A hybrid approach for de novo human genome sequence assembly and phasing (original) (raw)

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References

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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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5. Alex R Hastie
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6. Patrick Marks
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7. Joyce Lee
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8. Catherine Chu
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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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12. Stephen A Schlebusch
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13. Kristina Giorda
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14. Michael Schnall-Levin
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15. Jeffrey D Wall
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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 toPui-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).

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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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• Received: 12 January 2016
• Accepted: 08 April 2016
• Published: 09 May 2016
• Issue Date: July 2016
• DOI: https://doi.org/10.1038/nmeth.3865