Guidelines to laboratories to grant the accreditation for SNPs and STRs based parentage testing in cattle
Considered the need for defined high quality standards in bovine parentage testing due to the relevant impact that wrong parentage may have in the estimation of genetic indexes and in national and international genetic evaluations and based on the two year work of the genetic analysis task force, ICAR has decided to define minimum requirements for laboratories running DNA analyses for breeding purposes. Guidelines for accreditation are presently given for parentage testing in cattle based on microsatellite analyses and SNP-based analysis. Minimum requirements for additional species and DNA tests will be defined in the near future.
Laboratories requesting microsatellite- and/or SNP-based accreditation will have to apply by downloading and filling out the appropriate forms (Annex II for microsatellites; Annex V for SNPs) on the ICAR website. The forms must be filled out accurately and completely, providing necessary documentation as required. The application will be evaluated by a panel of Experts appointed by ICAR that will either approve it, request additional information, or reject it. In case of rejection, the applicant may submit a new form at least one year after her/his failed application.
For both the above accreditations, applicants have to provide the ISAG membership number, issued at the time of the submission. Certification can be provided in any language if a translation into English is attached to the original documents.
Accreditation will be given for a two-year period, at the end of which a new application is to be completed and submitted after participation in additional ISAG comparison tests.
Rules for microsatellite and SNP-based testing parentage verification for cattle
- The file containing the rules for microsatellite-based testing parentage verification for cattle is available here
- The file containing the rules for SNP-based testing parentage verification for cattle is available here
Accreditation for the microsatellite-based parentage testing in cattle
For the laboratory accreditation for the microsatellite-based parentage testing in cattle, the following documents have to be considered:
- Annex I – The file contains he application form for laboratories using microsatellites for the parentage verification
- Annex II – The file contains the list of recommended ISAG microsatellite markers to be considered in the accreditation
Accreditation for the SNP-based parentage testing in cattle
For the laboratory accreditation for the SNPs-based parentage testing in cattle, the following documents have to be considered:
- Annex III – The file contains the application form for laboratories using SNPs for the parentage verification
- Annex IV – The file contains the list of recommended SNPs markers to be considered in the accreditation
Already accredited laboratories
For the renewal of an already accredited laboratory, please complete the Annex VII
Minimum requirements for accreditation of Microsatellite based and SNP-based parentage testing in cattle
The present Rules contain Minimum requirements for accreditation of Microsatellite based and SNP-based parentage testing in cattle.
1 – LABORATORY IDENTIFICATION
The applicant should be unambiguously identified:
- Name of the laboratory.
- Institution if relevant.
- Address and Country.
- A reference person as well as all information necessary for quickly getting in touch with her/him is to be given.
2 – EDUCATION AND TRAINING OF LAB SUPERVISOR AND OPERATORS
The minimum requirements for education and training of laboratory supervisor and operators are:
- At least a bachelor degree in a scientific discipline is required to the laboratory head or supervisor.
- At least 5 years experience in molecular diagnostics is required to the laboratory senior operator.
Experience is considered a key factor both in data production and in the interpretation of results.
3 – EQUIPMENT
- Equipment used to run and score microsatellite is to be described.
- The year of purchase and last revision is to be made available, to check the appropriateness of technologies used and the following of a proper maintenance program ensuring the production of high quality data.
- Yearly revision is considered as a minimum requirement.
- A personal opinion on the performance of the laboratory set up available is asked to foresee the need for improvements in quality standards.
4 – CERTIFICATION
- International or national certification should be declared.
- International certification will become a minimum requirement for ICAR accreditation within 3 years after the approval of these Rules.
5 – PARTICIPATION AND PERFORMANCE IN RING TEST
- The participation to international and national ring test is to be declared and the performance in these ring tests disclosed.
- The participation in at least two international ring tests is considered a minimum requirement.
The Committee of Experts, considering the structure of the ring test and the average performance of laboratories in the ring test and year, will decide performance thresholds.
6 – MICROSATELLITE MARKERS
- Name of all microsatellites typed on all animals (marker set I) and of the additional ones assayed in the case of unresolved parentage (marker set II) is to be declared, as well as the number of animals typed in the last two years.
- Minimum requirement is the use on all animals typed of the complete set of 9 micorsatellites recommended by ISAG (see Annex III).
- The upgrade of the number of markers assayed on all animals to a minimum of 11 is envisaged in the short period, with the perspective of increasing this minimum requirement to the use of 16 microsatellites.
- d) To ensure sufficient experience within the lab, a number of 500 animals analysed per year is set as minimum requirement for certification.
- Exclusion probability (2 parents and 1 parent) of each and every marker and of complete marker sets is to be calculated and declared.
- The type of population and the number of animals used for computations are to be described. ICAR recommends using Holstein as reference when possible. The ICAR Committee of Experts will evaluate that an appropriate PE is reached for accreditation, on the basis of the population analyzed.
7 – SNP MARKERS
- The name of all SNPs typed on all animals (marker set I) and of the additional markers assayed in the case of unresolved parentage (marker set II) must be declared, as well as the number of animals typed in at least the last two years.
- It is a minimum requirement to use at least 95 SNPs from the set recommended by ISAG (see Annex VI) on all animals typed.
- To ensure sufficient experience within the lab, genotyping 500 animals per year is set as a minimum requirement for accreditation.
- Exclusion probability (PE; 2 parents and 1 parent) of the complete marker sets used must be calculated and declared. The type of population and the number of animals (minimum 150) used for computations are to be described. ICAR recommends using Holstein as a reference group when possible. The ICAR Committee of Experts will evaluate that an appropriate PE is reached for accreditation, on the basis of the population analyzed.
8 – MARKER NOMENCLATURE
For Microsatellite Parentage
- Nomenclature of markers and SNP has to be described.
- Minimum requirement is the use of ISAG nomenclature at least for the ISAG marker set.
For SNP-based Parentage
- Nomenclature of markers must be described.
- ISAG nomenclature is required for the ISAG SNP marker set