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Downloads and Upgrades: UCSC Genome Browser Group and Opal 1.7


The genome browser group at the University of California, Santa Cruz has released an updated genes track for the human genome browser. The new release has 82,960 total transcripts, compared with 80,922 in the previous version and the total number of canonical genes has increased from 31,227 to 31,848.

The group has also released assembly data hubs, which extend the functionality of track data hubs to assemblies that are not hosted natively on the browser. These hubs were developed to help researchers annotate sequences for which UCSC does not provide an annotation database. They let users include the underlying reference sequence, as well as data tracks that annotate that sequence. Sequences are stored in the UCSC twoBit format, and the annotation tracks are stored in the same manner as track data hubs.

Omicia has released version 1.7 of Opal, its cloud-based genome interpretation software.

Opal offers tools to analyze genomes and prioritize disease-causing variants and genes. These include a pipeline that lets users assess and compare the quality of genome variant files, methods to filter out polymorphic genes, and a reporting tool that lets users share results.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.