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Long-range polony haplotyping of individual human chromosome molecules


We report a method for multilocus long-range haplotyping on human chromosome molecules in vitro based on the DNA polymerase colony (polony) technology. By immobilizing thousands of intact chromosome molecules within a polyacrylamide gel on a microscope slide and performing multiple amplifications from single molecules, we determined long-range haplotypes spanning a 153-Mb region of human chromosome 7 and found evidence of rare mitotic recombination events in human lymphocytes. Furthermore, the parallel nature of DNA polony technology allows efficient haplotyping on pooled DNAs from a population on one slide, with a throughput three orders of magnitudes higher than current molecular haplotyping methods. Linkage disequilibrium statistics established by our pooled DNA haplotyping method are more accurate than statistically inferred haplotypes. This haplotyping method is well suited for candidate gene–based association studies as well as for investigating the pattern of recombination in mammalian cells.

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Figure 1: Multi-locus long-range haplotyping.
Figure 2: Haplotyping on intact chromosomes.


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We thank N. Reppas, F. Isaacs, J. Akey and L. Jin for critical review of the manuscript, C. Varma for assistance in polony image analyses. This work was supported by the US National Human Genome Research Institute-Center of Excellence in Genome Science grants.

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Correspondence to Kun Zhang.

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Supplementary information

Supplementary Fig. 1

Multi-locus polony haplotyping on CD36 and NOS3. (PDF 134 kb)

Supplementary Fig. 2

Effects of sample size on LD patterns revealed by pooled polony haplotyping. (PDF 164 kb)

Supplementary Table 1

Summary statistics of polony haplotyping on pooled DNA of 24 African Americans. (PDF 50 kb)

Supplementary Table 2

CD36 haplotypes determined by polony haplotyping. (PDF 31 kb)

Supplementary Table 3

Comparison of LD statistics in NOS3 determined by four methods. (PDF 54 kb)

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Zhang, K., Zhu, J., Shendure, J. et al. Long-range polony haplotyping of individual human chromosome molecules. Nat Genet 38, 382–387 (2006).

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