1. Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases
- Author
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M. Ryan Corces, S. Tansu Bagdatli, Stephen B. Montgomery, Maxwell R. Mumbach, Anna Shcherbina, Bryan H. Louie, Kathleen S. Montine, Soumya Kundu, Shadi Shams, Michael J. Gloudemans, Howard Y. Chang, Anshul Kundaje, Tiffany Eulalio, Jeffrey M. Granja, Laure Fresard, Boxiang Liu, William J. Greenleaf, and Thomas J. Montine
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Adult ,Epigenomics ,Population ,tau Proteins ,Locus (genetics) ,Genome-wide association study ,Disease ,Biology ,Polymorphism, Single Nucleotide ,Article ,Cohort Studies ,Machine Learning ,Genetic Heterogeneity ,03 medical and health sciences ,Atlases as Topic ,0302 clinical medicine ,Artificial Intelligence ,Alzheimer Disease ,Genetics ,Humans ,Genetic Predisposition to Disease ,Promoter Regions, Genetic ,education ,030304 developmental biology ,Genetic association ,Neurons ,0303 health sciences ,education.field_of_study ,Genetic heterogeneity ,Haplotype ,Brain ,Parkinson Disease ,Chromatin Assembly and Disassembly ,Enhancer Elements, Genetic ,Biological Variation, Population ,Haplotypes ,030217 neurology & neurosurgery ,Genome-Wide Association Study - Abstract
Genome-wide association studies (GWAS) of neurological diseases have identified thousands of variants associated with disease phenotypes. However, the majority of these variants do not alter coding sequences, making it difficult to assign their function. Here, we present a multi-omic epigenetic atlas of the adult human brain through profiling of single-cell chromatin accessibility landscapes and three-dimensional (3D) chromatin interactions of diverse adult brain regions across a cohort of cognitively healthy individuals. We developed a machine-learning classifier to integrate this multi-omic framework and predict dozens of functional single-nucleotide polymorphisms (SNPs) for Alzheimer’s disease (AD) and Parkinson’s disease (PD), nominating target genes and cell types for previously orphaned GWAS loci. Moreover, we dissected the complex inverted haplotype of the MAPT (encoding tau) PD risk locus, identifying putative ectopic regulatory interactions in neurons that may mediate this disease association. This work expands our understanding of inherited variation and provides a roadmap for the epigenomic dissection of causal regulatory variation in disease.
- Published
- 2020
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