Data Release - CARD-Dementia Long Read Project
Posted: March 7, 2023
Long-read DNA sequencing, which sequences genomes in larger segments than traditional short-read sequencing does, is providing more detailed views of genetic variants associated with disease. The NIH Center for Alzheimer's and Related Dementias (CARD) is using long-read sequencing technologies to uncover more of the genetic architecture of Alzheimer's disease and related dementias (AD/ADRD).
CARD has now released its first set of long-read DNA sequencing data from cell lines and brain tissue samples useful in the study of neurodegenerative disease. This data release includes nanopore data from 14 frontal cortex brain samples from a North American Brain Expression Consortium study (NABEC, dbGaP:phs001300) and three commonly used cell lines ( HG002, HG00733, and HG02723, dbGaP:phs003224).
In addition to raw sequencing data, CARD researchers are developing and publishing wet lab protocols, workflows, and computational pipelines to optimize the extraction of long DNA fragments from tissue samples and assemble final sequences with extreme accuracy. CARD-developed computational workflows for long-read sequencing analysis can also differentiate maternal and paternal chromosomes (phased sequencing) and detect DNA methylation patterns. These workflows are described here and can be found on Dockstore here. Additional information can be found in the preprint Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.
CARD aims to build a framework for the large-scale application of Oxford nanopore sequencing while filling knowledge gaps about genomic variation in Alzheimer’s disease and other neurological disorders. CARD makes its long-read sequencing data, protocols, and pipelines open access for other researchers. CARD’s cell line data is available without limitations on the AnVIL portal, while the brain data is available after dbGaP registration. Future releases will include long-read sequencing data from thousands of healthy and disease-affected brain samples.
CARD is a collaboration between the National Institute of Neurological Disorders and Stroke (NINDS) and the National Institute on Aging (NIA). Learn more about CARD’s long-read sequencing efforts for AD/ADRD here and here.
The CARD long-read consortium includes researchers from National Institute on Aging, UC Santa Cruz Genomics Institute, National Cancer Institute, National Human Genome Research Institute, Baylor College of Medicine, Johns Hopkins University, University of Southern California and Northeastern University College of engineering.