A method for developing high-density SNP maps and its application at the type 1 angiotensin II receptor (AGTR1) locus

Evaluating the potential genetic components of complex disease will likely be aided through the use of dense polymorphism maps. Previously, we reported evidence for linkage with diabetic nephropathy on chromosome 3q in a region encompassing the type 1 angiotensin II receptor (AGTR1) gene. To further investigate any role for this gene in disease onset, we set out to design a dense polymorphism map spanning the AGTR1 locus for the purpose of association studies. Toward this goal, we have developed a technique for rapid identification of polymorphisms in long stretches of genomic DNA. This approach uses long-range PCR, DNA pooling, and transposon-based DNA sequencing. Using this technique, we efficiently validated and genotyped 18 polymorphisms spanning the 60.5-kb AGTR1 locus. Our panel of polymorphisms has an average spacing of 3.2 kb and an average minor allele frequency of 24%.