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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

Unwrapping Mummies' Faces

LiveScience reports that Parabon NanoLabs researchers have reconstructed how three Egyptian mummies may have looked.

Study on Hold

The Spectrum 10K study has been put on hold due to a backlash, leading the researchers to conduct consultations with the autism community, Nature News reports.

Others Out There Already

Reuters reports that Sanofi is no longer developing an mRNA-based vaccine for SARS-CoV-2.

PNAS Papers on GWAS False Discovery, PRAMEF2 Role in Tumorigenesis, RNA Virus Reverse Genetics

In PNAS this week: strategy to account for GWAS false-discovery rates, role of PRAMEF2 in cancer development, and more.