On the design of clone-based haplotyping

Lo, C., Liu, R., Lee, J., Robasky, K., Byrne, S., Lucchesi, C., Aach, J., Church, G., Bafna, V., Zhang, K. (2013) On the design of clone-based haplotyping. Genome Biol, 14 (9). R100. ISSN 1465-6914 (Electronic)1465-6906 (Linking)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/24028704
DOI: 10.1186/gb-2013-14-9-r100

Abstract

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

Item Type: Paper
Uncontrolled Keywords: Algorithms Chromosomes, Artificial, Bacterial Cloning, Molecular Contig Mapping/ methods/statistics & numerical data Genome, Human HLA Antigens/ genetics Haplotypes Humans Molecular Typing/ methods/statistics & numerical data Polymorphism, Single Nucleotide Sequence Analysis, DNA
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosome
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosomes, structure and function > chromosome

Investigative techniques and equipment > cloning
Investigative techniques and equipment > assays > cloning

bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > single nucleotide polymorphism > haplotype
CSHL Authors:
Communities: CSHL labs > Lee lab
Depositing User: Matt Covey
Date: 2013
Date Deposited: 22 Jul 2015 15:50
Last Modified: 22 Jul 2015 15:50
PMCID: PMC4053695
Related URLs:
URI: http://repository.cshl.edu/id/eprint/31636

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