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

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Single Molecule and Single Cell Sequencing

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 1129))

Abstract

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.

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References

  • 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.

    Article  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Cao H, et al. Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology. Gigascience. 2014;3:34.

    Article  Google Scholar 

  • 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. https://doi.org/10.1101/239251.

    Article  CAS  Google Scholar 

  • de Koning AP, et al. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet. 2011;7(12):e1002384.

    Article  Google Scholar 

  • Gabrieli T, et al. Cas9-assisted targeting of CHromosome segments (CATCH) for targeted nanopore sequencing and optical genome mapping. 2017. https://doi.org/10.1101/110163.

  • Grunwald A, et al. Reduced representation optical methylation mapping (R2OM2). 2017. https://doi.org/10.1101/108084.

  • Huddleston J, Eichler EE. An incomplete understanding of human genetic variation. Genetics. 2016;202(4):1251–4.

    Article  CAS  Google Scholar 

  • Huddleston J, et al. Discovery and genotyping of structural variation from long-read haploid genome sequence data. Genome Res. 2017;27(5):677–85.

    Article  CAS  Google Scholar 

  • Jaratlerdsiri W, et al. Next generation mapping reveals novel large genomic rearrangements in prostate cancer. Oncotarget. 2017;8:23588–602.

    Article  Google Scholar 

  • Jiao Y, Peluso P, Ware D. Improved maize reference genome with single-molecule technologies. Nature. 2017;546(22):524–7. https://doi.org/10.1038/nature22971.

    Article  CAS  PubMed  Google Scholar 

  • Klein K, et al. Genome-wide identification of early-firing human replication origins by optical replication mapping. 2017. https://doi.org/10.1101/214841.

  • Lam ET, et al. Genome mapping on NanoChannel arrays for structural variation analysis and sequence assembly. Nat Biotechnol. 2012;30:771–6.

    Article  CAS  Google Scholar 

  • Lee H, et al. Clinical exome sequencing for genetic identification of rare mendelian disorders. JAMA. 2014;312(18):1880–7.

    Article  Google Scholar 

  • Mak A, et al. Genome-wide structural variation detection by genome mapping on NanoChannel arrays. Genetics. 2016;202:351–62.

    Article  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • McCaffrey J, et al. High-throughput single-molecule telomere characterization. Genome Res. 2017;27:1904–15.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Sudmant PH, et al. An integrated map of structural variation in 2,504 human genomes. Nature. 2015;526(7571):75–81.

    Article  CAS  Google Scholar 

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Correspondence to Sven Bocklandt .

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Bocklandt, S., Hastie, A., Cao, H. (2019). Bionano Genome Mapping: High-Throughput, Ultra-Long Molecule Genome Analysis System for Precision Genome Assembly and Haploid-Resolved Structural Variation Discovery. In: Suzuki, Y. (eds) Single Molecule and Single Cell Sequencing. Advances in Experimental Medicine and Biology, vol 1129. Springer, Singapore. https://doi.org/10.1007/978-981-13-6037-4_7

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