd	24	23	38.87	0	1	true	12.775	IVW	null	false	MR-Egger	-0.18826	0.101709	0.078291	-0.399775	0.023255	null	null	-0.004215	0.546808
adhd	ptsd	24	23	38.87	0	1	true	12.775	IVW	null	false	Weighted-Median	-0.333746	0.208195	0.108924	-0.741807	0.074315	null	null	null	null
adhd	schizophrenia	24	21	38.87	0	3	true	11.687	IVW	0.001185	true	IVW	-0.238954	0.065973	0.000292	-0.368261	-0.109646	55.954922	0.00003	null	null
adhd	schizophrenia	24	21	38.87	0	3	true	11.687	IVW	null	false	MR-Egger	-0.242143	0.067502	0.001965	-0.383427	-0.100859	null	null	0.00223	0.612132
adhd	schizophrenia	24	21	38.87	0	3	true	11.687	IVW	null	false	Weighted-Median	-0.250238	0.120383	0.037646	-0.486188	-0.014287	null	null	null	null
anxiety	adhd	60	56	37.76	0	4	true	23.795	IVW	0	true	IVW	-0.452731	0.06015	0	-0.570626	-0.334837	114.859509	0.000004	null	null
anxiety	adhd	60	56	37.76	0	4	true	23.795	IVW	null	false	MR-Egger	-0.441368	0.063092	0	-0.567859	-0.314876	null	null	-0.001356	0.529652
anxiety	adhd	60	56	37.76	0	4	true	23.795	IVW	null	false	Weighted-Median	-0.360966	0.067178	0	-0.492636	-0.229297	null	null	null	null
anxiety	autism	62	62	37.64	0	0	true	31.807	MR-Egger	0.888249	false	IVW	0.015004	0.086633	0.862503	-0.154797	0.184804	134.227666	0	null	null
anxiety	autism	62	62	37.64	0	0	true	31.807	MR-Egger	null	false	MR-Egger	-0.022769	0.086955	0.794334	-0.196704	0.151166	null	null	0.005789	0.057389
anxiety	autism	62	62	37.64	0	0	true	31.807	MR-Egger	null	false	Weighted-Median	0.057465	0.135936	0.672486	-0.208969	0.323899	null	null	null	null
anxiety	bipolar	61	52	37.64	0	9	true	10.866	MR-Egger	0	true	IVW	-0.65503	0.060094	0	-0.772814	-0.537247	94.546239	0.000203	null	null
anxiety	bipolar	61	52	37.64	0	9	true	10.866	MR-Egger	null	false	MR-Egger	-0.627964	0.062109	0	-0.752715	-0.503214	null	null	-0.003046	0.1428
anxiety	bipolar	61	52	37.64	0	9	true	10.866	MR-Egger	null	false	Weighted-Median	-0.597659	0.083012	0	-0.760362	-0.434955	null	null	null	null
anxiety	bpd	54	47	37.27	0	7	true	9.364	IVW	0	true	IVW	-0.894725	0.140734	0	-1.170563	-0.618888	143.411924	0	null	null
anxiety	bpd	54	47	37.27	0	7	true	9.364	IVW	null	false	MR-Egger	-0.906891	0.142593	0	-1.194088	-0.619694	null	null	0.003402	0.488677
anxiety	bpd	54	47	37.27	0	7	true	9.364	IVW	null	false	Weighted-Median	-1.120803	0.155983	0	-1.42653	-0.815077	null	null	null	null
anxiety	eating_disorders	61	60	37.64	0	1	true	48.607	IVW	0.313433	false	IVW	0.210962	0.156319	0.177158	-0.095424	0.517348	88.702982	0.007442	null	null
anxiety	eating_disorders	61	60	37.64	0	1	true	48.607	IVW	null	false	MR-Egger	0.199478	0.161436	0.22157	-0.123671	0.522626	null	null	0.001766	0.746443
anxiety	eating_disorders	61	60	37.64	0	1	true	48.607	IVW	null	false	Weighted-Median	0.009953	0.242926	0.967319	-0.466182	0.486088	null	null	null	null
