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  • Structural Variant Detection of short and long reads with NextGENe® 2nd Generation S

    September 30, 2009, State College PA SoftGenetics announced the new capability of whole genome structural variant detection in both short and long reads generated by 2nd generation systems such as the Roche Genome Analyzer II, Illumina GAII and Life Science SOLiD System with its NextGENe software.

    Structural variations, including insertions, deletions, inversions, gene fusions and copy number variants, occur frequently across the human genome and have been shown to be important in a number of diseases. Although there are several useful technologies for detecting SV’s all have their limitations. Paired-end read mapping has been used to detect shorter deletions and to hone in on breakage sites but is unable to detect structural variants larger than the library size.

    NextGENe makes it easy to find and map structural variants with sequence data from the Roche FLX Titanium system and short paired read data of the GAII and SOLiD using the NextGENe’s new pair linking technology which allows large mismatches when aligning to genome reference in order to detect SV’s. NextGENe then displays the information about those regions in a special structural variant report.

    Short paired reads such as those generated by the Illumina GAII and AB SOLiD System can be utilized by NextGENe to detect the SV’s. NextGENe’s analysis wizard allows users to choose between short paired reads and longer reads to perform structural variant detection.

    “The structural variant technology of NextGENe,” indicated Dr. Jonathan Liu, VP R&D, “provides an exciting new dimension in genomic disorder research. NextGENe’s technology, when used to perform the analysis of short and long read sequences, provides unerring detection of SV’s not possible with micro arrays and other older technologies.”

    The structural variant report uses a specialized algorithm to list regions of high variant frequency. Interference from false positives causes by sequencing errors is rarely detected in this report since multiple errors are unlikely to occur in a local region, thus providing high specificity and accuracy in the SV detection.

    For long reads NextGENe generates pseudo-paired reads for the sequence aligned to these regions by breaking the original reads into pairs. The pseudo pairs are then aligned to the reference genome mapping the structural variants with 99.9% accuracy. Detailed information on where these reads align is available in NextGENe’s Paired Read reports.

    The company offers no-cost 30-day trials as well as web-based training on its genetic analysis software packages. Interested parties may request the software on the company website: www.softgenetics.com or via email: [email protected]

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