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Calling all variant types

Structural variation accounts for most of the base pairs that differ between two human genomes, and causes many genetic disorders. The ability to study structural variants, in addition to smaller single nucleotide variants and indels, is critical to understanding how genetic variation impacts health and disease in the era of Precision Medicine.

Variation between two human genomes, by number of base pairs impacted – Single nucleotide variants (SNVs); insertions and deletions (indels) involve fewer than 50 base pairs; structural variants consist of greater than 50 base pairs. Explore this research further.

 

Robust variant discovery, full assembly not required

Single Molecule, Real-Time (SMRT) Sequencing enables structural variant (SV) discovery using low-coverage, long-read whole genome sequencing. With high consensus accuracy, uniform coverage and a low false discovery rate, SMRT Sequencing de novo assembly allows scientists to:

  • Detect novel SV of all types and lengths with base pair resolution
  • Reach five-fold higher sensitivity in SV detection over other technologies
  • Phase SV and single nucleotide variants into allele-specific haplotype blocks
  • Target complex regions to resolve allelic indels, copy number variants and pseudogenes to map causal variants and solve the genetic etiology of disease

PacBio Structural Variant Coverage
Insertions Deletions Duplications
Translocations Inversions Tandem Repeats

 

 

 

 

 

Spotlight: Structural variant discovery with PacBio long-read sequencing

Explore human genetic variation and learn how SMRT Sequencing uncovers the full spectrum of structural variants to advance understanding of genetic disease and broaden our knowledge of human diversity.

Infographic: Structural Variants and Disease

 

Explore the types of human genomic variation and the diseases known to be caused by structural variants.

 

Download the infographic

Whitepaper: Structural variation in the human genome

 

Learn how long-read sequencing is enabling detection of the full spectrum of structural variants to advance the study of human disease, evolution, and genetic diversity.

 

Download the whitepaper

Structural Variation Project Calculator

 

Explore our project calculator for structural variant discovery and receive an estimate on the time and materials needed for PacBio sequencing using the Sequel System.


 

Workflow: from DNA to structural variation detection

 

Library Preparation

 

SMRT Sequencing with PacBio Systems

  • Achieve ~10 kb average read lengths and ~5 Gb yield per Sequel SMRT Cell 1M
  • Scale throughput based on project needs
    • 5 to 10-fold: population genetics studies
    • 10-fold: rare undiagnosed disease studies
    • >20-fold: de novo SV detection in trios

Data analysis with SMRT Analysis or PacBio DevNet

  • Detect all structural variant types with the highest sensitivity
  • Use SMRT Link Structural Variant Calling powered by pbsv
  • Visualize structural variants with IGV 3 and GenomeRibbon

 

 

Learn more about Best Practices in whole genome sequencing for structural variation

 

Tutorial: PacBio Structural Variant Calling

This tutorial provides an overview of the Structural Variant Calling application in SMRT Link featuring a live demonstration of how to launch an analysis in SMRT Link and interpret the results. This application identifies large (default: ≥50 bp) insertions and deletions in a sample relative to a reference from whole genome sequence data.

Spotlight: Stanford Scientists Use PacBio Whole Genome Sequencing to Identify a Disease-Causing Mutation

With 8-fold coverage long-read sequence data generated on the Sequel System allowed scientists uncovered a 2.2 kb deletion in PRKAR1A, a gene involved in the Carney complex. This pathogenic variant went undetected using clinical single gene testing a whole genome short-read sequencing. Explore this research further.

Merker, J.D. et al., 2017. Long-read genome sequencing identifies causal structural variation in a Mendelian disease. Genetics in Medicine, ePub Ahead of Print.

Spotlight: Detect the most comprehensive SV callsets with long reads

Dr. Michael Schatz highlighted the ability of PacBio long-read sequencing to identify more types of structural variants, including long tandem repeat expansions, over other technologies. Explore this further:

Schatz, M., 2017. AGBT Conference: Personalized phased diploid genomes of the EN-TEx samples. Advances in Genome Biology and Technology.

To learn more about how SMRT Sequencing resolves structural variation, contact us.

Selected Resources