npj Parkinson's Disease

Table 2 Skat-O analysis of TMEM175, SCARB2 and CTSB

From: TMEM175, SCARB2 and CTSB associations with Parkinson’s disease risk across populations

TMEM175						SCARB2				CTSB
Ancestry	Variants	Num Var	rho	P-value	FDR corrected P-value	NumVar	rho	P value	FDR corrected P-value	NumVar	rho	P value	FDR corrected P-value
AAC	exonic	59	0	0.63	0.96	21	0	1.87e-03*	0.11	28	0	0.75	0.96
AAC	Nonsyn and LoF	38	0	0.52	0.96	12	0	0.050	0.59	15	0	0.28	0.96
AFR	exonic	76	1	0.74	0.96	19	1	0.78	0.96	46	0	0.83	0.96
AFR	Nonsyn and LoF	47	1	0.74	0.96	10	1	0.28	0.96	25	0.30	0.15	0.89
AJ	exonic	24	0	0.75	0.96	5	0	0.021*	0.35	13	1	0.73	0.96
AJ	Nonsyn and LoF	15	1	0.58	0.96	4	NA	NA	NA	11	1	0.88	0.96
AMR	exonic	72	0	0.62	0.96	18	0	0.85	0.96	39	0	0.75	0.96
AMR	Nonsyn and LoF	42	1	0.83	0.96	14	0	0.50	0.96	27	0	0.47	0.96
CAS	exonic	39	1	0.18	0.96	15	0	0.13	0.89	18	1	0.86	0.96
CAS	Nonsyn and LoF	26	0	0.26	0.96	10	0.2	0.091	0.77	12	1	0.76	0.96
EAS	exonic	52	0	0.86	0.96	17	0	0.024*	0.35	24	1	1	1
EAS	Nonsyn and LoF	34	0	0.40	0.96	12	0	0.019*	0.35	17	1	0.54	0.96
EUR	exonic	128	0	0.41	0.96	43	0	0.52	0.96	93	0	0.57	0.96
EUR	Nonsyn and LoF	69	1	0.86	0.96	27	0	0.54	0.96	59	1	0.56	0.96
MDE	exonic	47	0	0.42	0.96	21	1	1	1	24	1	0.40	0.96
MDE	Nonsyn and LoF	24	0	0.066	0.65	15	1	1	1	15	1	0.57	0.96
SAS	exonic	25	0	0.52	0.96	10	0	0.29	0.96	19	1	0.42	0.96
SAS	Nonsyn and LoF	18	1	0.55	0.96	7	0.8	0.15	0.89	12	0	0.64	0.96
CAH	exonic	47	1	0.64	0.96	16	1	1	1	28	0	0.73	0.96
CAH	Nonsyn and LoF	30	0	0.43	0.96	9	1	1	1	14	1	0.82	0.96

P values were corrected for multiple testing across ten ancestries, three genes and two variant categories using the Benjamini–Hochberg method to control the false discovery rate.
AAC African American, AFR African, AJ Ashkenazi Jewish, AMR Latino and indigenous Americas, CAS Central Asian, EAS East Asian, EUR European, MDE Middle Eastern, SAS South Asian, CAH Complex Admixture History, Nonsyn non-synonymous variants, LoF and Loss of function, NA not available, NumVar number of variants.
* p value < 0.05.

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