Long-read sequencing reveals genomic and epigenomic variation in the dark genome of human Alzheimer's disease.

INTRODUCTION: Faulty DNA repair and epigenetic regulation contribute to neurodegeneration in Alzheimer's disease. Long-read sequencing enables analysis of "dark regions" that are difficult to study via traditional sequencing methodologies. METHODS: Using nanopore whole-genome DNA sequencing of post mortem brain from early- and late- stage Alzheimer's disease cases and controls, we analyzed retrotransposition, non-allelic homologous recombination (NAHR), structural variation, and DNA methylation within repetitive regions. RESULTS: Retrotransposon insertions and NAHR were enriched in centromeric/pericentromeric and ribosomal DNA (rDNA) in the aged brain. Putatively somatic AluY retrotransposon insertions trended upward in late-stage disease. Enrichment of NAHR between repetitive regions and DNA demethylation were detected in early disease. Differential methylation of dark regions within specific Alzheimer's disease risk genes and repetitive elements occurred across disease stage. DISCUSSION: This study provides the first long-read analysis of repetitive elements in the aged human brain and identifies these regions as hotspots for genomic variation in Alzheimer's disease. HIGHLIGHTS: Long-read sequencing enables analysis of "dark" regions Alzheimer's disease brains Somatic AluY retrotransposon insertions may be elevated in late-stage disease Retrotransposon-associated non-allelic homologous recombination (NAHR) is enriched in repetitive regions in early disease DNA demethylation within the centro/pericentromere and ribosomal DNA (rDNA) occur across disease stage Dark regions of risk genes are differentially methylated across disease stage.