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Gain comprehensive access to human genetic variation

There is a growing awareness that SNVs do not tell the whole story of human genetic diversity, and that structural variation can be an important driver of health and disease susceptibility1. In fact, the majority of variant bases in the human genome occur in structural variants2. With complete de novo genomes, you gain access to all variant types, which is important for identifying causative alleles in pedigrees or de novo mutations in parent-child trios and large cohort studies. As our understanding of human genetic diversity grows, it becomes clear that reference selection is not a one-size-fits-all proposal3. Eventually, we may conclude each person will be his or her own best reference genome.

Generate exceptional de novo assemblies

Single Molecule, Real-Time (SMRT) Sequencing delivers the read lengths, uniform coverage, and the highest consensus accuracy required to access the complete spectrum of sequence variant types. From single nucleotides to complex structural variants, the PacBio Systems provide direct variant-phasing information through multi-gene regions and allows you to:

  • Generate gold-standard references unique to a population, disease, or individual
  • Increase power by matching references to the genetic background of studies
  • Access novel types of genetic variation and difficult-to-characterize regions
  • Evaluate all loci across the full spectrum of variant types without bias

Workflow: from DNA to gold-standard human de novo genomes

  • SMRT Sequencing with PacBio Systems
    • Take advantage of the Sequel System to reduce project costs and generate 7X more reads compared with the PacBio RS II
    • Achieve ~10 kb average read lengths, with some reads as long as 60 kb
    • Scale throughput based on project needs
      • 8-12 X coverage per sample for structural variant surveys
      • 50X coverage per sample for high-quality de novo assembly
    • Simultaneously capture epigenetic information
  • Read more about recommendations for large-genome assembly

To learn more about PacBio’s true whole genome sequencing solutions for human biomedical research, contact us.

 

“The PacBio technology has matured to a point where it is possible, and even advantageous, to use it for human-genome applications, because it is the only technology that can easily resolve complex regions and uncover genetic variations beyond single nucleotide polymorphisms.”
—Jeong-Sun Seo, Macrogen4

 

 References

  1. Baker, M., (2012) Structural variation: the genome’s hidden architecture. Nature Methods. 9, 133–137.
  2. Levy, S., et al., (2007) The Diploid Genome Sequence of an Individual Human. PLOS Biology. 5(10), e254.
  3. Church, DM., et al., (2011) Modernizing Reference Genome Assemblies. PLOS Biology. 9(7), e1001091.
  4. Seo, JS., (2015, February) High-quality Asian genome supports population-specific variant analysis. Presented at PacBio workshop at Advances in Genome Biology and Technology (AGBT).

Selected Resources