Access diverse and hidden variant types
Though they have been historically difficult to see, germline structural variation events (SVs) in the human genome account for a greater number of variable bases than single nucleotide variants (SNVs)1,2 and are known to cause a number of well-characterized genetic disorders3. Even when using a multiple algorithm approach, SV calling with next-generation sequencing data often leads to false positives, low sensitivity, or otherwise ambiguous or erroneous results4. This is due to factors such as amplification bias or trying to assemble short reads within complex repeat regions.
Resolve structural variation with low coverage
Uncovering the connection between genetics and heritable diseases requires an approach that looks at all the variant bases and types in a genome. While a PacBio de novo assembly resolves the most novel SV variants5, 8–12X PacBio coverage of single genomes or trios reveals triple the SVs detectable by short-read data4.
With Single Molecule, Real-Time (SMRT) Sequencing, you can access structural variations having a broad range of sizes, types, and GC content with the ability to:
- Uncover missing heritability linked to structural variation
- Unambiguously identify genomic context and variant breakpoints at the sequence level to unravel the genetic etiology of disease
- Resolve structural variation across the complete size spectrum with basepair resolution
Workflow: from DNA to structural variation detection
- Long-insert library preparation
- SMRT Sequencing with PacBio Systems
- Achieve ~10 kb average read lengths
- Scale throughput based on project needs:
- 8–12X coverage per sample for structural variant surveys
- 50X coverage per sample for high-quality de novo assembly
- Simultaneously capture epigenetic information
- Data analysis with SMRT Analysis or PacBio DevNet
- Create exceptional de novo assembly with megabase-size contig N50s and consensus accuracies > 99.999%
- Generate diploid assemblies with haplotype information
- Utilize community-developed structural variation calling tools such as Parliament, which DNAnexus includes in their toolset
- Read more recommendations for large genome assemblies
Featured research: assess structural variation in a personal genome
“Applying multiple Parliament workflows, we demonstrate that while method integration is optimal for SV detection in Illumina paired-end data, the addition of long-read data can more than triple the number of SVs detectable in a personal genome4.”
Explore this research further.
Featured research: discover novel structural variants
“Notably, less than 1% of these variants are present in newer assemblies of the human genome, including GRCh38 and CHM1.1 (ref. 22, derived primarily by Illumina sequencing technology) 5.”
Explore this research further.
To learn more about how SMRT Sequencing resolves structural variation, contact us.
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- English, Adam C et al. (2015) Assessing structural variation in a personal genome-towards a human reference diploid genome. BMC Genomics
- Chaisson, Mark J P et al. (2015) Resolving the complexity of the human genome using single-molecule sequencing. Nature
- Ummat, Ajay et al. (2014) Resolving complex tandem repeats with long reads. Bioinformatics
- Steinberg, Karyn Meltz et al. (2014) Single haplotype assembly of the human genome from a hydatidiform mole. Genome Research
- English, Adam C et al. (2014) PBHoney: identifying genomic variants via long-read discordance and interrupted mapping. BMC Bioinformatics
- Davis, Caleb F et al. (2014) The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell
- Cho, Yun Sung et al. (2016) An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes. Nature Communications
- Sevim, Volkan et al. (2016) Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing. Bioinformatics
- Zook, Justin M et al. (2016) Extensive sequencing of seven human genomes to characterize benchmark reference materials. Scientific Data
- Roses, Allen et al. (2016) Understanding the genetics of APOE and TOMM40 and role of mitochondrial structure and function in clinical pharmacology of Alzheimer’s disease. Alzheimer's & Dementia
- Sudmant, Peter H et al. (2015) An integrated map of structural variation in 2,504 human genomes. Nature
- Rhoads, Anthony et al. (2015) PacBio sequencing and its applications. Genomics, Proteomics & Bioinformatics
- Zhao, Hui et al. (2015) BreakSeek: a breakpoint-based algorithm for full spectral range INDEL detection. Nucleic Acids Research
- Linthorst, Jasper et al. (2015) Scalable multi whole-genome alignment using recursive exact matching bioRxiv
- Henikoff, Jorja G et al. (2015) A unique chromatin complex occupies young a-satellite arrays of human centromeres. Science Advances
- Ritz, Anna et al. (2014) Characterization of structural variants with single molecule and hybrid sequencing approaches. Bioinformatics
- Layer, Ryan M et al. (2014) LUMPY: a probabilistic framework for structural variant discovery. Genome Biology
- 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: Watson, C. T. et al. (2016) Characterizing haplotype diversity at the immunoglobulin heavy chain locus across human populations using novel long-read sequencing and assembly approaches
- Poster: Wenger, A. et al. (2016) Effect of coverage depth and haplotype phasing on structural variant detection with PacBio long reads
- Poster: Ranade, Swati et al. (2016) Immune regions are no longer incomprehensible with SMRT Sequencing
- Poster: Chin, Jason et al. (2016) Un-zipping diploid genomes ?- revealing all kinds of heterozygous variants from comprehensive hapltotig assemblies
- Presentation: Nattestad, Maria et al. (2015) Comprehensive genome and transcriptome structural analysis of a breast cancer cell line using PacBio long read sequencing
- Poster: Sedlazeck, Fritz J. et al. (2015) Detection of structural variants using third generation sequencing
- Poster: Rescheneder, Philipp et al. (2015) Highly accurate read mapping of third generation sequencing reads for improved structural variation analysis
- Presentation: Lindsay, Tina et al. (2015) ASHG – GRC Workshop
- Presentation: Salit, Marc et al. (2015) Genome in a Bottle: You’ve sequenced. How well did you do?
