A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples

Sebastiani, Paola; Zhao, Zhenming; Abad-Grau, Maria M; Riva, Alberto; Hartley, Stephen W; Sedgewick, Amanda E; Doria, Alessandro; Montano, Monty; Melista, Efthymia; Terry, Dellara; Perls, Thomas T; Steinberg, Martin H; Baldwin, Clinton T

doi:10.1186/1471-2156-9-6

Table 4 List of SNPs that were found associated with exceptional longevity in different studies, and results based on the analysis of pooled DNA samples.

From: A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples

				Males							Females
Index	SNP	Band	Gene	Validated	Distance	D'	BF	P_L	P_C	OR	Validated	Distance	D'	BF	P_L	P_C	OR
1	rs1870377	4q12	*KDR*	rs2305945	1128	1.00	1.5	0.84	0.75	1.71	rs2305945	1128	1.00	1.1	0.77	0.68	1.62
2	rs2866164	4q23	MTP	rs7693203	9187	NA	3.4	0.82	0.72	1.83	rs1057613	14042	NA	8.6	0.64	0.49	1.90
3	rs750032	4q24	PPP3CA	rs2850971	3819	NA	41.4	0.87	0.74	2.39	rs2850971	3819	NA	10.8	0.82	0.69	2.12
4	rs951085	4q24		rs9999238	29363	0.98	0.2	0.81	0.83	0.85	rs9999238	29363	0.98	10.9	0.81	0.67	2.09
5	rs28360135	5q14.2	XRCC4	rs1382367	40462	NA	295053.4	0.32	0.59	0.33	rs1382367	40462	NA	2.6	0.50	0.63	0.58
6	rs1799945	6p22.2	HFE	rs1572982	3188	0.99	28228.6	0.67	0.42	2.78	rs1572982	3188	0.99	11.2	0.44	0.61	0.51
7	rs9380254	6p21.33	MICA	rs1131896	780	1.00	5744.1	0.67	0.87	0.32	rs1131896	780	1.00	0.8	0.83	0.84	0.96
8	rs2227956	6p21.33	HSPA1L	rs2227956	0		12.6	0.10	0.20	0.42	rs2227956	0		0.3	0.18	0.14	1.31
9	rs1800797	7p15.3	IL6	rs2056576	5019	0.64	0.2	0.70	0.72	0.91	rs2056576	5019	0.99	1.7	0.75	0.64	1.70
10	rs662	7q21.3	PON1	rs662	0		0.2	0.33	0.29	1.21	rs662	0		2.8	0.32	0.21	1.77
11	rs1799983	7q36.1	NOS3	rs2373929	18701	0.16	6.1	0.50	0.64	0.57	rs2373929	18701	0.07	0.6	0.63	0.54	1.45
12	rs2251621	8p12	PURG	rs13269094	8189	0.66	1936.2	0.07	0.22	0.26	rs1362911	23018	0.47	>10^6	0.69	0.96	0.10
13	rs2725362	8p12	WRN	rs3024239	158	NA	4942.7	0.34	0.57	0.39	rs2725362	0		27.2	0.48	0.66	0.48
14	rs1346044	8p12	WRN	rs1346044	0		257.9	0.36	0.19	2.44	rs1346044	0		0.4	0.28	0.21	1.46
15	rs5744256	11q23.1	IL18	rs243908	16909	0.61	>10^6	0.63	0.29	4.02	rs243908	16909	0.96	0.2	0.28	0.28	1.01
16	rs675	11q23.2	APOA4	rs581015	5559	0.28	1.3	0.61	0.51	1.55	rs10502189	371	1.00	4.8	0.05	0.00	56.22
17	rs1467558	11p33	CD44	rs1467558	0		2.0	0.91	0.83	1.97	rs1467558	0		0.2	0.84	0.86	0.87
18	rs9536314	13	KL	rs9536314	0		5.1	0.24	0..36	0.55	rs9536314	0		99.0	0.36	0.18	2.56
19	rs861539	14	*XRCC3*	rs861539	0		0.15	0.75	0.74	1.05	rs861539	0		68.7	0.74	0.55	2.27
20	rs8052394	16q12.2	*MT1A*	rs7189840	9798	NA	0.14	0.59	0.57	1.09	rs7189840	9798	NA	54.1	0.56	0.37	2.18
21	rs1800776	16q13	*CETP*	rs3764261	1910	NA	1.1	0.59	0.69	0.65	rs3764261	1910	NA	0.15	0.66	0.67	0.97
22	rs5882	16q13	CETP	rs5882	0		0.19	0.39	0.35	1.19	rs5882	0		0.17	0.37	0.40	0.88
23	rs704	17q11.2	*VTN*	rs2027993	12085	0.99	17.3	0.45	0.61	0.53	rs2027993	12085	0.99	1.1	0.58	0.47	1.57
24	rs4344	17q23.3	*ACE*	rs4343	693	1.00	1.4	0.69	0.78	0.61	rs4343	693	1.00	6.4	0.66	0.51	1.87
25	rs2252673	19p13.2	*INSR*	rs2059807	15691	0.23	1.5	0.63	0.73	0.63	rs2059807	15691	0.31	0.2	0.75	0.72	1.16
26	rs1799782	19	*XRCC1*	rs9394611128	11001	NA	1.4	0.05	0.10	0.47	rs939461	11001	NA	12.6	0.09	0.02	5.88

Column 1: row number; Column 2: SNP ID; Column 3: Cytogenic band; Column 4: Genes tagged by the SNP; Column 5: SNP in the Illumina array that was used to compare the association as described in the caption of Table 3; Column 6: distance between the two SNPs; Column 7: Bayes D' between the two SNPs; Column 8: Bayes Factor; Column 9–10: estimates of allele frequencies in the pools of DNA from male centenarians and younger controls; Column 11: Odds ratio. Columns 12–18: as columns 5–11 but for the pools comparing female centenarians to younger controls. The SNPs 8, 10, 14, 16–19, 22 are in the array and SNPs 8, 14, 17–19 were found associated with longevity in females and/or males. Highlighted in bold are the associations confirmed by our analysis.

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