Comparative study of three PCR-based copy number variant approaches, CFMSA, M-PCR, and MLPA, in 22q11.2 deletion syndrome.

Small submicroscopic DNA copy number variants represent an important source of variation in the human genome, human phenotypic diversity, and disease susceptibility. Consequently, there is a pressing need for the development of methods allowing the efficient, accurate, and cheap measurement of genomic copy number polymorphisms in clinical cohorts. The PCR-based strategies, being cost-effective and sensitive, are considered important in the development of screening techniques. PCR-based techniques such as multiplex PCR; multiplex ligation-dependent probe amplification; and a new single-tube assay technique, the competitive fluorescent multiplex STRP assay, have been applied to 22q11.2 detection, a typical example of deletion syndromes. In this study, we compared the reliability and application of these three techniques in a cohort of 17 patients affected with 22q11.2 deletion and 300 normal controls. All three techniques shared 100% sensitivity; however, the competitive fluorescent multiplex STRP assay had the lowest possibility of concurrent false-positive signals from two adjoining probes in a genomic region. Moreover, it is a relatively fast and low-cost procedure to detect the deletion of 22q11.2 in numerous patients with several minor symptoms of deletion syndromes. Multiplex PCR, a rapidly developing and cheap technique, allows detection of atypical deletions.