Masao Nagasaki from Tohoku University presents in his ASHG 2015 poster on typing of HLA class I genes using SMRT Sequencing. By using long-read sequencing he was able to successfully type these genes for 220 individuals. This included samples that he had previously been unsuccessful typing using short-read sequencing.
PacBio scientist Cheryl Heiner describes new low-input protocols for SMRT Sequencing library construction. With these revised methods, 2 kb libraries can be generated from as little as 10 ng of DNA, while 10 kb libraries require only 100 ng of sample.
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.
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.
In this AGBT poster, Cheryl Heiner from PacBio describes results from a variety of experiments optimizing a protocol for full-length 16S amplification for 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
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.
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.
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.
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.
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.
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.
Dan Geraghty from the Fred Hutchinson Cancer Research Center presents his AGBT poster on a new PacBio-based solution to sequence extended genomic regions — in this case, KIR and MHC, two of the most variable regions of the human genome. He reports data revealing for the first time regions that may be associated with autoimmune diseases such as diabetes, rheumatoid arthritis, and multiple sclerosis, and also shows that sequences were phased, complete, and highly accurate.
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.