Anne Deslattes Mays from Georgetown University presents her AGBT poster on the balancing act of discovering transcriptome isoforms. Using SMRT Sequencing to study differentiated and undifferentiated cells from human bone marrow, she analyzed full-length isoforms and confirmed unexpected findings with mass spec. She says access to unfragmented long reads allows scientists to move from transcripts to proteins.
Ulf Gyllensten from Uppsala University describes his AGBT poster showing the use of SMRT Sequencing for HLA allele typing. He says long reads are essential for sequencing the HLA genes because they link exons in a single read and do not introduce bias, as short-read sequencers can. Looking at fusion transcripts from CML patients generated information that couldn't be achieved with any other technology, he adds.
Yunfei Guo, from the University of Southern California, presents his ASHG 2015 poster on a de novo assembly of a diploid Asian genome. The uniform coverage of long-read sequencing helped access regions previously unresolvable due to high GC bias or long repeats. The assembly allowed scientists to fill some 400 gaps in the latest human reference genome, including some as long as 50 kb.
Alex Dainis, a graduate student in Euan Ashley’s lab at Stanford University, presents her ASHG 2015 poster on haplotyping for genes linked to hypertrophic cardiomyopathy. Using the Iso-Seq method with SMRT Sequencing, she sequenced full transcripts of two genes of interest, generating data on 150 different isoforms. Rare variants, which could not be found with other technologies, were associated with haplotypes.
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.
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.
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.
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.
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.
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.
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