Copy number analysis
Encyclopedia
Copy number analysis usually refers to the process of analyzing data produced by a test for DNA copy number variation in patient's sample. Such analysis helps detect chromosomal copy number variation 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
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. 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.
Copy number variation can be detected with various types of tests such as fluorescent in situ hybridization
Fluorescent in situ hybridization
FISH is a cytogenetic technique developed by biomedical researchers in the early 1980s that is used to detect and localize the presence or absence of specific DNA sequences on chromosomes. FISH uses fluorescent probes that bind to only those parts of the chromosome with which they show a high...
, comparative genomic hybridization
Comparative genomic hybridization
Comparative genomic hybridization or Chromosomal Microarray Analysis is a molecular-cytogenetic method for the analysis of copy number changes in the DNA content of a given subject's DNA and often in tumor cells....
and with high-resolution array-based tests based on array comparative genomic hybridization
Array comparative genomic hybridization
Array-comparative genomic hybridization is a technique to detect genomic copy number variations at a higher resolution level than chromosome-based comparative genomic hybridization .-Process:DNA from...
(or aCGH) and SNP array
SNP array
In molecular biology and bioinformatics, a SNP array is a type of DNA microarray which is used to detect polymorphisms within a population. A single nucleotide polymorphism , a variation at a single site in DNA, is the most frequent type of variation in the genome. For example, there are around 10...
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
Virtual Karyotype
Virtual karyotype detects genomic copy number variations at a higher resolution level than conventional karyotyping or chromosome-based comparative genomic hybridization .-Background:...
. 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
Microarray
A microarray is a multiplex lab-on-a-chip. It is a 2D array on a solid substrate that assays large amounts of biological material using high-throughput screening methods.Types of microarrays include:...
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
PerkinElmer
PerkinElmer, Inc. is an American multinational technology corporation, focused in the business areas of human and environmental health, including environmental analysis, food and consumer product safety, medical imaging, drug discovery, diagnostics, biotechnology, industrial applications, and life...
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. 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
- Array comparative genomic hybridizationArray comparative genomic hybridizationArray-comparative genomic hybridization is a technique to detect genomic copy number variations at a higher resolution level than chromosome-based comparative genomic hybridization .-Process:DNA from...
- BioinformaticsBioinformaticsBioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
- DNA microarrayDNA microarrayA DNA microarray 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 genotype multiple regions of a genome...
- Virtual KaryotypeVirtual KaryotypeVirtual karyotype detects genomic copy number variations at a higher resolution level than conventional karyotyping or chromosome-based comparative genomic hybridization .-Background:...