Mechanisms of Ageing and Development xxx (2013) xxx–xxx

Contents lists available at SciVerse ScienceDirect Mechanisms of Ageing and Development journal homepage: www.elsevier.com/locate/mechagedev   aye TouSects 

Mechanisms of Ageing and Development

journal homepage: www.elsevier.com/locate/mechagedev

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

Han a,1, Seungjin Ryu a,1, David M. Moskowitz b, Devorah Rothenberg a, Daniel J. Leahy c, Atzmon a,d, Nir Barzilai a,d, Yousin Suh a,d,e,*

aDepartment of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA bDepartment of Biomedical Informatics, Stanford University, Stanford, CA 94305, USA cDepartment of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA dDepartment of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA eInstitute of Aging Research, Guangdong Medical College, Dongguan, China

A B S T R A C T

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. Published by Elsevier Ireland Ltd.

1. Introduction

Alzheimer’s disease (AD), cardiovascular disease, cancer, and type 2 diabetes, as compared to age- and gender- matched controls. Therefore, centenarians have been utilized as a model system for genetics studies of human longevity, with extreme age used as a phenotype to discover genetic variations predisposing people to longevity. Genetic studies of centenarians are based on the premise that they may lead to the identification of alleles that are either particularly enriched in these populations due to positive effects on extreme longevity or under-represented due to negative impact on human health (Tazearslan et al., 2012).

Longevity is known to have a genetic component. The heritability of average life expectancy has been estimated to be 15–25% (Murabito et al., 2012). Family studies on centenarians, those who are 100 years of age or above, suggest that the relationship between genetics and longevity is stronger in the oldest-old adults (Perls et al., 2002; Robine and Allard, 1998). For example, male and female siblings of centenarians have 17 and 8 times, respectively, greater probability of surviving to age 100 than the siblings of people who have an average life expectancy (Perls et al., 2002). Furthermore, offspring of centenarians are healthier with a lower prevalence of age-related diseases such as

Genome-wide analyses have been performed to identify genomic regions linked to longevity followed by identification of the genetic variation causal to the trait. Both the genome-wide linkage studies (GWLS) in family-based designs and genome-wide association studies (GWAS) in population-based designs con- firmed the role of APOE alleles in human longevity. These studies suggest that centenarians are likely to harbor rare protective variants with strong effects (Deelen et al., 2011; Passtoors et al., 2012). Considering the frequency of centenarians is only (cid:2)1/5000 individuals in the population (Andersen et al., 2012), these alleles

* Corresponding author at: Albert Einstein College of Medicine, Departments of Genetics and Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA. Tel.: +1 718 678 1111; fax: +1 718 678 1113.

Please cite this article in press as: Han, J., et al., Discovery of novel non-synonymous SNP variants in 988 candidate genes from 6 centenarians by target capture and next-generation sequencing. Mech. Ageing Dev. (2013), http://dx.doi.org/10.1016/

J. Han et al./Mechanisms of Ageing and Development xxx (2013) xxx–xxx

may not be detectable in general populations. Indeed, a comprehensive candidate approach demonstrated the presence of rare protective alleles enriched in centenarians (Suh et al., 2008; Tazearslan et al., 2011).