Today we’re pleased to announce the release of Sequel System 6.0, including new software, consumable reagents and a new SMRT Cell. Combined, the enhancements in the release improve the performance and affordability of Single Molecule, Real-Time (SMRT) Sequencing by providing individual long reads with greater than 99% accuracy, increasing the throughput up to 50 Gb per SMRT Cell, and delivering average read lengths up to 100,000 base pairs, depending on insert size. These improvements are expected to greatly enhance the accuracy and cost effectiveness of applications such as whole genome sequencing, human structural variant detection, targeted sequencing and RNA transcript isoform sequencing (Iso-Seq method). [caption…
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…
[caption id="attachment_25415" align="alignright" width="300"] Photo by John Cobb on Unsplash[/caption] In eukaryotic organisms, the majority of genes are alternatively spliced to produce multiple transcript isoforms. Gene regulation through alternative splicing can dramatically increase the protein-coding potential of a genome. Therefore, understanding the functional biology of a genome requires knowing the full complement of isoforms. Microarrays and high-throughput cDNA sequencing are useful tools for studying transcriptomes, yet these technologies provide only small snippets of transcripts. Accurately reconstructing complete transcripts to study gene isoforms has been challenging [1, 2]. The Iso-Seq method produces full-length transcripts using Single Molecule, Real-Time (SMRT) Sequencing [3].…
[caption id="attachment_24559" align="alignright" width="300"] The coast of Panay Island in the Philippines. U.S. Navy photo by Jennifer S. Kimball[/caption] 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…
[caption id="attachment_24213" align="alignright" width="225"] Photo by H. Zell[/caption] A new preprint from scientists at the University of California, Davis, demonstrates the usefulness of SMRT Sequencing and the Iso-Seq method to enable comprehensive transcriptome analysis even in the absence of a reference genome assembly. The team conducted this study on the grape used to make Cabernet Sauvignon. Lead author Andrea Minio, senior author Dario Cantu, and collaborators used SMRT Sequencing to generate full-length transcripts of Vitis vinifera cv. Cabernet Sauvignon, analyzing RNA collected from four replicates at each of four important stages of ripening. Previously, this team used PacBio sequencing to…
[caption id="attachment_14026" align="alignright" width="288"] Photo of ruby-throated hummingbird by Michelle Lynn Reynolds[/caption] UPDATED February 21, 2018 Congratulations to Winston Timp's team on the publication of their Iso-Seq analysis of hummingbird! The paper is now available at GigaScience. ORIGINAL POST April 4, 2017 A new preprint offers an enticing look at transcriptome results from analysis of a hummingbird using SMRT Sequencing. In this study, scientists found new clues to explain unique attributes of the bird’s metabolism. The work was made possible through full-length isoform sequencing, which allowed deep, assembly-free analysis even though no reference genome was available. “Single molecule, full-length transcript…
We’re pleased to announce the winner of this year’s ‘Open Your Eyes to Isoform Diversity’ SMRT Grant, which was launched during the American Association for Cancer Research annual meeting. The grant program, co-sponsored by PacBio and GENEWIZ, received many compelling entries, and it was a challenge choosing just one winner. Congratulations to Andrew Ludlow, a new faculty member at the University of Michigan, who impressed reviewers with his proposal to investigate the splicing of transcripts regulated by the oncogene NOVA1. Ludlow notes that in lung cancer cells, NOVA1 acts as a splicing enhancer to produce full-length hTERT and promote telomerase…
[caption id="attachment_20677" align="alignright" width="300"] Photo of Panax ginseng by Eugene Kim[/caption] Three recent publications report results from transcriptome studies of plants often used for medicinal purposes, all powered by SMRT Sequencing and the Iso-Seq method. The papers on ginseng, Huangqi, and tea collectively show the importance of sequencing full-length isoforms for the most accurate and comprehensive gene expression analysis; they also demonstrate the usefulness of characterizing gene models for complex species in the absence of a reference genome assembly. In “Isoform Sequencing Provides a More Comprehensive View of the Panax ginseng Transcriptome,” scientists from the National Institute of Horticultural and Herbal Science,…
