Ordered subset analysis of copy number variation association with age at onset of Alzheimer's disease

Abstract

Genetic heterogeneity is a common problem for genome-wide association studies of complex human diseases. Ordered-subset analysis (OSA) reduces genetic heterogeneity and optimizes the use of phenotypic information, thus improving power under some disease models. We hypothesized that in a genetically heterogeneous disorder such as Alzheimer's disease (AD), utilizing OSA by age at onset (AAO) of AD may increase the power to detect relevant loci. Using this approach, 8 loci were detected, including the chr15 : 30,44 region harboring CHRFAM7A. The association was replicated in the NIA-LOAD Familial Study dataset. CHRFAM7A is a dominant negative regulator of CHRNA7 function, the receptor that facilitates amyloid-β1-42 internalization through endocytosis and has been implicated in AD. OSA, using AAO as a quantitative trait, optimized power and detected replicable signals suggesting that AD is genetically heterogeneous between AAO subsets.

Keywords: Age at onset; Alzheimer's disease; copy number variation.

Fig. 1

Genotyping, validation, and genomic context of the CHRFAM7A fusion gene. (a) Genome-Wide Human SNP Array 6.0 is presented as a plot of normalized probewise log2ratio data in the four panels for duplication, diploid, heterozygous and homozygous deletion carriers (CN = 3,2,1,0). (b) Validation of the 4 CN states using TaqMan Copy Number Assay. (c) Genomic context of the structure of the CHRFAM7A region. Top: Chromosomal location and orientation of genes based on the human reference genome. The horizontal lines indicate the 9 CNV probes located in the CHRNA7 exons of the fusion gene (grey line: duplicated sequence, *: the site of the TaqMan probe). Bottom: The three structures of the CHRFAM7A allele. The ancestral allele contains both the CHRNA7 and FAM7A but no hybrid gene. Partial duplication and fusion of CHRNA7 and FAM7A generated the hybrid gene, CHRFAM7A (CHRNA7 and CHRFAM7A in direct orientation). Inversion of the fusion gene results in opposite orientation of CHRNA7 and CHRFAM7A.

Fig. 2

CHRFAM7A and CHRNA7 gene expression. Expression level of CHRFAM7A correlates with the (A) disease state (p = 0.018) and (B) CNV state (p = 10⁻⁵) in human temporal lobe samples. Expression of CHRNA7 is similar in AD versus controls (A) or in deletion carriers and non-carriers (B) consistent with in vitro experiments suggesting that the presence of the fusion gene decreases the number of functional receptors reaching the cell membrane without changes in CHRNA7 expression levels.