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 ALL 195 SNP used in the attached list for parentage verification and discovery (See ICAR documentation)
    • In order for data to qualify for ICAR parentage certification, there has to be at least 95% of the ICAR 195 with calls (at minimum 185/195 of the SNPs have to have calls / not be missing).
  • 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.
    • QDisc based on the ICAR 550 SNP subset: from the total ICAR 554 SNP list for parentage discovery , 4 SNP are excluded as per ICAR guidelines recommendation .
  • 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 https://www.ncbi.nlm.nih.gov/assembly/GCA_002263795.2/)

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

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

Name,Index,Chr,Position
SNP_Name_1,1,19,123456789
SNP_Name_2,2,30,11223344
SNP_Name_3,3,5,98765432
SNP_Name_4,4,1,123400000

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

2) Genotypes (Final Report file):

[Header]
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
[Data]
        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):

[Header],,,,,,,,,,,,,,,,,,,,,,,
Investigator Name,"Doe, John",,,,,,,,,,,,,,,,,,,,,,
Project Name,2023031411_ABC_AB,,,,,,,,,,,,,,,,,,,,,,
Experiment Name,,,,,,,,,,,,,,,,,,,,,,,
Date,44916,,,,,,,,,,,,,,,,,,,,,,
[Manifests],,,,,,,,,,,,,,,,,,,,,,,
A,A_Dairy_Chip,,,,,,,,,,,,,,,,,,,,,,
[Data],,,,,,,,,,,,,,,,,,,,,,,
Sample_ID,Sample_Plate,Sample_Name,Project,AMP_Plate,Sample_Well,SentrixBarcode_A,SentrixPosition_A,Scanner,Date_Scan,Replicate,Parent1,Parent2,Gender,Sample Type
AB01234567,123456,HOUSA000000000001,Project1,222222,E1,200000000000,R01C01,,,,,,,Tissue
AB01234568,123456,HOUSA000000000002,Project1,222222,B2,200000000001,R01C02,,,,,,,Tissue
AB01234569,123456,HOUSA000000000003,Project1,222222,C3,200000000002,R01C03,,,,,,,Tissue

• 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:
https://redmine.uscdcb.com/projects/cdcb-customer-service/wiki/CDCB_Accepted_genotype_file_formats