Analysis of genome-wide sequencing data from NIAGADS: Searching for gene variants related to gender-Alzheimer's disease (AD) association

Objectives: Analyze the approximately 3,500 DNA sequences from GWAS at NIAGADS for associations between gender, AD, and frequency of SNPs in chromosomal DNA using the P-Link software analytical tool. Rationale: We have performed such analyses of the DNA sequences (VCF files) made available by ADNI and have identified a significantly higher incidence of SNPs (p<10-7) in a few chromosomal genes in males vs. females with the diagnosis of AD. We would like to perform similar analyses to the DNA sequences (in VCF files) of the greater than 3,000 sequenced DNAs at NIAGADS.
Plan: The SNP association analyses will be performed on the DNA sequences using information about the gender and diagnosis of each individual whose DNA sequence we would analyze. We will use the P-Link software to generate data tables (Tab delimited P-Link association files) and Manhattan plots of genome-wide associations (gnuplot). There are no multiple research sites participating in the planned analysis of the DNA sequences. All work will be performed at the University of Kansas AD Center.

Variations in the sequences of DNA in our chromosomes and their association with the incidence of Alzheimer's disease (AD) have been identified in the last 10 years and have brought about new thinking regarding possible causes of AD. These variations in DNA do not directly cause the disease but increase the likelihood of the onset of AD in some individuals late in their life. For many years, it has been known that among various populations there is differential incidence of AD between males and females. In our initial study of a relatively small number of individuals with or without AD, we identified that there was a significant association between a few of the variants in DNA sequences and the incidence of AD in males as compared with females. The study planned will use the DNA sequences in the NIAGADS repository to conduct a similar analysis for variants in DNA sequences. The NIAGADS sequences represent a substantially larger population than that which we analyzed previously and should allow us to explore the possible association of gender and AD with variants of DNA.