We were delighted to have so many ASHG attendees join our workshop, titled “Discovering and Targeting Causative Variation Underlying Human Genetic Disease Using SMRT Sequencing.” If you missed it, check out the video recordings, or read our summary below.
The event featured three impressive customer presentations, beginning with Euan Ashley from Stanford University. In his presentation titled “Towards Precision Medicine,” He started off by acknowledging that “genomic medicine is here” and described how genomes and exomes are now routinely sequenced on a daily basis, with impressive genetic discovery results. For patients with rare and undiagnosed disease, Ashley reported that current sequencing efforts now solve approximately 30% of patient cases — a real improvement over years past. Despite these gains, he said there is still a need for new approaches to make sense of the remaining 70%. “If you can’t see it, you can’t call it,” “the genome is complex,” and “repeat tracts cause disease.” These are a few of the reasons Ashley mentioned that explain why current short-read NGS methods sometimes fail to achieve the same high accuracy levels establish by Sanger sequencing for calling known causal pathogenic variants in Precision Medicine studies.
Ashley then told attendees about the unique attributes of PacBio SMRT Sequencing that make it very well suited to address these challenges. He described how longer read lengths expand both the size and types of variants that can be studied. Toward that end, he said that accurately calling structural variants (SVs) is a major need, since short-read technologies work well for single nucleotide variants (SNVs) but not for longer variants. “Long read approaches reveal previously unseen structural variation,” he said, noting that this information is critical for research into repeat expansion disorders and other diseases tied to such variants.
In the first of its kind study, Ashley described the results of a new low-fold long-read WGS method using the PacBio Sequel System (recently published bioRxiv pre-print of this study). He reported sequencing a translational research sample from his clinic to an average depth of 8.6-fold coverage. Following mapping and genome-wide SV calling, Ashley said that SMRT Sequencing then allowed his team to identify six novel SVs occurring in OMIM genes in an individual with complex and varied symptoms. One gene was associated with Carney syndrome, which was a match for the person’s physiology and was later validated. He also called for the establishment of a massive SV resource, something like the ExAc repository, that would allow scientists to understand common and rare SVs and further facilitate discovery of causative pathogenic SVs in Precision Medicine studies. In separate work, his team used the Iso-Seq method with personalized haplotyping to determine how precision gene silencing could be used for people with hypertrophic cardiomyopathy.
Our next speaker, Melissa Laird Smith from the Icahn School of Medicine at Mount Sinai, spoke about “SMRT Sequencing as a Translational Research Tool to Investigate Germline, Somatic and Infectious Diseases.” In a fascinating and wide-ranging talk, she offered examples of how the Sequel System has been deployed at Mount Sinai for applications including pharmacogenomics, immune profiling, cancer profiling, and more. She cited Stuart Scott’s CYP2D6 work, which involves amplicon sequencing to understand an individual’s drug metabolism profile. Laird Smith said the team can now multiplex 384 samples on each SMRT Cell for 100-fold coverage on the Sequel System. She also presented work on Fabry’s disease spectrum, for which amplicon sequencing resolves phased mutations to make sense of the X-linked disease. In a personalized cancer therapy pipeline, low-coverage PacBio sequencing is used to validate somatic variants found in tumors. Finally, Laird Smith talked about immune profiling, where SMRT Sequencing of full-length single molecule VDJ sequences provides complete, accurate contigs of this highly variable and complex region.
In the final customer presentation, Michael Lutz from the Duke University Medical Center gave a talk entitled “Identification and Characterization of Informative Genetic Structural Variants for Neurodegenerative Diseases.” Focusing on Alzheimer’s disease, ALS, and Lewy body dementia, Lutz spoke about a recently published software tool that can be used in a pipeline with SMRT Sequencing data to find structural variant biomarkers. His team is particularly interested in short sequence repeats and short tandem repeats, which have already been implicated in neurodegenerative disease. In one example, they used SMRT Sequencing to characterize haplotypes of the low-complexity SNCA gene that could explain the differences between traditional Alzheimer’s and the Lewy body form of Alzheimer’s. In another project, Lutz used SMRT Sequencing to phase haplotypes across APOE alleles — something that wasn’t possible with short-read data — for insight into Alzheimer’s patterns of onset, severity, and more.
Lutz spoke in place of Allen Roses, who was originally scheduled to participate in the workshop but sadly passed away last month. Our CSO Jonas Korlach began the workshop with a tribute to the human genetics visionary, whose legacy in neurodegenerative diseases will be felt for decades to come.
Korlach also spoke about recent SMRT Sequencing updates, such as the Integrative Genomics Viewer update that is now optimized for PacBio data and the recently announced Sequel System chemistry (v 1.2.1) release. It offers a 50-fold reduction in DNA input requirements for 20 kb and 30 kb libraries, with SMRT Cell output ranging from 4 Gb to 8 Gb. He noted the recent data release of structural variation detected in the NA12878 genome, including many more insertions and deletions than short-read-based technologies were able to find. Korlach also congratulated the community of SMRT Sequencing users for their impressive publication rate. In 2016 alone there were more than 1,000 papers published citing the technology! Those include de novo human genomes, deep dives into structural variation and gene expression, plenty of novel findings in human genetic variation, and much more.
Thanks to everyone who participated in the event, and also to the great scientists everywhere who are applying SMRT Sequencing to any number of complex problems to reveal new information about our species and the world around us.
January 18, 2017 | General