Whole-genome sequencing of the world's oldest people

Abstract

Supercentenarians (110 years or older) are the world's oldest people. Seventy four are alive worldwide, with twenty two in the United States. We performed whole-genome sequencing on 17 supercentenarians to explore the genetic basis underlying extreme human longevity. We found no significant evidence of enrichment for a single rare protein-altering variant or for a gene harboring different rare protein altering variants in supercentenarian compared to control genomes. We followed up on the gene most enriched for rare protein-altering variants in our cohort of supercentenarians, TSHZ3, by sequencing it in a second cohort of 99 long-lived individuals but did not find a significant enrichment. The genome of one supercentenarian had a pathogenic mutation in DSC2, known to predispose to arrhythmogenic right ventricular cardiomyopathy, which is recommended to be reported to this individual as an incidental finding according to a recent position statement by the American College of Medical Genetics and Genomics. Even with this pathogenic mutation, the proband lived to over 110 years. The entire list of rare protein-altering variants and DNA sequence of all 17 supercentenarian genomes is available as a resource to assist the discovery of the genetic basis of extreme longevity in future studies.

Figure 1. Pipeline to test supercentenarians for enrichment of rare protein-altering variants or genes harboring them.

All female Caucasian supercentenarian genomes were annotated for protein-altering variants. (A) To test for enrichment of a single variant, we filtered against dbSNP131 and compared each remaining rare protein-altering variant against 1000G EUR. No single variant was significantly enriched. (B) To test for enrichment of a gene with rare protein-altering variants, we collapsed all variants in to their respective genes and filtered against 1000G EUR (MAF<0.015). We tested for enrichment against 34 control genomes from PGP using the RVT1 burden test or a gene-based Fisher’s Exact (for recessive model). No gene was significantly enriched for rare protein-altering variants in supercentenarians. We then Sanger validated TSHZ3 as the best candidate from our burden-test for follow-up.

Figure 2. Rare protein-altering variants in TSHZ3 in the Georgia Centenarian cohort versus NHLBI cohort.

To see if TSHZ3 is enriched for rare protein-altering variants in long-lived individuals, Sanger sequencing was performed on TSHZ3 in 99 Caucasians with extreme longevity (age 98–105). There was not a significant enrichment comparing the allele frequency of all rare protein-altering variants in the centenarians (4.0%; black bar) to 4300 Caucasian controls from the NHLBI exome project (2.5%; white bar). Both cohorts were annotated for protein-altering variants and filtered against 1000G EUR (MAF<0.015).

Figure 3. A supercentenarian with a known pathogenic mutation implicated in cardiomyopathy.

(A) Sanger validation confirmed that one supercentenarian possessed a known pathogenic mutation in a splice acceptor site of Desmocollin-2 (DSC2), a component of the myocardial desmosome. (B) This rare mutation has been reported in 2 independent cases of Arrhythmogenic Right Ventricular Cardiomyopathy and has been shown to cause cryptic splicing and mRNA degradation , .