anxiety	mdd	62	47	37.64	0	15	true	8.334	IVW	0.037586	true	IVW	0.217092	0.086401	0.011984	0.047747	0.386437	203.0682	0	null	null
anxiety	mdd	62	47	37.64	0	15	true	8.334	IVW	null	false	MR-Egger	0.202495	0.094376	0.037335	0.012412	0.392578	null	null	0.001255	0.687907
anxiety	mdd	62	47	37.64	0	15	true	8.334	IVW	null	false	Weighted-Median	0.259269	0.137951	0.060185	-0.011114	0.529652	null	null	null	null
anxiety	ocd	60	55	37.76	0	5	true	15.95	IVW	0.001959	true	IVW	-0.33468	0.096307	0.000511	-0.523442	-0.145918	185.647658	0	null	null
anxiety	ocd	60	55	37.76	0	5	true	15.95	IVW	null	false	MR-Egger	-0.312297	0.099724	0.002829	-0.512317	-0.112277	null	null	-0.002961	0.37793
anxiety	ocd	60	55	37.76	0	5	true	15.95	IVW	null	false	Weighted-Median	-0.473216	0.138514	0.000635	-0.744704	-0.201729	null	null	null	null
anxiety	ptsd	62	60	37.64	0	2	true	12.243	IVW	0.047591	true	IVW	0.318986	0.133944	0.017243	0.056456	0.581517	183.174606	0	null	null
anxiety	ptsd	62	60	37.64	0	2	true	12.243	IVW	null	false	MR-Egger	0.342107	0.1378	0.015957	0.06627	0.617943	null	null	-0.00351	0.448888
anxiety	ptsd	62	60	37.64	0	2	true	12.243	IVW	null	false	Weighted-Median	0.582182	0.306856	0.057795	-0.019256	1.183621	null	null	null	null
anxiety	schizophrenia	61	42	37.77	0	19	true	30.938	IVW	0.280376	false	IVW	0.130307	0.089694	0.146283	-0.045494	0.306108	101.682017	0	null	null
anxiety	schizophrenia	61	42	37.77	0	19	true	30.938	IVW	null	false	MR-Egger	0.146172	0.100028	0.151739	-0.055991	0.348336	null	null	-0.00125	0.709506
anxiety	schizophrenia	61	42	37.77	0	19	true	30.938	IVW	null	false	Weighted-Median	0.169752	0.16499	0.303545	-0.153629	0.493132	null	null	null	null
anxiety	substance_use	4	4	38.13	0.9145	0	true	36.935	IVW	0.034382	true	IVW	0.487973	0.190607	0.010464	0.114384	0.861562	0.51995	0.914487	null	null
anxiety	substance_use	4	4	38.13	0.9145	0	true	36.935	IVW	null	false	MR-Egger	0.081877	0.364995	0.843337	-1.48857	1.652324	null	null	-0.017572	0.373295
anxiety	substance_use	4	4	38.13	0.9145	0	true	36.935	IVW	null	false	Weighted-Median	0.463029	0.16401	0.004755	0.141569	0.784489	null	null	null	null
bipolar	adhd	42	39	40.48	0	3	true	39.977	IVW	0.461019	false	IVW	-0.032902	0.035123	0.348881	-0.101744	0.03594	75.781753	0.00026	null	null
bipolar	adhd	42	39	40.48	0	3	true	39.977	IVW	null	false	MR-Egger	-0.038575	0.036635	0.299197	-0.112805	0.035655	null	null	-0.001521	0.548163
bipolar	adhd	42	39	40.48	0	3	true	39.977	IVW	null	false	Weighted-Median	-0.015969	0.053981	0.767365	-0.121772	0.089834	null	null	null	null
bipolar	anxiety	44	36	40.1	0	8	true	43.265	IVW	0.000013	true	IVW	-0.11235	0.023577	0.000002	-0.158561	-0.066139	101.751082	0	null	null
