A genome-wide association study for late-onset Alzheimer's disease using DNA pooling

Abraham, Richard; Moskvina, Valentina; Sims, Rebecca; Hollingworth, Paul; Morgan, Angharad; Georgieva, Lyudmila; Dowzell, Kimberley; Cichon, Sven; Hillmer, Axel M; O'Donovan, Michael C; Williams, Julie; Owen, Michael J; Kirov, George

doi:10.1186/1755-8794-1-44

BMC Medical Genomics

Table 1 Individually genotyped SNPs that show significant association with LOAD.

From: A genome-wide association study for late-onset Alzheimer's disease using DNA pooling

SNP ID	Chrom	Position	Gene Symbol	SNP Type	Minor Allele	Pooled fcas	Pooled fcon	Ind fcas	Ind fcon	Ind f 1958	Comb Z-test pools	p Cases vs MRC Cons	p Cases vs All Cons
Rs6859 α	19	50073874	PVRL2	T/C	A	0.423	0.324	0.519	0.419	0.417	6.00E-07	1.73E-10	6.09E-14
Rs157580 α	19	50087106	TOMM40	A/G	G	0.653	0.583	0.693	0.595	0.616	6.43E-05	8.24E-11	3.87E-11
Rs8106922α	19	50093506	TOMM40	A/G	G	0.622	0.507	0.698	0.599	0.596	5.89E-09	1.21E-10	3.96E-14
Rs405509 α	19	50100676	APOE	A/C	G	0.547	0.468	0.558	0.463	0.521	7.33E-06	2.08E-09	4.77E-06
Rs439401 α	19	50106291	APOE	T/C	T	0.303	0.372	0.276	0.361	0.357	8.97E-05	7.97E-09	9.15E-11
Rs727153 ‡	4	156012026	intergenic	T/C	C	0.425	0.515	0.475	0.540	0.535	0.0009	0.00002	3.37E-06
Rs3754675	2	101008361	NPAS2	T/C	C	0.814	0.741	0.939	0.905	0.936	5.70E-06	0.00003	0.0144
Rs4699852	4	95699967	intergenic	T/C	A	0.392	0.468	0.431	0.493	0.451	0.0008	0.00004	0.0032
Rs2905990	5	11160513	CTNND2	A/G	T	0.298	0.369	0.300	0.356	0.327	3.79E-05	0.00009	0.0014
Rs9600764	13	76208794	intergenic	T/C	G	0.904	0.860	0.974	0.953	0.964	9.98E-05	0.00019	0.0027
Rs1032412	2	163464614	KCNH7	A/G	G	0.536	0.484	0.726	0.673	0.711	0.0024	0.00019	0.0097
Rs12510838	4	73326573	NPFFR2	A/G	G	0.627	0.558	0.828	0.783	0.810	0.0008	0.00024	0.0047
Rs7140253	14	106305044	intergenic	T/C	G	0.772	0.711	0.898	0.862	0.875	3.18E-05	0.00024	0.0007
Rs1455280	4	61600197	intergenic	T/C	G	0.870	0.820	0.900	0.864	0.882	0.0001	0.00027	0.0026
Rs13397414	2	154056922	intergenic	A/G	G	0.529	0.428	0.895	0.859	0.867	3.44E-09	0.00028	0.0003
Rs587259	19	39348246	LSM14A	T/C	T	0.515	0.450	0.397	0.344	0.364	0.0002	0.00028	0.0009
Rs13115107	4	183493069	intergenic	T/C	G	0.466	0.537	0.687	0.736	0.722	0.0001	0.00032	0.0005
Rs1373900	2	193561888	intergenic	T/C	T	0.259	0.322	0.329	0.380	0.346	5.38E-05	0.00037	0.0087
Rs1911014	4	127131703	intergenic	A/G	A	0.145	0.205	0.124	0.162	0.155	3.56E-06	0.00037	0.0003
Rs17228994	5	14095376	intergenic	A/C	C	0.668	0.736	0.849	0.885	0.870	3.60E-05	0.00060	0.0025
Rs407146	16	13223156	LOC729993	A/C	T	0.294	0.239	0.416	0.365	0.399	0.0007	0.00060	0.0137
Rs7937776	11	94336790	HSPC148	A/G	C	0.576	0.642	0.797	0.837	0.826	0.0006	0.00067	0.0007
Rs3819902	21	42973084	PDE9A	A/G	C	0.623	0.555	0.914	0.883	0.887	0.0009	0.00068	0.0004
Rs16916856	8	52901703	PCMTD1	T/C	C	0.745	0.677	0.887	0.852	0.868	7.80E-06	0.00069	0.0036
Rs393195	19	49184982	ZNF155	A/C	G	0.600	0.525	0.760	0.715	0.745	0.0002	0.00071	0.0147
Rs12146414	10	17108257	CUBN	A/G	G	0.829	0.759	0.933	0.905	0.920	1.37E-05	0.00086	0.0067
Rs7798395	7	70326814	WBSCR17	T/C	C	0.691	0.777	0.923	0.948	0.941	2.20E-06	0.00090	0.0011
Rs741477 ‡	2	64977962	intergenic	A/G	G	0.852	0.795	0.898	0.867	0.858	5.44E-05	0.00124	3.05E-05
Rs10161338‡	12	114328023	intergenic	T/C	C	0.759	0.682	0.902	0.872	0.875	3.52E-05	0.00176	0.0009
Rs10406335‡	19	49325793	ZNF225	A/G	G	0.637	0.571	0.905	0.878	0.876	0.0003	0.00390	0.0009
Rs9324088 ‡	14	106041164	intergenic	T/C	G	0.616	0.544	0.751	0.718	0.699	0.0003	0.01295	0.0002

Pooled fcas: Predicted Allele Frequency in MRC Case Pools. Pooled fcon – Predicted Allele Frequency in MRC Control Pools
Ind fcas: Actual Allele Frequency in MRC Cases.
Ind fcon: Actual Allele Frequency in MRC Controls.
Ind f1958: Allele Frequency in 1958 Birth Cohort
Comb Z-test pools: the p-value of combined Z-test for allelic association in pooled data.
p Cases vs MRC Cons: refers to p-value for allelic association in LOAD case subjects vs LOAD MRC control subjects matched for age, gender ethnicity.
p Cases vs All_Cons: refers to p-value for allelic association in LOAD case subjects vs MRC LOAD control subjects combined with genotype data obtained from the 1958 Birth Cohort
α : SNPs in the region of APOE
‡ : SNPs that show an approximately 10 fold increase in significance when additional controls from the 1958 Birth Cohort are combined with controls from the MRC sample (p Cases vs All Cons)

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ISSN: 1755-8794

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