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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

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Workflow: from DNA to structural variation detection

Featured research: assess structural variation in a personal genome

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“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

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“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.

 

References

  1. Levy, S., et al., (2007). The diploid genome sequence of an individual human. PLoS Biology. 5(10), e254.
  2. Redon, R., et al. (2006) Global variation in copy number in the human genome. 444, 444–454.
  3. Gonzaga-Jauregui, C., et al., (2012) Human genome sequencing in health and disease. Annual Review Medicine. 63, 35–61.
  4. English, A., et al. (2015) Assessing structural variation in a personal genome – towards a human reference diploid genome. BMC Genomics. 16:286.
  5. Chaisson, M., et al. (2014) Resolving the complexity of the human genome using single molecule sequencing. Nature. 517, 608–611.

Selected Resources