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Target your critical genomic regions

Targeted sequencing optimizes resources by focusing data collection on the most relevant genomic regions. However, neither time nor money is saved if the information you need isn’t captured. Homopolymeric stretches, repetitive elements, or short tandem repeats (STRs) within genes interfere with short-read approaches when targeted regions are prone to structural variation. Similarly, haplotype reconstruction from short reads relies on imputation, which is not always reliable — particularly when structural variants or de novo mutations are a factor1.

Resolve complex genomics underlying human disease

Targeted sequencing with PacBio long reads provides single-molecule observations of genomic regions linked to human disease. The result is continuous sequence data though polymorphic or repetitive regions and in-depth information on complex mixtures. These reads deliver standalone de novo solutions, but also resolve ambiguities in short-read data sets.

Single Molecule, Real-Time (SMRT) Sequencing enables a wide range of applications, giving you the ability to:

  • Definitively phase polymorphisms over entire genes
  • Sequence through STRs and other low-complexity regions within genes
  • Detect common or de novo structural variants and map breakpoints with precision
  • Fully characterize minor variants in polyclonal samples

spotlight-human-icon

Workflow: from targeted region to accurate variant or haplotype

  • 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-molecule consensus accuracies through multiple observations of single circularized templates for complex population resolution

Featured research: targeting structural variants in Potocki-Lupski Sydrome

Targeted-Sequencing.Spotlight

“Interestingly, when all of the junctions are examined, 3 of the 5 breakpoints resulted in Alu-Alu chimeras, which may be difficult to detect with shorter reads. Additionally, in a cohort of 123 PTLS (Potocki-Lupski syndrome) patients, about 60% of the non-recurrent rearrangements have one or more breakpoint within an LCR (low copy repeat)2.”

Explore this research further.

To learn more about how to access the full spectrum of genetic variation with SMRT Sequencing, contact us.


References

  1. Willems, T., et al., (2014) The landscape of human STR variation. Genome Research. 24(11), 1894-1904.
  2. Wang, M., et al., (2015) PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations. BMC Genomics. 16, 214.

Selected Resources