One major candidate gene for longevity that has not yet been explored is LMNA. Defects in the LMNA gene, which encodes the nuclear envelope proteins lamin A and lamin C, have been associated with at least 13 diseases, including Hutchinson-Ganalysis of LMNA SNPs in four populations of long-lived individuals and controls. The haplotype GTCT, comprised of SNPs 6, 7, 13, and 15, was the most significant haplotype associated with longevity in a meta-analysis across all samples. The association remained significant after adjustment for multiple testing. The association was not substantially affected by inclusion of principal components of ancestry informative markers as covariates in the analysis, suggesting that the observed haplotype association is not driven by population stratification. The association with GTCT was observed in two of the three US samples, but not in the European samples, suggesting possible regional differences in environmental exposures that interact with aging-related genes to affect longevity. Replication of genetic associations for longevity across diverse populations has been difficult in the literature, and reasons for lack of replication include regional differences in environmental exposures and lack of gender stratification in analyses.the case-control status within each of the five samples, (ii) computing trend test statistics for all haplotypes and SNPs in the permuted Stage 1 sample, (iii) selecting the most significant 6-SNP haplotype from the permuted Stage 1 analysis for follow-up, (iv) performing trend tests of association for all six SNPs and haplotypes composed of 26 SNP combinations of these six SNPs in the four permuted Stage 2 samples, and (v) computing meta-analysis statistics for all haplotypes and SNPs tested on all five permuted samples, recording the value of the most significant meta-analysis test statistic. We performed 10,000 permutations and computed the empirical P-value as the proportion of permutations in which the best statistic from the permutation was greater in magnitude than the best statistic from the original data analysis.

We used MaCH 1.0 software to infer 16-SNP haplotypes for all individuals in Stage 1 and 6-SNP haplotypes for all individuals in Stage 2. For individuals with missing genotypes, we inferred the most likely genotype based on haplotype frequencies within the sample. We imputed genotypes for SNP rs1468772 that was not genotyped in the French sample using MaCH and phased haplotype information from the HapMap CEU sample.

We performed association tests in all five samples and combined them in a meta-analysis using R. We performed all SNP and haplotype association tests as Cochran-Armitage tests for a linear trend between the number of copies of a reference allele (0, 1, or 2) and the likelihood that an individual belongs to the case or control group. We first tested each SNP or haplotype for association with centenarian status. We computed meta-analysis statistics for all followed-up SNPs and haplotypes as the weighted sum of z-statistics from the trend tests. The weights for sample i were defined as sqrt(n_i). 

We also genotyped AIMs from a published panel specific to European genetic substructure for the Stage 1 sample, and computed principal components to adjust for potential population stratification. We included the top principal components as covariates in the original analysis. Principal components based on genotypes from the 370K Illumina SNP chip were available for a subset of the NECS sample, and we used EIGENSTRAT to compute the principal components and include them as covariates in the original analysis.

Our initial haplotype association was replicated in one of four follow-up samples, and the association was sufficiently strong in those two samples to remain significant when combined in a meta-analysis of all five. The meta-analysis results complement a growing body of experimental evidence suggesting a potential role for LMNA and progerin in aspects of normal aging. However, given the incomplete replication observed, further work is needed to validate and interpret the results reported here. One of the four SNPs in our reported haplotype, rs4641, is a coding SNP for which allele-specific expression has been demonstrated, with 2.3-fold greater expression for transcripts with the C allele, which is part of the GTCT haplotype associated with greater longevity in our meta-analysis. Another SNP in our reported haplotype, rs915179, was associated with longevity in a recent genome-wide association study. Additional association studies of LMNA variants in independent samples and additional experiments focusing on functional consequences of the associated variants would be particularly valuable in establishing and elucidating the role of LMNA in the normal aging process.