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GeneSpring, SNP Software AQ, ISIS, SonarMS/MS

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Version 4.0 of Redwood City, Calif.-based Silicon Genetics’ GeneSpring gene expression analysis software will be available March 31.

Improvements over version 3.2 include the ability to load different file formats and determine which normalizations are appropriate, as well as the ability to compute error models.

Pyrosequencing of Uppsala, Sweden, has released SNP Software AQ for allele frequency determination.

SNP Software AQ can be used with SNP reagent kits and Pyrosequencing’s PSQtm96 system to automatically quantify allele frequencies in pooled DNA samples.

MDL Information Systems, based in San Leandro, Calif., has released a free database containing information on selected compounds found to be active in the National Cancer Institute’s AIDS antiviral screen.

The database is accessible to researchers who use MDL’s ISIS (Integrated Scientific Information System) software and allows them to view chemical structures, compound names, registry numbers, and quantitative screening results.

New York-based ProteoMetrics has released the SonarMS/MS search engine to identify proteins using MS/MS information from digest peptides. It can search DNA from the genome as well as translated protein sequences, allowing for detection of exons, alternate splice sites, and novel genes.

SonarMS/MS takes a protein/ EST/chromosome segment and looks at a compilation of mass spectra to see whether there is good evidence for that sequence.

 

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The Scan

Drug Response Variants May Be Distinct in Somatic, Germline Samples

Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.

Breast Cancer Risk Gene Candidates Found by Multi-Ancestry Low-Frequency Variant Analysis

Researchers narrowed in on new and known risk gene candidates with variant profiles for almost 83,500 individuals with breast cancer and 59,199 unaffected controls in Genome Medicine.

Health-Related Quality of Life Gets Boost After Microbiome-Based Treatment for Recurrent C. Diff

A secondary analysis of Phase 3 clinical trial data in JAMA Network Open suggests an investigational oral microbiome-based drug may lead to enhanced quality of life measures.

Study Follows Consequences of Early Confirmatory Trials for Accelerated Approval Indications

Time to traditional approval or withdrawal was shorter when confirmatory trials started prior to accelerated approval, though overall regulatory outcomes remained similar, a JAMA study finds.