Display Settings:


Send to:

Choose Destination
See comment in PubMed Commons below
Genome Res. 2003 Dec;13(12):2717-24.

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

Author information

  • 1Max-Planck-Institute for Molecular Genetics, D-14195 Berlin-Dahlem, Germany. burgtorf@molgen.mpg.de

Erratum in

  • Genome Res. 2004 Feb;14(4):327.


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.

[PubMed - indexed for MEDLINE]
Free PMC Article

Images from this publication.See all images (4)Free text

Figure 2
Figure 1
Figure 3
Figure 4
PubMed Commons home

PubMed Commons

How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for HighWire Icon for PubMed Central
    Loading ...
    Write to the Help Desk