Denaturing high-performance liquid chromatography (DHPLC) for nucleic acid analysis

1.1. DNA Sequence Variants Since the completion of the Human Genome Project, it is clear that the human genome carries about 30,000 genes occupying less than 5% of the 3 billion base pairs (bp) of DNA sequence. Meanwhile, the human genome was also found to carry a very large number of sequence variations (1). On average, there are about 3 million sequence differences (0.1% of the whole genome) between any two unrelated individuals from a population. The analysis of DNA sequence variations is very important in genetic studies. Two broad types of DNA sequence variations are classified: polymorphisms and diseasecausing mutations. Polymorphisms refer to those sequence variations that are found in normal individuals and do not result in diseased phenotypes. They include single nucleotide polymorphisms (SNPs), microsatellites, and minisatellites. A SNP (pronounced as snip) is a sequence variation owing to change in a single nucleotide. Microsatellites and minisatellites are caused by variations in the number of repeat units that are themselves a short stretch of DNA sequence. They are very useful in research for locating the position of genes in our chromosomes, a process known as gene mapping. On the other hand, disease-causing mutations are those sequence variations that result in diseased phenotypes because they adversely affect the functions of the proteins, either qualitatively or quantitatively. The identification of mutations is important for the diagnosis of genetic diseases in clinical medicine. To examine DNA sequence variations in various genetic studies, both unknown and known variations can be investigated (2). Unknown sequence variations refer to those that are not known to exist previously and have to be detected by a group of methods called screening or scanning methods. Known sequence variations are known to exist and their genotypes can be determined by a group of methods known as diagnostic methods. Numerous techniques are available for detecting and identifying sequence variations, and vary from each other in terms of the principle of the method, cost, ease of optimization and use, requirement of special instruments, and turnaround time. Examplesof methods for analysis of sequence variations include DNA sequencing, single strand conformation analysis (SSCP), denaturing high-performance liquid chromatography (DHPLC), denaturing gradient gel electrophoresis (DGGE), restriction endonuclease digestion, allele-specific hybridization and allelespecific polymerase chain reaction. For DHPLC, the WAVE DNA fragment analysis system (Transgenomic) provides an automatic medium-Throughput analytical tool for both screening unknown sequence variations and genotyping known sequence variations.