1. How much DNA do I need to send?  That depends on the chemistry.
    1. Illumina Golden Gate Chemistry: 25 µl @ 75-150ng/µl genomic DNA; 200-300 ng/ul WGA sample
    2. Illumina Infinium Chemistry: 25 µl @ 50 ng/µl genomic DNA; WGA DNA is not recommended
    3. Taqman OpenArray Chemistry: 10 ul @ 50 ng/ul genomic DNA; 200-300 ng/ul WGA sample
    4. Individual Assays: Amount required depends on assay.  Please contact us for details.
  2. Can I send Whole Genome Amplified (WGA) samples? WGA samples will always preform worse than whole genomic DNA.  They are usually somewhat successful for Golden Gate and Taqman chemistries, but they do not preform well with the Infinium chemistry.  This means that for GWAS products, we would prefer to work with you on lower volumes and/or concentration and avoid using WGA samples if at all possible.
  3. Will the entire DNA be used?  Under normal circumstances, no.
  4. Will excess DNA be returned?  Yes, with the release of your project data.
  5. If I don’t have any family structure in my samples, do I need to provide a pedigree file? Yes, for all Illumina projects. Our computer scripts require a pedigree file to function. Files without family structure are generally very easy to create following the instructions provided in your initioation documents. If you have misplaced the directions, please contact your project manager.
  6. Can I use my own plates for DNA transport? For Illumina genotyping, no. We will provide plates for DNA transport. These plates will be provided along with Individual tube caps and labels. For other types of genotyping, yes.  Plate maps can be created for these projects to assist with control placement.
  7. What is the best method to send our samples? DNA samples must be frozen prior to boxing and shipping.  Verify that the rack is locked (Illumina projects).  Place each rack in a separate bubble bag.  Place the racks in a shipment container and fill all empty space in the shipment container with dry ice so that the plates stay frozen and do not move during shipment.  Ship all packages overnight for delivery on Tuesday, Wednesday, Thursday, or Friday.  Send tracking number to your Project Coordinator. We cannot accept samples until all necessary documents and/or order forms have been filled out.  Do not ship samples until all necessary documentation has been received and reviewed by the Project Coordinator.
  8. Do you verify DNA concentration?  Do your adjust volumes to achieve correct concentration? No. We do not verify DNA concentration. We will run one plate through the process to make sure the samples are performing well before proceeding with the remainder of the project. Due to the numbers of samples we process, we do not adjust concentrations.
  9. Do you provide DNA controls? Yes, for human and mouse genotyping projects. All plates processed have HapMap controls on them. These spots will be reserved in the DNA manifest. We use these positive controls to: 1) Monitor assay performance 2) Evaluate experimental DNA quality 3) Aid in definition of cluster boundaries for each SNP locus 3) To assess marker performance and quality assurance 4) Evaluate plate to plate performance variation. For non-human projects, the investigator must supply their own controls.
  10. Do we need to provide our own internal controls? Yes. We recommend cross plate duplicates on each plate.
  11. What is the timeline for my project’s data to be released? This is dependent on the size and complexity of the project. Ask your Project Coordinator for a time estimate.
  12. Can we visit the GRCF? Yes. We welcome all project PIs to visit the lab. Talk to your Project Coordinator to arrange a visit.
  13. Who do we contact for information about our project? Each study will be assigned a Project Coordinator who will be your primary contact for information about the project and will let you know if there are any issues with the samples, DNA manifest, etc. that need to be resolved.
  14. I am uncertain about the quality and identity of all of my samples and would like some sort of QC done before committing to the full study? All GWAS projects are pretested with our fingerprint DNA panel.  This will provide gender information to compare against your records and a general measure of the quality of the DNAs. However, this is not the same chemistry the GWAS chips use, so highly degraded samples may work in pretesting and fail on the actual chips. You should try to send us intact DNA for use on GWAS chips.
  15. What is the difference between Golden Gate and Infinium chemistry? For detailed information on the different chemistries, please see Illumina’s website.