bipolar	anxiety	44	36	40.1	0	8	true	43.265	IVW	null	false	MR-Egger	-0.102528	0.025127	0.000257	-0.153592	-0.051464	null	null	0.001834	0.276851
bipolar	anxiety	44	36	40.1	0	8	true	43.265	IVW	null	false	Weighted-Median	-0.075509	0.047347	0.110753	-0.168308	0.01729	null	null	null	null
bipolar	autism	44	42	40.1	0	2	true	24.32	IVW	0.506047	false	IVW	-0.044549	0.053313	0.403371	-0.149044	0.059945	90.850911	0.000012	null	null
bipolar	autism	44	42	40.1	0	2	true	24.32	IVW	null	false	MR-Egger	-0.051695	0.056027	0.361704	-0.164931	0.06154	null	null	-0.001748	0.647801
bipolar	autism	44	42	40.1	0	2	true	24.32	IVW	null	false	Weighted-Median	-0.059619	0.100034	0.551186	-0.255685	0.136448	null	null	null	null
bipolar	bpd	37	33	41.02	0	4	true	19.947	IVW	0	true	IVW	0.40248	0.079348	0	0.246958	0.558001	76.504229	0.000016	null	null
bipolar	bpd	37	33	41.02	0	4	true	19.947	IVW	null	false	MR-Egger	0.401625	0.090767	0.000111	0.216505	0.586745	null	null	-0.000128	0.983784
bipolar	bpd	37	33	41.02	0	4	true	19.947	IVW	null	false	Weighted-Median	0.387304	0.101064	0.000127	0.189218	0.58539	null	null	null	null
bipolar	eating_disorders	44	43	40.1	0.0012	1	true	47.632	IVW	0.482383	false	IVW	0.082382	0.093353	0.377517	-0.10059	0.265355	65.246691	0.012277	null	null
bipolar	eating_disorders	44	43	40.1	0.0012	1	true	47.632	IVW	null	false	MR-Egger	0.034951	0.098313	0.72403	-0.163596	0.233498	null	null	-0.00924	0.168699
bipolar	eating_disorders	44	43	40.1	0.0012	1	true	47.632	IVW	null	false	Weighted-Median	0.148088	0.170001	0.3837	-0.185115	0.481291	null	null	null	null
bipolar	mdd	44	39	40.1	0	5	true	14.17	IVW	0.24754	false	IVW	-0.059106	0.038218	0.121976	-0.134014	0.015802	104.362189	0	null	null
bipolar	mdd	44	39	40.1	0	5	true	14.17	IVW	null	false	MR-Egger	-0.064142	0.042096	0.136081	-0.149436	0.021152	null	null	-0.00083	0.763333
bipolar	mdd	44	39	40.1	0	5	true	14.17	IVW	null	false	Weighted-Median	-0.11679	0.083437	0.161595	-0.280327	0.046748	null	null	null	null
bipolar	ocd	42	39	40.48	0	3	true	27.318	IVW	0.046983	true	IVW	0.119254	0.049665	0.016342	0.021911	0.216597	100.077666	0	null	null
bipolar	ocd	42	39	40.48	0	3	true	27.318	IVW	null	false	MR-Egger	0.126048	0.053916	0.02491	0.016804	0.235292	null	null	0.001249	0.730068
bipolar	ocd	42	39	40.48	0	3	true	27.318	IVW	null	false	Weighted-Median	0.127368	0.076147	0.094393	-0.02188	0.276616	null	null	null	null
bipolar	ptsd	45	45	39.89	0	0	true	19.312	IVW	0.461019	false	IVW	-0.061703	0.066036	0.350105	-0.191132	0.067727	114.123026	0	null	null
bipolar	ptsd	45	45	39.89	0	0	true	19.312	IVW	null	false	MR-Egger	-0.037041	0.070437	0.60168	-0.179091	0.10501	null	null	0.004829	0.32037
bipolar	ptsd	45	45	39.89	0	0	true	19.312	IVW	null	false	Weighted-Median	-0.130703	0.096456	0.1754	-0.319756	0.058351	null	null	null	null
