Copy number variation

Copy number variation (CNV) is a phenomenon in which sections of the genome are repeated and the number of repeats in the genome varies between individuals. Copy number variation is a type of structural variation: specifically, it is a type of duplication or deletion event that affects a considerable number of base pairs. Approximately two-thirds of the entire human genome may be composed of repeats and 4.8–9.5% of the human genome can be classified as copy number variations. In mammals, copy number variations play an important role in generating necessary variation in the population as well as disease phenotype. Copy number variations can be generally categorized into two main groups: short repeats and long repeats. However, there are no clear boundaries between the two groups and the classification depends on the nature of the loci of interest. Short repeats include mainly dinucleotide repeats (two repeating nucleotides e.g. A-C-A-C-A-C...) and trinucleotide repeats. Long repeats include repeats of entire genes. This classification based on size of the repeat is the most obvious type of classification as size is an important factor in examining the types of mechanisms that most likely gave rise to the repeats, hence the likely effects of these repeats on phenotype. One of the most well known examples of a short copy number variation is the trinucleotide repeat of the CAG base pairs in the huntingtin gene responsible for the neurological disorder Huntington's disease. For this particular case, once the CAG trinucleotide repeats more than 36 times in a trinucleotide repeat expansion, Huntington's disease will likely develop in the individual and it will likely be inherited by his or her offspring. The number of repeats of the CAG trinucleotide is inversely correlated with the age of onset of Huntington's disease. These types of short repeats are often thought to be due to errors in polymerase activity during replication including polymerase slippage, template switching, and fork switching which will be discussed in detail later.