A new Nature Communications paper shows how scientists continue to make progress elucidating some of the most complex regions of the human genome by deploying long-read PacBio sequencing technology. In this case, lead author PingHsun Hsieh (@phhBenson), senior author Evan Eichler, and collaborators at the University of Washington resolved the TCAF gene locus and identified more than 100 kb that had been missing in the human reference genome. Since the publication comes from the Eichler lab, it’s no surprise that the target genes in this project emerged in a segmental duplication (SD) region. The TCAF genes — which…
Hibernating bears have heart rates of 10-15 beats per minute, yet they do not develop congestive heart failure. Despite accumulating enormous amounts of fat and acquiring insulin resistance, they do not suffer metabolic diseases. And they maintain muscle strength in the near absence of weight-bearing activity.Iso-Seq study has revealed differential tissue-specific isoform changes in brown bears If we could crack these feats of physiology, perhaps we could apply the knowledge towards therapeutic targets for the prevention and treatment of numerous human diseases. The Project that Shed Light on the Metabolic Mystery of Brown Bears Washington State University researchers have…
Been itching to talk about your latest single-cell experiments, your favorite differentially expressed isoforms, or your latest and greatest software for visualizing alternative splicing, but thwarted by a worldwide pandemic preventing in-person scientific events? We were too, so we organized a virtual social club to easily enable scientists to geek out together. And we weren’t disappointed by our first event, which attracted dozens of self-proclaimed Iso-Seq analysis geeks and other curious researchers to share their work (published, unpublished and in progress) and discuss the benefits and challenges of incorporating long-read transcript sequencing into their research. Welcome to the Iso-Seq Analysis…
The study of genomics has revolutionized our understanding of science, but the field of transcriptomics grew with the need to explore the functional impacts of genetic variation. While different tissues in an organism may share the same genomic DNA, they can differ greatly in what regions are transcribed into RNA and in their patterns of RNA processing. By reviewing the history of transcriptomics, we can see the advantages of RNA sequencing – using a full-length transcript approach – become clearer. Reaching for the Transcriptome Even before genome sequencing became commonplace, scientists were able to measure gene expression activity using hybridization…
It’s not unusual for progeny to outperform their parents, and it’s often the goal in plant breeding. But tracing the molecular basis of such heterosis can be difficult, especially in diploid species with high genetic diversity and allele-specific expression like maize. Cold Spring Harbor scientists have tackled the challenge using the PacBio Iso-Seq method and a new tool, IsoPhase. As reported in Nature Communications Biology, Bo Wang, Doreen Ware, and colleagues performed an isoform-level phasing study in maize using the temperate line B73 and the tropical line Ki11, as well as their reciprocal crosses (B73 × Ki11; Ki11 × B73),…
It was a pleasure to attend the annual Advances in Genome Biology & Technology meeting in sunny Marco Island, Fla., last month. The conference has a long history of supporting sequencing innovation, and during the 20th anniversary celebration this year, the tradition continued. Video and synopses from several presentations featuring SMRT Sequencing are below. Adam Ameur (@_adameur) from Uppsala University spoke about the use of long-read PacBio sequencing to detect off-target edits from CRISPR/Cas9. In a method known as SMRT-OTS, Ameur’s team used a clever adaptation of the standard PacBio library preparation to enrich for molecules bound by a guide…
With the release of the award-winning Sequel II System, 2019 was an exciting year for the SMRT Sequencing community. We were inspired by our users’ significant contributions to science across a wide range of disciplines. As the year draws to a close, we have taken this opportunity to reflect on the many achievements made by members of our community, from newly sequenced plant and animal species to human disease breakthroughs. “It has been another phenomenal year for science. The introduction of the Sequel II System will accelerate discovery even more, and I can’t wait to see what 2020 will…
