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

Jeehae Han, Seungjin Ryu, David M. Moskowitz, Devorah Rothenberg, Daniel J. Leahy, Gil Atzmon, Nir Barzilai, Yousin Suh

Research output: Contribution to journalArticle

11 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)478-485
Number of pages8
JournalMechanisms of Ageing and Development
Volume134
Issue number10
DOIs
StatePublished - Oct 2013

Fingerprint

Single Nucleotide Polymorphism
Genes
Genome-Wide Association Study
Lipid Metabolism
DNA Repair
Cognition
Maintenance
Genome

Keywords

  • Candidate genes
  • Centenarian
  • Functional variant
  • Human longevity
  • Target capture and next-generation sequencing

ASJC Scopus subject areas

  • Aging
  • Developmental Biology

Cite this

Discovery of novel non-synonymous SNP variants in 988 candidate genes from 6 centenarians by target capture and next-generation sequencing. / Han, Jeehae; Ryu, Seungjin; Moskowitz, David M.; Rothenberg, Devorah; Leahy, Daniel J.; Atzmon, Gil; Barzilai, Nir; Suh, Yousin.

In: Mechanisms of Ageing and Development, Vol. 134, No. 10, 10.2013, p. 478-485.

Research output: Contribution to journalArticle

Han, Jeehae ; Ryu, Seungjin ; Moskowitz, David M. ; Rothenberg, Devorah ; Leahy, Daniel J. ; Atzmon, Gil ; Barzilai, Nir ; Suh, Yousin. / Discovery of novel non-synonymous SNP variants in 988 candidate genes from 6 centenarians by target capture and next-generation sequencing. In: Mechanisms of Ageing and Development. 2013 ; Vol. 134, No. 10. pp. 478-485.
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