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content/news/2023/03/17/data-release-card-dementia-long-read-project.md
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author: "AnVIL" | ||
date: "2023-03-17" | ||
description: "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." | ||
featured: true | ||
title: "Data Release - CARD-Dementia Long Read Project" | ||
--- | ||
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# Data Release - CARD-Dementia Long Read Project | ||
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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](https://card.nih.gov/research-programs/long-read-sequencing) to uncover more | ||
of the genetic architecture of Alzheimer's disease and related dementias (AD/ADRD). | ||
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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). | ||
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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](https://doi.org/10.1101/2023.01.12.523790) and can be found | ||
on [Dockstore](https://dockstore.org/) [here](https://dockstore.org/organizations/NIHCARD). Additional information can | ||
be found in the preprint [Scalable Nanopore sequencing of human genomes provides a comprehensive view of | ||
haplotype-resolved variation and methylation](https://pubmed.ncbi.nlm.nih.gov/36711673/). | ||
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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](https://card.nih.gov/data-resources/access-data). 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. | ||
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*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](https://www.genomeweb.com/sequencing/nih-researchers-deploy-nanopore-sequencing-large-scale-alzheimers-study#.ZBRJZuyZPjn) | ||
and [here](https://card.nih.gov/research-programs/long-read-sequencing).* | ||
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*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.* |
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content/news/2023/05/08/data-management-1000-genomes.md
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--- | ||
author: "AnVIL" | ||
date: "2023-05-08" | ||
description: "We’re writing to inform you of a data management incident which led to a temporary unavailability of a limited number of files hosted in the 1000G-high-coverage-2019 workspace from March 8, 2023 to May 8, 2023." | ||
featured: true | ||
title: "Reporting Temporary Data Unavailability for 1000 Genomes" | ||
--- | ||
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# Reporting Temporary Data Unavailability for 1000 Genomes | ||
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We’re writing to inform you of a data management incident which led to a temporary unavailability of a limited number of | ||
files hosted in the 1000G-high-coverage-2019 workspace from March 8, 2023 to May 8, 2023. Below is the list of files | ||
that were impacted during this time period; these files have been restored as of May 8, 2023. | ||
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`HG00257.final.cram` | ||
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`HG00369.final.cram` | ||
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`HG00657.final.cram` | ||
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`HG00684.final.cram` | ||
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`HG01079.final.cram` | ||
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`HG01110.final.cram` | ||
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`HG01122.final.cram` | ||
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`HG01491.final.cram` | ||
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`HG01697.final.cram` | ||
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`HG01777.final.cram` | ||
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`HG01976.final.cram` | ||
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`HG02164.final.cram` | ||
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`HG02312.final.cram` | ||
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`HG02380.final.cram` | ||
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`HG02512.final.cram` | ||
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`HG02557.final.cram` | ||
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`HG02681.final.cram` | ||
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`HG02769.final.cram` | ||
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`HG03063.final.cram` | ||
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`HG03563.final.cram` | ||
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`HG03844.final.cram` | ||
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`HG03898.final.cram` | ||
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`HG03937.final.cram` | ||
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`HG04141.final.cram` | ||
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`NA18912.final.cram` | ||
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`NA19060.final.cram` | ||
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`NA19238.final.cram` | ||
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`NA19360.final.cram` | ||
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`NA19474.final.cram` | ||
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`NA20790.final.cram` | ||
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`NA21126.final.cram` | ||
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`HG00408.final.cram` | ||
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`HG00639.final.cram` | ||
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`HG01096.final.cram` | ||
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`HG01529.final.cram` | ||
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`HG02821.final.cram` | ||
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`HG03047.final.cram` | ||
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`HG03487.final.cram` | ||
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`NA18487.final.cram` | ||
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`NA18500.final.cram` | ||
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`NA20279.final.cram` | ||
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`HG01141.haplotypeCalls.er.raw.vcf.gz` | ||
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`NA10830.haplotypeCalls.er.raw.vcf.gz` | ||
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`NA18863.haplotypeCalls.er.raw.vcf.gz` | ||
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If you have any questions about this incident, please reach out to us | ||
at [[email protected]](mailto:[email protected]). |
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