- Presentation: English, Adam et al. (2015) PBHoney: Detecting SVs with long-read sequencing
- Poster: Chin, J. et al. (2016) Phased human genome assemblies with Single Molecule, Real-Time Sequencing
- Presentation: Zook, Justin et al. (2015) Reference materials for clinical applications of human genome sequencing
- Presentation: Bashir, Ali et al. (2015) Structural variation with Pacific Biosciences long reads
- Poster: Korlach, Jonas et al. (2014) Resolving the ‘dark matter’ in genomes.
- Korlach, Jonas (2017) AGBT PacBio Workshop: SMRT Sequencing roadmap: better throughput, lower costs
- Schatz, Michael (2017) AGBT Conference: Personalized phased diploid genomes of the EN-TEx samples
- Korlach, Jonas (2016) ASHG PacBio Workshop: A future of high-quality genomes, transcriptomes, and epigenomes
- Ashley, Euan (2016) ASHG PacBio Workshop: Towards precision medicine
- Wenger, A. and Kujawa, S. and Hickey, L. and Chin, J. and Korlach, J. (2016) ASHG Virtual Poster: Effect of coverage depth and haplotype phasing on structural variant detection with PacBio long reads
- Wenger, Aaron (2016) Video: Using the Integrative Genomics Viewer (IGV) to visualize PacBio long-read SMRT Sequencing data
- Nattestad, Marie (2016) Webinar: Analysis and visualization tools for long reads, assemblies and complex variation
- Carroll, Andrew (2016) DNAnexus Webinar: Accurate calling of structural variation in PacBio data
- Meltz Steinberg, Karyn (2016) AGBT Conference: The first African reference genome assembly
- Ameur, Adam (2016) AGBT Roche and PacBio Workshop: Clinical SMRT Sequencing – from single genes to complete genomes
- Ashley, Euan (2016) AGBT Roche and PacBio Workshop: Towards precision medicine
- Ranade, Swati (2016) AGBT Virtual Poster: Immune regions are no longer incomprehensible with SMRT Sequencing
- Chin, Jason (2016) AGBT Virtual Poster: Unzipping diploid genomes – revealing all kinds of heterozygous variants from comprehensive haplotig assemblies
- Lupski, Jim (2015) Mendelspod: The goal is de novo assembly in the clinic, says Jim Lupski, Baylor
- Nattestad, Maria (2015) ASHG Conference: Comprehensive genome and transcriptome structural analysis of a breast cancer cell line using PacBio long read sequencing
- Korlach, Jonas (2015) ASHG PacBio Workshop: Going beyond the $1,000 genome? – the future of high quality de novo human genomes, epigenomes and transcriptomes?
- Gibbs, Richard (2015) ASHG PacBio Workshop: Medical diagnostic challenges and structural variation detection using the PacBio Platform
- Wilson, Richard (2015) ASHG PacBio Workshop: Of reference genomes and precious metals
- Guo, Yunfei (2015) ASHG Virtual Poster: De novo assembly of a diploid Asian genome
- Gerstein, Mark (2015) Mendelspod: Going beyond the $1,000 genome with Mark Gerstein
- Salit, Marc (2015) Mendelspod: Marc Salit discusses creating the foundation of genomics
- Korlach, Jonas (2016) AGBT Roche and PacBio Workshop: Closing remarks
- Schatz, Michael and Nattestad, Maria (2016) Mendelspod: Frontiers of sequencing – Putting long reads and graph assemblies to work
- Guo, Yunfei (2015) Customer Experience: Benefits of long reads
- McCombie, Richard (2015) AGBT PacBio Workshop: PacBio long-read sequencing and structural analysis of a breast cancer cell line
- Schatz, Mike (2015) Customer Experience: At CSHL, new achievements with long-read sequencing
- Gyllensten, Ulf (2015) Customer Experience: For human genomes, we can’t live with just 80%
- Eichler, Evan (2014) ASHG PacBio Workshop: Resolving complexity of the human genome
- Application Brief: Low-coverage, long-read whole genome sequencing for structural variation – Best Practices (2017)
- PacBio Certified Service Providers (2017)
- Cancer Brochure: Discover the hidden landscape of cancer variants (2017)
- Human Biomedical Research Brochure: The most comprehensive view of the human genome (2017)
- Case Study: Improving precision medicine studies in Asia using ethnicity-specific human reference genomes and PacBio long-read sequencing (2017)
- Application Brief: Large genome whole genome sequencing – Best Practices (2017)
- SMRT Sequencing Brochure: Revolutionize genomics with SMRT Sequencing (2017)
- SV Application Brochure: Track the full extent of structural variation in a genome (2016)
- Case Study: Scientists deconstruct cancer complexity through genome and transcriptome analysis (2016)
- De Novo Assembly Application Brochure: Bring the “W” back to Whole genome sequencing (2015)
- Case Study: Precise sizing and SMRT Sequencing offer unprecedented read length for clinical studies. (2014)