Human DNA polymorphisms find application in many areas of research and clinical testing, particularly in the linkage mapping of genes responsible for disease. Short tandem repeat polymorphisms are currently the markers of choice for these applications, but diallelic polymorphisms will likely eventually replace STRPs because of more efficient analysis on miniaturized DNA arrays (DNA chips). Goals of this research project are first, to develop 1,500 new human diallelic polymorphisms of the short insertion/deletion class, second, to investigate new approaches and to enhance existing approaches for the analysis of the insertion/deletion polymorphisms on flow through DNA genosensors, and third, to gradually introduce the chip-based analysis of the diallelic polymorphisms into the genotyping factory at Marshfield. Diallelic short insertion/deletion polymorphisms have a number of advantages over base substitution polymorphisms, especially that of improved hybridization discrimination between alleles. New, putative insertion/deletion polymorphisms will be identified by comparing publicly available overlapping genomic and coding DNA sequences. Putative polymorphisms will be confirmed by laboratory typing. Allele frequencies will be measured in groups of individuals with American, European, African, and Asian ancestry. Drs. Beattie and Doktycz at Oak Ridge National Laboratory have pioneered work on novel, porous DNA chip materials, particularly capillary channel glass. The porous chips support increased hybridization reaction kinetics compared to flat chips. Protocols will be enhanced for production of chips, for hybridization of DNA targets to the chips, and for detection of the hybridized DNA. A number of novel polymorphism analysis methods that bypass the requirement for PCR amplification of hybridization targets will be explored. Instrumentation for chip arraying and reading will be improved. Finally, DNA chips for typing short insertion/deletion polymorphisms will be gradually introduced into the genotyping factory at Marshfield to supplement STRP typing in linkage analysis of disease genes.
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