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Nucleic Acids Research, 2002, Vol. 30, No. 19 e96
© 2002 Oxford University Press

Molecular haplotyping at high throughput

Jörg Tost1, Ole Brandt1,2, Francis Boussicault1, David Derbala1, Christophe Caloustian1, Doris Lechner1 and Ivo Glynne Gut*,1

1 Centre National de Génotypage, Bâtiment G2, 2 Rue Gaston Crémieux, CP 5721, 91057 Evry Cedex, France and 2 Technische Universität Berlin, Berlin, Germany

*To whom correspondence should be addressed. Tel: +33 160 878 359; Fax: +33 160 878 383; Email: ivogut{at}cng.fr

Reconstruction of haplotypes, or the allelic phase, of single nucleotide polymorphisms (SNPs) is a key component of studies aimed at the identification and dissection of genetic factors involved in complex genetic traits. In humans, this often involves investigation of SNPs in case/control or other cohorts in which the haplotypes can only be partially inferred from genotypes by statistical approaches with resulting loss of power. Moreover, alternative statistical methodologies can lead to different evaluations of the most probable haplotypes present, and different haplotype frequency estimates when data are ambiguous. Given the cost and complexity of SNP studies, a robust and easy-to-use molecular technique that allows haplotypes to be determined directly from individual DNA samples would have wide applicability. Here, we present a reliable, automated and high-throughput method for molecular haplotyping in 2 kb, and potentially longer, sequence segments that is based on the physical determination of the phase of SNP alleles on either of the individual paternal haploids. We demonstrate that molecular haplotyping with this technique is not more complicated than SNP genotyping when implemented by matrix-assisted laser desorption/ionisation mass spectrometry, and we also show that the method can be applied using other DNA variation detection platforms. Molecular haplotyping is illustrated on the well-described ß2-adrenergic receptor gene.


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