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 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|
Workflow: from DNA to structural variation detection
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SMRT Sequencing with PacBio Systems
Structural Variation – Best Practices
Learn more about best practices in low-coverage, long-read whole genome sequencing for structural variation
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.
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.
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.
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, 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.
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- Elghraoui, Afif et al. (2017) SMRT genome assembly corrects reference errors, resolving the genetic basis of virulence in Mycobacterium tuberculosis. BMC Genomics
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- Bashir, Ali et al. (2017) Genomic confirmation of vancomycin-resistant Enterococcus transmission from deceased donor to liver transplant recipient. PLoS One
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- Poster: Vogelsang, R. et al. (2018) Population-scale discovery of structural variants with PacBio SMRT Sequencing
- Poster: Concepcion, G., et al. (2018) Structural variant detection in crops using PacBio SMRT Sequencing
- Poster: Kingan, S. et al. (2017) Structural Variant Detection with Low-Coverage PacBio Sequencing
- Poster: Hickey, L. et al. (2017) Detecting pathogenic structural variants with low-coverage PacBio sequencing.
- Poster: Wenger, Aaron et al. (2017) Structural variant detection with low-coverage Pacbio sequencing
- Poster: Concepcion, G. et al. (2017) Phased diploid genome assembly with single-molecule real-time sequencing
- Ameur, A. and Graves-Lindsay, T. and Peluso, P. (2018) Webinar: Assembling high-quality human reference genomes for global populations
- Korlach, Jonas (2018) Podcast: Why the diversity of genomic data matters
- Hoischen, A. and Wenger, A (2018) Webinar: Sequencing Structural Variants for Disease Gene Discovery and Population Genetics
- Wenger, Aaron (2017) Video: Structural variant detection with SMRT Sequencing
- Brunner, Han (2017) ASHG PacBio Workshop: Long-read sequencing for detecting clinically relevant structural variation
- Lee, Charles (2017) ASHG PacBio Workshop: Multiplatform discovery of haplotype-resolved structural variation in human genome
- Korlach, Jonas (2017) ASHG PacBio Workshop: PacBio applications updates & future roadmap
- Wenger, Aaron (2017) Webinar: Detecting structural variants in PacBio reads – tools and applications
- (2017) Tutorial: Minor variant analysis [SMRT Link v5.0.0]
- (2017) Tutorial: Structural variant calling [SMRT Link v5.0.0]
- Wenger, Aaron (2017) Webinar: Structural variant detection in SMRT Link 5 with PBSV
- Singh, Siddharth (2017) Webinar: Beginner’s Guide to PacBio SMRT Sequencing Data Analysis
- Schatz, Michael (2017) AGBT Conference: Personalized phased diploid genomes of the EN-TEx samples
- Glyllensten, Ulf (2017) AGBT Virtual Poster: Generation of local reference genomes using PacBio and BioNano data, and analysis of the “dark matter” of structural variants in 1000 Swedish genomes
- Application Brief: Low-coverage, long-read whole genome sequencing for structural variation – Best Practices. (2018)
- Sequel System Brochure: The premier solution for long-read sequencing. (2018)
- SMRT Sequencing Brochure: Revolutionize genomics with SMRT Sequencing. (2018)
- PacBio Certified Service Providers (2018)