Euan Ashley speaks about precision medicine and said clinical-grade analysis has been limited by complex regions in the human genome. His key theme,”Precision medicine needs to be accurate medicine,” was illustrated with several examples where short-read sequencing or traditional clinical sequencing methods failed to be accurate. Also included: targeted RNA sequencing and gene phasing with long-read sequencing.
Karyn Meltz Steinberg presents the first high quality African reference genome assembly of the Yoruban individual, NA19240, produced from SMRT Sequencing data. She said PacBio sequencing offers significant improvement over short-read sequence data for high-quality assemblies.
In this AGBT virtual poster video, Jason Chin, a bioinformatician at PacBio, describes a polyploidy-aware de novo assembly approach called FALCON and a new algorithm, dubbed FALCON-unzip, that involves “unzipping” diploid genomes for de novo haplotype reconstructions from SMRT Sequencing data. These methods are illustrated in a studies of fungal, Arabidopsis and human datasets for the resolution of structural variation and characterization of haplotypes.
PacBio bioinformatician Lawrence Hon describes using Targeted Locus Amplification Technology from Cergentis with SMRT Sequencing to analyze extremely large portions of chromosomes. He reports an 81 kb BRCA1 example, sequenced and phased into a single, error-free haplotype block.
Swati Ranade from PacBio presents her AGBT poster demonstrating the use of SMRT Sequencing to characterize complex immune regions from human, macaque, and hummingbird. Included: a de novo assembly of complete KIR haplotypes, the MHC region, and MHC alleles.
In his closing remarks, PacBio CSO Jonas Korlach comments on the trends of whole genome sequencing, and the recognition of the need for higher-quality human genome assemblies. He also demonstrated that long-read sequencing allows scientists to find SNPs and structural variants while also analyzing epigenetics and phasing genes or variants.
Jonas Korlach presents data from the new Sequel System and discussed the value of SMRT Sequencing for addressing complex disease. He shows comparisons of Sequel data to PacBio RS II data in applications such as targeted sequencing of structural variants, somatic variation detection of cancer samples, and full-length isoform transcript sequencing.
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…
Melissa Laird Smith discussed how the Icahn School of Medicine at Mount Sinai uses long-read sequencing for translational research. She gave several examples of targeted sequencing projects run on the Sequel System including CYP2D6, phased mutations of GLA in Fabry’s disease, structural variation breakpoint validation in glioblastoma, and full-length immune profiling of TCR sequences.
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.
PacBio Sequencing is characterized by very long sequence reads (averaging > 10,000 bases), lack of GC-bias, and high consensus accuracy. These features have allowed the method to provide a new gold standard in de novo genome assemblies, producing highly contiguous (contig N50 > 1 Mb) and accurate (> QV 50) genome assemblies. We will briefly describe the technology and then highlight the full workflow, from sample preparation through sequencing to data analysis, on examples of insect genome assemblies, and illustrate the difference these high-quality genomes represent with regard to biological insights, compared to fragmented draft assemblies generated by short-read sequencing.
PacBio bioinformatician Aaron Wenger presents this ASHG 2016 poster demonstrating human structural variation detection at varying coverage levels with SMRT Sequencing on the Sequel System. Results were compared to truth sets for well-characterized genomes. Results indicate that even low coverage of SMRT Sequencing makes it possible to detect hundreds of SVs that are missed in high-coverage short-read sequencing data.
This tutorial provides an overview of the Long Amplicon Analysis (LAA) application. The LAA algorithm generates highly accurate, phased and full-length consensus sequences from long amplicons. Applications of LAA include HLA typing, alternative haplotyping, and localized de novo assemblies of targeted genes. This tutorial covers features of SMRT Link v5.0.0.
At PAG 2017, Rockefeller University’s Erich Jarvis offered an in-depth comparison of methods for generating highly contiguous genome assemblies, using hummingbird as the basis to evaluate a number of sequencing and scaffolding technologies. Analyses include gene content, error rate, chromosome metrics, and more. Plus: a long-read look at four genes associated with vocal learning.
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…