The routine detection of large and medium copy number variants (CNVs) is well 
established. Hemizygotic deletions or duplications in the large Duchenne 
muscular dystrophy DMD gene responsible for Duchenne and Becker muscular 
dystrophies are routinely identified using multiple ligation probe amplification 
and array-based comparative genomic hybridization. These methods only map 
deleted or duplicated exons, without providing the exact location of 
breakpoints. Commonly used methods for the detection of CNV breakpoints include 
long-range PCR and primer walking, their success being limited by the deletion 
size, GC content and presence of DNA repeats. Here, we present a strategy for 
detecting the breakpoints of medium and large CNVs regardless of their size. The 
hemizygous deletion of exons 45-50 in the DMD gene and the large autosomal 
heterozygous PARK2 deletion were used to demonstrate the workflow that relies on 
real-time quantitative PCR to narrow down the deletion region and Sanger 
sequencing for breakpoint confirmation. The strategy is fast, reliable and 
cost-efficient, making it amenable to widespread use in genetic laboratories.