INVESTIGATING GENETIC VARIATION IN ALZHEIMER’S DISEASE USING WHOLE-EXOME SEQUENCING

Abstract

Alzheimer's disease (AD) is an incurable neurodegenerative disorder; in which the death of brain cells characteristically result in memory loss and cognitive decline. It is the most common form of dementia, affecting around 850,000 people in the UK. Sporadic late-onset AD (LOAD) accounts for 95% of all cases and is genetically complex in nature. It is believed that combinations of genetic and environmental factors are at play. Recent genome-wide association studies (GWAS) have uncovered over 20 new gene candidates for AD risk, however these exhibit small effect sizes. We are now utilising next generation sequencing (NGS) to explore the contribution made by rare variants (MAF<5%). Recently this approach highlighted the role of TREM2 and SORL1 variants in AD risk and emerging NeuroX chip and NGS data is set to generate more genes of interest. DNA was extracted from post-mortem brain tissue obtained from the BDR for healthy and diseased individuals. Whole-exome sequencing was performed on 292 samples, including 133 AD cases, 53 controls and 106 other phenotypes. Samples were screened for mutations in APP, PSEN1 and PSEN2 to distinguish early-onset AD cases and known LOAD risk genes. Using a combination of bioinformatics and statistical tools variants were tested for association with AD and their functionality assessed in silico. Presently over 340,000 variants have been identified in the whole-exome dataset, with 18% predicted to be novel. Coding variants account for ∼55% of all variants, with >50% of these being missense or frameshift mutations. A total of 653 SNPs were found in GWAS nominated genes. APOEε4 SNP rs429358 reached genome-wide significance (p<5x10-8, OR=6.5) in single SNP association without adjusting for covariates. It is well known that APOEε4 significantly increases AD risk. Although no other SNPs reached genome-wide significance, it is likely that important variants could lie below this threshold. Therefore AD risk gene variants and other neurodegenerative disease risk genes will also be investigated further.