Simple detection of large InDeLS by DHPLC: the ACE gene as a model

Abstract

Insertion-deletion polymorphism (InDeL) is the second most frequent type of genetic variation in the human genome. For the detection of large InDeLs, researchers usually resort to either PCR gel analysis or RFLP, but these are time consuming and dependent on human interpretation. Therefore, a more efficient method for genotyping this kind of genetic variation is needed. In this report, we describe a method that can detect large InDeLs by DHPLC (denaturating high-performance liquid chromatography) using the angiotensin-converting enzyme (ACE) gene I/D polymorphism as a model. The InDeL targeted in this study is characterized by a 288 bp Alu element insertion (I). We used DHPLC at nondenaturating conditions to analyze the PCR product with a flow through the chromatographic column under two different gradients based on the differences between D and I sequences. The analysis described is quick and easy, making this technique a suitable and efficient means for DHPLC users to screen InDeLs in genetic epidemiological studies.

Figure 1

Observed chromatograms patterns in the DHPLC system at 50°C after submitting the same samples to the two conditions. (a) ACE I sequence and chromatogram. (b) ACE D sequence and chromatogram. The lines in the upper part of both chromatograms show I/I genotype, the line in the middle is the D/D genotype, and the line below is the I/D genotype. The homozygotes show a peak when their sequences are analyzed, and the heterozygotes show a peak in both analyses.