ArticleAlzheimer's & dementia : the journal of the Alzheimer's Association2025
Long-read sequencing reveals genomic and epigenomic variation in the dark genome of human Alzheimer's disease.
Article in Alzheimer's & dementia : the journal of the Alzheimer's Association, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
3 citing papers in PubMed.
- Review
- Long-read sequencing reveals genomic and epigenomic variation in the dark genome of human Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Article
- Exploring the Relationship of Transposable Elements and Ageing: Causes and Consequences.Genome biology and evolution · 2025Review
Corrections and comments
- Update of
Authors and funding
9 authors.
Funding
Abstract
introductionFaulty 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.
methodsUsing 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.
resultsRetrotransposon 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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.