ArticleGenome biology2013
On the design of clone-based haplotyping.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling.PLoS genetics · 2018Article
- Ultraaccurate genome sequencing and haplotyping of single human cells.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies.Genome research · 2017Article
- An accurate clone-based haplotyping method by overlapping pool sequencing.Nucleic acids research · 2016Article
- InPhaDel: integrative shotgun and proximity-ligation sequencing to phase deletions with single nucleotide polymorphisms.Nucleic acids research · 2016Article
- A hybrid approach for de novo human genome sequence assembly and phasing.Nature methods · 2016Article
- Haplotype-resolved genome sequencing: experimental methods and applications.Nature reviews. Genetics · 2015Review
- SDhaP: haplotype assembly for diploids and polyploids via semi-definite programming.BMC genomics · 2015Article
- Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing.Nature genetics · 2014Article
- In vitro, long-range sequence information for de novo genome assembly via transposase contiguity.Genome research · 2014Article
- Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes.Nature communications · 2014Article
- Whole-genome haplotyping approaches and genomic medicine.Genome medicine · 2014Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
backgroundHaplotypes 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.
resultsWe 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.
conclusionsOur results provide practical guidelines for the development and design of clone-based methods to achieve long range, high-resolution and accurate haplotypes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.