Structural Variation Detection and Analysis Using Bionano Optical Mapping

• Published in: Methods in molecular biology (Clifton, N.J.) Vol. 1833; p. 193
• Main Authors: Chan, Saki, Lam, Ernest, Saghbini, Michael, Bocklandt, Sven, Hastie, Alex, Cao, Han, Holmlin, Erik, Borodkin, Mark
• Format: Journal Article
• Language: English
• Published: United States 01-01-2018
• Subjects: Alleles; Chromosome Mapping - methods; Genetic Variation; Genome, Human; Humans; Sequence Analysis, DNA - methods; Translocation; Genome structure; Long reads; Genomics; Deletion; Insertion; Inversion; Optical mapping; Structural Variation
• ISSN: 1940-6029
• DOI: 10.1007/978-1-4939-8666-8_16

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.