ASHG Day 2: Population and Clinical Genetics, Plus a SMRT Sequencing Roadmap
Thursday, October 19, 2017
The PacBio team hosted a luncheon workshop at ASHG yesterday titled “Population and Clinical Genetics Studies Using Long-read SMRT Sequencing.” Thanks to all the conference attendees who took time out of a very busy meeting to join us! If you couldn’t attend, we summarized the highlights below and will share recordings of the presentations soon.
Long-read Sequencing – for Detecting Clinically Relevant Structural Variation
Han Brunner, Head of Clinical Genetics at Radboud University Medical Center, kicked off the event with a talk about using SMRT Sequencing to detect clinically relevant structural variation. Introducing himself as a consumer of sequencing data, rather than a technology expert, he described a collaboration with PacBio to uncover structural variants associated with intellectual disability. Patients with this symptom often never receive a diagnosis, and while that situation has improved with exome and whole genome sequencing, it still isn’t fully addressed. In an assessment of 100 patients with severe disability, Brunner said, 38 of them still had no diagnosis even with WGS.
To overcome the challenge, his team turned to the Sequel System. In preliminary results from sequencing five trios, his team found 21 Mb of sequence revealed with SMRT Sequencing that had gone unresolved with short-read sequencing. They also found as many as 25,000 structural variants per genome, two-thirds of which were invisible to short-read technology. Brunner noted that the ability to phase data with PacBio sequencing provides “very useful information.” He also predicted that this approach could be implemented in the clinic within a year, based on the time it took to move exome sequencing toward patient care.
Expansion Sequence Variations Underlie Distinct Disease Phenotypes in SCA10
Next up was Karen McFarland, Research Assistant Professor at the University of Florida, who spoke about recent efforts to resolve repeat expansion regions associated with spinocerebellar ataxia type 10 (SCA10), a progressive neurodegenerative disorder. SCA10 is associated with a repeat expansion in the ATXN10 gene, ranging from nine repeats in unaffected individuals to as many as 4,500 in affected people. That’s as much as 22.5 kb of sequence, which has precluded thorough characterization of the region in the past. With SMRT Sequencing, though, McFarland and her team have not only successfully sequenced the region, but have also been able to accurately detect interruptions in the sea of ATTCT repeats that appear to have clinical consequence. Recently, they used the Cas9 enzyme to perform target capture of the region directly from genomic DNA of family members with different ataxia-related phenotypes.
Multi-platform Discovery of Haplotype-resolved Structural Variation in Human Genomes
Charles Lee, Scientific Director of The Jackson Laboratory for Genomic Medicine, gave the final user talk. He focused on a study from the Human Genome Structural Variation Consortium to assess many different technologies for discovering structural variants. The analysis of Yoruban, Han Chinese, and Puerto Rican trios showed that no single tool is currently capable of capturing the full range of human structural variants, which can be larger than a megabase. SMRT Sequencing, though, was found to dramatically increase the number of variants that could be detected and contributed to a seven-fold overall increase in structural variation discovery, he said. Among the variants he finds particularly interesting to pursue are inversions and mobile element insertions.
PacBio Applications Updates and Future Roadmap
Our CSO Jonas Korlach spoke as well, offering updates on structural variation, targeted sequencing and Iso-Seq analysis, as well as a look at future SMRT Sequencing developments. On the structural variation front, he noted that tools have evolved enough now that PacBio users can access a full SV detection workflow — including sequencing, read mapping, variant calling, and visualization — in the new SV Calling Software. Learn more about it or try our new project calculator on our new structural variation web page. For amplification-free target enrichment using the Cas9 protocol mentioned by McFarland, Korlach said that development is currently underway to adapt it for the Sequel System. If you’re attending ASHG, you can find out more at the CoLab session on Friday or check out the amp-free targeted sequencing web page.
Looking ahead, he told attendees that by the end of the year there will be a new accelerated protocol for library prep, a doubling of sequencing yield, and updated analysis tools in SMRT Link 5.1. Another 2-fold improvement is expected in 2018, and with the introduction of a new SMRT Cell with 8 million ZMWs (8-fold increase) in early 2019, a combined 30-fold capacity boost compared to current throughput will be achievable. These advances will help support the rising number of population studies that require an ever-increasing number of high-quality human genome assemblies.
We’ll be reporting on more from ASHG in the coming days, so stick with us!