New SNP Chip Validation Process Requirements

  • Submit a completed CDCB SNP array validation form. NOTE: All the requested information MUST be provided.
    • For SNP Array Full Name, please follow the format below:
      [Technology (e.g. Illumina or Affymetrix)] - [Company/Collaborator name] - [SNP array name] - [description / version # (if applicable)]
  • Paid the corresponding CDCB SNP array validation fees.
  • The following SNP must be included on the new chip:
    • Chips are required to have at least 3480 of the 3552 SNP (fast discovery) in the attached list, including all the first 96 labeled critical.
    • Chips are required to have at least 350 of the 550 SNP, used for quick discovery service (QDisc) in the attached list.
    • Chips are required to have at minimum 10 Y SNP for gender verification. See the attached file for examples of Y SNP commonly used for genotyping.
  • Provide one of the following two, to assess the accuracy of the genotype calls:
    • At least 50 genotypes from the new chip for animals already genotyped with a Chips Used in CDCB Evaluation that includes most of the SNPs in the new chip.
    • Genotypes from animals (min 50) which at least one parent has been genotyped with a Chips Used in CDCB Evaluation with substantial overlap with the new chip.
  • SNP coordinates should be based on the ARS-UCD1.2 assembly (Rosen et al. 2018 WCGALP, vol. Molecular Genetics 3, p. 802 and


The above data is to be submitted to CDCB in 3 files

1) Description of the SNP (SNP manifest/map file):

  • The above columns are REQUIRED, with the preferred order as shown

2) Genotypes (Final Report file):

Version    1.1.1
Processing Date 14-Mar-2023 03:44:44 PM
Content Test
Num SNPs        4
Total SNPs      4
Num Samples     3
Total Samples   3
        AB01234567        AB01234568        AB01234569
SNP_Name_1        BB        AA        AB
SNP_Name_2        AB        AB        AB
SNP_Name_3        AA        AB        AA
SNP_Name_4        BB        BB        BB
  • Matrix format is preferred (rows are SNP, columns are samples)
    • Standard format (all data in rows) can be submitted if matrix format is not available
  • Sample_ID in the genotype file should match the Sample_ID in the sample sheet file
  • SNP names have a maximum of 44 characters allowed

3) Information about the submitted samples (Sample sheet file):

Investigator Name,"Doe, John",,,,,,,,,,,,,,,,,,,,,,
Project Name,2023031411_ABC_AB,,,,,,,,,,,,,,,,,,,,,,
Experiment Name,,,,,,,,,,,,,,,,,,,,,,,
Sample_ID,Sample_Plate,Sample_Name,Project,AMP_Plate,Sample_Well,SentrixBarcode_A,SentrixPosition_A,Scanner,Date_Scan,Replicate,Parent1,Parent2,Gender,Sample Type
  • At minimum, the Sample sheet file must contain columns for Sample_ID, Sample_Name, Barcode, and Position

For additional details on the file formats, please see:


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