Despite advances in some of these technologies, in many cases, measurements are not sufficiently precise for determining copy number differences where the ratios between the target and reference are very small. Digital PCR, a technology capable of highly precise measurements, enables the detection of low percent copy number differences to be detected and accurately quantified.
A representative panel of 9 genomic DNA samples, procured from the Coriell repository, was analyzed using the QuantStudio™ 3D system and a standard TaqMan® Copy Number Assay specific to the CCL3L1 genetic locus found on the long arm of chromosome 17, 6, or 8. Replicate measurements indicated that the samples represent copy number variations from 0 to 8 copies per genome (Figure 1A). A statistically significant difference between samples containing 7 and 8 copies was clearly discernable as a result of the high degree of precision achieved, confirming that digital PCR can differentiate less than a 1.2-fold difference (Figure 1B).
Figure 1. Precision demonstrated for copy number analysis of the CCL3L1 genetic locus on chromosome 17. (A) Copy number was measured across 9 DNA samples. The CV (column 6) was below 2.5% for each set of replicates, demonstrating a high degree of measurement reproducibility within each replicate group. (B) As demonstrated by non-overlapping error bars, the achieved measurement precision enables statistical discernment of the CCL3L1 copy number in samples containing 7 and 8 copies.