Affymetrix SNP typing Microarray

Hybridization array-based methods for detecting common and rare single nucleotide polymorphisms (SNPs), copy-number variants (CNV) and other genetic variations that can contribute to complex disease.

 

Affymetrix SNP typing Microarray

Platform
Affymetrix Microarray
Category
Genotyping
Primary Contact

Christopher Krebs, Manager, UM DNA Sequencing Core

ckrebs@umich.edu

734-763-8891

Typical Cost Click here to view internal pricing list!
Click here to view external pricing list!
Typical Output

SNP 6.0 array interrogates 1.8 million genetic markers, including more than 900,000 SNPs with over 900,000 probes for detecting CNVs.

Axiom BioBanking arrays detect ~675,000 SNPs and indels. GWAS markers are common variants selected for genome-wide coverage of European, Asian, African and Latino populations allowing efficient imputation of additional markers.

OncoScan arrays reveal copy number and loss-of-heterozygosity (LOH) profiles from solid tumors obtained from highly degraded FFPE samples.

Raw data is exported as .CEL files. Analytical software is available for download on the Affymetrix website. Additional help is available through the Bioinformatics Core (Bioinformatics link) on a fee-for-service basis.

How to Request

Sample Submission: go to https://seqcore.brcf.med.umich.edu/ ​​ then choose “Microarray Genotyping Analysis”

Sample Requirements

SNP 6.0: 750 ng genomic DNA in 15 ul (50 ng/ul)

Axiom BioBanking: 200 ng genomic DNA in 20 ul (10 ng/ul)

OncoScan: 80 ng tumor DNA in 12 ul (6.67 ng/ul)

Typical Turnaround

3 to 4 weeks, however, timing is dependent on availability of arrays, which are purchased as needed.

Critical Information

For standard genotyping arrays (SNP 6.0, Axiom) DNA must be of high quality and free of protein, detergents or intercalating dyes (e.g., ethidium bromide). OncoScan arrays are designed to work with DNA recovered from FFPE tissue.

For all arrays, avoid subjecting DNA to multiple freeze-thaw cycles, high temperatures (> 65ºC) and pH extremes.

For Axiom arrays, samples must be submitted in AB-gene 96 Square Well Storage plates (ThermoScientific Cat# AB-0932). If samples require Sequencing Core personnel to transfer them to the correct plate, an additional fee will be added to the cost of your project.

More Information

For a list of arrays available, product descriptions and additional technical information, go to the Affymetrix website at: http://www.affymetrix.com

For DNA isolation services, go to: FAQ for Genomic DNA isolation

For other options for genotyping go to: FAQ for Next Generation Sequencing (NGS).