DNA Requirements
For Custom SNP panels:
All DNAs must be provided at a concentration between 75 ng/µl and 150 ng/µl. Whole genome amplified (WGA) products should be at a concentration between 200 ng/µl and 300 ng/µl, depending on source of original DNA. We advise you to discuss issues concerning WGA samples with our staff prior to beginning your study. Please be sure of your concentrations. We will not adjust concentrations for you.
The required volume of DNA depends on the number of SNP sets that will be assayed for the sample.
Depending on your experiment’s design, a SNP set (OPA) may contain 384, 768, or 1536 SNPs.
- Single SNP Set (OPA): Send 25µl
- Two SNP Sets (OPAs): Send 40µl
- Three SNP Sets (OPAs): Send 55µl
- Etcetera
Poor quality DNAs or DNAs that have been amplified may not perform as well as unamplified genomic DNA. In particular there may be allele loss in the heterozygotes and a reduced call rate for whole genome amplified samples. Additionally, samples contaminated with heme may not work. Clients should be aware of these limitations prior to committing to a study.
DNAs must be sent in bar-coded plates provided by the SNP Center, 92 samples per plate. Four wells on each plate are reserved for controls. Plates will be provided after arrangements for payment have been made, a pedigree file has been approved (required for both family based studies and case-control studies) and a copy of your IRB approval letter has been received. A DNA manifest template will be sent to you. Please read the instructions provided with the manifest carefully and follow them precisely. The manifest is our only record tying sample ID to plate and well location so please take care to ensure the accuracy of this document. The Illumina software has required fields, such as patient sex, shown in the manifest. This was implemented so that switched samples might be more easily identified. You can provide this information if you choose but we do not require it. Plates must be shipped on dry ice for arrival on Tuesday through Friday.
For Illumina Genome Wide Association and Human Linkage panels:
All DNAs should be provided at a concentration between 50 ng/µl and 100 ng/µl, (genomic DNA) or 100ng/µl and 200ng/µl (whole-genome amplified DNA), 25 µl total volume. Concentrations at the higher end of the spectrum and high molecular weight DNA is recommended for downstream copy number analysis.
A note regarding the use of amplified DNA for Genome Wide products: The final concentration of WGA samples is not indicative of sample quality. Depending on the input DNA quality and quantity, the final WGA'ed product may not be a good genetic representative of the starting material, especially if the starting concentration was low or if contaminating DNA was present. As a result, we discourage use of WGA samples at this time. If you do submit WGA samples, you should anticipate a higher missing data rate and perhaps a slightly higher error rate than for genomic DNA samples.
For Affymetrix 6.0 panel:
All DNAs should be provided at a concentration between 75 ng//µl and 100 ng//µl. ONLY blood or cell-line derived genomic DNA is accepted for this product.
Methylation products:
Bisulfite conversion must be carried out in the investigator's lab, prior to submission to the SNP Center. At this time, Illumina recommends the use of the Zymo EZ-DNA Methylation kit in either the tube format or the plate format for the conversion process. The SNP Center does not offer bisulfite modification at this time.
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.
DNA should be sent in the solution they are in at the end of the conversion process. Due to automated handling procedures, 1 µg of DNA in 20 µl volume is required for each sample.
Please note that at this time, you also need to provide your own fully methylated and completely unmethlyated control samples in addition to your experimental samples.
It is the policy of the SNP Center, as well as all units of the GRCF, to protect the confidentiality of an investigator's data. We ask that you not submit any patient identifiers with your samples and that you do not indicate affected status. We do not even need to know what disorder you are studying unless there are special circumstances that may impact data quality (e.g., DNAs from buccal swabs, fixed tissue, or the products of whole genome amplification).