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New Product Watch: Apr 7, 2009

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BioDiscovery last week launched Nexus Copy Number Version 4, a platform-independent application for DNA copy number analysis of microarray-derived data.

The latest version of the Nexus Copy Number software includes a new algorithm for SNP arrays that combines log ratio and B-allele frequency values to segment the genome; detection of loss of hetrozygosity and allelic imbalance calls for SNP array data; predictive power analysis for continuous data types; a query tool for listing genomic events for multiple genes or regions; and a one-click data loading tool.

Nexus Copy Number can integrate and process together data from commercial array platforms such as Agilent, Affymetrix, Illumina, and Roche NimbleGen, as well as custom arrays, BioDiscovery said.

The software is available in two editions. The standard edition enables copy number analysis of CGH and SNP arrays including customizable reports listing aberrant regions and copy number and allele event calls, minimum regions of aberration among a set of samples, individual sample results, and a genomic browser with customizable annotation tracks; Meantime, the discovery edition enables clustering based on similar aberration profiles, identification of statistically different regions of change between sample sub-groups, gene ontology enrichment analysis, survival analysis, and integration of external data such as gene expression.


Fluidigm last week launched SlingShot, a sample-quantification system that allows researchers to sequence their libraries of rare samples for use in second-generation DNA sequencing applications.

SlingShot relies on Fluidigm's integrated fluidic circuit microfluidic chips to detect only amplifiable molecules within the sample mixture. Since IFCs use small amounts of sample, SlingShot opens up the ability to sequence rare libraries where suboptimal amounts of the tissue are available. Using digital PCR, users can also count individual molecules using Fluidigm's technology, eliminating the need for library titration in preparation for sequencing, the company said.

Fluidigm's SlingShot kit includes an IFC chip, library-specific assays for second-generation DNA-sequencing platforms, the sample-loading agent, and the assay-loading agent.

The Scan

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.

Study Explores Animated Digital Message Approach to Communicate Genetic Test Results to Family Members

In the Journal of Genetic Counseling, the approach showed promise in participants presented with a hypothetical scenario related to a familial hereditary breast and ovarian cancer syndrome diagnosis.

Computational Tool Predicts Mammalian Messenger RNA Degradation Rates

A tool called Saluki, trained with mouse and human messenger RNA data, appears to improve mRNA half-life predictions by taking RNA and genetic features into account, a Genome Biology paper reports.

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.