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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. [1] 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. [2]
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.
A locally decodable code (LDC) is an error-correcting code that allows a single bit of the original message to be decoded with high probability by only examining (or querying) a small number of bits of a possibly corrupted codeword.
Multiplex ligation-dependent probe amplification (MLPA) is a variation of the multiplex polymerase chain reaction that permits amplification of multiple targets with only a single primer pair. [1] It detects copy number changes at the molecular level, and software programs are used for analysis.
This LDPC code fragment represents a three-bit message encoded as six bits. Redundancy is used, here, to increase the chance of recovering from channel errors. This is a (6, 3) linear code, with n = 6 and k = 3. Again ignoring lines going out of the picture, the parity-check matrix representing this graph fragment is
The code-rate is hence a real number. A low code-rate close to zero implies a strong code that uses many redundant bits to achieve a good performance, while a large code-rate close to 1 implies a weak code. The redundant bits that protect the information have to be transferred using the same communication resources that they are trying to protect.
Array CGH has proven to be a specific, sensitive, fast and high-throughput technique, with considerable advantages compared to other methods used for the analysis of DNA copy number changes making it more amenable to diagnostic applications. Using this method, copy number changes at a level of 5–10 kilobases of DNA sequences can be detected. [15]
If the average number of nearest neighbors per transmitted bit () is equal to one, the effective coding gain () is approximately equal to the nominal coding gain ().