In this presentation, Shawn Levy from the HudsonAlpha Institute for Biotechnology and HudsonAlpha Discovery offers a look at his team’s early access experience with the Sequel II System. Recent work includes a project designed to improve sequencing results from FFPE samples with long-read data. The protocol is still being optimized, but preliminary results indicate that SMRT Sequencing improves the quality of data that can be produced from these highly degraded samples. Looking ahead, Levy’s team will be using SMRT Sequencing to generate about 7,000 long-read genome assemblies for the All of Us program.
Penelope Bonnen, an assistant professor at Baylor College of Medicine, discusses her use of PacBio SMRT sequencing to look at whole mitochondrial genomes as she reviews her AGBT 2012 poster. Dr. Bonnen is studying a Micronesian population with unusually high rates of obesity, diabetes, and cardiovascular disease to figure out how mitochondrial genetics contributes to adult-onset metabolic syndrome. She describes two approaches in a pilot project for full-length mitochondrial sequencing: one using a 500-base pair insert library and another directly sequencing the single 17 kb amplicon.
Simon Chan, UC Davis on how PacBio long read sequencing revealed higher order repeats in centromeres of switchgrass which would have been hidden if you are restricted by the much shorter Sanger reads.
Computational biologist Mauricio Carneiro, PhD, describes a Broad Institute technology comparison to determine how PacBio, Ion Torrent, and Illumina MiSeq perform in discovering and validating human SNPs. Noted PacBio advantages: no bias in GC regions, no systematic errors, and no sequence degradation over increased read length. In a study using samples from the 1,000 Genomes project, PacBio outperformed MiSeq and Ion Torrent in sensitivity and specificity.
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.
In this AGBT talk, Mount Sinai’s Eric Schadt uses PacBio sequencing on human genomes and reports finding uncharacterized structural variation that could have diagnostic utility. Schadt says that SMRT sequencing is advantageous for long-range genetic information, extreme GC content, and highly repetitive regions. He presents sequence data for a CEPH individual studied for repeat expansions, showing that long reads can resolve the majority of these regions.
Ali Bashir from the Icahn Institute for Genomics and Multiscale Biology at Mount Sinai describes a tool to detect tandem repeats (PACMonSTR), which he believes are dramatically underrepresented in the human genome reference but that can be discovered with PacBio sequencing. In a collaboration with Cold Spring Harbor Laboratory and Cornell, Bashir and his team generated shotgun, whole-genome sequence data from human genomic DNA using PacBio sequencing. Their goal was to find structural variation features that are not present in the existing reference. He shows numerous examples wherein the long PacBio reads were able to resolve inversions in the sample,…
Shane Brubaker from renewable oil manufacturer Solazyme reports using the PacBio system to sequence the genome of a GC-rich strain of algae that couldn’t be fully assembled with short-read sequence data. He notes that CCS reads exceed Sanger quality at significantly lower cost.
In this BioConference Live webinar, PacBio CSO Jonas Korlach highlights how multi-kilobase reads from SMRT Sequencing can resolve many of the previously considered ‘difficult-to-sequence’ genomic regions. The long reads also allow phasing of the sequence information along the maternal and paternal alleles, demonstrated by full-length, fully phased HLA class I & II gene sequencing. In addition, characterizing the complex landscape of alternative gene products is currently very difficult with short-read sequencing technologies, and he describes how long-read, full-length mRNA sequencing can be used to describe the diversity of transcript isoforms, with no assembly required. Lastly, in the exciting area of…
Swati Ranade from PacBio presents recent efforts to look at challenging regions of the human genome using SMRT Sequencing. She highlights a study just published that fully sequences a particular mucin gene for the first time, as well as work on KIR haplotypes in humans and other primates.
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.