[caption id="attachment_20594" align="alignright" width="300"] Photo by Forest & Kim Starr[/caption] Scientists at Huazhong Agricultural University in China and collaborating institutions recently published results of an Iso-Seq analysis of allotetraploid cotton. The team’s findings are expected to be particularly useful for functional genomics, driving advances for cotton breeders as well as research biologists. “A global survey of alternative splicing in allopolyploid cotton: landscape, complexity and regulation” was published in New Phytologist by lead authors Maojun Wang and Pengcheng Wang, senior author Xianlong Zhang, and collaborators. Existing genome assemblies for polyploidy cotton were not “released with a well-annotated transcript isoform set,” the…
[caption id="attachment_18776" align="alignright" width="300"] Anna's hummingbird photo by Pat Durkin[/caption] If you’re interested in avian vocal learning or want to explore a PacBio Iso-Seq data set generated with the Sequel System, we have good news. We’ve just released data from Iso-Seq interrogations of brain tissue from two avian models of vocal learning, Anna’s hummingbird (Calypte anna) and zebra finch (Taeniopygia guttata), sequenced in collaboration with the Erich Jarvis and Olivier Fedrigo labs at the Rockefeller University. If you’re not familiar with the Iso-Seq method, it’s the long-read sequencing answer to short-read RNA-seq studies. By using SMRT Sequencing for a transcriptome…
A new publication in Clinical Cancer Research from scientists at the Mayo Clinic, University of Minnesota, and other institutions presents results from a study to evaluate androgen receptor (AR) isoforms as biomarkers for chemotherapy resistance in prostate cancer patients. The team used the Iso-Seq method with SMRT Sequencing to better characterize the structures of AR variants, discovering that the exon structure of this prostate cancer driver had previously been misreported due to the limitations of short-read sequencing. “Androgen receptor variant AR-V9 is co-expressed with AR-V7 in prostate cancer metastases and predicts abiraterone resistance” comes from lead authors Manish Kohli and…
[caption id="attachment_16831" align="alignright" width="300"] Photo by Timophey Tkachik[/caption] A new publication in BMC Genomics explores the use of RNA normalization and 5’ cap selection to enhance results from Iso-Seq studies using SMRT Sequencing. Scientists from the University of Edinburgh report that these modifications significantly boosted transcriptome coverage in a study of chicken. “Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human” comes from lead author Richard Kuo, senior author David Burt, and collaborators. The team chose this project because existing chicken annotation resources have far fewer genes than expected, with very little evidence of alternative splicing.…
A preprint from scientists at the University of Florida, Centro de Investigaciones Principe Felipe, and other institutes describes a new analysis tool to help boost quality of transcriptome studies. “SQANTI: extensive characterization of long read transcript sequences for quality control in full-length transcriptome identification and quantification” comes from lead author Manuel Tardaguila, senior author Ana Conesa, and collaborators. The automated pipeline for Structural and Quality Annotation of Novel Transcript Isoforms (SQANTI) was developed as a quality-assessment tool for transcripts discovered with SMRT Sequencing. SQANTI “calculates up to 35 different descriptors of transcript quality and creates a wide range of summary graphs to…
We’re excited to be heading to Washington, DC, for the annual meeting of the American Association for Cancer Research. The PacBio team always enjoys hearing about the latest in cancer translational research at AACR, along with thousands of leading scientists in the field. Many of those scientists have already learned that SMRT Sequencing provides a unique view into cancer, revealing structural variation, phasing distant variants, and delivering full-length isoform sequences. With uniform coverage, industry-leading consensus accuracy, and reads extending to tens of kilobases, PacBio long-read sequencing gives researchers the ability to monitor and make sense of even the most complex…
We’re thrilled to be at the AGBT conference this week, taking place this year in Hollywood, Fla. On the first full day of the meeting, everyone’s mandatory wristbands look shiny and new (we suspect by the end of the week they’ll be as wilted as us). And we've even been getting that work/life balance down thanks to some beach volleyball with our friends from BioNano Genomics and Swift Biosciences. At the opening session on Monday, Eimear Kenny from the Icahn School of Medicine at Mount Sinai showed why it’s essential to fully understand natural genetic diversity in a fascinating talk…