Discovery of novel non-synonymous SNP variants in 988 candidate genes from 6 centenarians by target capture and next-generation sequencing.

Authors: Han J; Ryu S; Moskowitz DM; Rothenberg D; Leahy DJ; Atzmon G; Barzilai N; Suh Y

Abstract: Despite evidence of a substantial genetic component, the genetic factors that underlie longevity in humans remain to be identified. Previous genome-wide linkage and association studies have not found strong evidence for the contribution of common variants besides the APOE gene, suggesting the role of rare variants in human longevity. To discover rare variants that might contribute to longevity, we selected 988 candidate genes and performed a pilot study to identify novel non-synonymous variants in 6 Ashkenazi Jewish centenarians older than 105. Our candidate genes act in pathways implicated in aging and longevity, including neurodegeneration, cognitive function, lipid metabolism, DNA repair, and genome maintenance. By implementing custom-designed Agilent SureSelect target capture and next-generation sequencing, we discovered a total of 89 novel non-synonymous SNPs (nsSNPs) and validated 51 nsSNPs by iPLEX MassArray assays. Genotyping analysis of these novel SNPs in 410 Ashkenazi Jewish controls and 390 centenarians showed significant enrichment (5.3 fold, p=0.02) of the p.Y318C variant in PMS2 and significant depletion (7.5 fold, p=0.04) of the p.V465A variant in GABRR3 in centenarians compared to controls. Our study presents the potential of targeted next-generation sequencing for discovery of rare but functional genetic variation which may lead to exceptional longevity in humans.

Journal: Mechanisms of ageing and development
Date: Feb. 5, 2013
PMID: 23376243
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Notes:

Next-generation sequencing was employed to identify novel variants in 988 candidate genes in 6 centenarians, revealing 89 novel non-synonymous SNPs. These were genotyped in 410 Ashkenazi Jewish controls and 390 centenarians.

Without correcting for multiple testing, the p.Y318C variant in PMS2 was significantly enriched while the p.V465A variant in GABRR3 was significantly depleted in centenarians.



Categories: Single-Nucleotide Polymorphism
Citation:

Han J, Ryu S, Moskowitz DM, Rothenberg D, Leahy DJ, Atzmon G, Barzilai N, Suh Y (2013) Discovery of novel non-synonymous SNP variants in 988 candidate genes from 6 centenarians by target capture and next-generation sequencing. Mechanisms of ageing and development.


Lifespan Factors:
  • PMS2 PMS2 postmeiotic segregation increased 2 (S. cerevisiae)

  • Longevity Variant Associations (p-value):
  • Y318C (0.02)
  • V465A (0.04)

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