Long-read sequencing to resolve the genomic architecture of dementia

The National Institute of Neurological Disorders and Stroke awarded Mayo Clinic Jacksonville $1,879,248 on September 3, 2026, under the Extramural Research Programs in the Neurosciences and Neurological Disorders program (CFDA 93.853) to employ long-read sequencing technologies to identify genomic variation and disease-relevant transcripts contributing to Lewy body dementia and frontotemporal lobar degeneration.

The research will detect structural variants, copy number variants, translocations, inversions, and repeat expansions that remain hidden with standard short-read sequencing and have stayed undetected despite discovery of multiple disease-associated loci in the majority of patients with these conditions. The project comprises two primary aims: resolving genomic architecture through structural-variation detection and identifying isoform-specific transcripts using long-read sequencing of post-mortem brain tissue. A third component will interrogate the long-read transcriptome using single-nuclei RNA sequencing to capture splicing events and dysregulated expression patterns implicated in neurodegeneration.

Place of performance is Jacksonville, Florida. The period of performance extends from the award date through July 31, 2029. The assistance type is a Project Grant.

Abstract

To date, no effective therapies or prevention strategies have been developed for two of the major forms of dementia, lewy body dementia (LBD) and frontotemporal lobar degeneration (ftld). With no strategies to prevent or delay the onset of these devastating diseases, their toll on the patient, family/caregiver, as well as community and social healthcare will be an ever-increasing burden. Hence, IT is imperative to develop a thorough understanding of their molecular pathogenesis to identify key targets and pathways for clinical intervention. As such, we seek to reveal the 'missing' genomic variation and determine isoform-specific, disease-relevant transcripts that contribute to these progressive and ultimately fatal neurodegenerative dementias. Given the fact that the vast majority of LBD and ftld patients remain etiologically unexplained, despite the discovery of multiple disease-associated loci, we will employ long-read sequencing technologies, which have the capacity to detect structural variation (aim 1) and individual transcripts (aim 2), which would have stayed hidden with standard short-read sequencing technologies. Our approach enables US to span the entire range of genomic variation from single-nucleotide variants and small insertions/deletions, to larger copy number variants, translocations, inversions, and repeat expansions, uncovering variants that contribute to the development of these diseases. In addition to these genomic studies, we are proposing to obtain a comprehensive, isoform- specific transcriptome of post-mortem brain tissue, using the latest long-read sequencing technology. Obtaining the full-length transcriptome is especially important since splicing events and dysregulated expression have been shown to play a central role in both neurodegenerative diseases. Finally, we propose to use single-nuclei RNA sequencing, interrogating the long-read transcriptome at the single-nucleus level. This will not only give US an unprecedented opportunity to reliably detect and quantify relevant individual transcripts and dysregulated pathways/networks, but also to define the cellular signatures of LBD and ftld in human brain tissue. Taken together, we are leveraging state-of-the-art long-read sequencing technologies to perform detailed genomic and transcriptomic assessments of our unique cohorts of LBD and ftld patients, which allows US to unravel their genomic architecture, pointing towards disease drivers and modifiers, as well as much-needed preclinical biomarkers and druggable targets.