An efficient method for multi-locus molecular haplotyping.
Many methods exist for genotyping--revealing which alleles an individual carries at different genetic loci. A harder problem is haplotyping--determining which alleles lie on each of the two homologous chromosomes in a diploid individual. Conventional approaches to haplotyping require the use of several generations to reconstruct haplotypes within a pedigree, or use statistical methods to estimate the prevalence of different haplotypes in a population. Several molecular haplotyping methods have been proposed, but have been limited to small numbers of loci, usually over short distances. Here we demonstrate a method which allows rapid molecular haplotyping of many loci over long distances. The method requires no more genotypings than pedigree methods, but requires no family material. It relies on a procedure to identify and genotype single DNA molecules, and reconstruction of long haplotypes by a 'tiling' approach. We demonstrate this by resolving haplotypes in two regions of the human genome, harbouring 20 and 105 single-nucleotide polymorphisms, respectively. The method can be extended to reconstruct haplotypes of arbitrary complexity and length, and can make use of a variety of genotyping platforms. We also argue that this method is applicable in situations which are intractable to conventional approaches.
Konfortov
Bernard A
BA
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
Bankier
Alan T
AT
Dear
Paul H
PH
D002891:Chromosomes, Human, Pair 21; D041321:Chromosomes, Human, X; D004247:DNA / Q000737:chemistry; D003627:Data Interpretation, Statistical; D004171:Diploidy; D006239:Haplotypes; D006801:Humans; D008297:Male; D016133:Polymerase Chain Reaction / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
D004247:DNA