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.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Sudmant PH, Rausch T, Gardner EJ, Handsaker RE et al (2016) An integrated map of structural variation in 2504 human genomes. Nature 526:75–81
Chiang C, Scott AJ, Davis JR et al (2017) The impact of structural variation on human gene expression. Nat Genet 49:692–699
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 18:36
Zack TI, Schumacher SE, Carter SL et al (2013) Pan-cancer patterns of somatic copy number alteration. Nat Genet 45:1134–1140
Jiao Y, Peluso P, Shi J et al (2017) Improved maize reference genome with single-molecule technologies. Nature 546:524–527
Alkan C, Coe BP, Eichler EE (2011) Genome structural variation discovery and genotyping. Nat Rev Genet 12:363–376
Escaramís G, Docampo E, Rabionet R (2015) A decade of structural variants: description, history and methods to detect structural variation. Brief Funct Genomics 14:305–314
Greer SU, Nadauld LD, Lau BT et al (2017) Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases. Genome Med 9:57
Huddleston J, Eichler EE (2016) An incomplete understanding of human genetic variation. Genetics 202:1251–1254
Schwartz DC, Li X, Hernandez LI et al (1993) Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science 262:110–114
Deschamps S, Zhang Y, Llaca V et al (2018) A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping. bioRxiv 327817
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer International Publishing AG, part of Springer Nature
About this protocol
Cite this protocol
Chan, S. et al. (2018). Structural Variation Detection and Analysis Using Bionano Optical Mapping. In: Bickhart, D. (eds) Copy Number Variants. Methods in Molecular Biology, vol 1833. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8666-8_16
Download citation
DOI: https://doi.org/10.1007/978-1-4939-8666-8_16
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-8665-1
Online ISBN: 978-1-4939-8666-8
eBook Packages: Springer Protocols