Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly

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Abstract

We describe genome mapping on nanochannel arrays. In this approach, specific sequence motifs in single DNA molecules are fluorescently labeled, and the DNA molecules are uniformly stretched in thousands of silicon channels on a nanofluidic device. Fluorescence imaging allows the construction of maps of the physical distances between occurrences of the sequence motifs. We demonstrate the analysis, individually and as mixtures, of 95 bacterial artificial chromosome (BAC) clones that cover the 4.7-Mb human major histocompatibility complex region. We obtain accurate, haplotype-resolved, sequence motif maps hundreds of kilobases in length, resulting in a median coverage of 114× for the BACs. The final sequence motif map assembly contains three contigs. With an average distance of 9 kb between labels, we detect 22 haplotype differences. We also use the sequence motif maps to provide scaffolds for de novo assembly of sequencing data. Nanochannel genome mapping should facilitate de novo assembly of sequencing reads from complex regions in diploid organisms, haplotype and structural variation analysis and comparative genomics.

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Figure 1: Nanochannel arrays.
Figure 2: Genome mapping.
Figure 3: Genome mapping of mixtures of 95 BACs from the PGF and COX libraries.
Figure 4: Sequence motif map of the MHC region.
Figure 5: De novo sequence assembly of the MHC region.
Figure 6: Haplotype resolution and structural variation detected by genome mapping.

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Acknowledgements

The authors thank A. Pool and P. Ling-Fung Tang for their assistance in sequencing. O. Hampton and H. VanSteenhouse provided critical comments. This research is supported in part by US National Institutes of Health (NIH) award to P.-Y.K. and M.X. (R01 HG005946). E.T.L. was supported in part by NIH Training Grant T32 GM007175.

Author information

E.T.L., M.X. and P.-Y.K. conceived the study. M.X. and P.-Y.K. supervised the project. E.T.L., C.L. and D.E. maintained BAC cultures and extracted DNA. A.H., S.K.D., M.D.A., P.D., D.E., N.N., E.L.T., H.C., M.X. and P.-Y.K. participated in data generation and analysis. E.T.L., A.H., M.X. and P.-Y.K. wrote the manuscript. All authors were involved in discussion of the manuscript.

Correspondence to Ming Xiao or Pui-Yan Kwok.

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Competing interests

A.H., S.K.D., M.D.A., P.D., H.C. and M.X. are employees of the commercial company BioNano Genomics. P.-Y.K. serves as a scientific advisor at BioNano Genomics.

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Lam, E., Hastie, A., Lin, C. et al. Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nat Biotechnol 30, 771–776 (2012) doi:10.1038/nbt.2303

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