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New Software Release: SMRT Analysis Upgrade for Iso-Seq Analysis and HLA Allele Phasing

Monday, March 31, 2014

Today we announced the release of a software upgrade for our Single Molecule, Real-Time (SMRT®) DNA Sequencing platform. SMRT Analysis 2.2 provides enhanced functionality to support two additional applications that uniquely benefit from our long-read sequencing technology: Iso-Seq™ full-length transcript /isoform sequencing, and human leukocyte antigen (HLA) allele phasing.

The study of mRNA transcript isoforms has been challenging due to the short read lengths of other sequencing technologies. Since Iso-Seq analysis allows for the capture of full-length transcripts, scientists can use this approach to identify alternatively spliced forms of a gene, detect novel genes and isoforms, or perform transcriptome-wide analysis to annotate genes. For an example of isoform sequencing using the PacBio® platform, check out this recent PNAS paper.

The software also generates consensus sequences that can be used with third-party software for HLA analysis. This data has successfully been used with the Conexio Genomics Assign MPS sequence analysis software.

This addition is particularly useful due to the nature of the HLA complex, which includes a number of genes critical to immune system function. In humans, these genes are extraordinarily polymorphic, with several thousand alleles described so far. Correct HLA allele-specific genotyping is critical for autoimmune disease-association studies, drug hypersensitivity research, and other applications. The long reads provided by PacBio sequencing are ideally suited for accurate allele-level genotyping with unambiguous allele phasing.

Additional features of the new SMRT Analysis 2.2 upgrade include:
•    Support for detecting minor variants in genome samples with as low as 0.5% frequency
•    Speed improvements to the Hierarchical Genome Assembly Process (HGAP)
•    Workflow enhancements to SMRT Portal, the user interface for the SMRT Analysis software suite.

The new SMRT Analysis software upgrade, along with data and documentation, can be found on our DevNet site: DevNet.

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