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Identification and Comparison of BRCA1 and BRCA2 Variants

CLC bio
7 May 2013

Combined use of Mutiplicom’s BRCA MASTR assay with Ion Torrent’s sequencing technology and data analysis using CLC Genomics Workbench results in high sensitive and specific detection and annotation of cancer relevant mutations in BRCA1 and BRCA2. This application note shows how to analyze amplicon sequencing data and identify cancer relevant variants in these two highly-studied tumor-suppressor genes using CLC Genomics Workbench.

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CLC DNA Workbench Software

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The New Standard for Desktop-Based Bioinformatics Tools CLC DNA Workbench provides a software environment which enables users to perform advanced DNA sequence analyses such as assembly of DNA sequence data, graphically and algorithmically advanced primer design, while offering user-friendly molecular cloning tools. CLC DNA Workbench is a bioinformatics software package containing a range of specialized DNA analyses and bioinformatics tools for molecular biology. It is based on the CLC Free Workbench framework, and has similar work environment, user interface, and framework for graphical viewing. When using CLC DNA Workbench, researchers working in molecular biology labs will be able to do most daily bioinformatics work, including data management and reporting, in one single integrated and user-friendly software package. Platform independent CLC DNA Workbench is from the new generation of bioinformatics software - software that also runs on the latest versions of Mac OS X, Windows, and Linux. Efficient collaboration support The full compatibility between all types of CLC workbenches provides strong support for efficient collaboration within research groups; advanced analyses and data searches can be performed on a CLC DNA Workbench, while more basic work tasks may be performed by the remaining researchers equipped with CLC Free Workbenches. Throughout the project, all researchers can be given easy access to knowledge obtained through sharing of sequence data and sharing of research results. Examples could be figures showing annotated sequences, alignments and their underlying sequences, reports on DNA characteristics, phylogenetic trees, BLAST results etc.

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Genome AnalysisGenomics, the study of genomes, includes functional genomics, evolutionary genomics and comparative genomics. There are many genomic technologies such as DNA sequencing of whole genomes, computational biology and bioinformatics. DNA and nucleic acids must be isolated and concentrated from cells for analysis with kits, automated analyzers and software. Other useful technologies for studying genomics include PCR, microarrays and electrophoresis.Data AnalysisData analysis hardware and software is available to make data processing straight-forward yet powerful. Data software can be used for math and stats, technical graphing and image analysis. In addition, software is available for specific data analysis of electrophoresis, densitometry, ELISA and DNA sequencing.Chem / BioinformaticsCheminformatics and bioinformatics are computational techniques used in chemistry and biology, respectively, for data acquisition, processing and storage. Cheminformatics focuses on compound information, whereas bioinformatics is mainly applied to analysis and modeling of genomics, genetic and sequencing information. Hardware and software is available for data acquisition, analysis, management and storage.DNA SequencingDNA sequencing, such as sanger sequencing, is a biological technique that determines the precise order of nucleotide bases in a fragment or template of DNA. DNA sequencers and genetic analyzers are based on capillary electrophoresis, where labeled DNA fragments are electrophoretically separated by size as they migrate through a polymer. Find the best DNA sequencing products, including DNA sequencing kits, genomic libraries and genetic identity kits in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Next Generation SequencingNext-generation sequencing (NGS), also known as whole-genome sequencing, high-throughput sequencing and massive parallel sequencing, produces and analyses thousands to millions of nucleotide sequences at once. Sequencing systems operate via varying technologies depending on the manufacturer, including sequencing by synthesis, ligation, pyrosequencing, ion semiconductor and single-molecule real-time sequencing. For NGS, library preparation is paramount to successful sequencing. In this section, explore a range of library preparation kits, from targeted, amplicon-based or hybridization-based kits including epigenomic, transcriptomic and genomic workflows to fragmentation kits. Find the best next-generation sequencing products in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Target-EnrichmentNGS SoftwareMutationMutations are changes in the DNA sequence that can lead to diseases, including cancer and genetic disorders. Analyzing mutations is crucial in diagnostics, drug development, and personalized medicine. Explore mutation detection tools in our peer-reviewed product directory; compare products, check reviews, and get pricing directly from manufacturers.BRCA1Genetic VariationBreast CancerBreast cancer is a type of cancer that begins in the cells of the breast and can spread to other parts of the body. Early detection, accurate diagnosis, and targeted treatments are essential for improving patient outcomes. Browse our peer-reviewed product directory to find the best breast cancer research and diagnostic tools, compare products, check reviews, and get pricing directly from manufacturers.

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Identification and Comparison of BRCA1 and BRCA2 Variants