Studying copy number variations using a nanofluidic platform

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

Variation in the human genome occurs on multiple levels, from single nucleotide polymorphisms (SNPs) to duplications or deletions of contiguous blocks of DNA sequences (1) (2) (3) (4) (5) . Copy number variation (CNV) is an important polymorphism of DNA segments across a wide range of sizes and one of the primary sources of variation in the human genome (6) . Recently, CNV has been studied extensively because of its close association with large numbers of human disorders (7, 8) . An understanding of this variation is important not only to understand the full spectrum of human genetic variation but also to assess the significance of such variation in disease-association studies. The first human CNV map was constructed from a study of 270 normal individuals with a total of 1447 CNV regions in the whole genome (9) ; more than 15 000 CNVs have been found in the human genome (http://projects. tcag.ca/variation). A recent paper demonstrated the presence of 525 novel insertion sequences across the genomes of eight unrelated individuals, which were not present in the human reference genome, and showed that many of these have different copy numbers (10) . However, the current CNV analysis is mainly dependent upon microarray-based SNP and comparative genomic hybridization (CGH) platforms, or DNA sequencing, and is therefore subject to low sensitivity and low resolution. These techniques are high throughput but lack the flexibility of analyzing individual genes or sequences of interest. Other existing technologies, such as quantitative polymerase chain reaction (PCR), are limited because of their inability to reliably distinguish less than a twofold difference in copy number of a particular gene in DNA samples (11) (12) (13) .