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Downloads and Upgrades: SVS 8, Variant Interpreter App, ProteomeXchange, and more


Golden Helix has released the eighth version of SNP & Variation Suite, its genomic analysis software.

In this version of the software, the company has integrated SVS with GenomBrowse, its visualization application for viewing sequence pile-up and coverage data. Other features include a new file format for annotation tracks, haplotype trend regression to associate phenotypes with haplotype frequencies of individuals, and new sequence analysis tools including one to classify variants by inheritance pattern and one to filter based on VCF quality metrics.

N-of-One has released a new application for Illumina's BaseSpace Apps store.

According to the company, the Variant Interpreter app gives oncologists and researchers access to relevant biological and clinical knowledge and insights that are related to the mutation profile of tumors that are identified by targeted sequencing.

This first version of the app will cover 30 cancer associated genes that are commonly tested. Future releases will include additional genes.

The National Center for Biotechnology Information has added two new data retrieval options to E-utilities, the application programming interface to the NCBI Entrez system. They are the &sort parameter and the JSON format.

The NCBI has also developed an online system for researchers to register studies, submit data, and access data in dbGaP. Tutorials on the online forms for study registration and data access are available on YouTube.

The ProteomeXchange consortium has launched a public portal for exchanging proteomics data and information. They've also published a paper that describes their efforts to develop the portal in Nature Biotechnology.

TATAA Biocenter and MultiD Analyses have launched GenEx version 6, the latest installment of the software which is used for analyzing qPCR data in a manner that complies with current regulatory guidelines.

This version includes tools for estimating PCR efficiency, testing for outliers and linear models; estimating dynamic range, random error, limit of detection, and quantification; and evaluating and verifying precision among other updates.

The Scan

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.

SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data in nearly 335,700 samples — a set known as the 300K-RNA resource.

Automated Sequencing Pipeline Appears to Allow Rapid SARS-CoV-2 Lineage Detection in Nevada Study

Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.