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

Item Type:Article
Title:Clone-based systematic haplotyping (CSH): a procedure for physical haplotyping of whole genomes
Creators Name:Burgtorf, C. and Kepper, P. and Hoehe, M. and Schmitt, C. and Reinhardt, R. and Lehrach, H. and Sauer, S.
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 approximately 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.
Keywords:Haplotypes, Human Genome, Molecular Cloning, Single Nucleotide Polymorphism
Source:Genome Research
Publisher:Cold Spring Harbor Laboratory Press (U.S.A.)
Page Range:2717-2724
Date:December 2003
Additional Information:Erratum in: Genome Res. 14(4):327.
Official Publication:https://doi.org/10.1101/gr.1442303
PubMed:View item in PubMed

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