Studying copy number variations using a nanofluidic platform

Qin, Jian; Jones, Robert C.; Ramakrishnan, Ramesh

We performed three experiments to test the feasibility of the digital array in the CNV study. First we measured the copy numbers of the RPP30 gene of a series of mixtures made of a human genomic DNA and a synthetic RPP30 construct. We observed a very good correlation between the results and the expected outcome. We then studied the CYP2D6 copy numbers of some DNA samples that were either genotyped elsewhere or characterized by us using conventional techniques. The results were also consistent. Lastly, we screened 40 breast cancer samples for the amplification of the ERBB2 gene. Although the clinical data (other than pathological classification) of these samples were lacking, about 35% of the samples had an increased number of this gene above 5, very close to the ERBB2 amplification frequency reported in the literature (67) .