Figure 7. Discrimination of the classification rule based on the ensemble of 281 genetic risk models. Panel A: Posterior probability of exceptional longevity (EL) and average longevity (AL) (x axis) in the centenarians (red boxplots) and controls (AL1: Illumina controls, blue boxplots, AL2: NECS controls, green boxplots) of the discovery set (NECS, top left). Both sensitivity and specificity were 89%. The boxplots in blue and green show that the distributions of the posterior probability of EL in the two control groups are not statistically different (p-value from t-test comparing the posterior probability of EL=0.21). Panel B: Posterior probability of EL and AL (x axis) in the centenarians (red boxplots) and controls of the replication set 1. Sensitivity and specificity were 60% and 58% and the distributions of the predictive score are significantly different (t-test p- value=0.001). Panel C: Median values of the posterior probability of EL (predictive score) in subsets of centenarians of the replication set 1 with increasing ages. The barplot shows that the median score increases with older ages. Panel D: Sensitivity of the classification rule in subsets of centenarians of the replication set 1 with increasing ages. The barplot shows the increasing sensitivity in older groups that reaches 85% in 20 subjects aged 106 and older. Panel E: Distribution of the posterior probability of exceptional longevity in the 253 cases of the replication set divided into two age groups (,103 years, pale blue, mean age 99 years, and $103 years, red, mean age 106). The sensitivities in the two groups are 57% and 71.4%. The three distributions are significantly different (p-value=0.04 from t-test comparing Illumina controls and centenarians aged ,103; p-value=0.004 from t-test comparing the centenarians stratified by age). Panel F: Sensitivity and specificity in an additional set of 2863 controls from the Illumina database (blue), and an additional set of 60 centenarians that include 39 centenarians enrolled since June 2009 (mean age 108) and 21 centenarians that were excluded from older analysis because of genetic matching (mean age 106). The specificity in the additional Illumina controls is 61.2%. The sensitivity in the additional centenarians was 71.5% in the set of 21, and 82% in the additional 39 for a total of 78% (p-value from t-test comparing the posterior probabilities of EL in controls and centenarians ,1e-10).

more than 70% posterior probability, and 67% predict average longevity (Figure S14). The most predictive genetic signatures that characterize exceptional longevity are rare amongst control subjects, and only 0.6% of the genetic signatures of control subjects have a posterior probability of exceptional longevity .0.95.

predictive) or cluster C26 (the least predictive), and the median survival in centenarians with signature C1 was 105 years compared to 104 years in centenarians with signature C2 or 103 years in centenarians with signature C26. We observed a similar result when we compared the survival of centenarians with the most predictive signatures in the merged replication sets (R1 and R2), and when we compared the survival of centenarians with the most and the least predictive signatures (R1 and R15) (See Figure 9). However, not all signatures correlated with different survival, for example centenarians with signatures C1 and C3 did not demonstrate different survival (See Figure S16). Preliminary analyses provided in the supplemen- tary material (in need of replication) suggest that the different genetic signatures of exceptional longevity associate with varying prevalences and ages of onset of various age-related diseases (Figure S17, Table S2).

Interestingly, the patterns of genetic risk profiles that cluster into genetic signatures distinctly differ from clusters of genetic risk profiles generated from SNPs selected at random (Figure S15). We also investigated if some clusters were enriched for specific ethnicities, but no clusters showed enrichment for any specific European ethnicity.

We next investigated whether different genetic signatures correlate with different life spans (Figure 9). Some genetic signatures were indeed associated with significantly different life spans. For example, the most predictive signature (C1) was comprised of centenarians with significantly longer survival

Probability of EL Probability of ELProbability of ELDiscovery SetoooS°aa)=Probability of EL6 ‘°C1 (N=66; 0.97)140Number of SNPsC5 (N=67; 0.91)140Number of SNPs (N=37; 0.72)440Number of SNPs281 281    281        a 1w.°20523£ C2 (N=94; 0.95)= OF 140 281Number of SNPsaw.°23z£ C6 (N=76; 0.89)& oF 140 281Number of SNPsa 15 C25 (N=16; 0.31)2Zos2822* oF 140 281Number of SNPsProbability of EL2C3 (N=46; 0.93)140Number of SNPsC10 (N=30; 0.82)140Number of SNPs_ ©26 (N=28; 0.17)Number of SNPs 281 281 Replication Set|R1 (N=18; 0.96)140 Probability of EL°281Number of SNPs Probability of ELa=R2 (N=14; 0.92)140 281Number of SNPsR15 (N=22; 0.08)Probability of EL Number of SNPs

and 2. In each plot, the x-axis reports the number of SNPs in each genetic risk model (1,…,281), and the y-axis reports the posterior probability of exceptional longevity predicted by each model. The boxplots (one for each SNP set on the x axis) display the genetic risk profiles of the centenarians grouped in the same cluster. Numbers N in parentheses are the cluster sizes, and the average posterior probability of exceptional longevity. Color coding represents the strength of the genetic risk to predict EL (Blue: P(EL|g ).0.95; Red: 0.5,P(EL|g ),0.95; Orange: 0.20,P(EL|g ),0.5; 281 281 281 Green: P(EL|g ),0.2). The full set of 26 clusters is in Figure S11 and includes more than 90% of centenarians in the discovery set. 281 doi:10.1371/journal.pone.0029848.g008