Direct determination of haplotypes from single DNA molecules


Determining the long-range haplotypes in a diploid individual is a major technical challenge. Here we report a method of molecular haplotyping by directly imaging multiple polymorphic sites on individual human DNA molecules simultaneously. We demonstrate the utility of this technology by accurately determining the haplotypes consisting of up to 16 single-nucleotide polymorphisms in genomic regions up to 50 kilobases.

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Figure 1: Allele-specific labeling of SNPs and regeneration of dsDNA.
Figure 2: Molecular haplotyping of four SNPs across a 12.5 kb region.
Figure 3: Molecular haplotyping of 16 SNPs across the 50 kb PLAT gene region.


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This work is supported by the US National Human Genome Research Institute (R01-HG01720).

Author information




M.X. designed and performed experiments, analyzed data and wrote the paper. E.W. and C.C. performed experiments and analyzed the data. Y.C. performed experiments. W.-C.H. performed statistical analysis. P.Y.K. designed the study and wrote the paper.

Corresponding authors

Correspondence to Ming Xiao or Pui-Yan Kwok.

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Competing interests

M.X. and P.-Y.K. have filed patent applications on the technologies described in this paper: US 11/957,216 (inventors: M.X., P.-Y.K., Paul Selvin and Matthew Gordon) and US 10/976,546 (inventors: Paul Selvin, Matthew Gordon, P.-Y.K., M.X. and Ting-Fung Chan).

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Supplementary Figure 1, Supplementary Tables 1–5, Supplementary Methods (PDF 383 kb)

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Xiao, M., Wan, E., Chu, C. et al. Direct determination of haplotypes from single DNA molecules. Nat Methods 6, 199–201 (2009).

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