Copy number analysis
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Copy number analysis usually refers to the process of analyzing data produced by a diagnostic test for DNA copy number variation in patient's sample.[1] schizophrenia,[2][3]
Copy number variation can be detected with various types of tests such as fluorescent in situ hybridization, comparative genomic hybridization and with high-resolution array-based tests based on array comparative genomic hybridization (or aCGH) and SNP array technologies. Array-based methods have been accepted as the most efficient in terms of their resolution and high-throughput nature 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 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). PerkinElmer and Bluegnome are the leading providers of BAC-based aCGH platforms. Data produced by such platforms are usually low to medium resolution in terms of genome coverage. But still, a proper statistical analysis of such data is required for reliable detection of copy number variation. Usually, log-ratio measurements are calculated to represent diviation 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).
Software
Currently infoQuant provides 2 software packages. oneClickCGH is designed to facilitate array-based copy number analysis for Cytogenetics. CGH Fusion is utilized in advanced multi-sample copy number and loss of heterozygosity studies. It automates large array-based studies and provides information about common regions of copy number change for participating individuals.
See also
External links
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Sebat, J.; et al. (2007). "Strong association of de novo copy number mutations with autism". Science. 316: 445. doi:10.1126/science.1138659. PMID 17363630.
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Cookwas invoked but never defined (see the help page). - ^ St Clair D (2008). "Copy number variation and schizophrenia". Schizophr Bull. 35: 9. doi:10.1093/schbul/sbn147. PMID 18990708.