Correlation of genetic signatures with lifespan.

<p><b>Panel A:</b> Some genetic signatures are associated with significantly different life-span. For example the most predictive signature (C1) comprises centenarians with significant longer survival compared to centenarians with signatures C2 or C26. (p-value 0.01 and 0.02) More examples are in <b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029848#pone.0029848.s015" target="_blank">Figure S15</a></b>. <b>Panel B:</b> The two most predictive genetic signatures and the least predictive signature in the centenarians of the merged replications sets show consistent results. The comparison between survival of centenarians with the most predictive signature R1 and the least predictive signature R15 reaches statistical significance, (p-value = 0.003) while the comparison between survival distributions of centenarians with signatures R1 and R2 does not reach statistical significance (p-value 0.10).</p

Distribution of age of last contact or age at death of centenarians included in the study.

<p>NECS: centenarians of the discovery set, ELIX: nonagenarians and centenarians from the ELIX replication set, NECS 2: additional NECS replication set of 60 centenarians. The y-axis reports the density, and the x-axis reports the age, in group of 2 years. The frequency of subjects with ages between x and x+2 is 2*density*(sample size).</p

Distribution of NECS cases (row 2), NECS controls (row 3) and Illumina controls (row 4) in clusters of genetic ethnicity (columns).

<p>The table shows the 20 clusters of genetic ethnicity that were discovered using a clustering algorithm described in reference <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029848#pone.0029848-Solovieff1" target="_blank">[20]</a>. Note that no centenarians were allocated to cluster 1 or 15. These clusters are represented by full red dots in <b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029848#pone.0029848.s001" target="_blank">Figure S1</a></b> and denote Franks and Celtics- Alpine ethnicities.</p

Schematic showing the methodology used to discover genetic signatures of exceptional longevity (EL).

<p>The analysis included genetic matching to remove confounding by population stratification between cases and controls of the discovery and replication set 1, discovery and replication of single SNP associations, multivariate genetic risk modeling and generation of predictive genetic profiles, and cluster analysis of genetic risk profiles to discover genetic signatures of EL.</p

Genes in the genetic risk models have been linked to coronary artery disease and Alzheimer's disease.

<p>The two networks display 38 of the 130 genes in the genetic risk model that are linked to Alzheimer's disease (top) and 24 of the 130 genes that are linked to coronary artery disease (bottom) in the literature, either by functional or genetic association studies. The nodes that are linked by an edge represents either genes that are “co-cited” (dashed lines) or “associated by expert curation” (continuous lines). The arrow head means that the associations are activation (triangle), inhibition (circle), modulation (diamond), conversion (arrow head). The node shape informs about known roles of the genes (see inset). The nodes that are singleton were linked to AD/CAD in the literature but not together with other genes. The number of genes linked to each disease was compared to what is expected by chance using Fisher exact test, and the p-values show that the gene seta are unluckily the result of chance. (Networks generated with Genomatix).</p

Replication of the association of rs207650 in TOMM40/APOE.

<p>The table shows the replicated associations of the SNP rs207650 in <i>TOMM40/APOE</i> in the replication set 1 and the additional control set from the Parkinson's Disease study. Column legends: <b>SNP</b> = official dbSNP identifier. <b>Gene</b> = official gene name for SNPs that are within 20 kb from transcribed regions. <b>Chrom</b> = Chromosome and physical position of SNP in hg18. <b>Alleles</b> = the two SNP alleles (allele 1 v allele 2) in the genetic model that reached strongest significance in the Bayesian analysis. <b>LOG10(BF)</b> = the logarithm 10 Bayes Factor for the association relative to the null model of no association. Assuming uniform prior probabilities for the two hypotheses, the BF represents the posterior odds for association. <b>P-value</b> = p-value for 1 degree of freedom test for the dominant model AG/GG versus AA. <b>OR</b> = odds ratio for exceptional longevity in subjects who carry allele 1 relative to allele 2. For example, subjects who carry the allele 1 (AG/GG) of SNP rs2075650 have 0.49 times the odds for exceptional longevity compared to subjects who carry the allele 2 (AG/GG: either the genotype AG or GG). <b>P(A)</b> = prevalence of allele 1 in cases and controls. For example, 15% of centenarians carry the allele AG/GG of SNP rs2075650 compared to 26% of controls. Row 1 shows the results in the discovery set; row 2 in the ELIX set, row 3 the combined discovery and ELIX datasets and row 4 is the set in which the 914 matched controls of the discovery set were replaced with the unmatched Coriel controls.</p

Notation of genotype frequencies.

