FAQ
- How much DNA do I need to send?
Total: about 2.5 µg (25 µl @ 75-150ng/µl) for linkage panels, custom SNP projects and focused content products.
Total: about 1.2 µg (25 µl @ 50 ng/µl) for genome wide association chips
Total: about 1 µg (in 20 ul) for methylation.
- Will the entire DNA be used?
Under normal circumstances, no.
- Will DNA not used be returned?
Yes, with the release of your project data.
- Can I use my own plates for DNA transport?
No. We will provide plates for DNA transport. These plates will be provided along with Individual tube caps and labels. Labels need to be placed on the column 12 side of the plate to be automation friendly.
- Will informatics tools be provided in reference to sample location, concentrations and family file information?
The SNP Center will provide you with an excel workbook including instructions, project information, forms to record sample location, concentrations, and family file information.
- 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. 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. The SNP Center cannot accept samples until all Project Initiation Documents are complete. Do not ship samples until all necessary documentation has been received and reviewed by the Project Coordinator.
- Do you verify DNA concentration? Do your adjust volumes to achieve correct concentration?
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 at the SNP Center.
- Do you provide DNA controls?
Yes, for genotyping projects. All plates processed have parent-parent-child CEPH trios and one replicate of the child. 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) Marker performance and quality assurance 4) Plate to plate performance variation.
For methylation projects, the investigator must supply their own fully methylated and completely unmethlyated control samples.
- Do we need to provide our own internal controls?
Yes. Illumina strongly suggests that at least 10 parent-parent-child trios be included for a project. If you are unable to accommodate this request, the SNP Center may need to reserve space for additional CEPH trios. We also recommend for family based studies, and require for case-control studies, a minimum of 2 duplicated samples from another plate on each plate. Genome Wide Association projects may use only one duplicate per plate, due to the expense of the product. The use of same plate duplicates is left to the investigators' discretion.
For methylation projects, it strongly recommended that samples with known methlyation status be supplied as well, though there are 20 genes with constant methlyation status included within the standard panel.
- What is the timeline for my project’s data to be released?
This is dependent on the size (DNA and # of OPAs) and complexity of the project. Ask your Project Coordinator for a time estimate.
- Can we visit the SNP Center?
Yes. We welcome all project PIs to visit the lab. Talk to your Project Coordinator to arrange a visit.
- 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.
- 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?
For an additional charge we can perform Taqman genotyping of the chr. X and Y amelogenin loci. This will provide gender information to compare against your records and a general measure of the quality of the DNAs. However, performance on another genotyping platform does not guarantee success on the Illumina system.
A pretest of samples can also be done using the DNA test panel available from Illumina. This is a panel of 348 SNPs across the genome, done on 92 samples. Cost is $6300.
- Can I look at LOH or copy number using the Illumina System?
Yes, any of the Genome Wide Association products can used to look at LOH and copy number using Illumina’s BeadStudio Genotyping Module. We do not do this analysis for you. If you would like to look at the data in this manner, you must purchase BeadStudio from Illumina. To do so, please contact your project manager. A BeadStudio license is available for internal JHU customers only. External customers should contact Illumina directly.
- Does your lab provide bisulfite conversion for methlyation studies?
No. Each investigator must carry out their own bisulfite conversion. At this time, Illumina recommends the use of the Zymo EZ-DNA Methylation kit for the conversion process
Bisulfited DNA is single stranded and unstable, so please be sure to arrange a slot in the SNP Center lab with your project manager before beginning the process.
- What is the difference between Golden Gate and Infinium chemistry?
For detailed information on the different chemistries, please see Illumina's website. A description of the Golden Gate Chemistry is here. A description of the Infinium Chemistry is here.
- If I don't have any family structure in my samples, do I need to provide a pedigree file?
Yes. 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.