SNP/CNV Arrays Track Settings
 
Microarray Probesets   (All Variation tracks)

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 Affy SNP 6.0  Affymetrix SNP 6.0   schema 
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 Affy SNP 6.0 SV  Affymetrix SNP 6.0 Structural Variation   schema 
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 Affy SNP 5.0  Affymetrix SNP 5.0   schema 
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 Affy 250KNsp  Affymetrix GeneChip Human Mapping 250K Nsp   schema 
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 Affy 250KSty  Affymetrix GeneChip Human Mapping 250K Sty   schema 
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 Affy CytoScan  Affymetrix Cytoscan CNV and SNP Array Probeset   schema 
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 Ag CGH 1x1m  Agilent SurePrint G3 Human CGH Microarray 1x1M AMADID 021529   schema 
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 Ag HRD 1x1m  Agilent SurePrint G3 Human High-Resolution Microarray 1x1M AMADID 023642   schema 
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 Ag SNP 2x400k  Agilent SurePrint G3 Human CGH+SNP Microarray 2x400K AMADID 028081   schema 
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 Ag CGH 2x400k  Agilent SurePrint G3 Human CGH Microarray 2x400K AMADID 021850   schema 
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 Ag Can 4x180k  Agilent SurePrint G3 Human CGH+SNP Cancer Microarray 4x180K AMADID 030587   schema 
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 Ag SNP 4x180k  Agilent SurePrint G3 Human CGH+SNP Microarray 4x180K AMADID 029830   schema 
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 Ag CGH 4x180k  Agilent SurePrint G3 Human CGH Microarray 4x180K AMADID 022060   schema 
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 Ag CGH 8x60k  Agilent SurePrint G3 Human CGH Microarray 8x60K AMADID 021924   schema 
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 Ag CGH 1x244k  Agilent SurePrint HD Human CGH Microarray 1x244K AMADID 014693   schema 
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 Ag CGH 2x105k  Agilent SurePrint HD Human CGH Microarray 2x105K AMADID 014698   schema 
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 Ag CGH 4x44k  Agilent SurePrint HD Human CGH Microarray 4x44K AMADID 014950   schema 
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 Illumina 550  Illumina Human Hap 550v3   schema 
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 Illumina 650  Illumina Human Hap 650v3   schema 
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 Illumina 300  Illumina Human Hap 300v3   schema 
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 Illumina 1M-Duo  Illumina Human1M-Duo   schema 
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 Illumina Cyto-12  Illumina Human CytoSNP-12   schema 
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 Illumina 660W-Q  Illumina Human 660W-Quad   schema 
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 Illumina Omni1-Q  Illumina Human Omni1-Quad   schema 
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 Illumina GDA  Illumina GDA   schema 
    

Affymetrix Arrays

Affymetrix Genome-Wide Human SNP Array 6.0 and SV

The SNP Array 6.0 includes more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation. The SNPs include the 482,000 SNPs from the 5.0 Array (unbiased selection). In addition, 424,000 new SNPs were chosen in the following areas:
  • Tag SNPs
  • SNPs from chromosomes X and Y
  • Mitochondrial SNPs
  • New SNPs added to dbSNP
  • SNPs in recombination hotspots

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.

Affymetrix Genome-Wide Human SNP Array 5.0

The SNP Array 5.0 is a single microarray featuring all single nucleotide polymorphisms (SNPs) from the original two-chip Mapping 500K Array Set, as well as 420,000 additional non-polymorphic probes that can measure other genetic differences, such as copy number variation.

Affymetrix 500K (250K Nsp and 250K Sty)

This annotation displays the SNPs available for genotyping with the GeneChip Human Mapping 500K Array Set from Affymetrix. It is comprised of two arrays: Nsp and Sty, which contain approximately 262,000 and 238,000 SNPs, respectively.

Affymetrix CytoScan HD

The CytoScan High-Density (HD) Array provides whole-genome coverage with enriched coverage of all constitutional and cancer-related genes on a single array. The complete CytoScan array includes:
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.

Agilent Arrays

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

Illumina Arrays

Illumina HumanHap650Y

This annotation displays the SNPs available for genotyping with Illumina's HumanHap650Y Genotyping BeadChip. The HumanHap650Y contains over 650,000 markers, extending the HumanHap550 by adding 100,000 additional Yoruba-specific tag SNPs. On average, there is 1 SNP every 5.3 kb, 6.2 kb and 5.4 kb across the genome in the CEU, CHB+JPT and YRI populations, respectively. The HumanHap650Y was derived from release 21 of the International HapMap Project.

