Bionano Genome Mapping: High-Throughput, Ultra-Long Molecule Genome Analysis System for Precision Genome Assembly and Haploid-Resolved Structural Variation Discovery

  • Sven BocklandtEmail author
  • Alex Hastie
  • Han Cao
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 1129)


Next Generation Sequencing (NGS) has rapidly advanced genomic research with tremendously increased throughput and reduced cost, through reading the fragmented genome content in massively parallel fashion. We have been able to sequence and map genomes to reference sequences with relative ease compared to the past. However, this mapping can only be accurately accomplished in the single copy regions of the genome, leaving out most duplicated genes and structural variation. Additionally, assembly of long genomic segments remains elusive since multi copy regions of the genome produce ambiguity when short read sequence is used.


  1. Barseghyan H, et al. Next-generation mapping: a novel approach for detection of pathogenic structural variants with a potential utility in clinical diagnosis. Genome Med. 2017;9:90.CrossRefGoogle Scholar
  2. Bickhart DM, et al. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nat Genet. 2017;49:643–50.CrossRefGoogle Scholar
  3. Cao H, et al. Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology. Gigascience. 2014;3:34.CrossRefGoogle Scholar
  4. De Carli F, Menezes N, Berrabah W, Barbe V, Genovesio A, Hyrien O. High-throughput optical mapping of replicating DNA. Small Methods. 2017;2(9):1800146. Scholar
  5. de Koning AP, et al. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet. 2011;7(12):e1002384.CrossRefGoogle Scholar
  6. Gabrieli T, et al. Cas9-assisted targeting of CHromosome segments (CATCH) for targeted nanopore sequencing and optical genome mapping. 2017.
  7. Grunwald A, et al. Reduced representation optical methylation mapping (R2OM2). 2017.
  8. Huddleston J, Eichler EE. An incomplete understanding of human genetic variation. Genetics. 2016;202(4):1251–4.CrossRefGoogle Scholar
  9. Huddleston J, et al. Discovery and genotyping of structural variation from long-read haploid genome sequence data. Genome Res. 2017;27(5):677–85.CrossRefGoogle Scholar
  10. Jaratlerdsiri W, et al. Next generation mapping reveals novel large genomic rearrangements in prostate cancer. Oncotarget. 2017;8:23588–602.CrossRefGoogle Scholar
  11. Jiao Y, Peluso P, Ware D. Improved maize reference genome with single-molecule technologies. Nature. 2017;546(22):524–7. Scholar
  12. Klein K, et al. Genome-wide identification of early-firing human replication origins by optical replication mapping. 2017.
  13. Lam ET, et al. Genome mapping on NanoChannel arrays for structural variation analysis and sequence assembly. Nat Biotechnol. 2012;30:771–6.CrossRefGoogle Scholar
  14. Lee H, et al. Clinical exome sequencing for genetic identification of rare mendelian disorders. JAMA. 2014;312(18):1880–7.CrossRefGoogle Scholar
  15. Mak A, et al. Genome-wide structural variation detection by genome mapping on NanoChannel arrays. Genetics. 2016;202:351–62.CrossRefGoogle Scholar
  16. McCaffrey J, et al. CRISPR-CAS9 D10A nickase target-specific fluorescent labeling of double strand DNA for whole genome mapping and structural variation analysis. Nucleic Acids Res. 2016;44:e11.CrossRefGoogle Scholar
  17. McCaffrey J, et al. High-throughput single-molecule telomere characterization. Genome Res. 2017;27:1904–15.CrossRefGoogle Scholar
  18. Miller DT, et al. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet. 2010;86(5):749–64.CrossRefGoogle Scholar
  19. Sudmant PH, et al. An integrated map of structural variation in 2,504 human genomes. Nature. 2015;526(7571):75–81.CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  1. 1.Bionano GenomicsSan DiegoUSA

Personalised recommendations