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PCR Applications Guide | 37
4 Copy Number
Variation Analysis
Overview
Analysis of copy number (CN) involves determining the number of copies of a given target
locus with respect to an invariant reference locus. An alteration in copy number state with
respect to the reference locus is copy number variation (CNV). CNV could be a deletion
or duplication of a locus with respect to the number of copies of the reference locus (and
hence genomes) present in the cell.
CNV is a prominent source of interindividual variability in the human genome, and CNV has
been associated with cancers, neurological and autoimmune diseases, and adverse drug
response. The major technical challenge in CN assessment is the ability to discriminate,
with statistical confidence, between consecutive CN states (Figure 4.1). Fundamentally,
as CN state increases, the percentage difference in target genomic material between
states decreases. For example, for a given target locus, a CN of 3 is 50% more abundant
in concentration per genome than a CN of 2, while a CN of 5 is only 25% more abundant
per genome than a CN of 4, and so on. Current methods to analyze CNV, including single
nucleotide polymorphism (SNP)–based microarrays, comparative genomic hybridization,
and quantitative PCR (qPCR), lack the sensitivity and resolution needed for this fine degree
of quantitative discrimination in CNV analysis.