Identification of genetic modifiers for Alzheimer disease: The Familial Alzheimer Sequencing (FASe) project.

Abstract

The Familial Alzheimer Sequencing (FASe) project aims to identify rare and high penetrant variants that have strong effect in the etiology of Alzheimer Disease (AD) by using sequencing data from families densely affected by late onset AD (fLOAD). We have generated whole genome sequence (WGS) data for 952 samples (758 cases, 194 controls) from the Knight-ADRC at Washington University (WASHU), the NIALOAD and NCRAD repositories. These samples are being added to our current dataset of whole exome (WES) and WGS from 1,235 non-Hispanic white participants (824 cases, 411 controls) across 285 fLOAD families. These samples have no or minimum overlap with the families sequenced by the ADSP consortia which will also be incorporated to our dataset; a total of 440 families and 3,187 samples (average of 5 cases and 2 controls per family) will be analyzed. We are processing all the data using the same bioinformatics pipeline. Briefly, sequence reads are aligned against reference build GRCh38 using BWA; variant calling is restricted to exonic regions following GATK v4.1.2 best practices. Data analysis includes single variant association, segregation, gene-based and pathway analysis. We have detected a genetic cross-over between AD, Frontotemporal Dementia and Parkinson disease, and we also identified rare variants in novel candidate genes for AD (PLD3, UNC5C, CPAMD8) highlighting the power of our dataset and the feasibility of our approach. We hope to identify novel variants and pathways implicated on AD, which will be followed-up in the case-control ADSP.