Gene frequency method

This method does not allow us to control for observed covariates. We compared gene frequencies in three age groups: 60–75, 75–85, and 85+ . The SNP allele was assigned to be a longevity allele if its frequency increased at the in- terval of aging and if this increase was statistically signifi- cant. We used p£ 10-4 as the level of significance for selecting longevity alleles. The use of smaller p values for selecting longevity alleles failed to select any genetic variant. As a result of this procedure, 52 GF-longevity alleles were selected.

To test whether longevity alleles obtained from the data on the FHS Original cohort jointly influence life span in the Offspring cohort, we calculated the values of the seven polygenic score indices for each of the 517 deceased indi- viduals from the FHSO cohort. Then we estimated parame- ters of seven linear regressions considering life span as a function of each of the polygenic score indices. The per- centages of life span variance in the FHSO cohort explained by each of seven sets of genetic variants selected from the data on the original cohort are shown in Table 2.

I-longevity alleles

The intersection of the four sets of longevity alleles se- lected by each of four methods resulted in the new set of 27 I- longevity alleles. All alleles passed the test for the linkage disequilibrium. The list of respective SNPs and change in their MAFs over age is shown in Table 1. Note that alto-

In each of seven cases and in both FHS cohorts, the esti- mates of the slope (as well as the intercept) parameter were positive and highly statistically significant (p £10-9). We also observed that individuals in the FHSO cohort having larger numbers of longevity alleles taken from the I-set with 27 such alleles had better survival than those from the same cohort who have a smaller number of such alleles in their genome (see Fig. S1 in Supplemental Data). Note that the difference in survival functions for carriers of different numbers of longevity alleles does not prove that the 27 de- tected genetic variants are true positive longevity alleles. The fact that individuals from both FHS cohorts were genotyped on the same chip can lead to apparently robust false-positive findings.

MAF MAF MAF P: 85–105 SNP (60–75) (75–85) (85–105) vs. 60–75 rs3800358 25.90% 28.10% 31.60% 5.41E-03 rs1974676 35.40% 38.80% 41.60% 4.96E-03 rs1834497 44.70% 47.20% 50.40% 9.79E-03 rs2590504 37.30% 38.90% 43.20% 8.54E-03 rs2024714 26.80% 30.00% 35.30% 7.43E-05 rs41383 25.00% 28.10% 31.00% 4.55E-03 rs16975963 46.70% 49.60% 53.30% 7.13E-03 rs13008689 23.20% 25.60% 28.50% 6.86E-03 rs3120819 42.10% 43.80% 48.40% 8.06E-03 rs9876781 34.90% 37.80% 42.40% 8.68E-04 rs9517320 30.80% 33.30% 37.70% 2.04E-03 rs139170 34.70% 37.70% 41.40% 3.32E-03 rs4648884 27.70% 30.50% 33.00% 9.92E-03 rs739401 32.40% 35.60% 39.50% 1.54E-03 rs10256972 36.50% 38.90% 43.60% 2.24E-03 rs10937739 41.90% 44.40% 48.40% 4.04E-03 rs5771675 30.90% 32.90% 36.50% 9.85E-03 rs12623542 36.70% 39.20% 44.00% 1.92E-03 rs9616906 22.70% 25.70% 30.80% 9.36E-05 rs13053175 28.00% 30.40% 33.60% 6.97E-03 rs4148544 24.60% 27.30% 29.70% 9.77E-03 rs2370413 35.20% 38.70% 42.60% 1.10E-03 rs10819510 26.50% 29.20% 32.00% 7.74E-03 rs1205035 36.20% 38.20% 42.00% 9.83E-03 rs432203 38.00% 40.90% 44.30% 7.79E-03 rs1327533 25.30% 28.90% 33.70% 3.56E-04 rs2826891 36.50% 40.00% 43.10% 4.02E-03

Additional arguments confirming that detected genetic are linked to life span could come from three of information from: (1) The new GWAS performed independent populations; (2) the results obtained in GWAS on independent populations performed by researchers; or (3) the fact that genes linked to detected belong to established metabolic pathways involved the regulation of aging and life span. Such pathways have identified in a number of earlier studies using inde- populations. In this paper we investigated the third of information mentioned above.

Genes closest to the 27 I-longevity SNPs: Their roles in aging and health

The fact that the 27 I-longevity alleles jointly significantly influenced life span, regardless of the statistical method used for their selection, indicates potential functional significance of respective genes in physiological aging and/or age- associated diseases, because both the aging and the diseases are major contributors to life span. To see if this is the case, we looked for where these 27 SNPs are located in the genome and conducted a review of current knowledge on biological functions (established or suggested) of genes closest to these

SNP,Single-nucleotidepolymorphism;MAF,minorallelefrequency.

Table Results of Analyses of Joint Effects of ‘‘Longevity’’ Alleles on Life Span 2.

GEE Normal Cox Logistic GF MM Intersection N 1,173 1,173 1,471 1,331 1,471 1,173 1,471 ind N 1,217 823 3,683 97 52 1,202 27 SNPs R2 16.6% 16.9% 13% 16% 16.1% 18.5% 14.4% orig R2 10.6% 10.3% 6% 9% 8.3% 10.2% 8.2% off

The first six columns show the effect of SNP alleles on life span for each of the six models used in the allele selection procedure. The last column shows this effect for the intersection set (of I-longevity alleles). The rows in the table denote: N , number of individuals from the ind FHS original cohort, which data were used in the alleles selection procedures; N , number of SNPs selected with respective model; R2 , SNPs orig percent of life span variance in the FHS original cohort explained by respective model; R2 , percent of life span variance in the FHS offspring off cohort explained by the respective model.

GEE, Generalized estimation equation; normal, normal linear regression; Cox, Cox regression; logistic, logistic regression; MM, model; GF, gene-frequency method; SNP, single-nucleotide polymorphism.