Studying copy number variations using a nanofluidic platform

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

When duplication occurs, multiple copies of a gene might be closely linked on the same chromosome and therefore might not be separated from each other, even on the digital array. As a result, multiple copies might behave as a single molecule and the total number of copies of the gene would be underestimated. When two copies are separated by a large genomic distance, some of them might be separated when DNA molecules are fragmented during purification. However, in most cases this would not be sufficient (see Table 2 , sample NA11994 genomic DNA data). Specific target amplification (STA) is a good solution to this problem. STA is a simple PCR reaction with primers for both the reference gene and the gene of interest. It is typically performed for a limited number of thermal cycles (five in this study). The copy numbers of both genes are proportionally increased. Using this process, multiple copies of the gene of interest will be amplified separately and later randomly partitioned into chambers in the digital array. Since the newly generated molecules of both genes reflect the original ratio and they are not linked any more, a digital chip analysis can quantitate the molecules of the two genes and measure their ratio, and therefore the copy number of the gene of interest, very accurately ( Figure 3 ). It is very important that the amplification efficiencies of the two pairs of primers be approximately equal in order not to introduce any bias in the ratio of the two gene copy numbers in the limited number of STA thermal cycles, although this is likely to have an insignificant effect on our results since we utilized only five cycles of preamplification. The amplification efficiency of any pair of primers can be easily measured using real-time PCR (18) .