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Structural Variation Detection and Analysis Using Bionano Optical Mapping

  • Saki Chan
  • Ernest Lam
  • Michael Saghbini
  • Sven Bocklandt
  • Alex Hastie
  • Han Cao
  • Erik Holmlin
  • Mark BorodkinEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1833)

Abstract

The need to accurately identify the complete structural variation profile of genomes is becoming increasingly evident. In contrast to reference-based methods like sequencing or comparative methods like aCGH, optical mapping is a de novo assembly-based method that enables better realization of true genomic structure. It allows for independently detecting balanced and unbalanced structural variants (SVs) from separate alleles and for discovering de novo events. Here we show how Bionano Genome Mapping creates de novo assemblies from native and intact, megabase-scale DNA molecules and uses those assemblies to detect a wide range of structural variants.

Key words

Structural Variation Insertion Deletion Inversion Translocation Long reads Genomics Genome structure Optical mapping 

References

  1. 1.
    Sudmant PH, Rausch T, Gardner EJ, Handsaker RE et al (2016) An integrated map of structural variation in 2504 human genomes. Nature 526:75–81CrossRefGoogle Scholar
  2. 2.
    Chiang C, Scott AJ, Davis JR et al (2017) The impact of structural variation on human gene expression. Nat Genet 49:692–699CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Collins RL, Brand H, Redin CE et al (2017) Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome. Genome Biol 18:36CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Zack TI, Schumacher SE, Carter SL et al (2013) Pan-cancer patterns of somatic copy number alteration. Nat Genet 45:1134–1140CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Jiao Y, Peluso P, Shi J et al (2017) Improved maize reference genome with single-molecule technologies. Nature 546:524–527PubMedGoogle Scholar
  6. 6.
    Alkan C, Coe BP, Eichler EE (2011) Genome structural variation discovery and genotyping. Nat Rev Genet 12:363–376CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Escaramís G, Docampo E, Rabionet R (2015) A decade of structural variants: description, history and methods to detect structural variation. Brief Funct Genomics 14:305–314CrossRefPubMedGoogle Scholar
  8. 8.
    Greer SU, Nadauld LD, Lau BT et al (2017) Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases. Genome Med 9:57CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Huddleston J, Eichler EE (2016) An incomplete understanding of human genetic variation. Genetics 202:1251–1254CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Schwartz DC, Li X, Hernandez LI et al (1993) Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science 262:110–114CrossRefPubMedGoogle Scholar
  11. 11.
    Deschamps S, Zhang Y, Llaca V et al (2018) A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping. bioRxiv 327817Google Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Saki Chan
    • 1
  • Ernest Lam
    • 1
  • Michael Saghbini
    • 1
  • Sven Bocklandt
    • 1
  • Alex Hastie
    • 1
  • Han Cao
    • 1
  • Erik Holmlin
    • 1
  • Mark Borodkin
    • 1
    Email author
  1. 1.Bionano GenomicsSan DiegoUSA

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