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Characterize complex somatic variants

Tumor samples often contain many unique and evolving genomes, and understanding how complex cancer cell populations adapt in response to treatment is a major focus of cancer research. Other tools for characterizing the range of mutations present within a cancer sample are limited primarily by their detection of standalone SNPs. This makes it difficult to resolve patterns of co-existing mutations or larger structural variation.

Resolve the full spectrum of genetic variation

Single Molecule, Real-Time (SMRT) Sequencing delivers a complete, accurate view of the clonal distribution of mutations in genes or genomic regions of interest. The PacBio Systems produce reads long enough to span full-length transcripts and to allow for the immediate detection of compound mutations and splice isoforms. With these sequencing technologies, you have the ability to:

  • Detect SNVs occurring at a frequency as low as 1%
  • Differentiate polyclonal from compound mutations
  • View splice variants in gene fusion transcripts
  • Discover every breakpoint in regions of genomic instability

Workflow: from sample to somatic variant detection

  • SMRT Sequencing with PacBio Systems
    • Take advantage of the Sequel System to reduce project costs and generate 7X more reads compared with the PacBio RS II
    • Achieve ~10 kb average read lengths, with some reads as long as 60 kb
    • Adjust run times (0.5 to 6 hours) to maximize sample throughput and turn-around time
    • Obtain consensus accuracies >99.999% by avoiding mapping and systematic errors
    • Produce high, single-molecular consensus accuracies through multiple observations of single circularized templates

Featured research: a comprehensive view of BCR-ABL1 fusion gene mutations

Detect_Somatic_Variation.Spotlight.BCR_ABL1_Fusion_Gene_Mutation

SMRT Sequencing provided a complete view of the clonal distribution of mutations in the BCR-ABL1 fusion gene implicated in chronic myeloid leukemia treatment resistance. The authors identified several mutations and novel transcript isoforms standard clinical assays had missed. PacBio sequencing provided clonal distribution frequencies for the compound mutations and isoforms1.

Explore this research further.

To learn more about how to resolve your complex somatic variant, contact us.


Reference

  1. 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.

Selected Resources