CDCB SNP-based parentage certification service¶

Table of contents
CDCB SNP-based parentage certification service

Introduction¶

This service is provided to national nominators and CDDR member studs that are also approved nominators.
A requester will be entitled to receive an official SNP-based parentage certificate for its own animals, based on the 195 ICAR-recommended Parentage SNPs, provided the animal is already in the CDCB cooperator database. In case of multiple usable genotypes are present for a given animal, or its relatives, a blending process will use all possible information available. Conflicting SNP calls will be removed. Note that since the compared set of SNPs is different from the parentage verification service normally provided by CDCB (where all SNPs are used), the results in the certificates may differ.

Policy document¶

The policy document for this service is available here

Operative information¶

Request file¶

File naming convention: Same as a format 1 naming convention, but with .par as an extension (YYYYMMDD.par*, where * means your own extension. Eg.: YYYYMMDD.par_thisismyfile)
File placement: The input file should be placed in your SFTP "in" directory
File content: The content of the file MUST contain 5 fields. Fields MUST be comma-separated, and no header should be included.
Fields:

Animal ID (valid id17)
Sire ID (valid id17)
Dam ID (valid id17)
Action required: values can be P (Parentage verification report only) or C (Parentage verification report + Parentage certificate for qualifying animals)
For the initial phase, this field must report 'CDCB' (no quotes) on each row. This field will be used later to allow users to submit genotypes for animals, not in CDCB DB (will require payment). But as
Example:
```
JE840003000000001,JEUSA000000000002,JE840003000000003,C,CDCB
HO840003000000004,HO840003000000005,HO840003000000006,P,CDCB
```

Output file¶

Output file: The output file will be placed in your out folder, and will be named as: CDCB_ICAR_parentage_YYYYMMDD_par<ext>_TTTTTT.zip , where:
- CDCB_ICAR_parentage_ and all the blue colored text as fixed.
- YYYYMMDD_par<ext> is the input file name provided by the user with underscore replacing dots in the name (e.g. YYYYMMDD.par1 = YYYYMMDD_par1)
- TTTTTT is a unique timestamp to avoid overwriting a the output file in case multiple files with the same name are sent on the same day.
- Example: input file called YYYYMMDD.par_thisismyfile. Expected output file_ will be CDCB_ICAR_parentage_YYYYMMDD_par_thisismyfile_123456.zip

Content of output file: The content of the zip file will be request-dependent.
- A report filename CDCB_ICAR_parentage_report_YYYYMMDD_par<ext>_TTTTTT.csv (e.g. CDCB_ICAR_parentage_report_YYYYMMDD_par_thisismyfile_123456.csv) will be provided irrespective of the option chosen. This file contains a detailed explanation for each animal provided in the input file. Fields in this file are:
  - CandidateID: The animal ID provided for the analysis
  - Candidate_SampleID: The sample ID of the genotype for the candidate animal used for the analysis (if genotype was retrieved from the CDCB cooperator database)
  - SireID: The sire ID provided for the analysis
  - Sire_SampleID: The sample ID of the genotype for the sire of candidate animal used for the analysis (if genotype was retrieved from the CDCB cooperator database)
  - DamID: The dam ID provided for the analysis
  - Dam_SampleID: The sample ID of the genotype for the dam of candidate animal used for the analysis (if genotype was retrieved from the CDCB cooperator database)
  - CalledSNP_Candidate: Number of non-missing SNPs out of the 195 used for the parentage verification for the candidate animal.
  - CalledSNP_Sire: Number of non-missing SNPs out of the 195 used for the parentage verification for the sire of the candidate animal.
  - Called_SNP_Dam: Number of non-missing SNPs out of the 195 used for the parentage verification for the dam of the candidate animal.
  - *ActionReqd: Action requested in the input file
  - Mend_SIRE: Count of mendelian conflicts between animal and sire. An explanation of what mendelian conflict means is provided in the CDCB Genomic Dictionary - section Mendelian inheritance conflicts.
  - Mend_DAM: Count of mendelian conflicts between animal and dam. An explanation of what mendelian conflict means is provided in the CDCB Genomic Dictionary - section Mendelian inheritance conflicts.
  - Mend_TRIO: Count of mendelian conflicts considering all 3 animals - candidate, sire and dam - together. This comparison is also known as "mating conflicts".
  - SIRE_REPORT: Outcome of the analysis. Possible values are: NOT CHECKED, LOW CALL, ACCEPTED, DOUBTFUL and EXCLUDED. The determination of each category and the thresholds used follow ICAR guidelines for SNP parentage verification
  - DAM_REPORT: Outcome of the analysis. Possible values are: NOT CHECKED, LOW CALL, ACCEPTED, DOUBTFUL and EXCLUDED. The determination of each category and the thresholds used follow ICAR guidelines for SNP parentage verification
  - MATING_REPORT: Outcome of the analysis. Possible values are: NOT CHECKED, LOW CALL, ACCEPTED, DOUBTFUL and EXCLUDED. The determination of each category and the thresholds used follow ICAR guidelines for SNP parentage verification
  - COMMENTS: If animals were excluded from the analysis or did not receive a certificate, the reason for the exclusion is explained in this field. If no errors or problems are found, this field will contain: "NO ERROR". Note not all comments in this section prevent an animal from receiving a certificate.
- If certificates are requested, all qualifying animals will have a separate certificate in pdf named Parentage_certificate_<ID_OF_THE_ANIMAL>.pdf (e.g. Parentage_certificate_HOUSA000000000001.pdf).
  - Not all requested animals may qualify for a certificate, and the user will find the reason in the "comments" section of the report. In general, except for formal problems in the input file, issues reported on candidate animals will result in no certificates being generated, whereas issues reported on sire/dam will not prevent a certificate to be issued. Since the initial phase is an ALPHA-TESTING phase, if you think an error was assigned by mistake by the system, please do not hesitate to submit a Redmine ticket to request a revision.
  - Please see an EXAMPLE SNP-parentage certificate.

Limitations¶

A maximum of 100 certificates per file can be requested.
No duplicates within file are allowed. In case duplicates are present, both duplicates will be excluded from the analysis (note that the genotype will be considered "unusable" by the program, even if the animal has usable genotypes. Please remove the duplicate and run the analysis again).
This service is provided to national nominators and for NAAB members that are also nominators.
Nominators can only request certificates for animals they have nominated. Breed associations can request certificates for any animal of the breed they represent. NAAB can request certificates for any AI male.
The certificate content cannot be modified and follows ICAR guidelines currently available. A discussion is ongoing at the ICAR DNA working group level - CDCB staff participates to it- to create international minimum standards of content and naming conventions. As of now, there is none so CDCB staff communicated with other countries issuing these certificates to be as much in line as possible with them. Note the requester of the certificate is embedded in the certificate.
Access rules for this phase are:
- AI bulls are released only to the stud controlling the animal.
- Non-AI bulls and females are released to any valid nominator.
- Exceptions apply for registered animals-breed associations and the NAAB organization.

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