Cancer genomics

More complete cancer transcriptomes and genomes

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Cancer genomics solutions

In order to fulfill the promise of cancer precision medicine, a better understanding of cancer’s complex biology is needed. PacBio highly accurate sequencing allows you to uncover novel isoforms, fusions, and structural variants with exceptional accuracy.

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Long-read RNA sequencing for isoform and fusion discovery

Cancer exhibits widespread RNA dysregulation. The Iso-Seq method uncovers the full repertoire of alternative splicing and fusion events.

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Long-read WGS for somatic variant detection

Structural variants (genomic differences ≥50 base pairs) are one of the main drivers of cancer. Most structural variants are too large to reliably discover with current short-read DNA sequencing technology.

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Highly accurate short-read sequencing for rare variant detection

Using the newly developed short-read sequencing platform you can achieve unprecedented sensitivity for detecting rare variants

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The Iso-Seq 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
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
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
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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1. Pan, Y., et al. (2021) RNA dysregulation: an expanding source of cancer immunotherapy targets. Trends in Pharmacological Sciences, 42(4), 268-282.
2. Viega, D.F.T., et al. (2022) A comprehensive long-read isoform analysis platform and sequencing resource for breast cancer. Science Advances, 8(3), eabg6711.
3. Mikheenko, A., et al. (2022) Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns.
Genome Research, 32(4), 726-737.
4. Nattestad, M., et al. (2018) Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome Research,
28(8), 1126-1135.
5. Miller, A. et al. (2022) PacBio Fusion and Long Isoform Pipeline (PB_FLIP) for Cancer Transcriptome–based Resolution of Isoform Complexity. The Journal of Molecular Diagnostics,
6. Cavelier, L. et al. (2015) Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing. BMC Cancer, 15:45
7. Olson, N. et al. (2022) PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions. Cell Genomics, 2, 100129

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The power of accurate long-read RNA sequencing for fusion gene detection in cancer research

Accurate and sensitive detection of fusion genes and their transcript structures is needed to interpret functional consequences, understand tumor biology and evolution, and identify potential therapeutic targets. PacBio full-length RNA isoform sequencing (Iso-Seq method) resolves complex fusions, providing more accurate breakpoints, and a complete sequence readout of associated fusion transcripts. And while several published studies show how long-read sequencing is more effective at discovering gene fusions accurately, researchers need a fusion calling tool to help them quantify and annotate fusions found in their Iso-Seq data.

In a collaboration between University of Calgary and PacBio, a new fusion gene detection software has been created – pbfusion. The pbfusion caller is specifically designed for long, accurate HiFi reads from PacBio Iso-Seq data; the tool applies to both bulk and single-cell Iso-Seq data, including those generated using the MAS-Seq for 10x Single Cell 3’ kit.

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Alternative splicing (AS) results in the generation of multiple RNA isoforms from a single gene, greatly increasing both transcriptomic and proteomic diversity. AS controls which introns are removed from premRNAs and which exons are combined to form the final messenger RNA (mRNA).¹

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Cancer genomics research in action

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Complex oncogene amplifications revealed

A detailed map of structural variations in breast cancer.

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Long reads reveal differences in drug response

Learn how PacBio’s accurate 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.

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Researchers are moving away from using only short-read sequencing, making new insights into the role of RNA dysregulation in tumor biology.

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Did you know we have a comprehensive library of articles, reports, papers, and videos related to cancer research?

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Long-read sequencing: the key to a more complete cancer transcriptome

Our understanding of the complex biology of cancers is currently limited by the sequencing technology that we have available. For example, a study previously published in Science Advances showed that short-read based RNA-seq approaches only capture a faction of RNA isoforms that occur in breast cancer samples. On the flip side, long-read sequencing using PacBio Iso-Seq method detects ~2.5 times the number of isoforms, including a substantial number of novel isoforms. These aberrant transcripts are often translated into cancer-specific proteins and have been shown to affect cancer initiation, progression, metastasis, and drug resistance. As a result, accurate long-read sequencing can offer new potential clues into how to detect, track and treat various forms of cancer.

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The RNA isoform landscape of cancer

Learn how PacBio’s accurate 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.

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PacBio sequencers empower you to better understand the complex biology of cancer.

Reveal novel isoforms, fusions, and structural variants with exceptional accuracy.

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