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A hybrid approach for de novo human genome sequence assembly and phasing

Nature Methods volume 13, pages 587–590 (2016)Cite this article

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Abstract

Despite tremendous progress in genome sequencing, the basic goal of producing a phased (haplotype-resolved) genome sequence with end-to-end contiguity for each chromosome at reasonable cost and effort is still unrealized. In this study, we describe an approach to performing de novo genome assembly and experimental phasing by integrating the data from Illumina short-read sequencing, 10X Genomics linked-read sequencing, and BioNano Genomics genome mapping to yield a high-quality, phased, de novo assembled human genome.

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Figure 1
Figure 2: Schematic of the relative sizes of scaffolds produced during the assembly process.
Figure 3: Alignment and phasing of the hybrid assembly.

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Sequence Read Archive

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Acknowledgements

This work was supported in part by R01 HG005946 (P.-Y.K.). The DNA sample was obtained from the Coriell Institute for Medical Research, and the Illumina sequence data were obtained from the US National Institute of Standards and Technology (NIST). We thank the expert sequencing staff at the Institute for Human Genetics at UCSF for generating some of the sequencing data.

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Authors and Affiliations

  1. Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, USA.,

    Yulia Mostovoy, Michal Levy-Sakin, Jessica Lam, Catherine Chu, Chin Lin & Pui-Yan Kwok

  2. BioNano Genomics, Inc., San Diego, California, USA

    Ernest T Lam, Alex R Hastie, Joyce Lee, Željko Džakula & Han Cao

  3. 10X Genomics, Inc., Pleasanton, California, USA

    Patrick Marks, Kristina Giorda & Michael Schnall-Levin

  4. Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa

    Stephen A Schlebusch

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

    Jeffrey D Wall & Pui-Yan Kwok

  6. Department of Dermatology, University of California, San Francisco, San Francisco, California, USA.,

    Pui-Yan Kwok

Authors
  1. Yulia Mostovoy
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  2. Michal Levy-Sakin
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  3. Jessica Lam
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  4. Ernest T Lam
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  7. Joyce Lee
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  9. Chin Lin
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  10. Željko Džakula
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  11. Han Cao
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  16. Pui-Yan Kwok
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Contributions

P.-Y.K., J.D.W., and Y.M. conceived the project and provided resources and oversight for sequencing and algorithmic analysis. K.G. prepared long libraries for 10XG GemCode sequencing. C.C. and C.L. performed long DNA preparation and BNG genome mapping experiments. E.T.L., A.R.H., Ž.D., J.Lee, and H.C. built initial genome maps and performed BNG alignment and structural variant calling. Y.M. and J.Lam performed scaffold analysis. E.T.L., A.R.H., and J.Lee performed hybrid genome assembly. P.M., K.G., and M.S.-L. performed scaffold phasing. Y.M., M.L.-S., E.T.L., J.Lam, J.Lee, and S.A.S. performed validation and quality measure analyses of the assembled data. Y.M., E.T.L., M.L.-S., and P.-Y.K. primarily wrote the manuscript and revisions, though many coauthors provided edits and Online Methods sections.

Corresponding author

Correspondence to Pui-Yan Kwok.

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Competing interests

E.T.L., A.R.H., J.Lee, Ž.D., and H.C. are employees of BioNano Genomics. P.M., K.G., and M.S.-L. are employees of 10X Genomics, and P.-Y.K. is on the scientific advisory board of BioNano Genomics.

Integrated supplementary information

Supplementary Figure 1 Ideograms showing scaffold boundaries and segmental duplication locations.

Blue lines mark the boundaries of assembly scaffolds. Black marks show the locations of segmental duplications. Magenta regions mark unassembled regions around the centromeres and telomeres. Ideogram were generated using The Genome Decoration Page, NCBI.

Supplementary Figure 2 Architecture of complex regions at the MHC and Amylase loci.

(a) MHC region (chr6: 28-32 Mb). Upper panel: green bar = reference, blue bars = hybrid assembly (bottom). Bottom panel: green phase blocks separated by SNVs in the hybrid assembly in the middle. (b) Amylase region (chr1: 160-163 Mb). Top panel: green bar = reference, blue bars = assemby. Assembly in the red box expanded to show nicking pattern in 450 kb region (bottom panel). (c) Haplotypes in increasing resolution to show alleles on the same phase block (green line = allele 1, grey line = allele 2).

Supplementary Figure 3 Assembly and phasing of Inversion.

Inversion at Chr10q 46-47.5 Mb with partial haplotyping.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–3 and Supplementary Tables 1–3 (PDF 786 kb)

Supplementary Data 1

NA12878 BNG assembly (TXT 16137 kb)

Supplementary Data 2

NA12878 hybrid assembly SV calls (TXT 278 kb)

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Mostovoy, Y., Levy-Sakin, M., Lam, J. et al. A hybrid approach for de novo human genome sequence assembly and phasing. Nat Methods 13, 587–590 (2016). https://doi.org/10.1038/nmeth.3865

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