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Sex-specific Associations of Gene Expression with Alzheimer's Disease Neuropathology and Ante-mortem Cognitive Performance.
bioRxiv
January 2025
Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA.
The biological mechanisms underlying women's increased Alzheimer's disease (AD) prevalence remain undefined. Previous case/control studies have identified sex-biased molecular pathways, but sex-specific relationships between gene expression and AD endophenotypes, particularly sex chromosomes, are underexplored. With bulk transcriptomic data across 3 brain regions from 767 decedents, we investigated sex-specific associations between gene expression and post-mortem β-amyloid and tau as well as antemortem longitudinal cognition.
View Article and Find Full Text PDFPre-processing of paleogenomes: mitigating reference bias and postmortem damage in ancient genome data.
Genome Biol
January 2025
Department of Biological Sciences, Middle East Technical University, Ankara, Turkey.
We investigate alternative strategies against reference bias and postmortem damage in low coverage paleogenomes. Compared to alignment to the linear reference genome, we show that masking known polymorphic sites and graph alignment effectively remove reference bias, but only starting from raw read files. We next study approaches to overcome postmortem damage: trimming, rescaling, and our newly developed algorithm, bamRefine (github.
View Article and Find Full Text PDFFatal Fulminant Epstein-Barr Virus (EBV) Encephalitis in Immunocompetent 5.5-Year-Old Girl-A Case Report with the Review of Diagnostic and Management Dilemmas.
Biomedicines
December 2024
Department of Pediatric Anesthesiology and Intensive Therapy, Medical University of Warsaw, 02-091 Warsaw, Poland.
Epstein-Barr virus (EBV) usually causes mild, self-limiting, or asymptomatic infection in children, typically infectious mononucleosis. The severe course is more common in immunocompromised patients. Neurological complications of primary infection, reactivation of the latent infection, or immune-mediated are well-documented.
View Article and Find Full Text PDFLong-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation.
bioRxiv
December 2024
Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
Structural variants (SVs) drive gene expression in the human brain and are causative of many neurological conditions. However, most existing genetic studies have been based on short-read sequencing methods, which capture fewer than half of the SVs present in any one individual. Long-read sequencing (LRS) enhances our ability to detect disease-associated and functionally relevant structural variants (SVs); however, its application in large-scale genomic studies has been limited by challenges in sample preparation and high costs.
View Article and Find Full Text PDFA personalized multi-platform assessment of somatic mosaicism in the human frontal cortex.
bioRxiv
December 2024
Gilbert S Omenn Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
Somatic mutations in individual cells lead to genomic mosaicism, contributing to the intricate regulatory landscape of genetic disorders and cancers. To evaluate and refine the detection of somatic mosaicism across different technologies with personalized donor-specific assembly (DSA), we obtained tissue from the dorsolateral prefrontal cortex (DLPFC) of a post-mortem neurotypical 31-year-old individual. We sequenced bulk DLPFC tissue using Oxford Nanopore Technologies (~60X), NovaSeq (~30X), and linked-read sequencing (~28X).
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