The present invention relates to an application of a target nucleic acid detection method using a clamping probe and a detection probe. The method of the present invention can effectively detect a small amount of variation or a specific gene sequence contained in a sample by selective amplification and detection of a trace amount of a target gene to be detected while inhibiting amplification of wild-type genes or undesired genes. Also, it is possible to determine a large number of genotypes at the same time through a melting curve analysis. In particular, the method can be used for diagnosis, prognosis and monitoring of the medical condition of a disease, treatment efficacy evaluation, and for aiding nucleic acid and protein delivery studies and so on, through a very small amount of a mutant genotype that is confirmed at a high detection sensitivity. The method of the present invention comprises a step for evaluating the detection of biomarkers such as EGFR, KRAS, NRAS etc. and the presence of mutations of biomarkers using invasive specimens such as tissues as well as non-invasive specimens (blood, urine, sputum, stool, saliva, and cells). The presence of the biomarker and mutations provides a method used for monitoring of the entire cycle of a related disease, disease prognosis and prediction, decision of disease treatment strategy, disease diagnosis / early diagnosis, disease prevention, and development of disease therapeutics.