Learn why it is critically important to understand accuracy in DNA sequencing to distinguish important biological information from sequencing errors.
In this short video, Aaron Wenger, a Principal Scientist at PacBio, explains what highly accurate long reads, or HiFi reads, are and how they help to detect all variant types including single nucleotide, indels, and structural variants. He goes on to recap the precisionFDA Truth Challenge V2 which used Genome in a Bottle (GIAB) benchmarks to evaluate various sequencing technologies. In the 2020 challenge, when ranked for accuracy, PacBio HiFi reads delivered the highest precision and recall in all categories.
In this webinar, Adam Ameur of SciLifeLab at Uppsala University shares how he uses Single Molecule, Real-Time (SMRT) Sequencing applications for medical diagnostics and human genetics research, including sequencing of single genes and de novo assembly of human genomes as well as a new method for detection of CRISPR-Cas9 off-targets.
In this presentation, Naomichi Matsumoto from Yokohama City University speaks about the use of SMRT Sequencing to solve Mendelian diseases, including the story of how his lab discovered a 12.4 kb structural variant that’s responsible for progressive myoclonic epilepsy in two siblings. He also reports progress in understanding repeat expansion disorders by pairing SMRT Sequencing with new analysis tools designed to highlight repetitive areas.
In this presentation, Shawn Levy from the HudsonAlpha Institute for Biotechnology and HudsonAlpha Discovery offers a look at his team’s early access experience with the Sequel II System. Recent work includes a project designed to improve sequencing results from FFPE samples with long-read data. The protocol is still being optimized, but preliminary results indicate that SMRT Sequencing improves the quality of data that can be produced from these highly degraded samples. Looking ahead, Levy’s team will be using SMRT Sequencing to generate about 7,000 long-read genome assemblies for the All of Us program.
To start Day 1 of the PacBio User Group Meeting, Jonas Korlach, PacBio CSO, provides an update on the latest releases and performance metrics for the Sequel II System. The longest reads generated on this system with the SMRT Cell 8M now go beyond 175,000 bases, while maintaining extremely high accuracy. HiFi mode, for example, uses circular consensus sequencing to achieve accuracy of Q40 or even Q50.
In this presentation, Emily Hatas of PacBio offers a look a how SMRT Sequencing has changed over the years as well as the most common applications in human genome analysis: high-throughput structural variant detection; comprehensive variant detection; and de novo assembly of reference genomes.
To comprehensively detect large variants in human genomes, we have extended pbsv – a structural variant caller for long reads – to call copy-number variants (CNVs) from read-clipping and read-depth signatures. In human germline benchmark samples, we detect more than 300 CNVs spanning around 10 Mb, and we call hundreds of additional events in re-arranged cancer samples. Long-read sequencing of diverse humans has revealed more than 20,000 insertion, deletion, and inversion structural variants spanning more than 12 Mb in a typical human genome. Most of these variants are too large to detect with short reads and too small for array…
Bipolar disorder (BD) is a phenotypically and genetically complex neurological disorder that affects 1% of the worldwide population. There is compelling evidence from family, twin and adoption studies supporting the involvement of a genetic predisposition with estimated heritability up to ~ 80%. The risk in first-degree relatives is ten times higher than in the general population. Linkage and association studies have implicated multiple putative chromosomal loci for BD susceptibility, however no disease genes have yet to be identified. Here, we have fully characterized a ~12 Mb significantly linked (lod score=3.54) genomic region on chromosome Xq24-q27 in an extended family from…
The latest advancements in Sequel II SMRT Sequencing have increased average read lengths up to 50% compared to Sequel II chemistry 1.0 which allows multiplexing of 2-3 small organisms (98% of conserved genes) for both individuals. For microbial multiplexing, we multiplexed 48 microbes with varying complexities and sizes ranging 1.6-8.0 Mb in single SMRT Cell 8M. Using a new end-to-end analysis (Microbial Assembly Analysis, SMRT Link 8.0), assemblies resulted in complete circularized genomes (>200-fold coverage) and efficient detection of >3-200 kb plasmids. Finally, the long read lengths (>90 kb) allows detection of barcodes in large insert SMRTbell templates (>15 kb)…