Illumina HumanHap550

This annotation displays the SNPs available for genotyping with Illumina's HumanHap550 Genotyping BeadChip. The HumanHap550 contains over 550,000 markers, the majority of which are tag SNPs derived from release 20 of the International HapMap Project. In addition, approximately 7800 non-synonymous SNPs, a higher density of tag SNPs in the MHC region, over 150 mitochondrial SNPs and over 4000 SNPs from regions with copy number polymorphism were included. In the CEU population, an r-squared threshold of 0.8 was used for common SNPs in genes, within 10 kb of genes or in evolutionarily conserved regions. For all other regions, an r-squared threshold of 0.7 was used. On average, there is 1 SNP every 5.5 kb, 6.5 kb and 6.2 kb across the genome in the CEU, CHB+JPT and YRI populations, respectively.

Illumina HumanHap300

This annotation displays the SNPs available for genotyping with Illumina's HumanHap300 Genotyping BeadChip. The HumanHap300 contains over 317,000 tagSNP markers derived from Phase I of the International HapMap Project. In addition, approximately 7300 non-synonymous SNPs and a higher density of tag SNPs in the MHC region were included. On average, there is 1 SNP every 9 kb across the genome and median spacing is 5 kb.

Illumina Human1M-Duo

This annotation displays the SNPs available for genotyping with Illumina's Human1M-Duo Genotyping BeadChip. The Human1M-Duo contains more than 1,100,000 tagSNP markers and a set of ~60,000 additional CNV-targeted markers. The median spacing is 1.5kb (mean - 2.4 kb).

Illumina HumanOmni1-Quad v1

The HumanOmni1-Quad BeadChip consists of 1,140,419 markers in a 4-sample format. The whole-genome content provides high genomic coverage rates of 93%, 92%, and 76% at r2 > 0.8 for the CEU, CHB+JPT, and YRI populations, respectively. High density markers with a median spacing of 1.2 kb ensure the highest level of resolution for CNV and breakpoint identification. The content has been derived from the 1,000 Genomes Project, all three HapMap phases, and recently published studies, including new coding variants identified by the 1000 Genomes Project and markers chosen in high-value regions of the genome: ABO blood typing SNPs, cSNPs, disease-associated SNPs, eSNPs, SNPs in mRNA splice sites, ADME genes, AIMs, HLA complexes, indels, introns, MHC regions, miRNA binding sites, mitochondrial DNA, PAR, promoter regions, and Y-chromosome.

Illumina Human660W-Quad v1

The Human660W-Quad BeadChip consists of 657,366 markers in a 4-sample format. The Human660W-Quad BeadChip provides 87%, 85%, and 56% coverage of CEU, CHB+JPT, and YRI populations at r2 > 0.8. For CNV and cytogenetic analysis, the dense backbone content is combined with an additional ~100,000 markers that target observed common CNVs.

HumanCytoSNP-12 v2.1

The 301,232 markers on the HumanCytoSNP-12 represents a complete 12-sample panel of genome-wide SNPs for a uniform backbone and additional markers targeting all regions of known cytogenetic importance. Backbone markers provide genome-wide marker spacing of 10kb. This is supplemented with dense coverage (at 6 kb spacing average) of ~250 genomic regions commonly studied in cytogenetics labs and targeted coverage in ~400 additional genes, subtelomeric regions, pericentromeric regions, and sex chromosomes. An efficiency-optimized tagging strategy provides a panel for GWAS (70% coverage in CEU at r2 > 0.8) in the highest throughput and most cost-effective whole-genome DNA Analysis BeadChip.

Illumina Global Diversity Array

The Global Diversity Array-8 v1.0 BeadChip includes coverage of the ACMG 59-gene clinical research variants and multi-ethnic, genome-wide content. The GDA is the commercial version of the array chosen by the All of Us Research Program and is designed to capture a wider range of the world's populationsthan traditional microarrays.

Methods

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:

References

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. Proc Natl Acad Sci U S A. 2004 Dec 21;101(51):17765-70. PMID: 15591353; PMC: PMC535426

More information on the Affymetrix arrays is available at these sites:

More information on the Illumina arrays is available at these sites:

Credits

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.