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 Launch of two new DNA-based services

by ICAR and Interbull Centre

 October 2016

During the ICAR and Interbull Meetings in Chile at the end of October 2016, two new services will be presented and discussed for an official launch by January 2017:

 

  • Parentage SNP Exchange (“GenoEx-PSE”) – a service for exchanging standardized sets of SNP for genotyped animals to facilitate parentage analysis activities.
  • A service for Accreditation of DNA Data Interpretation Centres.

 

Both services will be provided by ICAR through the Interbull Centre.

 

This page provides information about both services.

 

The main purpose of GenoEx-PSE is to provide a service for exchanging standardized sets of SNP for genotyped animals to facilitate parentage analysis activities carried out by authorized service users of the GenoEx-PSE service.  Three sets of SNP are envisioned for this exchange service, which have been defined as follows:

 

          Group A:       200 SNP recommended by ISAG for parentage verification

          Group B:       675 SNP in addition to Group A to be used for parentage verification and/or discovery

          Group C:       980 SNP, different from those in Groups A or B, to be used for the imputation of microsatellite SNP profiles for parentage verification

 

Each authorized service user for GenoEx-PSE will be required to achieve Parentage Analysis accreditation from Service-ICAR for the appropriate level of parentage analysis service it wishes to provide, which, for the immediate future, include either (a) only SNP-based parentage verification, or (b) SNP-based parentage verification and discovery.  Depending on the level of ICAR accreditation obtained, the GenoEx-PSE service user would upload and download the appropriate groups of SNP as outlined above but the service user may also decide to exchange the additional SNP (Group C) for microsatellite imputation in order to develop the service to impute microsatellite SNP profiles for parentage verification.

 

 

 

 

Included SNP and Exchange File Formats

Table 1 provides the number of SNP within each group by chromosome.

 

For a complete list of the SNP included in each group, an Excel file is available from the ICAR and Interbull websites.

 

 

 

 

The list of SNP included in Groups A, B and C have been discussed and recommended by the GenoEx-PSE Expert Group, which currently reports to the GenoEx-PSE Implementation Task Force, both of which were appointed by ICAR.  In addition to defining the list of SNPs to be initially included in the GenoEx-PSE service, the Expert Group has also recommended file formats for the uploading and downloading of data into the GenoEx-PSE database to be established and maintained by the Interbull Centre.  A document entitled "GenoEx-PSE File Exchange Formats" describes the Expert Group recommendations, and is available for download from the ICAR and Interbull websites.

 

Implementation and Documentation

The proposal to develop an International Genotype Exchange Platform “GenoEx” was originally presented during the Interbull Meeting in May 2014, in Berlin, Germany[1], with a view to establish an infrastructure able to support and develop international cooperation based on SNP data. The GenoEx infrastructure has since been developed at the Interbull Centre, with financial support from Interbull, SLU and ICAR. Parentage SNP Exchange (“GenoEx-PSE”) will be the first service provided through this platform.

 

The implementation of both GenoEx-PSE and Accreditation of DNA Data Interpretation Centres has taken place under the guidance of the ICAR-appointed GenoEx-PSE Implementation Task Force, responsible for developing GenoEx-PSE policies and business rules, and the GenoEx-PSE Expert Group, addressing specific scientific and technical issues for both GenoEx-PSE and the Accreditation of DNA Data Interpretation Centres, and resulting in the following documents which contain information on specific scientific, technical and legal issues and which are made available to (potential) users of these new services:

 

1)      GenoEx-PSE SNP Groups and Evolution

2)      GenoEx-PSE SNP list details.xls

3)      GenoEx-PSE File Formats

4)      GenoEx-PSE Service Agreement - DRAFT Version October 2016

5)      ICAR Accreditation of DNA Interpretation Centres

6)      Annex V Application Form for ICAR Accreditation of DNA Centres

 

Download all above pdf documents related to this ICAR-Interbull Centre GenoEx-PSE Communication by clicking here

 

 

Further details of both proposed new DNA-based services will be provided during the upcoming Interbull Business Meetings and ICAR plenary session in Puerto Varas, Chile, in late October 2016.

 

 

Sincerely,

Toine Roozen                                                Martin Burke

Interbull Centre Director                                ICAR Chief Executive

Toine.Roozen @ slu.se                                    Martin @ ICAR.org



[1] Dürr, J., Jorjani, H., Reents, R. 2014. International Genotype Exchange Platform (GENOEX). Proc. ICAR/Interbull Conference, Berlin, Germany, May 19-23, 2014. 10 p.

 

Interbull Centre - Department of Animal Breeding and Genetics, SLU - Box 7023, S-75007 Uppsala, Sweden - interbull@slu.se

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