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Downloads and Upgrades: St. Jude's Cancer Genomes; Omixon Target; and more.

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St. Jude Children's Research Hospital has released data for 520 cancer genomes — matched sets of normal and tumor genomes from 260 pediatric cancer patients participating in the Pediatric Cancer Genome project. The data is available for free for the global scientific community.

Researchers will be able to access the sequence data via the European Genome-Phenome Archive, which provides large datasets for free access on request.

The data release was accompanied by a perspective piece published in Nature Genetics last month.


Omixon has released Omixon Target, analysis software for targeted next-gen sequencing data.

According to the company, the new software is meant to help diagnostic labs replace or complement traditional capillary Sanger sequencing with next-generation sequencing.

The tool is able to perform analysis quality control based on repeat analysis with mutated reference as well as with simulated short reads. Users can navigate between variant tables, variant visualization, short read tracks, and final reporting as well as perform multi-sample comparison for controls and family trio analysis among other capabilities.


Ensembl Genomes 14 is available here.

This release includes a migration to version 67 of Ensembl and 11 new genomes, bringing the total genomes supported to 352. These include four new genomes in Ensembl Protists; the addition of Solanum lycopersicum, Setaria italica, and Oryza brachyantha to Ensembl Plants; and two new butterfly species, Danaus plexippus and Heliconius melpomene, which have been added to Ensembl Metazoa.


Version 4.1 of OpenMM, a software library and application for molecular dynamics simulations on high-performance computer architectures, is available here.

This release includes model building tools, custom integrators, and the ability to add virtual sites.


The Scan

Purnell Choppin Dies

Purnell Choppin, a virologist who led the Howard Hughes Medical Institute, has died at 91, according to the Washington Post.

Effectiveness May Decline, Data From Israel Suggests

The New York Times reports that new Israeli data suggests a decline in Pfizer-BioNTech SARS-CoV-2 vaccine effectiveness against Delta variant infection, though protection against severe disease remains high.

To See Future Risk

Slate looks into the use of polygenic risk scores in embryo screening.

PLOS Papers on Methicillin-Resistant Staphylococcus, Bone Marrow Smear Sequencing, More

In PLOS this week: genomic analysis of methicillin-resistant Staphylococcus pseudintermedius, archived bone marrow sequencing, and more.