We’d like to extend a sincere thanks to everyone who attended our two-day North America User Group Meeting, held this year at our Certified Service Provider, the University of Delaware Sequencing and Genotyping Center (@UD_DNAcore). With representation from 80+ organizations and over 160 attendees, the event was a great environment for sharing best practices and networking with the SMRT Sequencing community. Also, a big thanks to our host, Bruce Kingham (@bkingham) and team, as well as our partners: Agilent, Biosoft Integrators, Circulomics, Covaris, Diagenode, Perkin Elmer, Sage Science and Shoreline Biome. If you weren’t able to attend the meeting, we’ve…
We were delighted to host an educational workshop at last month’s annual meeting of the American Society of Human Genetics (ASHG), where we had the opportunity to feature talks from two customers as well as an overview of SMRT Sequencing. If you couldn’t attend, check out the videos or read the highlights below. Emily Hatas, our director of business development, kicked things off with a look at how SMRT Sequencing has evolved over the years. Compared to the first instrument we offered, the Sequel II System represents a 100-fold improvement in read length and a 10,000-fold improvement in throughput. As…
At ASHG 2019, PacBio scientists Aaron Wenger and Liz Tseng offered a CoLab presentation. At the annual meeting of the American Society of Human Genetics in Houston, PacBio scientists presented how our Sequel II System performs for structural variant (SV) detection and for whole transcriptome sequencing. The educational workshop focused on experiments that can be done using a single SMRT Cell 8M on the Sequel II System. The event kicked off with Aaron Wenger walking through SV analysis, which he said has mirrored the development path of single nucleotide variants, from proof-of-concept to individual rare disease studies and now to…
PingHsun Hsieh presents his findings at ASHG. In a new Science publication, researchers from the University of Washington and other institutions report detailed analyses revealing the adaptive importance of copy number variants (CNVs) acquired from Denisovan and Neanderthal ancestors, the closest relatives of modern humans, in the modern-day Melanesian population. The team used PacBio long-read sequencing to study these complex stretches of DNA and the Iso-Seq method to generate full-length transcript data. “Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes” comes from lead author PingHsun Hsieh (@phhBenson), senior author Evan Eichler, and collaborators.…
Variety is the spice of life, and one of the drivers of genetic variation is gene splicing. After a gene is transcribed, there are alternatively spliced transcripts that add even more variety to that gene’s expression and its menu of phenotypes. It appears that there are types of disorders that take advantage of these varieties. Top amongst them are myeloid disorders, where somatic mutations in splicing factors lead to cell proliferation in myelodysplastic syndromes (MDS) and blood cancers. Christopher R. Cogle, a physician-scientist at the University of Florida, would like to understand why, in hopes that such knowledge could be…
Seeking to sequence and characterize entire transcriptomes in one go? Our new Iso-Seq protocol and reverse-transcriptase PCR kit makes it easier, speedier and cheaper. Run on the new Sequel II System, the completely revamped Iso-Seq Express workflow achieves whole transcriptome characterization from a single SMRT Cell 8M delivering up to 400 Gb, and at a third of the cost, or less. Yield has also increased on the Sequel System, with 3.0 sequencing chemistry typically delivering up to 30 Gb per SMRT Cell 1M for our RNA sequencing application. The new protocol requires three times less RNA input (300 ng) and…
Single Molecule, Real-Time (SMRT) Sequencing continues to get smarter and more powerful, with the recent launch of the Sequel II system increasing capabilities and efficiencies of the long-read DNA and RNA PacBio sequencing technology even further. In a special issue devoted entirely to the technology in the MDPI open access journal Genes, guest editors Adam Ameur of Uppsala University and Matthew S. Hestand of the Cincinnati Children’s Hospital Medical Center present eight articles highlighting research conducted using SMRT Sequencing. As this special issue demonstrates, the benefits of SMRT Sequencing to many different areas of research are becoming evident, not only…
When looking to understand the functional implications of genetic variability, scientists should seek out the Iso-Seq method, according to Cold Spring Harbor researchers. In a recent paper published in Frontiers in Genetics, Doreen Ware, Bo Wang, and colleagues reviewed the state of transcript sequencing and analysis technologies, and concluded that single-molecule sequencing from PacBio provided several advantages over other methods. A major challenge in molecular biology continues to be the complex mapping of the same genome to diverse phenotypes in different tissue types, development stages and environmental conditions, the paper states. “A better understanding of the transcripts and expression of…