Genotyping Arrays

SNP Genotyping Arrays (Whole Genome Genotyping)

Whole Genome Genotyping (Genome-wide association studies) is supported by SNP genotyping arrays that can be run on both the Affymetrix GeneChip 3000 7G system and the Illumina iScan. These chips can interrogate (at the present time) up to 2.5 million SNPs per sample on a single chip.

The lab has extensive experience with processing Affymetrix SNP Array 6.0 chips, having competed a number of studies ranging from 500-1200 samples per study. Unlike previous Affymetrix SNP arrays, the SNP Array 6.0 probe sets are contained on a single chip. In addition to probing for 900,000 SNP markers, the chip also contains probes to over 900,000 copy number variants.

Illumina has a number of SNP BeadChip options, including the HumanOmniExpress, which allows analysis of over 700,000 SNP markers using a 12 sample per chip format. HumanOmni2.5-Quad allows analysis of about 2.5 million SNP markers using a 4 sample per chip format.

The lab provides a full service – investigators need only provide genomic DNA in a 96-well format, with two blank wells that will be used for controls. Data is provided back to the investigator for analysis. For those who would like support for analysis, the Bioinformatics group at the UM Institute for Genome Sciences is readily available to help.

For those who desire a custom-designed SNP Array chip, Illumina has the ability to provide this service in a cost-effective manner.

* Does not include the cost of the Affymetrix chip or the Affymetrix reagent kit.

** Pricing varies depending on format.

For any questions related to our genotyping services, please contact Jing Yin (jyin@umaryland.edu) or Nick Ambulos (nambulos@som.umaryland.edu).