Open Access Open Badges Research

On the design of clone-based haplotyping

Christine Lo1, Rui Liu2, Jehyuk Lee34, Kimberly Robasky3456, Susan Byrne3, Carolina Lucchesi4, John Aach3, George Church34, Vineet Bafna1* and Kun Zhang2*

Author Affiliations

1 Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA

2 Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA

3 Department of Genetics, Department of Genetics, Harvard Medical School, Boston, MA, USA

4 Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA

5 The Bioinformatics Program, Boston University, Boston, MA, USA

6 Present address: Expression Analysis, A Quintiles Company, Durham, NC 27713, USA

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Genome Biology 2013, 14:R100  doi:10.1186/gb-2013-14-9-r100

Published: 12 September 2013



Haplotypes are important for assessing genealogy and disease susceptibility of individual genomes, but are difficult to obtain with routine sequencing approaches. Experimental haplotype reconstruction based on assembling fragments of individual chromosomes is promising, but with variable yields due to incompletely understood parameter choices.


We parameterize the clone-based haplotyping problem in order to provide theoretical and empirical assessments of the impact of different parameters on haplotype assembly. We confirm the intuition that long clones help link together heterozygous variants and thus improve haplotype length. Furthermore, given the length of the clones, we address how to choose the other parameters, including number of pools, clone coverage and sequencing coverage, so as to maximize haplotype length. We model the problem theoretically and show empirically the benefits of using larger clones with moderate number of pools and sequencing coverage. In particular, using 140 kb BAC clones, we construct haplotypes for a personal genome and assemble haplotypes with N50 values greater than 2.6 Mb. These assembled haplotypes are longer and at least as accurate as haplotypes of existing clone-based strategies, whether in vivo or in vitro.


Our results provide practical guidelines for the development and design of clone-based methods to achieve long range, high-resolution and accurate haplotypes.