Code of Practice for the use of the Parentage SNP Exchange (PSE) services at the Interbull Centre (“GenoEx-PSE CoP”)

This GenoEx-PSE Code of Practice describes the practical aspects of the GenoEx-PSE services provided by the Interbull Centre. It is an integral part of the GenoEx-PSE Service Agreement that eligible Service Users have signed up for with the Interbull Centre.

1. Introduction

The International Genotype Exchange Platform “GenoEx” has been developed at the Interbull Centre, with financial support from Interbull, SLU and ICAR.

The first service provided through this platform is the Parentage SNP Exchange (GenoEx-PSE) service.

GenoEx-PSE is provided through the Interbull Centre.

The main purpose of GenoEx-PSE is to provide a service for exchanging standardized sets of SNP for genotyped animals to facilitate and streamline parentage analysis activities carried out by organizations that are already responsible and/or active in parentage integrity.

To accomplish this, a Genotype Exchange Parentage SNP Exchange (GenoEx-PSE) database for the storage and exchange of SNP data has been built at the Interbull Centre.

The concept is one of a “bucket” of genotypes with only parentage SNP with only authorized parties contributing to and extracting from that “bucket”.

The service does not include parentage analysis in its own right, nor does it seek to enable new entrants to gain easy access to parentage SNP. As such, the database and associated services are not a replacement for national authorities or historic providers of parentage verification.

2. Legal and Financial aspects

Prerequisites:

• Organisations wishing to join GenoEx-PSE shall have a valid ICAR Accreditation for DNA Interpretation Centre Details and application guidelines on “ICAR Parentage Analysis Accreditation for DNA Data Interpretation Centres” are available on the ICAR website: http://www.icar.org/index.php/certifications/certification-and-accreditation-of-dna-genetic-laboratories/

• Sign the GenoEx-PSE Service Agreement which includes (amongst others):

• The rules for participation in GenoEx-PSE

• The levels and types of Services Fees

  • The GenoEx-PSE Service Agreement is available on the GenoEx Website on: https://genoex.org/

3. GenoEx-PSE Principles

The GenoEx-PSE database and service are developed on the basis of a number of underlying principles:

3.1. GenoEx-PSE is a tool to facilitate only the exchange of SNP useful for parentage analysis. It is not a replacement for existing service providers.

3.2. GenoEx-PSE does not include the possibility for the Interbull Centre to carry out parentage analysis. Any such new service in the future would require approval from ICAR as well as Interbull and/or Interbeef.

3.3. All Service Users can access all SNP genotypes up to the level of service that they have signed up for (see Article 5 and 6 for details on SNP).

3.4. The SNP information exchanged via GenoEx-PSE must only be used for parentage analysis. Other uses, including the estimation of genomic predictions, are absolutely forbidden.

3.5. GenoEx-PSE is entirely a voluntary initiative allowing various countries to enter when comfortable.

4. Service User Rights & Obligations

Only organizations with a signed GenoEx-PSE Service Agreement can upload and download data: Each Service User has designated “population(s)” of animals under its responsibility, normally defined by country/region, breed(s), herdbook or not, etc. The Service User will define the level of service desired: Parentage Verification, Parentage Discovery, or Microsatellite Imputation.

4.1. Service User rights:

4.1.1. Access to GenoEx-PSE for uploading and downloading of its own data.

4.1.2. Access to GenoEx-PSE for downloading the SNP genotypes required to perform parentage analysis services for animals under its responsibility, which will primarily be males in A.I. but may include other males and potential dams. The groups of SNP included in the genotypes for downloading must be consistent with the groups of SNP uploaded, depending on whether the parentage services are restricted to parentage verification or also include parentage discovery and the use of microsatellite marker information.

4.2. Service User obligations:

4.2.1. Agree to use the data only for parentage analysis. Other uses, especially for genomic predictions, are strictly prohibited.

4.2.2. Must routinely (minimum 3 times per year) upload all genotypes for “targeted” animals to access desired genotypes for same group of SNP.

4.2.3 "Targeted" animals relate to the population of animals for which the Service User has the authority to conduct parentage analysis services.

Such a population is defined by breed, country of birth and registration status (i.e.: either in the national breed association herdbook or not registered).

A Service User may be authorized to carry out parentage analysis services for multiple breeds and/or multiple countries and/or both groups of registration status. For each such population, "Targeted" animals for uploading genotypes to GenoEx-PSE must minimally include:

1. Sires in the authorized population that are born in the authorized country and known to be in A.I.
   b. Sires in the authorized population that are not born in the authorized country for which the Service User has permission to share the required genotype for GenoEx-PSE services.
   c. Dams of all known A.I. sires in the authorized population for which the Service User has permission to share the required genotype for GenoExPSE services.
   d. Known embryo transfer (ET) donors within the authorized population for which the Service User has permission to share the required genotype for GenoEx-PSE services.
   e. Known parents of animals born in the authorized country for which a genotype was downloaded/received from GenoEx-PSE for which the Service User has permission to share the required genotype for GenoEx-PSE services
   

4.2.4. Shall report to the authorized organization in the animal’s country of birth, any pedigree conflicts identified via GenoEx-PSE.

