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Chromosome-Range Whole-Genome High-Throughput Experimental Haplotyping by Single-Chromosome Microdissection

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Haplotyping

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1551))

Abstract

Haplotype is fundamental genetic information; it provides essential information for deciphering the functional and etiological roles of genetic variants. As haplotype information is closely related to the functional and etiological impact of genetic variants, it is widely anticipated that haplotype information will be extremely valuable in a wide spectra of applications, including academic research, clinical diagnosis of genetic disease and in the pharmaceutical industry. Haplotyping is essential for LD (linkage disequilibrium) mapping, functional studies on cis-interactions, big data imputation, association studies, population studies, and evolutionary studies. Unfortunately, current sequencing technologies and genotyping arrays do not routinely deliver this information for each individual, but yield only unphased genotypes. Here, we describe a high-throughput and cost-effective experimental protocol to obtain high-resolution chromosomal haplotypes of each individual diploid (including human) genome by the single-chromosome microdissection and sequencing approach.

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Acknowledgment

This work was supported by US National Institutes of Health grants (R21HG006173, RC4MD005964, HL003676, RR014758, RR003034, GM74913, G12MD007602, U54MD007588), an American Heart Association grant (09GRNT2300003).

Author information

Authors and Affiliations

  1. 4DGenome Inc, Atlanta, GA, USA

    Li Ma M.D., Ph.D. & Qing Song M.D., Ph.D.

  2. Cardiovascular Research Institute and Department of Medicine, Morehouse School of Medicine, 720 Westview Dr SW, Atlanta, GA, 30310, USA

    Li Ma M.D., Ph.D., Wenzhi Li & Qing Song M.D., Ph.D.

  3. Center of Big Data and Bioinformatics, First Affiliated Hospital of Medicine School, Xi’an Jiaotong University, Xi’an, Shaanxi, China

    Wenzhi Li & Qing Song M.D., Ph.D.

  4. Research Wing D-203, 720 Westview Drive, Atlanta, GA, 30310, USA

    Qing Song M.D., Ph.D.

Authors
  1. Li Ma M.D., Ph.D.
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  2. Wenzhi Li
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  3. Qing Song M.D., Ph.D.
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Corresponding authors

Correspondence to Li Ma M.D., Ph.D. or Qing Song M.D., Ph.D. .

Editor information

Editors and Affiliations

  1. Johannes Kepler University Institute of Biophysics, Linz, Austria

    Irene Tiemann-Boege

  2. Vetmeduni Vienna InstitutPopulationsgenetik, Wien, Austria

    Andrea Betancourt

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Ma, L., Li, W., Song, Q. (2017). Chromosome-Range Whole-Genome High-Throughput Experimental Haplotyping by Single-Chromosome Microdissection. In: Tiemann-Boege, I., Betancourt, A. (eds) Haplotyping. Methods in Molecular Biology, vol 1551. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6750-6_9

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  • DOI: https://doi.org/10.1007/978-1-4939-6750-6_9

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6748-3

  • Online ISBN: 978-1-4939-6750-6

  • eBook Packages: Springer Protocols

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