Low-Cost Genome-Scale Phasing with Barcode-Linked Sequencing

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Haploty**

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2590))

Abstract

Complete comprehension of clinically relevant variation among human genomes is likely only to come from sequencing platforms that are cost-efficient, and which feature both accurate base calling and long-range DNA phasing capability. The NGS revolution has struggled to meet the latter of these needs. Here we describe a protocol to address this limitation by preserving the molecular origin of short sequencing reads with an insignificant increase to sequencing costs. Whole haplotype-resolved genomes with megabase-scale phase blocks can be obtained with this method; offering researchers a unique opportunity to tackle the hurdles of de novo sequencing without being limited by a lack of resources.

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References

  1. Chaisson MJP, Sanders AD, Zhao X et al (2019) Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat Commun 10(1784). https://doi.org/10.1038/s41467-018-08148-z

  2. Church DM, Schneider VA, Steinberg KM et al (2015) Extending reference assembly models. Genome Biol 16:13

    Article  PubMed  PubMed Central  Google Scholar 

  3. Schneider VA, Graves-Lindsey T, Howe K et al (2017) Evaluation of grch38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Res 27(5):849–864. https://doi.org/10.1101/gr.213611.116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Clarke J, Wu HC, Jayasinghe L et al (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol 4:265–270

    Article  CAS  PubMed  Google Scholar 

  5. Eid J, Fehr A, Gray J et al (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133–138

    Article  CAS  PubMed  Google Scholar 

  6. Zheng GXY, Lau BT, Schnall-Levin M et al (2016) Haploty** germline and cancer genomes with high-throughput linked-read sequencing. Nat Biotechnol 34:303–311. https://doi.org/10.1038/nbt.3432

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Amini S, Pushkarev D, Christiansen L et al (2014) Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nat Genet 46:1343–1349. https://doi.org/10.1038/ng.3119

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Peters BA, Kermani BG, Sparks AB et al (2012) Accurate whole-genome sequencing and haploty** from 10 to 20 human cells. Nature 487:190–195

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Lan F, Haliburton JR, Yuan A, Abate AR (2016) Droplet barcoding for massively parallel single-molecule deep sequencing. Nat Commun 7(11784). https://doi.org/10.1038/ncomms11784

  10. Redin D, Frick T, Aghelpasand H et al (2019) High throughput barcoding method for genome-scale phasing. Sci Rep 9(18116). https://doi.org/10.1038/s41598-019-54446-x

  11. Redin D, Frick T, Aghelpasand H et al (2018) Efficient whole genome haploty** and high-throughput single molecule phasing with barcode-linked reads. bioRxiv:356121. https://doi.org/10.1101/356121

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Correspondence to David Redin .

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Redin, D. (2023). Low-Cost Genome-Scale Phasing with Barcode-Linked Sequencing. In: Peters, B.A., Drmanac, R. (eds) Haploty**. Methods in Molecular Biology, vol 2590. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2819-5_6

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  • DOI: https://doi.org/10.1007/978-1-0716-2819-5_6

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2818-8

  • Online ISBN: 978-1-0716-2819-5

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