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.
|Primary Contact||Christopher Krebs, Manager, UM DNA Sequencing Core
|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||For sample submission, log-in at https://client-seqcore.brcf.med.umich.edu and follow the links for “Sample QC”. On the page showing Service Requested, select “Qubit Broad Range Double-Stranded DNA Assay”. In the “Reason” pull-down menu, choose “Affymetrix Microarray Submission”. Add additional information (e.g., “Please run DNA on SNP 6.0 chip”, “Samples are for Precision Medicine Array”, etc.) in the “Additional Notes” section.|
|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 the 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).