<p>The table defines the mathematical notation for the genotype frequencies used in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029848#s4" target="_blank">methods</a>.</p

Discrimination of the classification rule based on the ensemble of 281 genetic risk models.

<p><b>Panel A:</b> 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). <b>Panel B:</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). <b>Panel C:</b> 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. <b>Panel D: Sensitivity of the classification rule in subsets of centenarians of the replication set 1 with increasing ages.</b> The barplot shows the increasing sensitivity in older groups that reaches 85% in 20 subjects aged 106 and older. <b>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).</b> 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). <b>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).</b> 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).</p

Breakdown of genotyped samples by Illumina SNP array type (columns 3—7), laboratory (column 8), and case/control/study status (rows).

<p>The columns of the table denote the Illumina array types. The column “Lab” denotes the laboratory that performed the genotyping: BU = Boston University; CIDR = Center for Inherited Disease Research. The row Illumina I denotes the control samples included in the discovery set; Illumina II denotes the control samples included in the first replication set, and Illumina III denotes the residual samples from the Illumina repository; Coriell NINDs denotes the neurologically normal controls.</p

Examples of genetic risk profiles in 4 study subjects (3 centenarians with ages at death 107, 108 and 119 years, and a control).

<p>281 nested SNP sets were used to compute the posterior probability of exceptional longevity in the 4 subjects (y-axis) and were plotted against the number of SNPs in each set (x-axis). In the 107 year old, the first 5 SNP sets Σ₁ = [rs2075650], Σ₂ = [Σ₁, rs1322048], …, Σ₅ = [Σ₄, rs6801173] determine a posterior probability of exceptional longevity ranging between 0.54 and 0.28. This subject carries genotypes AA, AG, AG, CC, AA for the 5 SNPs respectively and, with the exclusion of genotype AA of rs2075650 that is more common in centenarians, the other genotypes are more common in controls than centenarians and determine a posterior probability of exceptional longevity that is lower than the posterior probability of average longevity. The sixth SNP set, Σ₆ = [Σ₅, rs337656], predicts an almost 30% chance of exceptional longevity. The subject carries the AA genotype for the SNP rs337656 that is more frequent in centenarians (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029848#pone.0029848.s022" target="_blank">Table S1</a>), and carrying this genotype increases the posterior probability of exceptional longevity. The probability predicted by the next SNP sets increases steadily and all models with more than 20 SNPs predict more than a 50% chance of exceptional longevity. This genetic profile shows that the subject carries some combinations of SNP alleles that are associated with exceptional longevity, while other alleles are associated with “average longevity”. However, the overall genetic risk profile determined by all 281 SNP sets makes a strong case for exceptional longevity because the majority of models predict more than an 80% chance of exceptional longevity. The genetic risk profile of the centenarian who died at age 119 years is even more convincing: with the exception of the first SNP, all subsequent SNP sets determine more than a 70% chance of exceptional longevity, and 272 of the 281 models predict more than an 80% chance for exceptional longevity. This profile shows that this subject is highly enriched for SNPs alleles that are more common in centenarians (longevity associated variants) and that probably played a determinant role in the extreme survival. The profile of the third subject, age 108 years, shows that different SNP sets determine different chances for exceptional longevity, and only the overall trend of genetic risk provides evidence for exceptional longevity. The fourth plot displays the profile of a control, and shows that this subject carries some longevity associated variants; however, the overall trend of genetic risk points to average longevity rather than exceptional longevity.</p