The structural variation copy number (SV) probes include 202,000 probes targeting 5,677 known CNV regions from the Toronto Database of Genomic Variants. The additional 744,000 probes are evenly spaced throughout the genome.
Genome build hg19 Total number of copy-number markers 2,696,550 Total number of non-polymorphic markers 1,953,246 Number of SNP markers 743,304 SNP markers with >99% genotype accuracy 749,157 Autosomal markers 2,491,915 Pseudoautosomal markers 4,624 Intragenic markers 1,410,535 Intergenic markers 1,286,015
Probes are colored green for CNV probesets and purple for SNP probesets. Some SNP probesets are also considered informative for CNV detection.
Non-SNP subtracks are colored in alternating shades of green and orange to highlight track boundaries. SNP subtracks are colored blue with SNP probes colored dark blue and CGH probes colored light blue.
The track consists of the following subtracks:
The arrays listed in this track are probes from the Agilent Catalog Oligonucleotide Microarrays. The following table summarizes the different Agilent arrays:Description | AMADID | Samples per Slide | Biological Features | Median Probe Spacing | Gene-biased | SNPs |
---|---|---|---|---|---|---|
SurePrint G3 Human CGH Microarray 1x1M | 021529 | 1 | 969,033 | 2.1 kb | Yes | 0 |
SurePrint G3 Human High-Resolution Microarray 1x1M | 023642 | 1 | 989,214 | 2.6 kb | No (evenly tiled) | 0 |
SurePrint G3 Human CGH+SNP Microarray 2x400K | 028081 | 2 | 411,434 | 7 kb | Yes | 65,000 |
SurePrint G3 Human CGH Microarray 2x400K | 021850 | 2 | 415,914 | 5.3 kb | Yes | 0 |
SurePrint G3 Human Cancer CGH+SNP Microarray 4x180K | 030587 | 4 | 172,595 | 25 kb | Yes (cancer genes) | 65,000 |
SurePrint G3 Human CGH+SNP Microarray 4x180K | 029830 | 4 | 172,595 | 25 kb | No (ISCA regions) | 65,000 |
SurePrint G3 Human CGH Microarray 4x180K | 022060 | 4 | 174,675 | 13 kb | Yes | 0 |
SurePrint G3 Human CGH Microarray 8x60K | 021924 | 8 | 59,175 | 41 kb | Yes | 0 |
SurePrint HD Human CGH Microarray 1x244K | 014693 | 1 | 238,331 | 8.9 kb | Yes | 0 |
SurePrint HD Human CGH Microarray 2x105K | 014698 | 2 | 100,034 | 22 kb | Yes | 0 |
SurePrint HD Human CGH Microarray 4x44K | 014950 | 4 | 43,143 | 43 kb | Yes | 0 |
Position, strand, and polymorphism data were obtained from Affymetrix and supplemented with links to corresponding dbSNP rsIDs based on a positional lookup into dbSNP. The Affy 6.0 Array is based on dbSNP build 127; the Affy 5.0 Array is based on dbSNP build 126. The Affy 500K Array is based on dbSNP build 125 and was translated from hg17 by UCSC using rsID lookup. In fewer than 2% of the cases, a dbSNP rsID was not present in dbSNP at the Affymetrix array position. Reference allele information was retrieved from the UCSC database based on dbSNP position and strand data.
Illumina data were supplied as rsIDs and position based on dbSNP build 126. Strand, polymorphism and reference allele information was retrieved from the UCSC database based on rsID and position. The Illumina arrays are comprised of probes for 4 of the possible single-base substitutions: A/C, A/G, C/T and G/T. A/T and C/G probes will be available in future arrays.
For Illumina Human1M-Duo, the position, strand, polymorphism and reference allele information was retrieved from the snp129 table of UCSC database if the marker ID can be found in dbSNP 129, otherwise the information is retrieved from the data provided by Illumina.
For Illumina HumanOmni1-Quad, Human660W-Quad, and HumanCytoSNP-12, the position, strand, polymorphism and reference allele information was retrieved from the snp130 table of UCSC database if the marker ID can be found in dbSNP 130, otherwise the information is retrieved from the data provided by Illumina.
Agilent's oligonucleotide CGH (Comparative Genomic Hybridization) platform enables the study of genome-wide DNA copy number changes at a high resolution. The CGH probes on Agilent aCGH microarrays are 60-mer oligonucleotides synthesized in situ using Agilent's inkjet SurePrint technology. The probes represented on the Agilent CGH microarrays have been selected using algorithms developed specifically for the CGH application, assuring optimal performance of these probes in detecting DNA copy number changes.
The Agilent SurePrint G3 CGH+SNP microarrays are designed for high quality human DNA copy-number profiling combined with the simultaneous detection of copy-neutral aberrations, such as lack or loss of heterozygosity (LOH) and uniparental disomy (UPD). Identification of LOH/UPD is enabled by the presence of a set of SNP probes on the CGH+SNP microarrays resulting in ~5-10 Mb resolution for copy neutral LOH/UPD detection across the entire genome.
The Agilent catalog CGH and CGH+SNP microarrays are printed on 1 in. x 3 in. glass slides and are available in several formats. The human catalog SurePrint G3 microarrays formats are the 1x1M (gene-biased or evenly tiled), 2x400K (CGH-only or CGH+SNP), 4x180K (CGH-only or CGH+SNP), and 8x60K. The legacy human catalog SurePrint HD microarrays are the 1x244K, 2x105K, and 4x44K.
Non-SNP subtracks are colored in alternating shades of green and orange to highlight track boundaries. SNP subtracks are colored blue with SNP probes colored dark blue and CGH probes colored light blue. The track consists of the following subtracks:
More information on Agilent Oligonucleotide Microarrays can be found on Agilent's website.
Barrett MT, Scheffer A, Ben-Dor A, Sampas N, Lipson D, Kincaid R, Tsang P, Curry B, Baird K, Meltzer PS et al. Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. PNAS. 2004 Dec 21;101(51):17765-70.
More information on the Affymetrix arrays is available at these sites:
Thanks to Shane Giles, Peter Webb, and Anniek De Witte from Agilent Technologies, Venu Valmeekam from Affymetrix, and Luana Galver and Jennifer L. Stone from Illumina for providing these data.