bipolar	schizophrenia	44	24	40.1	0	20	true	14.62	IVW	0.184719	false	IVW	-0.119089	0.06929	0.085667	-0.254897	0.016719	78.354692	0	null	null
bipolar	schizophrenia	44	24	40.1	0	20	true	14.62	IVW	null	false	MR-Egger	-0.130402	0.073797	0.091094	-0.283447	0.022644	null	null	-0.002484	0.612979
bipolar	schizophrenia	44	24	40.1	0	20	true	14.62	IVW	null	false	Weighted-Median	-0.206728	0.110659	0.061742	-0.42362	0.010164	null	null	null	null
bipolar	substance_use	9	9	39.63	0.3112	0	true	37.435	IVW	0.418793	false	IVW	0.044904	0.042403	0.28961	-0.038206	0.128015	9.381226	0.311163	null	null
bipolar	substance_use	9	9	39.63	0.3112	0	true	37.435	IVW	null	false	MR-Egger	-0.036701	0.081251	0.665148	-0.228829	0.155427	null	null	0.005289	0.281066
bipolar	substance_use	9	9	39.63	0.3112	0	true	37.435	IVW	null	false	Weighted-Median	0.057403	0.155834	0.712605	-0.248032	0.362838	null	null	null	null
bpd	adhd	6	4	34.37	0	2	true	7.878	IVW	0.033503	true	IVW	-0.183917	0.071122	0.009711	-0.323316	-0.044518	4.756404	0.190529	null	null
bpd	adhd	6	4	34.37	0	2	true	7.878	IVW	null	false	MR-Egger	-0.181626	0.075309	0.137369	-0.505654	0.142402	null	null	-0.00519	0.496467
bpd	adhd	6	4	34.37	0	2	true	7.878	IVW	null	false	Weighted-Median	-0.186617	0.069598	0.007332	-0.323029	-0.050205	null	null	null	null
bpd	anxiety	7	4	36.1	0	3	true	17.738	IVW	0.76624	false	IVW	-0.011748	0.031675	0.710715	-0.073831	0.050335	6.483486	0.090316	null	null
bpd	anxiety	7	4	36.1	0	3	true	17.738	IVW	null	false	MR-Egger	-0.011591	0.038633	0.792468	-0.177813	0.154632	null	null	0.000651	0.904199
bpd	anxiety	7	4	36.1	0	3	true	17.738	IVW	null	false	Weighted-Median	-0.047811	0.045908	0.297664	-0.13779	0.042168	null	null	null	null
bpd	autism	6	6	34.37	0.0324	0	true	15.233	MR-Egger	0.600307	false	IVW	0.053545	0.085408	0.530706	-0.113855	0.220946	12.183979	0.032352	null	null
bpd	autism	6	6	34.37	0.0324	0	true	15.233	MR-Egger	null	false	MR-Egger	0.049518	0.038917	0.272161	-0.058532	0.157568	null	null	-0.019619	0.010966
bpd	autism	6	6	34.37	0.0324	0	true	15.233	MR-Egger	null	false	Weighted-Median	0.035521	0.117663	0.762737	-0.195098	0.26614	null	null	null	null
bpd	bipolar	7	6	36.1	0.0012	1	true	24.655	IVW	0.92663	false	IVW	-0.005453	0.059214	0.92663	-0.121512	0.110607	13.304769	0.020684	null	null
bpd	bipolar	7	6	36.1	0.0012	1	true	24.655	IVW	null	false	MR-Egger	-0.000531	0.056343	0.992933	-0.156964	0.155902	null	null	0.00866	0.281106
bpd	bipolar	7	6	36.1	0.0012	1	true	24.655	IVW	null	false	Weighted-Median	-0.016358	0.073065	0.822844	-0.159565	0.126848	null	null	null	null
bpd	eating_disorders	6	6	34.37	0.6406	0	true	155.443	IVW	0.570764	false	IVW	0.078967	0.111745	0.479773	-0.140054	0.297987	3.386526	0.640623	null	null

