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  Fosmid-based whole genome haplotyping of a HapMap trio child: evaluation of Single Individual Haplotyping techniques

Duitama, J., McEwen, G. K., Huebsch, T., Palczewski, S., Schulz, S., Verstrepen, K., et al. (2011). Fosmid-based whole genome haplotyping of a HapMap trio child: evaluation of Single Individual Haplotyping techniques. Nucleic Acids Research. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/22102577 http://nar.oxfordjournals.org/content/early/2011/11/17/nar.gkr1042.full.pdf.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-78A2-4 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-78A3-2
Genre: Journal Article

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Duitama, J., Author
McEwen, G. K.1, Author              
Huebsch, T.2, Author              
Palczewski, S.1, Author              
Schulz, S.1, Author              
Verstrepen, K., Author
Suk, E. K.1, Author              
Hoehe, M. R.2, Author              
Affiliations:
1Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              
2Genetic Variation, Haplotypes, and Genetics of Complex Disease (Margret Hoehe), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479651              

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 Abstract: Determining the underlying haplotypes of individual human genomes is an essential, but currently difficult, step toward a complete understanding of genome function. Fosmid pool-based next-generation sequencing allows genome-wide generation of 40-kb haploid DNA segments, which can be phased into contiguous molecular haplotypes computationally by Single Individual Haplotyping (SIH). Many SIH algorithms have been proposed, but the accuracy of such methods has been difficult to assess due to the lack of real benchmark data. To address this problem, we generated whole genome fosmid sequence data from a HapMap trio child, NA12878, for which reliable haplotypes have already been produced. We assembled haplotypes using eight algorithms for SIH and carried out direct comparisons of their accuracy, completeness and efficiency. Our comparisons indicate that fosmid-based haplotyping can deliver highly accurate results even at low coverage and that our SIH algorithm, ReFHap, is able to efficiently produce high-quality haplotypes. We expanded the haplotypes for NA12878 by combining the current haplotypes with our fosmid-based haplotypes, producing near-to-complete new gold-standard haplotypes containing almost 98% of heterozygous SNPs. This improvement includes notable fractions of disease-related and GWA SNPs. Integrated with other molecular biological data sets, this phase information will advance the emerging field of diploid genomics.

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 Dates: 2011
 Publication Status: Published in print
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Title: Nucleic Acids Research
Source Genre: Journal
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Pages: - Volume / Issue: - Sequence Number: - Start / End Page: - Identifier: ISSN: 1362-4962 (Electronic) 0305-1048 (Linking)