SALRR: Scalable Analysis of Long-Read RNA-Seq Enables Comprehensive Transcriptome Profiling in Human Brain
Year: 2026
Type: preprint
Abstract: ABSTRACT Isoform-resolved transcriptomics is fundamental to decoding the molecular complexity of the human brain, yet population-scale long-read RNA sequencing has remained inaccessible due to labor-intensive library preparation, sensitivity to RNA degradation in postmortem tissue, and the absence of integrated, reproducible analysis pipelines. Here we present SALRR (Scalable Analysis of Long-Read RNA-seq), an integrated wet-lab and computational platform designed to overcome these barriers. Automated ONT long-read cDNA library preparation on the Hamilton Microlab NGS STAR platform reduces hands-on time by 67% and enables 24 libraries per operator per day while maintaining performance across RNA integrity values. A modular, Snakemake-based pipeline performs end-to-end processing from ONT signal data to isoform-level quantification, incorporating SIRV spike-in calibration, multi-stage quality control, and stringent isoform validation. Applied to 10 postmortem frontal cortex samples from the North American Brain Expression Consortium, SALRR identified 31,607 high-confidence isoforms from 10,075 genes, including 8,532 novel splice variants absent from GENCODE v49, and complex splicing events systematically missed by short-read sequencing at neurodegeneration-relevant loci, including GBA1 , CCNF , CHCHD10 , and TREM2 . All protocols and code are openly available, providing a scalable, community-ready framework for isoform-resolved transcriptomics in neurodegeneration, aging, and complex brain disease.
Authors: Cedric Kouam, Jackson Mingle, Pilar Álvarez Jerez, Allison Evans, Abraham Moller, Breeana Baker, Cory Weller, Kimberly Paquette, Janet Brooks, Spencer M Grant, Alexis Ayuketah, Melissa Meredith, Joanna Palade, Laksh Malik, Kristen Hise, Jessica Anderson, Robert Harbert, Yilei Fu, Xinchang Zheng, Sonia García-Ruiz, Emil K Gustavsson, Cornelis Blauwendraat, Mina Ryten, Fritz J Sedlazeck, Luigi Ferrucci, J. Raphael Gibbs, Jinhui Ding, Xylena Reed, Mike Nalls, Mark R Cookson, Kendall Van Keuren-Jensen, Elizabeth Hutchins, Miten Jain, Kimberley J Billingsley
Institutions: National Institutes of Health, National Institute of Neurological Disorders and Stroke, National Institute on Aging, UCL Queen Square Institute of Neurology, University College London, Data Tecnica International (United States), University of Cambridge, Oxford Nanopore Technologies (United Kingdom), Baylor College of Medicine, Coalition for Aligning Science, NIHR Cambridge Biomedical Research Centre, Rice University, Translational Genomics Research Institute, Northeastern University
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Awards: G1265246815, G1656305939, G2258677762, G6141462147, Center for Alzheimer's and Related Dementias (CARD): Long-read DNA sequencing of Alzheimers Disease and Related Dementias cases, Single-molecule sequence assembly and analysis, Center for Alzheimer's and Related Dementias (CARD): Harmonized Data-Derived Resources for the Alzheimer's Disease and Related Dementias Community
OpenAlex ID: W7204653425