Illumina BeadArray Genotyping

Using the Illumina BeadArray based assay, the DNA Sequencing Core performs high throughput custom genotyping, whole genome genotyping, copy number variation (CNV), cytogenetic analysis, and linkage analysis assays. The Core Genotyping Services for the Illumina BeadArray platform consist of the following:

  1. Verify DNA concentration with a PicoGreen/Qubit assay,
  2. Normalize sample
  3. Perform Illumina Genotyping assay,
  4. Record SNP loci intensities with an iScan Scanner,
  5. Create a GenomeStudio Project for DNA analysis, and
  6. Generate reports (i.e. genotypes, sample call rates, SNP call rates, etc).

 

Illumina BeadArray Genotyping

Platform
Illumina iScan
Category
Genotyping
Primary Contact

Susan Dagenais, Ph.D.
UM DNA Sequencing Core
e-mail: sdagenai@umich.edu
Phone: 734-615-8743
Fax: 734-763-8889

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

Typical call rates are >99% for all standard Illumina GoldenGate, Infinium, and LCG Array products.

How to Request

Sample Submission – Contact Susan Dagenais (sdagenai@umich.edu) and request a Project Quote. Please indicate the number of samples to be assayed and which Illumina BeadChip kit you would like used for the assay. We will e-mail you a Quote for the Illumina Kit costs and Estimated Core Processing fees. Once we a signed Quote, we will place an order with Ilumina, assign a Core Project Number, and you will be sent a BeadArray submission form for sample submission.

Sample Requirements

DNA Concentration Request – dependent upon how the stock DNA concentration was determined.

  1. PicoGreen/Qubit – 50-55ng/ul (10-12ul)
  2. NanoDrop - 100ng/ul (20-25ul)
Typical Turnaround

Typical turnaround time is 1-3 weeks.

Critical Information
  1. The Core will assign Core Sample ID numbers, which you will write on top of 1.5mL tubes containing your samples. For Plate submissions, the Core will assign Core Sample ID numbers and a Core Plate ID numbers, which will be written on the side of the plate.
  2. The Core offers Qubit/PicoGreen and Normalization service for $2/sample (see link in More Information).
  3. If samples need to be normalized to 50-55ng/ul, they should be submitted in 1.5mL tubes with the BeadArray Core Sample ID written on top.
  4. If samples are normalized to 50-55ng/ul (PicoGreen/Qubit), the samples can be submitted in either in 1.5mL tubes or in plates with samples arranged in columns (A1, B1, C1, etc).
  5. Unused DNA will be returned after project is completed.
  6. Computer Workstations are available for clients to perform their own analysis using the Illumina GenomeStudio DNA Analysis Software packages.
  7. For the Illumina BeadArray platform, the Client must perform their own data analysis or consult with a Bio-informatics specialist.
More Information