PacBio scientist Khai Luong reviews her AGBT poster which was the first example showing SMRT Sequencing could be used to directly detect epigenetic modification in a eukaryotic organism.
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.
Keith Robison, from Warp Drive Bio, discusses his experiences using PacBio for antibiotic drug discovery in GC-rich Streptomyces genomes
In this poster presentation, PacBio scientist Ellen Paxinos describes an improved algorithm for circular consensus reads. Using this new algorithm, dubbed CCS2, it is possible to reach arbitrarily high quality across longer insert lengths at a lower cost and higher throughput than Sanger Sequencing. She shows results from the application of CCS2 to the characterization of the HIV-1 K103N drug-resistance associated mutation, which is both important clinically, and represents a challenge due to regional sequence context.
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.
In this AGBT poster, PacBio bioinformatician Matthew Seetin presents a new assembly for Aedes aegypti cell line, the mosquito responsible for spreading viruses like Dengue and Zika. SMRT Sequencing generated a gapless assembly with a contig N50 of 1.4 Mb, compared to 82 kb in the previous assembly. The genome features a number of transposable elements and long tandem repeats.
In this poster presentation, PacBio scientist Richard Hall describes a collaboration with the University of Minnesota to use long-read metagenomic profiling with SMRT Sequencing to analyze the gut microbiome of a patient who had undergone a fecal transplant after chronic C. difficile infection.
Steve Kujawa from PacBio presents an AGBT poster reporting a study that characterized the use of SMRT Sequencing for the detection of low-frequency somatic variants. A multiplexed reference standard was amplified using the Multiplicom assay and sequenced on both the PacBio RS II and MiSeq System. Results indicate good concordance between the sequencing platforms, even at very low mutation frequencies.
Robert Morey, from Synthetic Genomics shows how his team uses SMRT Sequencing to quickly and accurately confirm the content of long pieces of synthetic DNA. Included: a cost comparison for sequencing clones with Sanger Sequencing vs. SMRT Sequencing.
Yoshihiko Suzuki, Graduate Student from University of Tokyo presents his poster (in Japanese) on characterizing a methylome of the human gut microbiome using SMRT Sequencing and metagenomic assembly
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.