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De novo assembly and genotyping of variants using colored de Bruijn graphs

Nature Genetics volume 44, pages 226–232 (2012)Cite this article

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Abstract

Detecting genetic variants that are highly divergent from a reference sequence remains a major challenge in genome sequencing. We introduce de novo assembly algorithms using colored de Bruijn graphs for detecting and genotyping simple and complex genetic variants in an individual or population. We provide an efficient software implementation, Cortex, the first de novo assembler capable of assembling multiple eukaryotic genomes simultaneously. Four applications of Cortex are presented. First, we detect and validate both simple and complex structural variations in a high-coverage human genome. Second, we identify more than 3 Mb of sequence absent from the human reference genome, in pooled low-coverage population sequence data from the 1000 Genomes Project. Third, we show how population information from ten chimpanzees enables accurate variant calls without a reference sequence. Last, we estimate classical human leukocyte antigen (HLA) genotypes at HLA-B, the most variable gene in the human genome.

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Figure 1: Schematic representation of four methods of variation analysis using colored de Bruijn graphs; line width represents coverage.
Figure 2: Simulation-based evaluation of Cortex.
Figure 3: Structural and complex variants identified in a single high-coverage genome.
Figure 4: Population analysis with Cortex.
Figure 5: HLA-B genotyping from HTS data using Cortex.

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Acknowledgements

We would like to thank the members of the 1000 Genomes Project Consortium for discussion, suggestions and sequencing data. We thank B. Ahiska, A. Auton, E. Birney, R. Durbin, G. Lunter, J. Woolf and D. Zerbino for discussion, two anonymous reviewers for their comments and members of the PanMap Project and the Genomics Core at the Wellcome Trust Centre for Human Genetics for access to sequence data. Z.I. is funded by a grant from the Wellcome Trust (WT086084/Z/08/Z to G.M.). The sequencing of NA12878 was performed by the Wellcome Trust Sequencing Core at Oxford, under a grant from the Wellcome Trust (090532/Z/09/Z).

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Author notes

  1. Zamin Iqbal and Mario Caccamo: These authors contributed equally to this work.

Authors and Affiliations

  1. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK

    Zamin Iqbal, Isaac Turner & Gil McVean

  2. European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK

    Zamin Iqbal & Paul Flicek

  3. The Genome Analysis Centre, Norwich Research Park, Norwich, UK

    Mario Caccamo

  4. Department of Statistics, University of Oxford, Oxford, UK

    Gil McVean

Authors
  1. Zamin Iqbal
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Contributions

Z.I. and G.M. designed the study, developed the mathematical models and wrote the manuscript. M.C. and Z.I. developed the variant discovery algorithms, designed the multicolor graph data structures and implemented software. Z.I. performed simulations and analyses for cases 1, 3 and 4. I.T. and Z.I. performed analyses for case 2. P.F. contributed to early plans for Cortex.

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Correspondence to Gil McVean.

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The authors declare no competing financial interests.

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Supplementary Note, Supplementary Figures 1–6 and Supplementary Tables 1–7 (PDF 1207 kb)

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Iqbal, Z., Caccamo, M., Turner, I. et al. De novo assembly and genotyping of variants using colored de Bruijn graphs. Nat Genet 44, 226–232 (2012). https://doi.org/10.1038/ng.1028

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