Rethink what’s possible in cancer transcriptomics
Move beyond gene expression to consider the full spectrum of RNA dysregulation in cancer
While cancer is often considered a disease of the genome, much of the effects of cancer-causing mutations are expressed at the level of RNA. Current short read methods rely on transcript assembly to identify isoforms and fusions, but fail to uncover much of the variation present in the tumor transcriptome. Long-read RNA sequencing with the Kinnex method offers an unprecedented look at alternative splicing, fusion events, and expressed somatic mutations, elevating our understanding of RNA dysregulation in cancer.
The Kinnex method offers robust detection of isoforms, fusions, and expressed mutations
| RNA variant type | Use cases | Iso-Seq advantage | Other short reads | Other long reads | PacBio long reads |
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| RNA isoforms | Discover RNA isoforms as source of cancer biomarkers and drug targets | Read length: >2.5X isoform discovery power compared to short reads.2 Accuracy: Superior accuracy offers more robust isoform discovery power than other long-read technologies.3 |
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| RNA fusions | Identify known, novel, and complex RNA fusions | Read length: More robust fusion discovery power than short-read approaches.4,5 Accuracy: Highly accurate sequencing allows for robust detection of fusion isoforms.5 |
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| Expressed mutations | Detect expressed mutations in RNA for genotyping and neoantigen discovery | Read length: Long reads provide phasing information of expressed mutations.6 Accuracy: Highly accurate mutation detection compared to other long-read technologies.6,7 |
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Whitepaper
Full-length bulk and single-cell RNA sequencing for cancer research
The Iso-Seq method (full-length RNA sequencing using PacBio HiFi sequencing) has been shown to advance cancer research by unambiguously characterizing isoforms at both the bulk and single-cell level. PacBio Kinnex RNA kits further increase throughput on HiFi long-read sequencers. This whitepaper highlights publications on cancer research to demonstrate how bulk and single-cell Iso-Seq data detects fusion genes, identifies novel isoforms that might serve as neoepitopes for vaccine candidates, and traces clonal evolution.
Blog
Long-read RNA sequencing for cancer neoantigen discovery
The development of cancer vaccines and personalized immunotherapies relies on the identification of tumor neoantigens that can serve as therapeutic targets. Most neoantigen studies to date have focused on small variants like SNVs due to limitations of short read sequencing technologies. However, neoantigens derived from novel isoforms or fusions are more likely to elicit an immune response, because they generate more sequence differences compared to small variants. Learn how researchers at the National University of Singapore used long-read single-cell RNA sequencing to identify and prioritize potential neoantigens in colorectal cancer.
Webinar
Detecting shared mis-splicing across blood cancers to identify therapeutic targets and biomarkers of progression
Discover how long-read single-cell RNA sequencing with the PacBio Kinnex single-cell RNA kit identified shared mis-splicing patterns in adult and pediatric leukemia, and learn about new computational tools for identifying alternative splicing to uncover novel biomarkers associated with progression and pinpoint new therapeutic targets, even for cases without targetable genetic mutations.
Cancer transcriptomes in action
Publication
Identifying novel isoforms and fusions in ovarian cancer
Learn how the Tumor Profiler Consortium used single-cell long-read RNA sequencing at scale to discover novel isoforms and fusions that were missed with other technology.
A comprehensive long-read isoform analysis platform for breast cancer
Long-read RNA sequencing identifies novel biomarkers and drug targets in breast cancer
Long reads reveal differences in drug response
Learn how accurate PacBio long-read RNA sequencing provides true discovery power of cancer-related RNA isoforms and allows for the understanding of molecular mechanisms underlying cancer biology in this webinar.
pbfusion for comprehensive fusion detection in long-read RNA sequencing
Computational methods for identifying fusion transcripts in long-read RNA sequencing data.
Explore
Did you know we have a comprehensive library of articles, reports, papers, and videos related to cancer research?
THIS IS YOUR MOMENT
PacBio sequencers empower you to better understand the complex biology of cancer.
Reveal novel isoforms, fusions, and structural variants with exceptional accuracy.