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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 through 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

Workflow: from targeted region to accurate variant or haplotype

 

 

 

Library Preparation – Enrich target regions of interest

 

 

SMRT Sequencing with PacBio Systems

  • Achieve ~10 kb average read lengths and up to 20 Gb yield per sequel SMRT Cell 1M (yields may vary based on insert size and complexity of templates in the mix)
  • Use long movies (up to 20 hrs) to increase throughput for insert sizes ≥ 2.5 Kb
    • Up to 2000 amplicons (2.5-6 kb) multiplex per SMRT Cell
    • High quality phased SNP information with 75-fold coverage with probe-based hybridization strategies
    • Increase the number of multiple single circularized template observations for improved Circular Consensus Sequence (CCS) accuracies (QV30) for complex population resolution
  

Data Analysis with SMRT Analysis and PacBio DevNet

Spotlight: SMRT Sequencing uncovers causative mutation within GC-rich region

PacBio long-read sequencing enabled scientists to detect a single causative mutation for autosomal dominate tubulointerstitial kidney disease (ADTKD) in MUC1 gene residing in a GC-rich variable number tandem repeat region (VNTR) that was previously intractable. Explore this research further:

Wenzel, A. et al., 2018. Single molecule real time sequencing in ADTKD-MUC1 allows complete assembly of the VNTR and exact positioning of causative mutations. Scientific Reports, 8(1), p.4170.

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