SNP Genotyping Project Information

DNA Preparation:

  • All samples should be diluted with filter sterilized distilled or deionized water to a concentration of 20 ng/µl. Please, DO NOT USE TE (Tris-EDTA) buffer. The EDTA will negatively impact the small volume PCR reactions that we perform for genotyping. Please notify us is if the EDTA concentration exceeds 0.05 mM per sample (after dilution).

  • The total volume required varies depending on project size; however we typically require 3 µl per sample per SNP being genotyped, with an absolute minimum of 15 µl. For example, if you have would like to genotype 25 SNPs, we would require a minimum of 75 µl per sample.

General Considerations

  • If needed, we can provide DNA extraction and reagent protocols. Alternatively, for an additional fee, we can perform this service at PreventionGenetics along with Biobanking services.

  • It is recommended that you retain some concentrated DNA stock from each sample for use in subsequent studies and also in the event we require additional DNA to complete the project (for example: cases in which the initial signal amplification is weak).

  • DNA obtained from a MDA (multiple displacement amplification) reaction is an acceptable template for SNP analysis. However, final genotyping quality with MDA-derived DNA is a function of the initial quality of the genomic DNA and the amplification reaction.

  • NOTE: Please contact us before sending DNA acquired via the Buccal swab method. It has been our experience that DNA obtained by this method tends to be of low concentration, which can complicate SNP analysis.

Sample Tubes, Labeling and Shipping

  • Our preferred sample system for SNP genotyping is the Matrix TrakMates 2-D barcode storage tube system along with the individual Sepraseal for each tube. There are other equivalent systems on the market but our experience has been with the Matrix system. If this is not a system used by your lab we can provide tubes, racks and SepraSeals for your samples. We will need the address and phone number of a contact person to ship the tubes.

    Other sample systems are acceptable provided they have a standard 96-well footprint. If you chose your own 96-well plate system, please group your plates in sets of four. One out of four plates should have either the top half or bottom half left empty. We genotype on a standard 384 well layout and will use these 48 empty wells for our control samples.
  • The data files (click here for an Excel template) for each 96-well plate should contain the kindred and individual numbers and the gender. It is also helpful to include the parental and ancestral information (if known). No patient identification information (such as names or phenotypic status) should be provided. Kindred numbers and individual numbers should be kept as simple as possible. DO NOT use any letters or hyphens in the kindred or individual identification numbers. Our software does not accept alphanumeric character strings. The data file can be returned via email to dave.s@preventiongenetics.com.

  • Your samples should be frozen to -80°C prior to shipment. In addition, freeze enough ice packs to -80°C to fill the Styrofoam shipping container. Once everything is frozen to -80°C, pack the samples and ice packs tightly into the container and send the shipment via overnight delivery to:

    PreventionGenetics
    Attn: David Schlesinger
    3700 Downwind Drive
    Marshfield, WI 54449

  • A brief e-mail message to the Director of Research Genotyping, notifying the lab of when to expect the shipment, including the TRACKING NUMBER, would be appreciated. It is also best if all DNA samples are shipped at one time, as opposed to being shipped in multiple batches.
  • Please be sure to include the name of the lead principal investigator (PI) of the project in the data file or on the shipping label.