To bring personalized medicine to all patients, cancer researchers need more reliable and comprehensive views of somatic variants of all sizes that drive cancer biology.
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…
Grant Cramer from the University of Nevada, Reno, and Dario Cantu from the Univeristy of Callifornia, Davis, discuss past challenges with sequencing Clone 8 of Cabernet Sauvignon (Vitis vinifera). An assembly of the genome was attempted with approximately 110x Illumina reads and 5x PacBio reads. The PacBio SMRT Sequencing read made major improvements in the assembly compared with the results of Illumina reads only. However, the assembly results were still unsatisfactory, so an additional 100-fold SMRT Sequencing coverage had been generated. An update on the current sequencing results and status of the assembly are presented.
Jonas Korlach spoke about recent SMRT Sequencing updates, such as latest Sequel System chemistry release (1.2.1) and updates to the Integrative Genomics Viewer that’s now update optimized for PacBio data. He presented the recent data release of structural variation detected in the NA12878 genome, including many more insertions and deletions than short-read-based technologies were able to find.
In this AGBT 2017 poster, Ulf Gyllensten from Uppsala University presents two local reference genomes generated with PacBio and Bionano Genomics data. These assemblies include structural variation and repetitive regions that have been missed with previous short-read efforts, including some new genes not annotated in the human reference genome.
Targeted sequencing experiments commonly rely on either PCR or hybrid capture to enrich for targets of interest. When using short read sequencing platforms, these amplicons or fragments are frequently targeted to a few hundred base pairs to accommodate the read lengths of the platform. Given PacBio’s long readlength, it is straightforward to sequence amplicons or captured fragments that are multiple kilobases in length. These long sequences are useful for easily visualizing variants that include SNPs, CNVs and other structural variants, often without assembly. We will review methods for the sequencing of long amplicons and provide examples using amplicons that range…
Tremendous flexibility is maintained in the human proteome via alternative splicing, and cancer genomes often subvert this flexibility to promote survival. Identification and annotation of cancer-specific mRNA isoforms is critical to understanding how mutations in the genome affect the biology of cancer cells. While microarrays and other NGS-based methods have become useful for studying transcriptomes, these technologies yield short, fragmented transcripts that remain a challenge for accurate, complete reconstruction of splice variants. The Iso-Seq method developed at PacBio offers the only solution for direct sequencing of full-length, single-molecule cDNA sequences needed to discover biomarkers for early detection and cancer stratification,…
At AGBT 2017, Margaret Roy from Calico Life Sciences discussed a de novo genome sequencing effort for the naked mole rat. This animal has a remarkably long life span and resistance to cancer, both of which make it interesting for studies of life extension. The team is using SMRT Sequencing for a more complete, contiguous assembly than the two existing short-read-based assemblies. Included: data from the Sequel System.
In this PacBio User Group Meeting presentation, Tim Smith of the USDA’s Agricultural Research Service describes efforts to generate reference-grade genome assemblies for various bovine species and analyze them to understand factors such as how selective breeding has affected certain breeds. Genome assemblies he presents span cattle, water buffalo, and gaur. Smith shows data for each assembly, noting that as data production shifted to the Sequel System, long-read PacBio data became even better at producing highly contiguous assemblies.
In this PacBio User Group Meeting presentation, Bruce Kingham of the DNA Sequencing & Genotyping Center at the University of Delaware describes tips on using the FEMTO Pulse for large-insert libraries.
In this PacBio User Group Meeting presentation, Tina Graves-Lindsay of the McDonnell Genome Institute and the Genome Reference Consortium speaks about the importance of phasing human reference genomes. Her team is now working on its fifteenth human genome assembly — part of a major effort to improve genomic representation of ethnic diversity — with a pipeline that generates 60-fold PacBio coverage for a de novo assembly, followed by scaffolding with other technologies. They are also using FALCON-Unzip to separate haplotypes, leading to reference-grade diploid assemblies. This approach has already helped resolve errors seen in other genomes and even the gold-standard…
In this PacBio User Group Meeting presentation, Garth Ehrlich of Drexel University College of Medicine shares his work on developing a microbiome assay that uses SMRT Sequencing to provide high-quality coverage of the 16S bacterial rRNA for species identification. The microbiome analysis pipeline, MCSMRT, takes advantage of PacBio circular consensus sequencing (CCS) technology and second-generation pathway analysis system for generating extremely high-fidelity sequences that provide the user with ultra-high-confidence species-level microbiome data.
In this PacBio User Group Meeting presentation, Jonas Korlach and Roberto Lleras share the latest updates to the structural variation application and analysis tools.
In this PacBio User Group Meeting presentation, Zev Kronenberg of PacBio presents on using the combination of PacBio and Phase Genomics data and analysis tools to create highly contiguous genome assemblies.