title: Clone-based systematic haplotyping (CSH): a procedure for physical haplotyping of whole genomes.
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.
authors.affiliation: Max-Planck-Institute for Molecular Genetics, D-14195 Berlin-Dahlem, Germany. burgtorf@molgen.mpg.de
authors.forename: Carola
authors.initials: C
authors.lastname: Burgtorf
authors.forename: Pamela
authors.initials: P
authors.lastname: Kepper
authors.forename: Margret
authors.initials: M
authors.lastname: Hoehe
authors.forename: Carsten
authors.initials: C
authors.lastname: Schmitt
authors.forename: Richard
authors.initials: R
authors.lastname: Reinhardt
authors.forename: Hans
authors.initials: H
authors.lastname: Lehrach
authors.forename: Sascha
authors.initials: S
authors.lastname: Sauer
mesh_terms: D003001:Cloning, Molecular / Q000379:methods*; D015894:Genome, Human; D006239:Haplotypes; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics