Genotyping

Illumina BeadArray Genotyping

Using the Illumina BeadArray based assay, the Advanced Genomics 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).
PlatformIllumina iScan
Primary ContactSusan Dagenais, Ph.D.
UM Advanced Genomics Core
e-mail: sdagenai@umich.edu
Phone: 734-615-8743
Typical OutputTypical call rates are >99% for all standard Illumina GoldenGate, Infinium, and LCG Array products.
Sample RequirementsDNA 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 TurnaroundTypical 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. For the Illumina BeadArray platform, the Client must perform their own data analysis or consult with a Bio-informatics specialist.

More Information

Frequently Asked Questions

What concentrations and volumes of DNA are required?

We request 10-12µl of DNA at a concentration of 50ng/µl based on Qubit or PicoGreen dsDNA Quantification and NOT NanoDrop.  If you do not have access to Qubit or PicoGreen dsDNA quantification kits, you may submit 25-30µl of DNA at a concentration of 100ng/µl based on NanoDrop.  In this case, the Core will determine the concentration with Qubit/PicoGreen and perform the normalization for an additional charge.

Do you verify DNA concentrations?

Unless the client requests verification of concentrations or the sample concentrations submitted is based on NanoDrop, we do not verify the concentrations of samples.

Can we use whole genome amplified DNA?

Illumina does not recommend using WGA DNA. The use of WGA DNA may lead to lower call rates and allelic bias.

Can we submit degraded DNA?

Yes, but DNA must be 2kb or greater in size.

Do you provide DNA controls?

No. The client must provide their own controls (i.e. HapMap controls, cross plate duplicates, etc)

What is the turnaround time?

We perform assays based on first come first served, but the typical turnaround time is 1.5-3 weeks.  However, the time frame for completion of your project may be longer as it is dependent upon the length of the queue and the number of samples in your project.

Do you perform methylation profiling assays?

Yes, we assay samples with the Illumina Infinium MethylationEPIC assay.

Do you perform bi-sulfite conversions?

No. Either the Epigenomics Core performs the bi-sulfite conversions (clalance@umich.edu) or the client submits bi-sulfite converted DNAs using the EZ DNA Methylation™ Kit from Zymo Research and following incubation conditions in Appendix 6 (Catalog Nos. D5001 & D5002): https://files.zymoresearch.com/protocols/_d5001_d5002_ez_dna_methylationga_o_kit.pdf).

Do you genotype FFPE DNA samples?

Yes.  However, we request that the client perform the Illumina FFPE QC assay (Link:https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/infinium_assays/infinium_hd_ffpe_qc_assay/infinium_ffpe_dna_qc_assay_insert_15020981_c.pdf) before we order kits for the FFPE restoration and Illumina Genotyping or MethylationEPIC kits.

How much DNA is needed for FFPE restoration?

A minimum of 100ng in a maximum volume of 8µl (i.e. 12.5ng/µl) is required, but if available, you may use up to 250ng of DNA.

What is included in the processing fees?

Core Processing fees include Tech time (labor) fees, consumables, and iScan time fees.