Channel Glass-based Detection of Human Short Insertion/Deletion Polymorphisms by Tandem Hybridization

The development and critical evaluation of newtechnologies for identifying genetic polymorphisms willrapidly accelerate the discovery and diagnosis of diseaserelatedgenes. We report a novel way for distinguishing anew class of human DNA polymorphisms, short insertion/deletion polymorphisms (indels). A sensor with cylindricalpores named channel glass in combination with tandemhybridization, which uses a 50-fluorescent labeled stackingprobe and microarray-based short allele-specificoligonucleotide (capture probe) was investigated. Thismethodology allows indels to be detected individuallyand rapidly with small quantities of target DNA. Thisestablishes a reliable quantitative test. Approaches forsimultaneously hybridizing different targets to arrayedprobes, designed to detect various indels in parallel, wereexamined. Five markers were consistently detected in asingle hybridization. Possible factors impeding thehybridization reaction process are discussed.