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dc.contributor.authorLo, Christineen_US
dc.contributor.authorLiu, Ruien_US
dc.contributor.authorLee, Jehyuken_US
dc.contributor.authorRobasky, Kimberlyen_US
dc.contributor.authorByrne, Susanen_US
dc.contributor.authorLucchesi, Carolinaen_US
dc.contributor.authorAach, Johnen_US
dc.contributor.authorChurch, Georgeen_US
dc.contributor.authorBafna, Vineeten_US
dc.contributor.authorZhang, Kunen_US
dc.date.accessioned2014-07-07T17:03:23Z
dc.date.issued2013en_US
dc.identifier.citationLo, Christine, Rui Liu, Jehyuk Lee, Kimberly Robasky, Susan Byrne, Carolina Lucchesi, John Aach, George Church, Vineet Bafna, and Kun Zhang. 2013. “On the design of clone-based haplotyping.” Genome Biology 14 (9): R100. doi:10.1186/gb-2013-14-9-r100. http://dx.doi.org/10.1186/gb-2013-14-9-r100.en
dc.identifier.issn1465-6906en
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:12406686
dc.description.abstractBackground: 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.en
dc.language.isoen_USen
dc.publisherBioMed Centralen
dc.relation.isversionofdoi:10.1186/gb-2013-14-9-r100en
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053695/pdf/en
dash.licenseLAAen_US
dc.titleOn the design of clone-based haplotypingen
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden
dc.relation.journalGenome Biologyen
dash.depositing.authorLee, Jehyuken_US
dc.date.available2014-07-07T17:03:23Z
dc.identifier.doi10.1186/gb-2013-14-9-r100*
dash.contributor.affiliatedLee, Jehyuk
dash.contributor.affiliatedLucchesi, Carolina
dash.contributor.affiliatedByrne, Susan M
dash.contributor.affiliatedAach, John
dash.contributor.affiliatedChurch, George


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