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Copy number analysis is the process of analyzing data produced by a test for DNA
Copy number analysis is the process of analyzing data produced by a test for DNA 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 ...
in an organism's sample. One application of such analysis is the detection of chromosomal 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 ...
that may cause or may increase risks of various critical disorders. Copy number variation can be detected with various types of tests such as fluorescent in situ hybridization, comparative genomic hybridization Comparative genomic hybridization (CGH) is a molecular cytogenetic method for analysing copy number variations (CNVs) relative to ploidy level in the DNA of a test sample compared to a reference sample, without the need for culturing cells. The ai ...
and with high-resolution array-based tests based on array comparative genomic hybridization (or aCGH), SNP array
In molecular biology, SNP array is a type of DNA microarray which is used to detect polymorphisms within a population. A single nucleotide polymorphism (SNP), a variation at a single site in DNA, is the most frequent type of variation in the gen ...
technologies and high resolution microarrays that include copy number probes as well an SNPs. Array-based methods have been accepted as the most efficient in terms of their resolution and high-throughput nature and the highest coverage (choose an array with over 2 million probes)
and they are also referred to as virtual karyotype. Data analysis for an array-based DNA copy number test can be very challenging though due to very high volume of data that come out of an array platform.
BAC (Bacterial Artificial Chromosome) arrays were historically the first microarray
A microarray is a multiplex lab-on-a-chip. Its purpose is to simultaneously detect the expression of thousands of genes from a sample (e.g. from a tissue). It is a two-dimensional array on a solid substrate—usually a glass slide or silic ...
platform to be used for DNA copy number analysis. This platform is used to identify gross deletions or amplifications in DNA. Such anomalies for example are common in cancer and can be used for diagnosis of many developmental disorders. Data produced by such platforms are usually low to medium resolution in terms of genome coverage. Usually, log-ratio measurements are produced by this technology to represent deviation of patient's copy number state from normal. Such measurements then are studied and those that significantly differ from zero value are announced to represent a part of a chromosome with an anomaly (an abnormal copy number state). Positive log-ratios indicate a region of DNA copy number gain and negative log-ratio values mark a region of DNA copy number loss. Even a single data point can be declared an indication of a copy number gain or a copy number loss in BAC arrays.
See also
*Bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combin ...
*DNA microarray
A DNA microarray (also commonly known as DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to ...
References
{{reflist, 30em Genetics Molecular biology