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Guidelines for laboratories seeking certification for SNP-based genotyping and STR microsatellite-based parentage testing in cattle

In recent years, genomics has greatly increased its range of applications and its results are now a regular part of the evaluation process of the performances of farm animals.

The need of getting reliable high-quality standards in bovine parentage testing is negatively affected by wrong parentage analysis, producing a negative impact on the estimation of genetic indexes and adversely affecting national and international genetic evaluations.

Following these considerations and for supporting its member organisations, ICAR decided to define minimum requirements for organisations running DNA analyses for breeding purposes in cattle. Guidelines for certification are presently given for parentage testing in cattle based on microsatellite analyses as well as SNP-based genotyping by laboratories and SNP-based parentage analysis by DNA Data Interpretation Centres.

Laboratories requesting microsatellite- and/or SNP-based certificationwill have to apply by downloading from the ICAR website the necessary forms below listed, filling them out and emailing them to DNA@icar.org 

The latest version of the forms must be filled out accurately and completely, providing necessary documentation as required. The application will be evaluated by experts appointed by ICAR that will either approve it, request additional information, or reject it. In case of rejection for some services, the applicant may submit a new form and pay the associated fees.

For the above laboratory certifications, applicants have to provide the ISAG membership number, and the Certificate of Participation issued at the most recent round of Cattle SNP and Cattle microsatellite (STR) comparison tests organised by ISAG. Certifications can be provided in any language if a translation into English (even an in-house translation) is attached to the original documents.

Certification will be given for a two-year period, at the end of which a new application is to be completed and submitted.

Rules for STR microsatellite-based certification and SNP-based genotyping certification in cattle

The “Rules for STR microsatellite-based certification and SNP-based genotyping certification in cattle containing the rules and the guidelines for STR microsatellite-based parentage verification in cattle” are available below in this page

  • The file containing the rules and the guidelines for SNP-based genotyping required for parentage analysis in cattle is available here
  • The file containing the rules and the guidelines for SNP-based parentage analysis as a DNA Data Interpretation Centre in cattle is available here
  • The list of recommended SNP to be considered in the SNP-based certification for genotyping and parentage analysis is available here
  • The list of recommended ISAG microsatellite markers to be considered in the certification is available here

Form for STR microsatellite-based parentage testing in cattle

For the laboratory certification for STR microsatellite-based parentage testing in cattle, the following application form has to be considered:

Form for SNP-based genotyping required for parentage analysis in cattle

For the laboratory certification for SNP-based genotyping in cattle that is required for parentage analysis, the following application form is required :

Previously certified laboratories

For the renewal of an already certified laboratory, please complete the specific form available here

Check list of the documents to be submitted for the application

  1. Application form for STR microsatellite-based and/or application form for the SNP-based genotyping certification (or the simplified form for the renewal of a previously certified laboratory)
  2. ISAG Certificate for SNP
  3. ISAG Certificate for STR
  4. For SNP-based genotyping and/or STR microsatellite-based certification, the ISO17025 Certificate of accreditation in original form and
    1. its translation into English (an in-house translation is also accepted)
    2. Scope of the ISO17025 Certificate of accreditation in original and its translation into English (an in-house translation is also accepted)

PARTICIPATORY FEE

The participatory fee is organised on ICAR Member/Non ICAR Member criteria and summarised in the below tables:

Class of application Euros
ICAR Member Laboratory (Full or Associate) 390€
Non-ICAR Member Laboratory 1,300€
Priority submission (i.e.: application out of schedule) 1,700€

Flat fee covers both STR and/or SNP certification and in case a laboratory is interested in becoming an ICAR Member the instructions and the form for the submission are available here

NOTE

  1. Please be aware that for ICAR certification to be granted to laboratories carrying out STR microsatellite-based parentage testing or SNP-based genotyping, ISO17025 accreditation is a mandatory minimum requirement as per the ICAR Guidelines.
  2. Please also be aware that for ICAR certification of SNP-based Parentage Verification or Discovery, the ICAR Parentage Analysis certification for DNA Data Interpretation Centres must be requested.

Minimum requirements for certification of STR Microsatellite-based parentage testing and SNP-based genotyping in cattle

The present rules contain minimum requirements for certification of STR Microsatellite-based parentage testing and SNP-based genotyping in cattle.

1 – LABORATORY IDENTIFICATION

The applicant should be unambiguously identified by:

  1. Name of the laboratory.
  2. Institution if relevant.
  3. Address and Country.
  4. 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:

  1. At least a bachelor’s degree in a scientific discipline is required to the laboratory head or supervisor.
  2. 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

  1. Equipment used to run and score microsatellite is to be described.
  2. 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.
  3. Yearly revision is considered as a minimum requirement.
  4. 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

  1. International or national certification should be declared.
  2. Effective 2022, international certification meeting ISO17025 standards will be a minimum requirement for both of these types of ICAR certification for laboratories.

5 – PARTICIPATION AND PERFORMANCE IN RING TEST

  1. The participation to international and national ring test is to be declared and the performance in these ring tests disclosed.
  2. 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

  1. 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.
  2. Minimum requirement is to use the complete set of 12 microsatellites recommended by ISAG (see Annex III) on all animals typed
  3. To ensure sufficient experience within the lab, a number of 500 animals analysed per year is set as minimum requirement for certification.
  4. Exclusion probability (2 parents and 1 parent) of each and every marker and of complete marker sets is to be calculated and declared.
  5. 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 certification, on the basis of the population analyzed.

7 – SNP MARKERS

  1. The name of all SNP genotyped on all animals and of the additional markers assayed in the case of unresolved parentage must be declared, as well as the number of animals genotyped in at least the last two years.
  2. It is a minimum requirement to use at least 200 SNP from the set recommended by ISAG (here) on all animals typed.
  3. To ensure sufficient experience within the lab, genotyping 500 animals per year is set as a minimum requirement for certification.

8 – MARKER NOMENCLATURE

For STR Microsatellite-based Parentage Testing

  1. Nomenclature of markers and SNP has to be described.
  2. Minimum requirement is the use of ISAG nomenclature at least for the ISAG marker set.

For SNP-based Genotyping required for Parentage Verification

  1. Nomenclature of markers must be described.
  2. ISAG nomenclature is required for the ISAG SNP marker
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