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Psychiatric MR Evidence Atlas

Overview

This repository contains a directed cross-disorder Mendelian randomization atlas built from the harmonized psychiatric GWAS summary-statistics dataset.

It evaluates pairwise directional genetic evidence between 11 psychiatric disorder groups. The atlas is intended as a research resource for structured secondary analysis alongside the harmonized dataset and graph-based prediction models.

This repository should not be interpreted as a clinical causal knowledge base. The results are better understood as a filtered MR evidence screen under explicit assumptions and with material limitations.

Source data

The atlas was generated from:

harmonized dataset: lighteternal/pgc-psychiatric-gwas-harmonized

That harmonized dataset was derived from public OpenMed / PGC Hugging Face repositories, including:

cross_disorder is excluded from this atlas.

Disorder panel

The 11 disorders considered in this release are:

ADHD
Anxiety
Autism
Bipolar disorder
Borderline personality disorder
Eating disorders
Major depressive disorder
Obsessive-compulsive disorder
Post-traumatic stress disorder
Schizophrenia
Substance use

Analysis design

For each directed exposure-outcome pair:

Select exposure instruments at genome-wide significance (p < 5e-8).
Greedily clump instruments to one SNP per 1 Mb window.
Harmonize exposure and outcome alleles on shared variant_id.
Filter instruments by approximate F-statistic (F >= 10).
Apply a PRESSO-style outlier screen.
Estimate directional effects using:
- IVW
- MR-Egger
- Weighted median
Record Steiger directionality, PRESSO-style outlier statistics, and a Rucker-style method recommendation.
Apply Benjamini-Hochberg FDR correction to IVW p-values across the atlas.

Coverage

This atlas attempted 110 directed disorder pairs (11 x 10).

Published results:

unique directed pairs with estimable MR results: 69
method-specific rows: 207
methods per estimable pair: 3
IVW rows passing the atlas filter: 25

The gap between attempted and estimable pairs is expected under the current rules. Not every disorder yields enough usable clumped exposure instruments after harmonization and F-stat filtering.

In this release, estimable exposure sets are concentrated in:

ADHD
Anxiety
Bipolar disorder
Borderline personality disorder
Major depressive disorder
Obsessive-compulsive disorder
Schizophrenia

Disorders such as autism, eating disorders, PTSD, and substance use remain underpowered as MR exposures under the present instrument-selection rule.

Output files

data/mr_results.parquet
summary.json

Result schema

The main result table contains:

exposure
outcome
method
beta
se
pval
ci_lower, ci_upper
n_instruments
n_instruments_after_presso
f_stat_mean
presso_global_pval
presso_outliers_removed
steiger_correct_direction
steiger_z2_ratio
rucker_recommended
heterogeneity_q, heterogeneity_pval
egger_intercept, egger_intercept_pval
fdr_qval
overall_pass

Interpretation

overall_pass = true is a conservative atlas summary flag. In this release it means:

method is IVW
IVW FDR q-value is below 0.05
Steiger directionality check favors the reported exposure-to-outcome direction
MR-Egger intercept does not indicate obvious directional pleiotropy

This flag is useful for ranking and filtering, but it is not equivalent to proof of causality.

Limitations

Summary-statistic MR in psychiatry is vulnerable to sample overlap and residual pleiotropy.
The atlas is only as strong as the available exposure instruments; several disorders are underpowered as exposures.
IVW significance can coexist with heterogeneity or method disagreement.
The implementation uses approximate clumping and summary-statistic harmonization rather than full LD reference-panel modeling.
Results are disorder-level research signals, not patient-level or mechanism-level claims.