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Whole-genome molecular haplotyping of single cells

Nature Biotechnology volume 29, pages 51–57 (2011)Cite this article

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Abstract

Conventional experimental methods of studying the human genome are limited by the inability to independently study the combination of alleles, or haplotype, on each of the homologous copies of the chromosomes. We developed a microfluidic device capable of separating and amplifying homologous copies of each chromosome from a single human metaphase cell. Single-nucleotide polymorphism (SNP) array analysis of amplified DNA enabled us to achieve completely deterministic, whole-genome, personal haplotypes of four individuals, including a HapMap trio with European ancestry (CEU) and an unrelated European individual. The phases of alleles were determined at ∼99.8% accuracy for up to ∼96% of all assayed SNPs. We demonstrate several practical applications, including direct observation of recombination events in a family trio, deterministic phasing of deletions in individuals and direct measurement of the human leukocyte antigen haplotypes of an individual. Our approach has potential applications in personal genomics, single-cell genomics and statistical genetics.

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Figure 1: Microfluidic device designed for the amplification of metaphase chromosomes from a single cell.
Figure 2: Whole-genome haplotyping.
Figure 3: Comparison of statistically determined phases with experimentally determined phases.
Figure 4: Direct observation of recombination events and deterministic phasing of heterozygous deletions in the family trio.
Figure 5: HLA haplotypes of P0 determined using DDP.

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Acknowledgements

We thank J. Melin and the Stanford Microfluidic Foundry for fabrication of microfluidic devices. We thank N. Neff and G. Mantalas for performing sequencing experiments. We thank D. Pushkarev for providing data and primers from the genome sequencing project of P0. We thank M. Anderson and D. Tyan at Stanford Histocompatibility Laboratory for providing HLA typing results. We thank Y. Marcy, P. Blainey, J. Jiang and A. Wu for helpful discussions. The project was supported by the US National Institutes of Health (NIH) Pioneer Award and an NIH U54 award. H.C.F. was supported by a scholarship from the Siebel Foundation. J.W. was supported by a scholarship from the China Scholarship Council.

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Authors and Affiliations

  1. Department of Bioengineering, Stanford University, Stanford, California, USA

    H Christina Fan, Jianbin Wang & Stephen R Quake

  2. Howard Hughes Medical Institute, Stanford University, Stanford, California, USA

    Anastasia Potanina & Stephen R Quake

  3. Department of Applied Physics, Stanford University, Stanford, California, USA

    Stephen R Quake

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  1. H Christina Fan
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Contributions

H.C.F. and S.R.Q. conceived the experiments. H.C.F. designed the microfluidic device. A.P. developed protocols for device fabrication. H.C.F. and J.W. performed the experiments. H.C.F., J.W. and S.R.Q. analyzed the data and wrote the manuscript.

Corresponding author

Correspondence to Stephen R Quake.

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Competing interests

S.R.Q. is a founder, consultant and shareholder of Fluidigm Corporation and Helicos Biosciences Corporation, and a consultant and shareholder of Artemis Health. H.C.F. was previously employed at Fluidigm Corporation. All other authors declare no conflict of interest.

Supplementary information

Supplementary Text and Figures

Supplementary Tables 1–6 and Supplementary Figs. 1–4 (PDF 979 kb)

Supplementary Data Set 1

Haplotypes 1 GM12891 haplotypes.txt (TXT 21809 kb)

Supplementary Data Set 2

Haplotypes 2 GM12892 haplotypes.txt (TXT 20361 kb)

Supplementary Data Set 3

Haplotypes 3 GM12878 haplotypes.txt (TXT 21341 kb)

Supplementary Data Set 4

P0 Omni1S (TXT 31433 kb)

Supplementary Data Set 5

P0 Omni1Quad (TXT 16458 kb)

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Fan, H., Wang, J., Potanina, A. et al. Whole-genome molecular haplotyping of single cells. Nat Biotechnol 29, 51–57 (2011). https://doi.org/10.1038/nbt.1739

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