Affymetrix GeneChip

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Specifications at a glance

Parameter estimates are based on a 10-plate (940 sample) study, and on current platform capacity, and assume immediate availability and usability of a customer’s DNA samples. These parameters are for comparison and planning purposes, and are not necessarily reflective of actual results. Time measures reflect laboratory time, and not post-lab data analysis.

Platform Description

Affymetrix GeneChip Arrays enable large scale, genome wide linkage analysis and association studies using high-density arrays. Utilizing photolithographic technology adapted from the semiconductor industry, arrays are produced with hundreds of thousands of unique probes packed at an extremely high density. Researchers are able to obtain high quality, genome-wide data using minimal amounts of starting DNA template. Affymetrix GeneChip DNA Analysis Software allows for rapid and accurate genotype calling with minimal user manipulation.

The Broad Institute has implemented the use of the BRLMM algorithm for genotype calling of the 500K (and 100K) GeneChips. An evaluation by Kuruvilla et al. of the BRLMM genotyping algorithm in comparison to the DM algorithm can be found here.

More recently, we have implemented the use of the BirdSeed algorithm for genotype calling of the Human SNP Array 5.0 and 6.0 arrays, and will soon be releasing the BirdSuite set of algorithms to detect and report SNP genotypes, common Copy-Number Variants (CNVs), and rare/de novo CNVs.

Services Offered

Genome-Wide Human SNP Array 5.0 and 6.0 (Single Chip)

• Genome-Wide Human SNP Array 6.0: http://www.affymetrix.com/products/application/genome_wide_snp_6_ad.affx

The Genome-Wide Human SNP Array 6.0 on one chip assays ~907,000 SNPs and also includes ~946,000 additional probes designed specifically for copy number assessment. These probes are designed to complement the SNP genotyping probes in terms of genome coverage.

• Genome-Wide Human SNP Array 5.0: http://www.affymetrix.com/products/arrays/specific/genome_wide/genome_wide_snp_5.affx

The Genome-Wide Human SNP Array 5.0 on one chip assays ~500,000 SNPs and also includes ~420,000 additional probes designed specifically with copy number assessment in mind. These probes are designed to complement the SNP genotyping probes in terms of genome coverage.

Human 500K and 100K Array Chip Sets

• Mapping 500K Array Set (250K x 2): http://www.affymetrix.com/products/arrays/specific/500k.affx
• GeneChip® Human Mapping 100K Set (50K x 2): http://www.affymetrix.com/products/arrays/specific/100k.affx

The 500K and 100K Chip Sets each utilize two unique high density arrays to genotype over 500,000 and 100,000 SNPs in one experiment, respectively. The 100K set is no longer offered.

Human Mapping 10Kv2.0 Array

http://www.affymetrix.com/products/arrays/specific/10k2.affx

The 10K Array is no longer offered.

Cost

Please refer to this page for current prices.

Contact

Contact information may be found here.