precise location of the repeat in the genome, and it can also detect other types of structural variation such as inversions. In addition, another way of detecting copy number variation is using single nucleotide polymorphisms (SNPs). Due to the abundance of the human SNP data, the direction of detecting copy number variation has changed to utilize these SNPs. Relying on the fact that human recombination is relatively rare and that many recombination events occur in specific regions of the genome known as recombination hotspots, linkage disequilibrium can be used to identify copy number variations. Efforts have been made in associating copy number variations with specific haplotype SNPs by analyzing the linkage disequilibrium, using these associations, one is able to recognize copy number variations in the genome using SNPs as markers. Next-generation sequencing techniques including short and long read sequencing are nowadays increasingly used and have begun to replace array-based techniques to detect copy number variations. In contrast to array-based techniques, sequencing-based detection methods readily identify other classes of structural variation such as inversions and translocations. Molecular mechanism There are two main types of molecular mechanism for the formation of copy number variations: homologous based and non-homologous based. Although many suggestions have been put forward, most of these theories are speculations and conjecture. There is no conclusive evidence that correlates a specific copy number variation to a specific mechanism. One of the best-recognized theories that leads to copy number variations as well as deletions and inversions is non-allelic homologous recombinations. During meiotic recombination, homologous chromosomes pair up and form two ended double-stranded breaks leading to Holliday junctions. However, in the aberrant mechanism, during the formation of Holliday junctions, the double-stranded breaks are misaligned and the crossover lands in non-allelic positions on the same chromosome. When the Holliday junction is resolved, the unequal crossing over event allows transfer of genetic material between the two homologous chromosomes, and as a result, a portion of the DNA on both the homologues is repeated. Since the repeated regions are no longer segregating independently, the duplicated region of the chromosome is inherited. Another type of homologous recombination based mechanism that can lead to copy number variation is known as break induced replication. When a double stranded break occurs in the genome unexpectedly the cell activates pathways that mediate the repair of the break. Errors in repairing the break, similar to non-allelic homologous recombination, can lead to