Table 3

Stage 2 validation of the 16 most significantly associated SNPs from the GWAS (stage 1).

Chr. Position B36 ID Min AF (LLI) AF (controls) P P P OR 95% C.I. Bonferroni adjusted P GC P CAT CCA CCG CCA 1 175309154 rs12741354 0.483 0.532 0.006 0.007 0.021 0.82 0.71–0.94 0.084 0.020 2 28515768 rs2338013 0.252 0.241 0.496 0.527 0.469 1.06 0.90–1.25 1 0.320 5 52022995 rs350450 0.264 0.26 0.775 0.802 0.948 1.02 0.87–1.21 1 0.711 6 29731718 rs29228 0.199 0.211 0.446 0.473 0.682 0.93 0.78–1.11 1 0.425 6 29753592 rs3129063 0.202 0.216 0.353 0.367 0.528 0.92 0.77–1.10 1 0.354 6 29778631 rs3129046 0.237 0.247 0.523 0.525 0.744 0.95 0.80–1.12 1 0.432 6 29785931 rs1610742 0.234 0.246 0.454 0.470 0.742 0.94 0.79–1.11 1 0.378 6 29808162 rs1610601 0.225 0.234 0.548 0.575 0.734 0.95 0.80–1.13 1 0.549 6 29834025 rs1633063 0.224 0.240 0.289 0.303 0.464 0.91 0.77–1.08 1 0.255 9 10715294 rs11790055 0.328 0.327 0.942 0.969 0.876 1.01 0.86–1.17 1 0.929 9 10726580 rs10959258 0.331 0.329 0.897 0.895 0.831 1.01 0.87–1.17 1 0.897 13 46905819 rs9595687 0.053 0.048 0.470 0.507 0.957 1.13 0.81–1.56 1 0.488 13 47001519 rs1575892 0.055 0.049 0.442 0.461 0.75 1.13 0.82–1.56 1 0.504 16 73418057 rs16947526 0.077 0.087 0.314 0.354 0.628 0.88 0.68–1.14 1 0.338 18 54052953 rs158869 0.450 0.425 0.169 0.175 0.308 1.11 0.96–1.28 1 0.226 19 50114786 rs4420638 0.104 0.174 1.9(cid:2)10(cid:3)08 1.1(cid:2)10(cid:3)08 8.8(cid:2)10(cid:3)08 0.55 0.44–0.68 1.3(cid:2)10(cid:3)07

P P P OR 95% C.I. Bonferroni adjusted P GC P value SNP call rate (LLI) SNP call rate (controls) CAT CCA CCG CCA 0.006 0.007 0.021 0.82 0.71–0.94 0.084 0.020 0.95 0.98 0.496 0.527 0.469 1.06 0.90–1.25 1 0.320 0.96 0.98 0.775 0.802 0.948 1.02 0.87–1.21 1 0.711 0.97 0.96 0.446 0.473 0.682 0.93 0.78–1.11 1 0.425 0.97 0.99 0.353 0.367 0.528 0.92 0.77–1.10 1 0.354 0.97 0.97 0.523 0.525 0.744 0.95 0.80–1.12 1 0.432 0.96 0.98 0.454 0.470 0.742 0.94 0.79–1.11 1 0.378 0.95 0.98 0.548 0.575 0.734 0.95 0.80–1.13 1 0.549 0.97 0.98 0.289 0.303 0.464 0.91 0.77–1.08 1 0.255 0.96 0.99 0.942 0.969 0.876 1.01 0.86–1.17 1 0.929 0.96 0.98 0.897 0.895 0.831 1.01 0.87–1.17 1 0.897 0.98 0.99 0.470 0.507 0.957 1.13 0.81–1.56 1 0.488 0.97 0.99 0.442 0.461 0.75 1.13 0.82–1.56 1 0.504 0.97 0.99 0.314 0.354 0.628 0.88 0.68–1.14 1 0.338 0.95 0.98 0.169 0.175 0.308 1.11 0.96–1.28 1 0.226 0.95 0.98 1.9(cid:2)10(cid:3)08 1.1(cid:2)10(cid:3)08 8.8(cid:2)10(cid:3)08 0.55 0.44–0.68 1.3(cid:2)10(cid:3)07 3.53(cid:2)10(cid:3)08 0.98 0.97 132 (2011) 324–330

Bonferroni adjustment was made for 13 tests (see Supplementary methods). For details see legend to Table 2.

Table 4

for SNPs included in the 5000 most significantly associated haplotypes yielded only 19 marker pairs with high-quality genotypes for both SNPs. Of these, two haplotypes including the APOE locus and four redundant haplotypes from a region of strong LD on chromosome 6 were not considered for follow-up. Thus, 13 haplotype pairs were chosen for validation in the stage 2 samples. However, none of them showed a significant haplotype association with longevity, neither in the stage 2 sample as a whole (Table 4) nor in the subset of centenarians (data not shown).

Association with longevity of 13 two-SNP haplotypes in stages 1 (detection) and 2 (validation).

Chromosome 1st SNP 2nd SNP P P score score (stage 1) (stage 2) 1 rs11577254 rs11205832 4.5(cid:2)10(cid:3)9 0.767 1 rs705536 rs7540568 2.8(cid:2)10(cid:3)8 0.466 2 rs11123531 rs13030366 2.4(cid:2)10(cid:3)7 0.209 2 rs4673981 rs4465766 4.4(cid:2)10(cid:3)7 0.205 4 rs4613559 rs16878067 1.3(cid:2)10(cid:3)11 0.411 4 rs6448493 rs4613559 7.1(cid:2)10(cid:3)8 0.233 4 rs17600829 rs10025735 2.3(cid:2)10(cid:3)6 0.922 6 rs16872733 rs6458227 <1.00(cid:2)10(cid:3)16 1.000 8 rs1389109 rs13254091 4.8(cid:2)10(cid:3)8 0.185 10 rs11597067 rs576289 6.1(cid:2)10(cid:3)9 0.621 10 rs11009149 rs12251479 1.3(cid:2)10(cid:3)7 0.382 11 rs4469890 rs10833433 7.6(cid:2)10(cid:3)12 0.280 14 rs17127261 rs747053 2.0(cid:2)10(cid:3)6 0.910

A recent GWAS identified 70 genome-wide significant SNPs, 33 of which were subsequently replicated in an additional sample (Sebastiani et al., in press). Here, we tested these 33 SNPs for association with longevity in our large German collection. Except for SNP rs2075650 (P value = 7.5  10(cid:3)6, Table 5), which is in high LD with the known APOE alleles (Sebastiani et al., in press; Yu et al., 2007), none of the other markers showed a significant association in our study.

3.6. Haplotype analysis

We also conducted a genome-wide haplotype-based associa- tion analysis, using a sliding window comprising pairs of consecutive SNPs. Out of the 677,291 two-marker haplotypes considered, 51,912 (7.7%) showed a nominally significant associa- tion with longevity in a score test assuming an additive risk model for haplotypes (P < 0.05). Visual inspection of the scatter plots score

4. Discussion

Our study confirmed the known association between APOE and survival at advanced age, but failed to identify any

Table 5

Association results of SNPs identified in the GWAS of Sebastiani et al. in the German GWAS data set. Markers not genotyped on the Affymetrix 6.0 Chip were