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Copy number analysis is the process of analyzing data produced by a test for DNA copy number variation in an organism's sample. One application of such analysis is the detection of chromosomal copy number variation that may cause or may increase risks of various critical disorders.
Copy number variation was initially thought to occupy an extremely small and negligible portion of the genome through cytogenetic observations. [12] Copy number variations were generally associated only with small tandem repeats or specific genetic disorders, [13] therefore, copy number variations were initially only examined in terms of specific loci.
Gene dosage is the number of copies of a particular gene present in a genome. [1] Gene dosage is related to the amount of gene product (proteins or functional RNAs) the cell is able to express. Since a gene acts as a template, the number of templates in the cell contributes to the amount of gene product able to be produced.
If an extra copy is present in the test sample, the signals are expected to be 1.5 times the intensities of the respective probes from the reference. If only one copy is present the proportion is expected to be 0.5. If the sample has two copies, the relative probe strengths are expected to be equal.
The remaining copy of the tumor suppressor gene can be inactivated by a point mutation or via other mechanisms, resulting in a loss of heterozygosity event, and leaving no tumor suppressor gene to protect the body. Loss of heterozygosity does not imply a homozygous state (which would require the presence of two identical alleles in the cell).
Copy number variation is a very important type of structural variation and has been studied extensively. A study on the influence of the CCL3L1 gene on HIV-1/AIDS susceptibility tested if the copy number of the CCL3L1 gene had any effect on an individual’s susceptibility to HIV-1
where is the number of segregating sites (an example of a segregating site would be a single-nucleotide polymorphism) in the sample and = = is the () th harmonic number. This estimate is based on coalescent theory. Watterson's estimator is commonly used for its simplicity.
Using this formula, one has to start from the tips of the tree , then move towards the root and compute the partial likelihoods of each necessary node on the way (4 partial likelihoods per node). Having finished at the root of the tree, the likelihood of the tree (for this particular site) is then the sum of the partial likelihoods of the root ...