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Science  25 Apr 2014:
Vol. 344, Issue 6182, pp. 431
DOI: 10.1126/science.344.6182.431-a

aCGH DATA ANALYSIS

Complimentary with all CytoSure array purchases, the latest version (4.5.3) of CytoSure Interpret Software is a powerful and easy-to-use package for the analysis of aCGH data, the gold-standard for copy number variation (CNV) detection. Offering an impressive combination of advanced features, including Automatic Aberration Classification, the software allows the choice of standardized or customized user-defined data analysis. With this latest version, OGT has introduced several innovative new features that further facilitate and standardize the data analysis workflow in order to deliver rapid access to meaningful results. By using information available in online databases such as DECIPHER and settings defined by the user, the Automatic Aberration Classification enables users to configure the software to automatically perform an initial classification of any detected CNV, accelerating analysis and standardizing the interpretation process. CytoSure Interpret Software allows simultaneous access to sample and experiment information across a network, providing the potential for labs on multiple sites to access a central database.

DNA COPY NUMBER ANALYSIS

Version 7.5 of Nexus Copy Number software introduces a new next generation sequencing (NGS) module for analysis of sequence variants from array or NGS platforms and detection of copy number from sequencing data. The software expands support for the Affymetrix platform with support for the OncoScan FFPE Assay Kit and Affymetrix Axiom Human Genotyping array. Notable features for the case review workflow include new filters that quickly cut variations down to potential pathogenic ones, including a trio analysis filter to remove parental calls from the proband, and the ability to display previous samples containing a variant under review. For cancer applications, improvements include ASCAT 2.1—which does not require a matched normal—and the ability to detect copy number variations from whole-genome and whole-exome sequencing. Nexus version 7.5 features integrated analysis allowing identification of sequence variants overlapping copy number aberrations or homozygous regions, along with the added ability to store and query sequence variants in the Nexus DB genomic data repository.

ICP-MS SOFTWARE

Syngistix software is a workflow-based software designed to improve efficiencies in the laboratory. It features an easy-to-use, intuitive interface, along with new automated method setup tools for faster implementation. The software's user-defined and customizable reporting capabilities facilitate support for a variety of peripherals, including online auto-dilution systems, laser ablation, flow injection, and field-flow fractionalization. The software's optional dedicated Nano Application Module can be combined with the NexION 350 ICP-MS for nanomaterial detection and characterization.

MLPA ANALYSIS

The latest version of the GeneMarker Software includes automated quality control evaluation in the widely used MLPA analysis module. Multiplex Ligation-dependent Probe Amplification (MLPA) is a powerful technique to detect deletions and insertions and is used in clinical research on a variety of genetic diseases and cancers. MLPA reactions are composed of several steps; quality control fragments in MLPA reactions indicate success or failure of polymerase chain reaction, denaturation, ligation, hybridization, and adequate DNA concentration for the reaction. Before the inclusion of this automated quality control evaluation feature, the analyst would review the raw data prior to analysis and identify any problematic samples. The automated evaluation of quality control fragments detects and flags any sample that does not meet the criteria of the MLPA kit, increasing efficiency of data analysis and improving workflow. The software processes and normalizes raw data files, allowing the user to load their raw data, process the data, and proceed directly to MLPA analysis.

NEXT GENERATION SEQUENCING LIMS

The Exemplar Next Generation Sequencing (NGS) Laboratory Information Management System (LIMS) will track multiple NGS platform workflows from request through processing and analysis. Exemplar's NGS LIMS features all of the following: prebuilt CLIA standard workflows for leading NGS platforms, instrument integrations with NGS platforms and leading QC instruments, support for automation via integration with leading robotic sample preparation platforms, a highly graphical and intuitive interface, graphical executive dashboard for viewing lab activity in any timeframe, and complete consumables management for reagents and other consumables with reorder alerts. It is a 100% web-based solution with no extra software required from the client and is usable on iPads and other tablets. The system is scalable for small labs to large multinational, multi-lab deployments. Exemplar NGS LIMS is targeted at NGS labs, but retains the full capability of the Exemplar ecosystem to address any lab's needs, such as genotyping and proteomics.

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  • Newly offered instrumentation, apparatus, and laboratory materials of interest to researchers in all disciplines in academic, industrial, and governmental organizations are featured in this space. Emphasis is given to purpose, chief characteristics, and availabilty of products and materials. Endorsement by Science or AAAS of any products or materials mentioned is not implied. Additional information may be obtained from the manufacturer or supplier.

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