STRP Genotyping Project Information

Requirements for Samples:

General Instructions:

  • We require 15-30 µg of DNA for a 10cM genome screen on each individual sample, (double the amount for a 5cM scan). 15 µg is the minimum amount, however additional DNA usually leads to higher quality results. For individual STRPs we require 150-300 ng of DNA per STRP per sample.

  • The samples should be diluted in filter sterilized distilled or deionized water to 15-30 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).

  • All samples should be at the SAME CONCENTRATION, and that concentration should be clearly noted.

  • It is recommended that you retain some concentrated stock for each sample to use in subsequent studies and also in the event we require additional DNA for.

  • Do NOT submit DNA acquired via Buccal swab without contacting us in advance.

Quality Control DNA:
  • Each project has the option of including Quality Control (QC) samples. THESE QC SAMPLES WILL BE INCLUDED IN YOUR TOTAL APPROVED SAMPLE NUMBER. The results of these controls will be for your use only as we include our own internal quality controls.

  • The identity of your QC samples should not be revealed to us. These samples should be disguised with individual numbers similar to those of the study subjects.

  • The best QC samples are those for which you have or will have genotypes for each marker. A preferred choice is to use duplicate DNA samples from study subjects. Other types of QC samples, such as water or CEPH family DNA may be used.

  • For the best indication of genotyping quality, the QC DNA should be at the same concentration and in the same solvent as the DNA from the test samples.

Sample Tubes, Labeling and Shipping:
  • We will send you labeled tubes, racks, and plate seals for your samples after we receive your datafile (see below). To ship the tubes, we will need the address and phone number of a contact person.

  • The data file entries (see example below) should contain ONLY the kindred #, individual #, Father ID, Mother ID, and Gender (1 for male and 2 for female). No other patient information (such as names, social security numbers, or phenotypic status) should be provided. Kindred numbers and individual numbers should be kept as simple as possible. Please send us the data file (ASCI tab-delimited computer file or as an Excel spreadsheet) via email (dave.s@preventiongenetics.com).

    • Kindred1

    Individual2

    Father3

    Mother3

    Gender4

    Ancestry5

    1

    001

    0

    0

    1

    German

    1

    002

    0

    0

    2

    German

    2

    004

    001

    002

    2

    African American

    2

    005

    001

    002

    1

    African American

    3

    007

    0

    0

    1

    Chinese

    3

    008

    0

    0

    2

    Chinese

    1Kindred involves a typical family with father, mother and three children.
    2DO NOT use any letters or hyphenated numbers in the kindred or individual identification numbers. Our programs do not accept alphanumeric character strings.
    3The individual numbers of both the father and mother of the sample donor if possible (0 = Not Available). Family structures are used to search for violation of Mendel's segregation rules as a final check of the genotyping results.
    4Gender information will be used to identify any sample mislabeling through typing of X and Y chromosome polymorphisms.
    5Ancestry of study participant. This information can be beneficial in making correct allele assignments. When possible, please include their country of origin and/or group or tribe. For example: German; Amish; African American; Nigerian/Yoruba; Native American/Sioux; Ashkenazi Jewish; Chinese; Vietnamese; etc.

  • The DNA samples should be sent to:


    • PreventionGenetics
    Attn: David Schlesinger
    3700 Downwind Drive
    Marshfield, WI 54449
    Phone: 715-387-0484

  • A brief e-mail message to dave.s@preventiongenetics.com , notifying the lab of when to expect the shipment, ALONG WITH THE SHIPMENT TRACKING NUMBER, would be appreciated. It is also best if all the DNA samples are shipped at one time, as opposed to being shipped in two or more batches.

  • Currently, the maximum number of individuals for any one family is 86. If you have a family that is larger than 86 individuals, you will need to break the family down into 2 or more branches. Please give each branch a different family number.

Genotyping Results:

Genotyping results will be reported to you as allele sizes of the polymorphic markers in nucleotides. Allele sizes for all test samples are determined relative to the allele sizes assigned to the parents of CEPH family 1331 (133101 and 133102). We use amplified DNA from these two individuals as standards. Note that there may be differences between the sizes assigned to alleles and the actual physical lengths of the amplified fragments. However, in nearly all cases these differences will be no more than a few nucleotides. Note also that alleles with the same electrophoretic mobility will occasionally differ in sequence. For example, an allele with 18 dinucleotide repeats with structure (AC)10(TC)8 will be indistinguishable from an allele with (AC)8(TC)10 structure.