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  Clone-based systematic haplotyping (CSH): A procedure for physical haplotyping of whole genomes

Burgtorf, C., Kepper, P., Hoehe, M., Schmitt, C., Reinhardt, R., Lehrach, H., et al. (2003). Clone-based systematic haplotyping (CSH): A procedure for physical haplotyping of whole genomes. Genome Research, 13(12), 2717-2724.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-8955-9 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-8956-7
Genre: Journal Article
Alternative Title : Genome Res.

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 Creators:
Burgtorf, Carola1, Author
Kepper, Pamela, Author
Hoehe, Margret2, Author              
Schmitt, Carsten, Author
Reinhardt, Richard3, Author              
Lehrach, Hans4, Author              
Sauer, Sascha5, Author              
Affiliations:
1Max Planck Society, ou_persistent13              
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              
3High Throughput Technologies, Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433552              
4Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              
5Nutrigenomics and Gene Regulation (Sascha Sauer), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479662              

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 Abstract: We present a novel methodology to determine the phase of single-nucleotide polymorphisms (SNPs) on a chromosome, which we term clone-based systematic haplotyping (CSH). The CSH procedure is based on separating the allelic chromosomes of a diploid genome by fosmid/cosmid cloning, and subsequent SNP typing of 96 clone pools, each representing 10% of the genome. The pools are screened by PCR for the sequence of interest, followed by SNP typing on the PCR products using the GOOD assay. We demonstrate that by CSH, the haplotype of SNPs separated by more than 50 kilobases can definitely be assigned. We propose this method as being suitable for constructing maps of ancestral haplotypes, analysis of complex diseases, and for diagnosis of rare defects in which the molecular haplotype is crucial. In addition, by amplifying the initial DNA by many orders of magnitude, the original DNA resource is effectively immortalized, enabling the haplotyping of hundreds of thousands of SNPs per individual.

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Language(s): eng - English
 Dates: 2003-12
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: -
 Identifiers: eDoc: 173635
ISI: 000186920200022
 Degree: -

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Title: Genome Research
  Alternative Title : Genome Res.
Source Genre: Journal
 Creator(s):
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Publ. Info: -
Pages: - Volume / Issue: 13 (12) Sequence Number: - Start / End Page: 2717 - 2724 Identifier: ISSN: 1088-9051