Copy number variation analysis
deCODE offers the leading comprehensive solution for copy number variation (CNV) analysis. In collaboration with Illumina, deCODE developed a next generation CNV content which is the first to specifically target regions in the genome that are more likely to present novel CNVs.
Genotyping platforms have up to now focused on the SNPable genome defined by the HapMap project. However, regions containing CNVs are typically very complex - making them difficult to target with current genotyping platforms. With this content, deCODE has addressed the important need for coverage of these complex regions (also referred to as the unSNPable or untaggable genome). Novel probes and SNPs are used to directly measure genome copy number by intensity. rather than using SNPs as surrogates for CNV alleles.
The CNV platform contains over 13,000 novel regions and all known regions that show common and rare CNVs using more than 55,000 SNPs or probes. The content covers the following regions:
Definition Size Approx. # of Segments Megasatellites Head to tail repeats covering hundreds of base pairs.
>500 bp 167 Duplicons All duplicons as well as segments flanked by duplicons within 500 kb. Superior coverage for 154 Mb of segmental duplications defined as duplicons separated by up to 3kb. Other platforms cover <30% of these regions.
>1000 bp 22700 Unstable regions Regions of the genome containing either no quality SNPs or containing at least 2 SNPs that failed quality checks in the HapMap project.
5-15 kb 2800 MHC region Missing information from large sections of this region missed by other arrays.
3.4 Mb 1500 Known CNVs All known rare and common CNVs from the Toronto Database of Genomic Variants
2100
deCODE offers the following services with the CNV content using the Illumina genotyping technology:
- iSelect BeadChip featuring CNV content alone
- 370K-Quad with the additional CNV content
- 610K-Quad with the additional CNV content
- 1M-Duo BeadChip with the additional CNV content
Our services include:
- Providing materials for shipping your samples to deCODE.
- Quality control.
- Setting-up and running of genotyping arrays.
- Delivering called alleles for SNPs and intensity report for CNV SNPs and probes.
For more information, please contact services@decode.com.
