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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- Redon, R., et al. (2006) Global variation in copy number in the human genome. 444, 444–454.
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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
- 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
- Xiao, Wenming et al. (2016) Challenges, solutions, and quality metrics of personal genome assembly in advancing precision medicine. Pharmaceutics
- Sevim, Volkan et al. (2016) Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing. Bioinformatics
- Rhoads, Anthony et al. (2015) PacBio sequencing and its applications. Genomics, Proteomics & Bioinformatics
- Sudmant, Peter H et al. (2015) An integrated map of structural variation in 2,504 human genomes. Nature
- 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 ?-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: Chin, Jason et al. (2016) Un-zipping diploid genomes - revealing all kinds of heterozygous variants from comprehensive hapltotig assemblies
- Poster: Ranade, Swati et al. (2016) Immune regions are no longer incomprehensible with SMRT Sequencing
- Poster: Sedlazeck, Fritz J. et al. (2015) Detection of structural variants using third generation sequencing
- Presentation: Nattestad, Maria et al. (2015) Comprehensive genome and transcriptome structural analysis of a breast cancer cell line using PacBio long read 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: Youve sequenced. How well did you do?
- Presentation: English, Adam et al. (2015) PBHoney: Detecting SVs with long-read sequencing
- Presentation: Bashir, Ali et al. (2015) Structural variation with Pacific Biosciences long reads
- Presentation: Zook, Justin et al. (2015) Reference materials for clinical applications of human genome sequencing
- Poster: Korlach, Jonas et al. (2014) Resolving the ‘dark matter’ in genomes.
- Carroll, Andrew (2016) DNAnexus Webinar: Accurate calling of structural variation in PacBio data
- Chin, Jason (2016) AGBT Virtual Poster: Unzipping diploid genomes – revealing all kinds of heterozygous variants from comprehensive haplotig assemblies
- Ranade, Swati (2016) AGBT Virtual Poster: Immune regions are no longer incomprehensible with SMRT Sequencing
- Ashley, Euan (2016) AGBT Roche and PacBio Workshop: Towards precision medicine
- Ameur, Adam (2016) AGBT Roche and PacBio Workshop: Clinical SMRT Sequencing – from single genese to complete genomes
- Meltz Steinberg, Karyn (2016) AGBT Conference: The first African reference genome assembly
- Guo, Yunfei (2015) ASHG Virtual Poster: De novo assembly of a diploid Asian genome
- Nattestad, Maria (2015) ASHG Conference: Comprehensive genome and transcriptome structural analysis of a breast cancer cell line using PacBio long read sequencing
- Gibbs, Richard (2015) ASHG PacBio Workshop: Medical diagnostic challenges and structural variation detection using the PacBio Platform
- Korlach, Jonas (2015) ASHG PacBio Workshop: Going beyond the $1,000 genome – the future of high quality de novo human genomes, epigenomes and transcriptomes
- Lupski, Jim (2015) Mendelspod: The goal is de novo assembly in the clinic, says Jim Lupski, Baylor
- 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
- Wilson, Richard (2015) ASHG PacBio Workshop: Of reference genomes and precious metals
- Schatz, Michael and Nattestad, Maria (2016) Mendelspod: Frontiers of sequencing – Putting long reads and graph assemblies to work
- Korlach, Jonas (2016) AGBT Roche and PacBio Workshop: Closing remarks
- Eichler, Evan (2014) ASHG PacBio Workshop: Resolving complexity of the human genome
- McCombie, Richard (2015) AGBT PacBio Workshop: PacBio long-read sequencing and structural analysis of a breast cancer cell line
- Gyllensten, Ulf (2015) Customer Experience: For human genomes, we can’t live with just 80%
- Schatz, Mike (2015) Customer Experience: At CSHL, new achievements with long-read sequencing
- Guo, Yunfei (2015) Customer Experience: Benefits of long reads
- PacBio Service Providers (2016)
- Case Study: Scientists deconstruct cancer complexity through genome and transcriptome analysis (2016)
- Cancer Brochure: Drive discovery with most complete view of cancer complexity (2016)
- De Novo Assembly Application Brochure: Bring the “W” back to Whole genome sequencing (2015)
- Sequel System Brochure: Introducing the scalable platform for SMRT Sequencing (2015)
- Case Study: Precise sizing and SMRT Sequencing offer unprecedented read length for clinical studies. (2014)