Paul Hagerman, MD/PhD, a professor in the biochemistry and molecular medicine department at UC Davis discusses the use of PacBio SMRT sequencing technology for the fragile X gene. Hagerman says the PacBio RS is able to sequence through more than a kilobase of the CGG trinucleotide repeat element underlying Fragile X Syndrome -- something no other sequencing platform has achieved. He also plans to use the data to study methylation of this gene, which tends to occur in cases where there are more than 200 copies of the CGG element.
Dr. Nezih Cereb, CEO & co-founder of HistoGenetics shares his reasons for adopting the PacBio DNA Sequencing platform for their operations and elaborates how the system's unique ability to sequence full-length HLA amplicons irrespective of insert size and to provide fully phased HLA alleles will be used for HLA typing.
Bobby Sebra from the Icahn School of Medicine at Mount Sinai talks about how he uses PacBio sequencing for disease biology, pathogen surveillance, metagenomic sequencing, and more. With reads 70 kb or even longer, SMRT Sequencing lets him characterize tandem repeats and other structurally relevant elements that are inaccessible with short-read sequencing.
Harold Swerdlow, who formerly ran the R&D department at Wellcome Trust Sanger Institute, discusses the Sanger team's use of the PacBio RS sequencer. He says the system is uniquely suited for de novo sequencing and genome assembly, methylation pattern identification, and low-level variant detection because of its long reads and high-accuracy, single-molecule sequencing. At Sanger, that makes a real difference for the large-scale projects they have in cancer biology, pathogen sequencing, and human genetics.
The Genome Analysis Centre's (TGAC) Matthew Clark, who leads the sequencing technology development group, says that high-accuracy PacBio sequencing is ideal for GC-rich or AT-rich genomes since it shows no GC bias. This has enabled his team to sequence several strains of Streptomyces and elucidate gene clusters thought to be important in antibiotic production. Clark says long reads from SMRT Sequencing are good for other hard-to-sequence regions, such as repeats or large transposable elements.
Chad Nusbaum from the Broad Institute talks about the sequencing projects that will now be possible with the new Sequel System from PacBio, including efforts to sequence human genomes that currently are limited by cost.
Yunfei Guo, a grad student at the University of Southern California, discusses the benefits of SMRT Sequencing: very long reads that make it possible to resolve long repetitive regions and discover structural variants, and a random error mode that allows for extremely high accuracy.
Alex Dainis from Stanford University says the Sequel System from PacBio will offer more power to multiplex samples more efficiently.
Lemuel Racacho at the Children's Hospital of Eastern Ontario says that his team chose SMRT Sequencing to detect longer isoforms of noncoding RNAs and to survey numerous transcripts. Continuous long reads offer a chance to see a lot of RNA missed by other technologies, he adds.
Anne Deslattes Mays from Georgetown University describes how long-read sequencing provided important biological answers after three years of short-read sequencing failed to generate enough information for her gene discovery project. She says long reads are essential for understanding alternative splicing, RNA editing, and genome rearrangements.
Mario Caccamo, head of bioinformatics at The Genome Analysis Centre (TGAC) in the UK, integrates many different sequencing technologies to get the best of each for optimal genome assemblies, analysis, and annotation. He uses PacBio's SMRT Sequencing due to its unique long reads for scaffolding and finishing genomes.
Dan Geraghty from the Fred Hutchinson Cancer Research Center says that PacBio sequencing “gives us access to genomic sequence data that's not available by any other means.” He's using it to understand the genetic basis of autoimmune diseases and has for the first time gotten answers to problems that have been challenging researchers for decades.
Mario Caccamo, head of bioinformatics at The Genome Analysis Centre (TGAC) in the UK, integrates many different sequencing technologies to get the best of each for optimal genome assemblies, analysis, and annotation. He uses PacBio's SMRT Sequencing due to its unique long reads for scaffolding and finishing genomes.
Yuta Suzuki from the University of Tokyo details his experience using SMRT Sequencing for generating data for haplotype-specific epigenetic analysis.
Commentary from PacBio users on their applications of SMRT Sequencing, including Ulf Gyllensten (Uppsala University), Tim Smith (USDA-ARS) and Bobby Sebra (Icahn School of Medicine)