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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 (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]
fastqp Simple FASTQ quality assessment using Python. Kraken: [9] A set of tools for quality control and analysis of high-throughput sequence data. HTSeq [10] The Python script htseq-qa takes a file with sequencing reads (either raw or aligned reads) and produces a PDF file with useful plots to assess the technical quality of a run.
Homogeneously staining regions (HSRs) are chromosomal segments with various lengths and uniform staining intensity after G banding.This type of aberration is also known as Copy Number Gains or Amplification.
Other examples of emerging RNA-Seq applications due to the advancement of bioinformatics algorithms are copy number alteration, microbial contamination, transposable elements, cell type (deconvolution) and the presence of neoantigens. [8] Prior to RNA-Seq, gene expression studies were done with hybridization-based microarrays.
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]
Gene amplification refers to a number of natural and artificial processes by which the number of copies of a gene is increased "without a proportional increase in other genes". [ 1 ] Artificial DNA amplification
Gains: A copy number gain represents the gain of genetic material. If the gain is of just one additional copy of a segment of DNA, it may be called a duplication (Fig 4). If there is one extra copy of an entire chromosome, it may be called a trisomy. Copy number gains in germline samples may be disease-associated or may be a benign copy number ...