4.2.5. Follow ICAR rules and regulations related to the GenoEx-PSE services.

• Interbull maintains a GenoEx-PSE Code of Practice

4.2.6. SNP data accessed via GenoEx-PSE may not be forwarded, shared or exchanged with any third party organization.

4.2.7. Follow ICAR accreditation rules and policies.

• ICAR Guidelines for Parentage Verification and Parentage Discovery Based on SNP Genotypes are available on the ICARwebsite:

  • https://www.icar.org/index.php/certifications/dna-certifications/guidelines-for-str-and-snp-based-parentage-testing-in-cattle/

5. SNP Exchange

The main purpose of GenoEx-PSE is to provide a service for exchanging standardized sets of SNP for genotyped animals to facilitate and streamline parentage analysis.

The exchange of SNP genotypes required for parentage analysis allows for flexibility in terms of the number of SNP to be included.

The list of SNP to be exchanged within GenoEx-PSE may be updated from time to time:

• The minimum requirement for parentage verification shall be those recommended by ISAG.
• The ICAR DNA Working Group shall define and specify the SNP for parentage discovery for the imputation of microsatellite markers.
• The list of SNP will be defined in order to assist multiple breeds of dairy and beef cattle.

6. Current list and sets of SNP

In line with the “ICAR Accreditation of DNA Data Interpretation Centres’, GenoEx-PSE provides at this stage the opportunity for exchange of a standardized set of 554 SNP according to the following specification:

Group A: Parentage Verification

• 200 SNP recommended by ISAG for parentage verification
• Consists of 100 core SNP plus 100 extra SNP.
• see genoex.org for list of SNPs for Parentage Verification

Group B: Parentage Discovery

• The 200 SNP as in group A, pluss additional 354 SNP recommended by ISAG for parentage discovery
• see genoex.org for list of SNPs specific for Parentage Discovery

7. Data Exchange Formats

GenoEx-PSE Service Users will be required to follow specific data exchange file formats.

Two files for each upload and download will be required, named in a standard way and zipped together. Both files should be in csv format and comma delimited. The records in one file should always have corresponding record(s) in the other file.

7.1. File 702 – meta.csv :

The first file contains information related to the animals with a SNP genotype to be transferred. This file includes details on the Service User, Source Country, Animal ID, Lab, Sample ID and fields associated with the full genotype (i.e.: LD, MD, HD) from which the parentage SNP were taken.

Only 1 record is permitted and required per Animal ID.

7.2. File 704 – snps.csv:

The second file includes information related to the actual SNP genotypes for the animals in the first file, and includes details on Animal ID, SNP Name, Allele 1 and 2 results. Note that all SNP-names must be written in capital letters.

The SNP results can be provided in either AB or TOP format.

For detailed description of the formats and the values allowed for each field, see User's Manual for detailed file formats

7.3. GenoEx-PSE will “time stamp” all data transfers by each Service User.

Therefore:

7.3.1. uploads only need to involve new animals but may also include more complete SNP genotypes,

7.3.2. downloads may be either:

• all new genotypes for males and/or females one or more breeds and countries, or
• a selection of genotypes based on an animal request list.
• AB or TOP standard, independently of the standard the data was uploaded in.

8. Resolution of Data Conflicts

The GenoEx-PSE service includes a defined process for reporting data conflicts back to those organizations involved with the submission of any genotype involved with the conflict, and for addressing such conflicts.

This process for resolution of data conflicts may be updated in line with recommendations by the ICAR DNA Working Group as needed.

The Service User agrees to handle such data conflicts as stipulated in this Code of Practice.

The following describes the types of data conflicts that are currently considered:

8.1. Conflicts arising from different SNP and/or microsatellite data being submitted for the same animal:

In such cases, the data quality assurance measures recommended by the ICAR DNA Working Group will be used to resolve the conflicts, which may involve the Service Users that submitted the data involved with the conflict.

8.2. Conflicts arising when the SNP and/or microsatellite data is inconsistent with the reported information for the animal’s pedigree:

In general, the integrity of animal pedigree information lies in the hands of the authorized organization in the country of birth of the animal. In principle, all parentage conflicts, and parentage discovery results when available, should be communicated directly to the authorized organization (as referred to in the GenoEx-PSE Service Agreement and the list compiled by ICAR), in the animal’s country of birth by the organization that identified the parentage conflict. The resolution of such conflicts will remain the responsibility of the authorized organization in the animal’s country of birth and any modified pedigree information would subsequently flow to GenoEx-PSE, Interbull Centre and/or Interbeef services, if applicable.