Cleo van Diemen, University Medical Center Groningen A hearty congratulations to Cleo van Diemen at the University Medical Center Groningen for winning the 2019 Neuroscience SMRT Grant! Van Diemen’s impressive proposal involves using PacBio long-read sequencing to find new genetic mechanisms associated with spinocerebellar ataxia (SCA). While some 70% of SCA patients can get clear diagnostic and prognostic information because they have one of the ~37 genes known to be associated with this condition, 30% of patients have no such clarity. In this project, van Diemen and her colleagues will use their SMRT Grant award to generate highly accurate long…
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…
Two recent review articles discuss the idea that structural variants (SVs) — genetic differences that involve at least 50 base pairs — are numerous, important to human biology, and best detected with long reads. The authors review years of studies that have applied PacBio SMRT Sequencing to identify around 20,000 SVs per human genome. The reviews also report on cases in which SMRT Sequencing has helped scientists discover pathogenic variants that explain diseases for which there had previously been no clear genetic cause. In Nature Reviews Genetics, Steve Ho, Alexander Urban, and Ryan Mills from the University of Michigan and…
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…
To enable better understanding of biology, sequencing data must be accurate and complete. This is especially true when seeking out variants and determining their implications. Luckily, technical and software improvements for SMRT Sequencing are making it easier to efficiently generate genome assemblies with unparalleled accuracy. As presented in a webinar by PacBio Staff Scientist Sarah Kingan (@drsarahdoom) and GoogleAI Genomics Project Lead Andrew Carroll (@acarroll_ATG), HiFi reads enabled by circular consensus sequencing (CCS) on the new Sequel II System challenge the notion that sequencing technologies require a tradeoff between length and accuracy. Highly accurate long reads (HiFi reads) offer the…
We’re thrilled to announce the launch of the Sequel II System, reducing project costs and timelines with approximately eight times the data output compared to the previous Sequel System. It enables customers to comprehensively detect human variants ranging in size from single nucleotide changes to large, complex structural variants. The system is also ideal for standard applications such as de novo assembly of large genomes and whole transcriptome analysis using the Iso-Seq method. The Sequel II System is based on the proven technology and workflow underlying the previous version of the system, but contains updated hardware to process the new…
In an effort to produce a comprehensive list of structural variants in the human genome, scientists from the University of Washington, the University of Chicago, Washington University, and Ohio State University sequenced 15 human genomes and have now released the results of their in-depth analysis. The Cell publication, “Characterizing the Major Structural Variant Alleles of the Human Genome,” comes from lead authors Peter Audano and Arvis Sulovari, senior author Evan Eichler, and collaborators. The data generated by this work “provide the framework to construct a canonical human reference and a resource for developing advanced representations capable of capturing allelic diversity,” the…
Scientists in Japan report using the unique properties of SMRT Sequencing to detect a structural variant (SV) responsible for a hereditary form of epilepsy. The 4.6 kb intronic repeat insertion was found from low-coverage whole genome sequence data, leading the team to suggest that this approach could be useful for determining the genetic mechanisms behind many unexplained diseases. “Detecting a long insertion variant in SAMD12 by SMRT sequencing: implications of long-read whole-genome sequencing for repeat expansion diseases” comes from lead author Takeshi Mizuguchi, senior author Satoko Miyatake, and collaborators at Yokohama City University and the University of Occupational and Environmental Health School…
In addition to the most common applications, like whole genome sequencing for de novo assembly, there are several other features you can utilize to advance your science or incorporate to offer your customers a broad range of the best PacBio services. Here’s a sampling of the most recent updates and releases. Iso-Seq Analysis for Genome Annotation or Targeted Isoform Discovery The isoform sequence (Iso-Seq) application generates full-length cDNA sequences – from the 5’ end of transcripts to the poly-A tail – eliminating the need for transcriptome reconstruction using isoform-inference algorithms. It’s even easier to help your customers annotate their…
In an exciting paper that made the cover of Genome Research, scientists from Cold Spring Harbor Laboratory and collaborating institutions report the genome sequence and transcriptome of a commonly used breast cancer cell line. They determined that the cell line harbors far more structural variants than previously thought with results that call into question cancer genome analysis based solely on short-read sequencing data. In “Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line,” lead author Maria Nattestad, senior author Michael Schatz, and collaborators describe an in-depth investigation of SK-BR-3, an important…
Justin Zook A map of every individual’s genome will soon be possible, but how will we know if it is correct? Benchmarks are needed in order to check the performance of sequencing, and any genomes used for such a purpose should be comprehensive and well characterized. Enter the Genome in a Bottle Project (GIAB), a consortium of geneticists and bioinformaticians committed to the creation and sharing of high-quality reference genomes. Unlike other initiatives, such as the 1000 Genomes Project, that are seeking to sequence many representatives of different populations, GIAB is interested in sequencing just a few individuals, but deeply…
Fritz Sedlazeck Nature Methods just published “Accurate detection of complex structural variations using single-molecule sequencing,” a publication that presents the NGMLR aligner and Sniffles structural variant caller, both designed for use with long-read sequencing data. We chatted with developer and lead author Fritz Sedlazeck from the Human Genome Sequencing Center at Baylor to learn more. Q: Why was a new alignment tool needed when many scientists already use BWA and other methods? A: When I started my postdoc in Mike Schatz’s lab at Cold Spring Harbor, I had the opportunity to look at the complex SK-BR-3 cell lines. We soon…
Structural variants account for most of the base pairs that differ between human genomes, and are known to cause more than 1,000 genetic disorders, including ALS, schizophrenia, and hereditary cancer. Yet they remain overlooked in human genetic research studies due to inherent challenges of short-read sequencing methods to resolve complex variants, which often involve repetitive DNA. At a recent webinar co-hosted by Nature Research, Professor Alexander Hoischen joined Principal Scientist Aaron Wenger to discuss how advances in long-read sequencing and structural variant calling algorithms have made it possible to affordably detect the more than 20,000 such variants that are…
The coast of Panay Island in the Philippines. U.S. Navy photo by Jennifer S. Kimball In an exciting new Cell paper, scientists report identification of an intronic structural variant that causes a neurodegenerative Mendelian disorder that primarily affects people on the island of Panay in the Philippines. The team used a number of approaches, including SMRT Sequencing and the Iso-Seq method, to solve the medical mystery. “Dissecting the Causal Mechanism of X-Linked Dystonia-Parkinsonism by Integrating Genome and Transcriptome Assembly” comes from lead authors Tatsiana Aneichyk, William Hendriks, Rachita Yadav, David Shin, and Dadi Gao; senior authors Cristopher Bragg and Michael Talkowski;…