A TOMM40 variable-length polymorphism predicts the age of late-onset Alzheimer's disease

Abstract

The ɛ4 allele of the apolipoprotein E (APOE) gene is currently the strongest and most highly replicated genetic factor for risk and age of onset of late-onset Alzheimer's disease (LOAD). Using phylogenetic analysis, we have identified a polymorphic poly-T variant, rs10524523, in the translocase of outer mitochondrial membrane 40 homolog (TOMM40) gene that provides greatly increased precision in the estimation of age of LOAD onset for APOE ɛ3 carriers. In two independent clinical cohorts, longer lengths of rs10524523 are associated with a higher risk for LOAD. For APOE ɛ3/4 patients who developed LOAD after 60 years of age, individuals with long poly-T repeats linked to APOE ɛ3 develop LOAD on an average of 7 years earlier than individuals with shorter poly-T repeats linked to APOE ɛ3 (70.5 ± 1.2 years versus 77.6 ± 2.1 years, P=0.02, n=34). Independent mutation events at rs10524523 that occurred during Caucasian evolution have given rise to multiple categories of poly-T length variants at this locus. On replication, these results will have clinical utility for predictive risk estimates for LOAD and for enabling clinical disease prevention studies. In addition, these results show the effective use of a phylogenetic approach for analysis of haplotypes of polymorphisms, including structural polymorphisms, which contribute to complex diseases.

Figure 1

Schematic overview of the TOMM40-APOE locus. (a) Genomic locations of the TOMM40 and APOE genes on chromosome 19 between 50 084 480 and 50 107 480 bp. The regions subjected to primary sequencing and phylogenetic analysis for the exploratory (R1) (23 kb) and confirmatory (R2) (10 kb) studies are highlighted on the genomic map (NCBI Build 36.3). (b) Distribution of SNP and insertion/deletion polymorphisms are shown on the gene structure of TOMM40 covered in the region that was subjected to primary sequencing. The region covers exons 6–10 and all associated intronic regions. The variable poly-T repeat (rs10524523) that is significantly associated with LOAD age of onset is depicted with the square labeled ‘P'.

Figure 2

Schematic of APOE allele and genotype frequencies associated with the major clades for the phylogenetic tree constructed for the TOMM40 R2 region (Figure 1) for the ES cohort. The percentage of each APOE allele that is present in clades A and B is indicated (column 2). The APOE genotypes that are represented in each clade are also given (column 3). n=300 subject haplotypes.

Figure 3

Distributions of the rs10524523 variable-length polymorphism for the AS (n=210 subject haplotypes) and ES (n=300 subject haplotypes) cohorts. (a) Histograms of rs10524523 length stratified by APOE genotype for the AS cohort. (b) Histograms of rs10524523 poly-T lengths and allele frequencies linked to specific APOE alleles for the ES cohort.

Figure 4

Phylogenetic tree showing separation of SNP variants that distinguish clades A and B. Separation of the two main branches has strong bootstrap support (973 of 1000). These SNPs distinguish the two clades for both the ES and AS cohorts.

Figure 5

Annotated phylogenetic tree shows that there are three groups of clades on the tree that have consistent and characteristic patterns of rs10524523 lengths (C1-C3). For the major clade B, which is associated with lower risk of LOAD and contains haplotypes linked to the APOE ɛ3 allele, rs10524523 lengths are characterized by a uniform short length (C1: mean=15.9, s.e.m.=0.4, n=63). There are two groups that branch from major clade A, one group is characterized by short lengths of rs10524523 (C2: mean length=21.4, s.e.m.=0.2, n=16) and the second by long rs10524523 lengths (C3: mean length=33.5, s.e.m.=0.3, n=30). Haplotypes in group C3 are linked uniquely to the APOE ɛ3 allele. The remaining subject haplotypes in clade A have a mean poly-T rs10524523 length of 30.2 (s.e.m.=0.3, n=101) and are associated with both APOE ɛ3 and ɛ4 alleles. There is a strong bootstrap support (973/1000) for the first major branch and moderate bootstrap support for the branches within clade A (247 of 1000 for C3 and 776 of 1000 for C2). Arrows indicate the branching point for each of the groups.