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Downloads and Upgrades: UCSC Genome Browser, RefSeq 60, and Cancer Genome Analysis Suite


The genome browser group at the University of California, Santa Cruz has added epigenomics data from the European BLUEPRINT epigenome project to the UCSC browser via its public hubs function.

The dataset currently contains 8 DNase-seq, 48 DNA methylation, 170 Histone modification, and 24 RNA-seq tracks, focused on displaying variation in human monocyte and neutrophil cells from 7 adult blood and 4 cord blood samples.

RefSeq 60 is now available from the National Center for Biotechnology Information via FTP.

This release incorporates genomic, transcript, and protein data available as of July. 19 and includes 40,913,699 records; 32,504,738 proteins; 4,243,209 RNAs; and sequences from 28,560 different organisms.

This week, Appistry has launched the Cancer Genome Analysis Suite, an integrated set of tools for analyzing next-generation sequence data from cancer genomes.

According to the company, the suite provides the high sensitivity required for identifying low-frequency point mutations and discrepancies in DNA sequences that mark tumor development and evolution. It includes the Broad's Genome Analysis Toolkit and MuTect, also developed by the Broad, which lets users identify somatic point mutations. It also includes tools for identifying somatic indels, an Appistry-built test dataset, results summary, and a Perl script that runs all of the tools in the suite across the test dataset or a customer's own data.

The Scan

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.

Machine Learning Improves Diagnostic Accuracy of Breast Cancer MRI, Study Shows

Combining machine learning with radiologists' interpretations further increased the diagnostic accuracy of MRIs for breast cancer, a Science Translational Medicine paper finds.

Genome Damage in Neurons Triggers Alzheimer's-Linked Inflammation

Neurons harboring increased DNA double-strand breaks activate microglia to lead to neuroinflammation like that seen in Alzheimer's disease, a new Science Advances study finds.

Long COVID-19 Susceptibility Clues Contained in Blood Plasma Proteome

A longitudinal study in eBioMedicine found weeks-long blood plasma proteome shifts after SARS-CoV-2 infection, along with proteomic signatures that appeared to coincide with long Covid risk.