Richard Gibbs, Director of Baylor College of Medicine’s Human Genome Sequencing Center, talked about the transition to genomic medicine. This hasn’t been as simple as people would like due to such issues as the incomplete reference genome, the difficulty in characterizing some variation, and the lack of knowledge about the function of some genes. At Baylor, most of the human genome sequencing is done for children with Mendelian disorders. He said that among 7,000 samples processed using short-read exome sequencing, only about 25% of these cases are solved. The relatively low diagnosis rate is likely due to structural variation and…
Michael Schatz of Cold Spring Harbor Laboratory and Johns Hopkins University discusses the challenges in detecting structural variations (SVs) in high throughput sequencing data, especially more complex SVs such as a duplication nested within an inversion. To overcome these challenges, Dr. Schatz and his team have been applying long-read sequencing to analyze SVs in a range of samples from small microbial genomes, through mid-sized plant and animal genomes, to large mammalian genomes. The increased read lengths, which currently average over 10kbp and some approach 100kbp, make it possible to span more complex SVs and accurately assess SVs in repetitive regions,…
Robert Sebra reports the use of SMRT Sequencing at the Icahn Institute and presents some early data from the new Sequel System. Topics include: Targeted sequencing applications for CYP2D6 metabolism and Gaucher disease, tandem repeat detection in FTD/ALS patients, structural variation detection for Goldenhar Syndrome, inverted PCR assays for detection of DNA damage in Glioblastome, whole gene BRCA sequencing, and sensitive somatic variant detection in heterogeneous tissues.
Chetana Pandya, a bioinformatician at the Icahn School of Medicine at Mount Sinai discusses how the institute is using their PacBio Systems in a variety of cancer research project including detecting somatic fusions events in patient-derived cancer samples and validating somatic variants.
Fritz Sedlazeck, a bioinformatician at John Hopkins, discusses why he’s excited to use long-read sequencing from PacBio to resolve structural variants.
Fritz Sedlazeck, a postdoc at Johns Hopkins University, describes his structural variant detection tool Sniffles in this poster from AGBT 2016. Included: examples of structural variants that could not be detected with other algorithms.
Bioinformatics scientist Chetanya Pandya from the Icahn School of Medicine at Mount Sinai presents a poster comparing short-read and long-read sequencing to detect somatic fusion events in cancer samples. SMRT Sequencing identified significantly more fusions, while many of the short-read calls may have been artifacts from challenging regions of the genome.
This presentation describes a new genome browser for read alignments around complex variation: genomeribbon.com. Ribbon was built for viewing genomic read alignments around structural variants. It is very useful for looking at long-read alignments where we can see a complicated set of variants captured within individual reads. Ribbon can also be used to view assembly alignments such as from MUMmer.
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.
At AGBT 2017, Mike Schatz from Johns Hopkins University and Cold Spring Harbor Laboratory presented data from sequencing, assembling, and analyzing personalized, phased diploid genomes with either Illumina, 10x Genomics, and PacBio SMRT Sequencing. Compared to the short-read-based methods, PacBio data assembled in large, complete contigs and contained the broadest range of structural variants with the best resolution. Plus: unexpected translocation findings with SMRT Sequencing, validated in follow-up studies.
SMRT Sequencing is a DNA sequencing technology characterized by long read lengths and high consensus accuracy, regardless of the sequence complexity or GC content of the DNA sample. These characteristics can be harnessed to address medically relevant genes, mRNA transcripts, and other genomic features that are otherwise difficult or impossible to resolve. I will describe examples for such new clinical research in diverse areas, including full-length gene sequencing with allelic haplotype phasing, gene/pseudogene discrimination, sequencing extreme DNA contexts, high-resolution pharmacogenomics, biomarker discovery, structural variant resolution, full-length mRNA isoform cataloging, and direct methylation detection.
In this PacBio User Group Meeting presentation, PacBio scientist Kristin Mars speaks about recent updates, such as the single-day library prep that’s now possible with the Iso-Seq Express workflow. She also notes that one SMRT Cell 8M is sufficient for most Iso-Seq experiments for whole transcriptome sequencing at an affordable price.
Dr. Wenger gives attendees an update on PacBio’s long-read sequencing and variant detection capabilities on the Sequel II System and shares recommendations on how to design your own study using HiFi reads. Then, Dr. Sund from Cincinnati Children’s Hospital Medical Center describes how she has used long-read sequencing to solve rare neurological diseases involving complex structural rearrangements that were previously unsolved with standard methods.
To bring personalized medicine to all patients, cancer researchers need more reliable and comprehensive views of somatic variants of all sizes that drive cancer biology.
During the past decade, the search for pathogenic mutations in rare human genetic diseases has involved huge efforts to sequence coding regions, or the entire genome, using massively parallel short-read sequencers. However, the approximate current diagnostic rate is