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Assembly and diploid architecture of an individual human genome via single-molecule technologies

Nature Methods volume 12, pages 780–786 (2015)Cite this article

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Abstract

We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality.

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Figure 1: De novo assembly and scaffold layout.
Figure 2: Tandem-repeat detection from single molecules predicts a large divergence from reference.
Figure 3: De novo maps identify large structural variants.
Figure 4: CLRs highlight multiple colocated SVs and complex SV structures.

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Sequence Read Archive

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Acknowledgements

This work was supported in part by institutional support from the Icahn Institute for Genomics and Multiscale Biology, R01 HG005946, U01 HL107388, R01 DK098242-01, R01 MH106531, US National Institutes of Health (NIH) U41HG007497, the Irma T. Hirschl and Monique Weill-Caulier Charitable Trusts, the STARR Consortium, the WorldQuant Foundation, the Pershing Square Foundation, the Genomics & Epigenomics Core Facilities and SMRT Sequencing Center at Weill Cornell Medical College, and through the computational resources and staff expertise provided by the Department of Scientific Computing at the Icahn School of Medicine at Mount Sinai. DNA samples were provided by the Coriell Institute for Medical Research and the US National Institute of Standards and Technology (NIST). We would also like to thank T. Zichner for assistance with the design of validations and M. Chaisson for assistance with running Blasr, the assembly-based SV pipeline, and in performing the CHM1 comparison.

Author information

Author notes

  1. Matthew Pendleton, Robert Sebra, Andy Wing Chun Pang and Ajay Ummat: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA

    Matthew Pendleton, Robert Sebra, Ajay Ummat, Oscar Franzen, Ariella Cohain, Gintaras Deikus, Eric E Schadt & Ali Bashir

  2. BioNano Genomics, San Diego, California, USA

    Andy Wing Chun Pang, William Stedman, Thomas Anantharaman, Alex Hastie, Heng Dai & Han Cao

  3. Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany

    Tobias Rausch, Adrian M Stütz, Markus Hsi-Yang Fritz & Jan O Korbel

  4. The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA

    Russell E Durrett, Roger Altman & Christopher E Mason

  5. Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA

    Scott C Blanchard

  6. Pacific Biosciences, Menlo Park, California, USA

    Chen-Shan Chin, Yan Guo & Ellen E Paxinos

  7. European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, UK

    Jan O Korbel

  8. Laboratory of Neuro-Oncology, The Rockefeller University, New York, New York, USA

    Robert B Darnell

  9. Howard Hughes Medical Institute, New York, New York, USA

    Robert B Darnell

  10. The Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA

    W Richard McCombie

  11. The Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA

    W Richard McCombie

  12. Institute for Human Genetics, University of California–San Francisco, San Francisco, California, USA

    Pui-Yan Kwok

  13. Department of Medicine, Division of Hematology/Oncology, Weill Cornell Medical College, New York, New York, USA

    Christopher E Mason

  14. The Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, New York, New York, USA

    Christopher E Mason

Authors
  1. Matthew Pendleton
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Contributions

E.E.S., A.B., R.S., C.E.M., W.R.M. and R.B.D. conceived the project and provided resources for sequencing and algorithmic analysis. A.B. and E.E.S. provided bioinformatics oversight. J.O.K., M.H.-Y.F., A.M.S. and T.R. performed Illumina SV analysis and PCR validation. R.S., M.P. and E.E.P. prepared long libraries for PacBio sequencing. R.S., Y.G., A.C., S.C.B., R.A. and R.E.D. performed PacBio sequencing and primary analysis of hdf5 data. A.W.C.P., H.D., A.H., T.A., W.S., H.C. and P.-Y.K. generated the BioNano Data, built initial Genome Maps and performed BioNano alignment and SV calling. O.F., A.B. and M.P. performed PacBio SV analysis and validation. A.U., A.B. and C.-S.C. performed error correction and assembly. A.W.C.P. and H.D. built the initial hybrid scaffolding pipeline. A.B. and M.P. refined the hybrid scaffolding pipeline. A.W.C.P., H.D. and A.B. performed scaffold analysis and phasing. A.B., A.W.C.P., M.P. and A.U. generated figures for the main text. A.B., E.E.S., R.S., M.P. and A.W.C.P. primarily wrote the manuscript, though many coauthors provided edits and methods sections.

Corresponding author

Correspondence to Ali Bashir.

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Competing interests

A.W.C.P., H.C., W.S., T.A., A.H. and H.D. are employees of BioNano Genomics. C.-S.C., Y.G. and E.E.P. are employees of Pacific Biosciences, and E.E.S. is on the scientific advisory board of Pacific Biosciences.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–15, Supplementary Tables 1–4 and 6–12, Supplementary Results and Supplementary Notes 1–3 (PDF 16327 kb)

Supplementary Software

Custom scripts for performing hybrid scaffolding and SV analysis (ZIP 23658 kb)

Supplementary Table 5

Insertion and deletion SVs with phasing (XLSX 1079 kb)

Supplementary Table 13

Alignment coordinates between sequence contigs and V2 hybrid scaffolds (XLSX 260 kb)

Supplementary Table 14

Alignment coordinates between BioNano genome maps and V2 hybrid scaffolds (XLSX 89 kb)

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Pendleton, M., Sebra, R., Pang, A. et al. Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat Methods 12, 780–786 (2015). https://doi.org/10.1038/nmeth.3454

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