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Copy Number Variation - Important Markers beyond SNPs

Copy Number Variations (CNVs) are structural alterations in a genome that results in an abnormal number of copies of one or more sections of the DNA. Copy Number Variations correspond to relatively large regions of the genome that have been deleted or duplicated.

Analysis of copy number variations via

Benefit from numerous microarray based solutions for Copy Number Variation (CNV) analyses

Affymetrix Arrays

With their new CytoScan HD, Affymetrix has launched a new high-density platform for cytogenetics research to replace their Whole Genome 2.7M array. With 2.6 million markers, the new chip offers, according to Affymetrix, a 100 percent coverage of cancer genes as well as X chromosome genes (because 25 percent of known syndromes are on the X chromosome); the array also offers 100 % coverage of constitutional genes.

Affymetrix Genome-wide Human SNP array 6.0. The human SNP 6.0 has already been used for several years as second-tier testing in cytogenetics. It provides 950,000 markers for CNV, incl. 202,000 probes targeting 5,677 CNV regions from the Toronto Database of Genomic Variants and 744,000 probes, evenly spaced along the genome. In addition it contains 900,000 SNP markers that enable you to detect loss of heterozygosity (LOH), uniparental disomies (UPD), and regions of the genome that are identical-by-descent.

Affymetrix’ arrays come with a specially developed Chromosomal Analysis Suite free of charge. Among others the software summarizes chromosomal aberrations across the genome, provides focus analysis on specific regions of known significance, analyzes the genome at different levels of resolution and has direct access to e.g. NCBI, UCSC Genome Browser, Ensembl, and OMIM. Also you can customize and load your own annotations and regions for focused analysis.

Illumina Bead Arrays

Illumina Omni-5 with close to 5 million markers, Illumina Omni-Express with 700,000 markers and Illumina CytoSNP-12 with 300,000 markers all belong to the Infinium Assays series.

As with other Illumina Infinium Assays it simultaneously measures intensity differences and allelic ratios, enabling the profiling of intercellular mosaicism and copy-neutral LOH events such as uniparental disomy (UPD), mitotic recombination, or gene conversion events, all of which cannot be detected on array-CGH platforms.

Analysis of Infinium HD BeadChip data is supported by Illumina's general BeadStudio Genotyping Module and the standalone KaryoStudio data analysis software package. The integrated chromosomal browser displays gene information, found regions, and regions previously associated with phenotypes. It enables the use of standard region lists, or customer-selected regions and phenotypes for cross-matching and links to databases such as the Database of Genomic Variants, UCSC genome browser, and DECIPHER.