In addition to examining the association of these 10 LOAD susceptibility genes with aging, we performed a genome-wide analysis which includes all SNPs on the Illu- mina platforms after QC. The genome-wide significance threshold was calculated (p  1.04  10(cid:3)7) using Bonfer-  roni correction for the number of independent tests (n 483,066), which was estimated using the method we have previously described (Shi et al., 2010).

There were 41 SNPs with p value IA 5  10(cid:3)5. These SNPs span the genome, representing 35 distinct signals (pairwise r2 ,— 0.8) across 13 chromosomes. Twenty-four of them are located within 20 kilobase (kb) of known human genes with a wide range of functions. SNPs with p values “— &  5 xX 10(cid:3)5 are shown in Table 3B. These signals are at best tentative but may merit study in larger sample sets.

Without conducting logistic regression comparison, ini- tial analysis of the association study suggested 2 genome- wide significant SNPs—rs4110518 (p fg 5.96 xX 10(cid:3)9) and

No variants appear to be associated with aging with a genome-wide level of significance (p  1.04 Ae 10(cid:3)7).

       . © UKUSAsa VY HapMap_cetUK .USAHapMap_ceU - oe anHapMap_JPTCHSHapMap_YRi eweeet    

Fig. 7. Multidimensional scaling (MDS) plot depicting the principal component analysis of Merged Data 3. Population stratification was tested using HapMap data #23 as reference. UK and USA and HapMap CEU samples formed a single cluster (shown inside the dashed rectangle). Up-pointing triangles represent Asian (CHB/JPT) population (bottom left), and right-pointing triangles represent Yoruba (YRI) population (top left). One HapMap individual from the Asian samples appears to have dual ethnicity. The diagram on the right shows a magnified section including UK, USA, and HapMap CEU samples.

Table 3

Summary of results SNP [major/minor] CHR BP Gene p Direction of effect (A) rs2075650 [T/C] 19 50087459 APOE 5.27E-04 — rs3764650 [A/C] 19 997520 ABCA7 1.35E-01 — rs610932 [C/A] 11 59695883 MS4A6A 1.76E-01 + rs3851179 [G/A] 11 85546288 PICALM 2.27E-01  rs11767557 [A/G] 7 142819261 EPHA1 2.67E-01 — rs3865444 [C/A] 19 56419774 CD33 4.42E-01 + rs3818361 [G/A] 1 205851591 CR1 5.63E-01  rs1485780 [A/C] 6 47664589 CD2AP 6.04E-01 — rs744373 [A/G] 2 127611085 BIN1 6.89E-01 + rs11136000 [G/A] 8 27520436 CLU 9.75E-01 — (B) rs987839 [T/C] 12 21266105 SLCO1B1 3.19E-06  rs17205854 [G/A] 5 64458658 3.74E-06  rs17811551 [T/C] 5 64462993 ADAMTS6 3.74E-06  rs1857821 [A/G] 4 77101003 NAAA 5.12E-06  rs7525717 [G/A] 1 56700226 5.76E-06 — rs4673651 [A/G] 2 212712848 ERBB4 6.08E-06 — rs17049647 [G/T] 2 130093855 7.12E-06 + rs10518142 [G/T] 4 77061898 NAAA 8.89E-06  rs2444861 [A/G] 8 99170108 C8orf47 8.99E-06  rs1418425 [G/A] 1 111270409 9.64E-06 — rs2271528 [C/T] 4 77107860 SDAD1 1.02E-05 + rs1555453 [A/C] 9 27316780 MOBKL2B 1.07E-05  rs13111494 [A/G] 4 77204512 ART3 1.28E-05  rs12740413 [C/T] 1 16388466 ARHGEF19 1.30E-05 — rs3210458 [C/T] 3 142494320 ACPL2 1.52E-05 + rs4859571 [G/A] 4 77076333 NAAA 1.56E-05  rs7803143 [T/C] 7 6211011 PSCD3 1.57E-05 — rs7622678 [T/C] 3 198798845 BDH1 1.93E-05 — rs4720752 [G/A] 7 7735965 RPA3 1.93E-05 — rs6962026 [C/T] 7 6213048 PSCD3 2.07E-05 — rs10901296 [C/T] 9 132755477 ABL1 2.37E-05 + rs680109 [C/A] 11 105255919 GRIA4 2.52E-05  rs1537438 [G/T] 13 26806973 2.53E-05  rs11206814 [C/T] 1 56690636 2.67E-05 — rs12562047 [A/C] 1 164095780 UCK2 2.70E-05 + rs2710548 [A/G] 4 126492980 FAT4 2.79E-05 — rs6454676 [C/T] 6 88934174 2.90E-05 + rs17047650 [C/T] 3 68547103 FAM19A1 3.19E-05  rs10433502 [C/T] 3 68569792 FAM19A1 3.49E-05  rs10485170 [T/C] 6 88939371 3.67E-05  rs12257410 [A/C] 10 13832528 FRMD4A 3.77E-05  rs3125524 [C/T] 10 133104931 3.83E-05  rs4280854 [A/G] 5 105923201 3.85E-05  rs1037381 [A/G] 2 105669675 3.99E-05 — rs6532496 [A/G] 4 95799427 PDLIM5 4.00E-05 — rs17618813 [G/A] 4 114153483 ANK2 4.16E-05 + rs7103504 [G/A] 11 99006474 CNTN5 4.39E-05 — rs10085518 [C/T] 7 6252040 PSCD3 4.59E-05 — rs4686837 [G/A] 3 188222371 ST6GAL1 4.60E-05 + rs6491207 [T/C] 13 26828900 4.63E-05  rs7952321 [G/T] 11 55539349 OR5AS1 4.68E-05 —

Results of the analysis of (A) the 10 documented late-onset Alzheimer’s disease (LOAD) susceptibility loci (APOE, CLU, PICALM, CR1, BIN1, ABCA7, MS4A6A, CD33, CD2AP, and EPHA1) with human aging. (B) Single-nucleotide polymorphisms (SNPs) (rs number [major/minor allele]) from our analysis with p values s<s 5 5 xX | 10(cid:3)5. Chromosome number (CHR), base pair position (BP), and gene name is shown together with p value and direction of effect: “(cid:4)” indicates the minor allele of any given SNP is protective, whereas “(cid:3)” means the minor allele of the SNP has a detrimental effect on aging. In (B), the gene name is shown if the SNP is within 20 kilobase of a known gene.

rs2944476 (p 2.19 Comparing SNPs between NIMH and WashU data showed no significant difference in allele frequency, whereas 5 SNPs showed significant difference in allele frequency comparing Mayo data with

for the major allele “A”. No effect was seen for the  viduals carrying “AG” genotype (p 0.891).

It is perhaps unsurprising that the 2 SNPs which showed genome-wide level of significance overlap with the 5 SNPs that showed significant bias between Mayo and WashU data, as the AAD of the Mayo data are significantly younger (as previously described). It is not possible to correct for center, as the spread of the AAD is considered crucial in detecting genuine aging-associated variants. The difference in allele frequency due to samples with young AAD in Mayo and old AAD in WashU may well represent genuine associations. Including center as a covariate would abolish our ability to detect this effect.