Parkinson disease polygenic risk score is associated with Parkinson disease status and age at onset but not with alpha-synuclein cerebrospinal fluid levels

Ibanez, Laura; Dube, Umber; Saef, Benjamin; Budde, John; Black, Kathleen; Medvedeva, Alexandra; Del-Aguila, Jorge L.; Davis, Albert A.; Perlmutter, Joel S.; Harari, Oscar; Benitez, Bruno A.; Cruchaga, Carlos

doi:10.1186/s12883-017-0978-z

Table 2 PD Genetic Risk Score Variants

From: Parkinson disease polygenic risk score is associated with Parkinson disease status and age at onset but not with alpha-synuclein cerebrospinal fluid levels

Variant	Chr	Position	Gene or Nearest Genes	Effect Allele	Known Loci			Current Study		GRS Weight
Variant	Chr	Position	Gene or Nearest Genes	Effect Allele	MAF	P.Value	OR	MAF	Call Rate	Log₂(OR)
rs35749011	1	155,135,036	GBA – SYT11	A	0.017	6.09 × 10⁻²³	2.307	0.021	0.999	1.206
rs823118	1	205,723,572	RAB7L1 – NUCKS1	T	0.559	1.36 × 10⁻¹³	1.109	0.412	0.945	0.149
rs10797576	1	232,664,611	SIPA1L2	T	0.140	1.19 × 10⁻⁰⁸	1.110	0.142	0.125	not included
rs6430538	2	135,539,967	ACMSD – TMEM163	T	0.430	5.56 × 10⁻¹⁵	0.882	0.430	0.998	−0.181
rs1474055	2	169,110,394	STK39	T	0.128	7.12 × 10⁻¹⁶	1.218	0.133	0.991	0.285
rs115185635	3	87,520,857	KRT8P25 – APOOP2	C	0.035	2.18 × 10⁻⁰⁸	0.931	0.035	0.123	not included
rs12637471	3	182,762,437	MCCC1	A	0.193	3.32 × 10⁻¹⁶	0.836	0.183	1.000	−0.258
rs34311866	4	951,947	TMEM175 – GAK - SGKQ	T	0.809	3.58 × 10⁻³³	0.791	0.779	0.998	−0.338
rs11724635	4	15,737,101	BST1	A	0.553	8.07 × 10⁻¹³	1.138	0.439	1.000	0.187
rs6812193	4	77,198,986	FAM47E – SCARB2	T	0.364	7.17 × 10⁻¹¹	0.935	0.347	1.000	−0.097
rs356182	4	90,626,111	SNCA	A	0.633	3.23 × 10⁻⁶⁷	0.822	0.599	0.872	−0.085
rs9275326	6	32,666,660	HLA – DQB1	T	0.094	5.82 × 10⁻¹³	0.900	0.100	0.995	−0.152
rs199347	7	23,293,746	GPNMB	A	0.590	2.37 × 10⁻¹²	1.072	0.595	0.996	0.100
rs117896735	10	121,536,327	INPP5F	A	0.014	1.21 × 10⁻¹¹	1.404	0.004	0.967	0.147
rs3793947	11	83,544,472	DLG2	A	0.443	2.59 × 10⁻⁰⁸	0.976	–	–	not available
rs329648	11	133,765,367	MIR4697	T	0.354	1.65 × 10⁻⁰⁸	0.121	0.359	0.126	not included
rs76904798	12	40,614,434	LRRK2	T	0.143	1.33 × 10⁻¹²	1.110	0.151	0.999	0.151
rs11060180	12	123,303,586	CCDC62	A	0.558	2.14 × 10⁻⁰⁸	1.114	0.560	0.872	0.156
rs11158026	14	55,348,869	GCH1	T	0.335	7.13 × 10⁻¹¹	0.889	0.314	0.123	not included
rs1555399	14	67,984,370	TMEM229B	A	0.468	5.53 × 10⁻¹⁶	0.872	0.509	0.125	not included
rs2414739	15	61,994,134	VPS13C	A	0.734	4.13 × 10⁻⁰⁹	1.114	0.781	0.127	not included
rs14235	16	31,121,793	BCKDK – STX1B	A	0.381	3.89 × 10⁻⁰⁸	1.094	0.391	0.995	0.130
rs17649553	17	43,994,648	MAPT	T	0.226	4.86 × 10⁻³⁷	0.771	0.201	0.991	−0.113
rs12456592	18	40,673,380	RIT2	A	0.693	5.12 × 10⁻⁰⁹	0.905	0.756	0.126	not included
rs62120679	19	2,363,319	SPPL2B	T	0.314	2.53 × 10⁻⁰⁹	1.141	–	–	not available
rs8118008	20	3,168,166	DDRGK1	A	0.657	2.32 × 10⁻⁰⁸	1.111	0.609	0.126	not included

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