feat: news item - CARD Consortia (#2782)

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"
+---
+
+# Data Release - CARD-Dementia Long Read Project
+
+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).
+
+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](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/).
+
+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.
+
+*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).*
+
+*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.*

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"
+---
+
+# Reporting Temporary Data Unavailability for 1000 Genomes
+
+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.
+
+`HG00257.final.cram`
+
+`HG00369.final.cram`
+
+`HG00657.final.cram`
+
+`HG00684.final.cram`
+
+`HG01079.final.cram`
+
+`HG01110.final.cram`
+
+`HG01122.final.cram`
+
+`HG01491.final.cram`
+
+`HG01697.final.cram`
+
+`HG01777.final.cram`
+
+`HG01976.final.cram`
+
+`HG02164.final.cram`
+
+`HG02312.final.cram`
+
+`HG02380.final.cram`
+
+`HG02512.final.cram`
+
+`HG02557.final.cram`
+
+`HG02681.final.cram`
+
+`HG02769.final.cram`
+
+`HG03063.final.cram`
+
+`HG03563.final.cram`
+
+`HG03844.final.cram`
+
+`HG03898.final.cram`
+
+`HG03937.final.cram`
+
+`HG04141.final.cram`
+
+`NA18912.final.cram`
+
+`NA19060.final.cram`
+
+`NA19238.final.cram`
+
+`NA19360.final.cram`
+
+`NA19474.final.cram`
+
+`NA20790.final.cram`
+
+`NA21126.final.cram`
+
+`HG00408.final.cram`
+
+`HG00639.final.cram`
+
+`HG01096.final.cram`
+
+`HG01529.final.cram`
+
+`HG02821.final.cram`
+
+`HG03047.final.cram`
+
+`HG03487.final.cram`
+
+`NA18487.final.cram`
+
+`NA18500.final.cram`
+
+`NA20279.final.cram`
+
+`HG01141.haplotypeCalls.er.raw.vcf.gz`
+
+`NA10830.haplotypeCalls.er.raw.vcf.gz`
+
+`NA18863.haplotypeCalls.er.raw.vcf.gz`
+
+If you have any questions about this incident, please reach out to us
+at [[email protected]](mailto:[email protected]).

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