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ASHG 2019: CoLab Session Highlights Structural Variation and Transcriptome Sequencing

Thursday, October 31, 2019

At ASHG 2019, PacBio scientists Aaron Wenger and Liz Tseng offered a CoLab presentation.

At the annual meeting of the American Society of Human Genetics in Houston, PacBio scientists presented how our Sequel II System performs for structural variant (SV) detection and for whole transcriptome sequencing. The educational workshop focused on experiments that can be done using a single SMRT Cell 8M on the Sequel II System.

The event kicked off with Aaron Wenger walking through SV analysis, which he said has mirrored the development path of single nucleotide variants, from proof-of-concept to individual rare disease studies and now to large cohort studies like SOLVE-RD in Europe and All of Us in the United States.

Wenger showed a variety of SV types that can be detected with highly accurate SMRT Sequencing, such as insertions, deletions, translocations, and inversions.  He also showed the standard SV discovery and analysis workflow, and the precision and recall performance of this method.  He noted that a single SMRT Cell is now sufficient to achieve high recall for SV discovery for two human samples.

Next up, Elizabeth Tseng (@magdoll) spoke about the Iso-Seq method for full-length transcript sequencing that eliminates the need for bioinformatics-driven isoform assembly and enables direct ORF prediction even without a reference genome. With the Iso-Seq Express Kit, she noted, customers can generate reliable results from as little as 60 nanograms of total RNA.

Using an Alzheimer’s brain Iso-Seq dataset released for ASHG, Tseng demonstrated the comprehensive, highly accurate results for full-length isoform detection using SMRT Sequencing. More than 99% of transcripts reported by the Iso-Seq method are more than 99% accurate, she added. She also looked at single-cell Iso-Seq experiments, showing examples of SMRT Sequencing paired with DropSeq or 10x Genomics workflows, and at how Iso-Seq analysis can be used to solve rare disease or characterize cancer fusion genes.

Thanks to all the attendees who took the time to listen to our presentations. We hope you enjoyed the meeting as much as we did!

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