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Frequently asked questions

General questions concerning the genotyping services
  1. What is the procedure to request genotyping services?
  2. What are the concentration and quantity of DNA for the sample which should be sent?
  3. If I do not have enough DNA, can I send you whole-genome amplified DNA?
  4. How should I send my DNA samples and primers?
  5. Is there a specific format I should use to create my DNA plate?
  6. Should I create a pedigree for the samples that do not have one?
  7. Is there a specific way to identify the samples?
  8. How will the genotypes be delivered?
  9. What are the validation and production steps?
  10. What are the validation and production genotypes?
  11. How much time is necessary for the completion of genotyping projects?
Questions on the microsatellite genotyping services
  1. How are the microsatellite markers groupings done?
  2. Do the selected SNPs have to be obtained from the Innovation Centre's database, Nanuq?
  3. How should I identify the selected SNPs?
Answers
General questions concerning the genotyping services
  1. What is the procedure to request genotyping services?

    You must contact the Client Management Office to request a quote. Once the quote is approved, you must fill out the request form, sent it by e-mail (along with a Purchase Order number (PO) and the ethics certificate if samples are of human origin) and send the first page, signed, by fax.

  2. What are the concentration and quantity of DNA for the sample which should be sent?

    The required concentration varies according to the technology used.

    For genotyping of microsatellites, TaqMan or Sequenom® iPLEX, the sent DNA should be in a minimum concentration of 20ng/ul and you need to provide at least 30ul. The quantity required can depend on the amplitude of the project. Ideally, the DNA should be solubilized in ultrapure water.

    For genotyping using the Illumina technology, the DNA should have a minimum concentration of 100ng/ul and the minimum required quantity is 25ul. The DNA should be diluted in a TE buffer (10mM Tris-HCl pH 8.0 / 1mM EDTA). If you prefer, you can send us your lyophilized samples.

  3. If I do not have enough DNA, can I send you whole-genome amplified DNA?

    Even if the genotyping ratio is not significantly different from that of non-amplified DNA, we have observed, for Illumina technologies, that for certain SNPs, the clusters behave differently between amplified and non-amplified DNA. Consequently, it is not recommended to mix amplified and non-amplified DNA samples in a same experiment. Note that if this is the only way to do it, the problematic SNPs will simply be taken out of the analyses.

    In the case of microsatellite technologies, TaqMan or Sequenom® iPLEX, we have not noted particular problems with the use of amplified genomic DNA.

  4. How should I send my DNA samples and primers?

    Samples should be sent in 96-well plates and safely sealed with an appropriate sealer. You must also include a schematic representation of your plate.

  5. Is there a specific format I should use to create my DNA plate?

    Please refer to the 'DNA' section for each technology for all the necessary information regarding the creation of this format.

  6. Should I create a pedigree for the samples that do not have one?

    If your DNA cohort is comprised of unrelated individuals, the creation of a pedigree is unnecessary. However, if your cohort is mostly comprised of samples with a pedigree and only a few unrelated individuals, please insert the unrelated individuals in the pedigree folder. These unrelated individuals will have no link with the other samples.

  7. Is there a specific way to identify the samples?

    Please have a unique identification (ID) for each sample. Please refer to the DNA section for each technology for all the necessary information to properly identify your samples.

  8. How will the genotypes be delivered?

    Data will be transmitted in our standard formats. The performance of each marker and the number of Mendelian errors will be summarized. The results will be sent as is indicated in the Request form 1 - General genotyping services. As soon as they are analysed and verified, the results will be sent to you via email or via FedEx on a CD-Rom.

  9. What are the validation and production steps?

    The validation step is the first step in the genotyping procedure. The objective of this step is to determine the optimal working conditions for your markers of interest by using a sub-group of samples. These conditions will then be used in the second step in the genotyping procedure: the production step. If no condition can be used to recuperate the markers which have failed the validation step, the client will be informed and will be asked to provide a new marker or to repeat the validation step. We will proceed to the production step only once acceptable results are obtained at the validation step.

  10. What are the validation and production genotypes?

    The validation genotypes are the genotypes obtained during the validation step. The production genotypes are the genotypes obtained during the production step.

  11. How much time is necessary for the completion of genotyping projects?

    The projects are completed on a 'first come first serve basis'. In addition, the time necessary to complete a project depends on the technology used, on the type of experiment and on the details of this experiment. Please, contact us for more information regarding how long your project will take to be completed.

Questions on the microsatellite genotyping services
  1. How are the microsatellite markers groupings done?

    The markers are put in groups of 8 in order to avoid overlap between the lengths of the fragments for two markers with the same fluorescent color.

  2. Do the selected SNPs have to be obtained from the Innovation Centre's database, Nanuq?

    No, however, it is always better to choose validated SNPs from public databases. Avoid SNPs localized in repetitive genomic regions.

  3. How should I identify the selected SNPs?

    The best way to identify your SNPs is to include the number « rs ». If it does not exist, give it a short and informative name. Avoid names containing more than 15 characters.