1. Identification of Novel Alzheimer’s Disease Loci Using Sex-Specific Family-Based Association Analysis of Whole-Genome Sequence Data
- Author
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Winston Hide, Nan M. Laird, Julian Hecker, Rudolph E. Tanzi, Rory Kirchner, Christoph Lange, Oliver Hoffman, Dawn L. DeMeo, Dmitry Prokopenko, Kristina Mullin, Lars Bertram, and Brad Chapman
- Subjects
0301 basic medicine ,Data Analysis ,Male ,Risk ,Population ,lcsh:Medicine ,Genome-wide association study ,Neuropathology ,Computational biology ,Disease ,Biology ,Genome-wide association studies ,Article ,03 medical and health sciences ,0302 clinical medicine ,Sex Factors ,Alzheimer Disease ,Databases, Genetic ,Humans ,Family ,DNA sequencing ,Allele ,education ,lcsh:Science ,Alleles ,Genetic Association Studies ,Whole genome sequencing ,Zinc finger ,education.field_of_study ,Multidisciplinary ,Whole Genome Sequencing ,lcsh:R ,Intracellular Signaling Peptides and Proteins ,Quality control ,Zinc Fingers ,Alzheimer's disease ,Minor allele frequency ,030104 developmental biology ,Genetic Loci ,BTB-POZ Domain ,Metalloproteases ,Female ,lcsh:Q ,030217 neurology & neurosurgery ,Genome-Wide Association Study - Abstract
With the advent of whole genome-sequencing (WGS) studies, family-based designs enable sex-specific analysis approaches that can be applied to only affected individuals; tests using family-based designs are attractive because they are completely robust against the effects of population substructure. These advantages make family-based association tests (FBATs) that use siblings as well as parents especially suited for the analysis of late-onset diseases such as Alzheimer’s Disease (AD). However, the application of FBATs to assess sex-specific effects can require additional filtering steps, as sensitivity to sequencing errors is amplified in this type of analysis. Here, we illustrate the implementation of robust analysis approaches and additional filtering steps that can minimize the chances of false positive-findings due to sex-specific sequencing errors. We apply this approach to two family-based AD datasets and identify four novel loci (GRID1, RIOK3, MCPH1, ZBTB7C) showing sex-specific association with AD risk. Following stringent quality control filtering, the strongest candidate is ZBTB7C (Pinter = 1.83 × 10−7), in which the minor allele of rs1944572 confers increased risk for AD in females and protection in males. ZBTB7C encodes the Zinc Finger and BTB Domain Containing 7C, a transcriptional repressor of membrane metalloproteases (MMP). Members of this MMP family were implicated in AD neuropathology.
- Published
- 2020
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