Paul Hagerman, MD/PhD, a professor in the biochemistry and molecular medicine department at UC Davis discusses the use of PacBio SMRT sequencing technology for the fragile X gene. Hagerman says the PacBio RS is able to sequence through more than a kilobase of the CGG trinucleotide repeat element underlying Fragile X Syndrome — something no other sequencing platform has achieved. He also plans to use the data to study methylation of this gene, which tends to occur in cases where there are more than 200 copies of the CGG element.
In this ASHG 2016 virtual poster, Flora Tassone from UC Davis describes her study of the molecular mechanisms linked to fragile X syndrome and associated disorders, such as FXTAS. She is using SMRT Sequencing to resolve the FMR1 gene in premutation carriers because it’s the only technology that can generate full-length transcripts with the causative CGG repeat expansion. Plus: direct confirmation of predicted isoform configurations.
PacBio’s Jenny Ekholm presents this ASHG 2016 poster on a new method being developed that enriches for unamplified DNA and uses SMRT Sequencing to characterize repeat expansion disorders. Incorporating the CRISPR/Cas9 system to target specific genes allows for amplification-free enrichment to preserve epigenetic information and avoid PCR bias. Internal studies have shown that the approach can successfully be used to target and sequence the CAG repeat responsible for Huntington’s disease, the repeat associated with ALS, and more. The approach allows for pooling many samples and sequencing with a single SMRT Cell.
Euan Ashley from Stanford University started with the premise that while current efforts in the field of genomics medicine address 30% of patient cases, there’s a need for new approaches to make sense of the remaining 70%. Toward that end, he said that accurately calling structural variants is a major need. In one translational research example, Ashley said that SMRT Sequencing with the Sequel System allowed his team to identify six potentially causative 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…
Michael Lutz, from the Duke University Medical Center, discussed a recently published software tool that can now be used in a pipeline with SMRT Sequencing data to find structural variant biomarkers for neurodegenerative diseases with a focus on Alzheimer’s disease, ALS, and Lewy body dementia. His team is particularly interested in short sequence repeats and short tandem repeats, which have already been implicated in neurodegenerative disease.
Jonas Korlach spoke about recent SMRT Sequencing updates, such as latest Sequel System chemistry release (1.2.1) and updates to the Integrative Genomics Viewer that’s now update optimized for PacBio data. He presented 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.
Tetsuo Ashizawa, Director of the Neuroscience Research Program at Houston Methodist Research Institute, presents a novel amplification-free targeted enrichment method using CRISPR-Cas9 for the disease-causing repeat expansion in SCA10. Using long-read sequencing, he has been able to span multi-kilobase repetitive regions and identify interruption sequence motifs that correlate with alternative clinical phenotypes in individuals from varying ethnic backgrounds. Webinar registration required.
In this video, PacBio scientists present ongoing improvements to the Integrative Genomics Viewer (IGV) and demonstrate how multiple new features improve visualization support for PacBio long-read sequencing data. The video describes these recent updates which include; quick consensus accuracy mode to hide random single-molecule errors, direct phasing of haplotypes using long-read evidence, and visual annotation of insertions and deletions relative to the reference with enumeration of gap size for individual reads. These new features are available now in the development version of IGV, which can be found at http://software.broadinstitute.org/software/igv/download_snapshot. The Sequel sequencing data used in this demonstration is also publicly…
At AGBT 2017, Lars Paulin from the University of Helsinki presented this poster on whole genome sequencing of the virus responsible for progressive multifocal leukoencephalopathy, a rare and dangerous brain infection. His team used long amplicon analysis to resolve the whole virus genome from three patient samples, pooled them for SMRT Sequencing, and identified variants and rearrangements. This work represents the first time the viral genome was sequenced from patients.
Adam Ameur from the National Genomics Infrastructure at SciLifeLab presented this poster at AGBT 2017. In it, he details a validation study for the use of CRISPR/Cas9 to capture genomic targets without the use of amplification. Results from 12 Huntington’s patients indicate that this approach paired with SMRT Sequencing generates accurate repeat counts in the HTT gene.
Targeted sequencing has proven to be an economical means of obtaining sequence information for one or more defined regions of a larger genome. However, most target enrichment methods are reliant upon some form of amplification. Amplification removes the epigenetic marks present in native DNA, and some genomic regions, such as those with extreme GC content and repetitive sequences, are recalcitrant to faithful amplification. Yet, a large number of genetic disorders are caused by expansions of repeat sequences. Furthermore, for some disorders, methylation status has been shown to be a key factor in the mechanism of disease. We have developed a…
In this ASHG 2017 presentation, Karen McFarland of the University of Florida presented research on spinocerebellar ataxia type 10 (SCA10), a progressive neurodegenerative disease caused by repeat expansions. She outlined efforts to sequence these repeat expansions including using CRISPR-Cas9 system coupled with SMRT Sequencing. McFarland shared findings from a study of a Parkinson’s disease patient and family that showed variations in expansion sequence can underlie distinct disease phenotypes.
In this ASHG workshop presentation, Janet Song of Stanford School of Medicine shared research on resolving a tandem repeat array implicated in bipolar disorder and schizophrenia. These psychiatric diseases share a number of genomic risk variants, she noted, but scientists continue to search for a specific causal variant in the CACNA1C gene suggested by previous genome-wide association studies. SMRT Sequencing of this region in 16 individuals identified a series of 30-mer repeats, containing a total of about 50 variants. Analysis showed that 10 variants were linked to protective or risk haplotypes. Song aims to study the function of these variants…