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GenoEx-PSE

2018

Two DNA-based services were first announced during the ICAR and Interbull Meetings in Chile at the end of October 2016.

 

  • 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 are now provided by ICAR through the Interbull Centre. This page provides information about GenoEx-PSE.

Please visit the ICAR website for more information about Accreditation of DNA Data Interpretation Centres.

 

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 were envisioned for this exchange service, among which only the first (Group A) is currently available. The groups are as follows:

 

            Group A:  200 SNP recommended by ISAG for parentage verification

            Group B:  354 SNP in addition to Group A to be used for parentage 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 requires first completing ICAR Accreditation for DNA Data Interpretation Centres from Service-ICAR for the appropriate level of parentage analysis service it wishes to provide, which, right now, includes only SNP-based parentage verification. Depending on the level of ICAR accreditation obtained, the GenoEx-PSE service user would be able to upload and download the group of SNP as outlined above but the service user may also decide in the future to exchange the additional SNPs (Group B or C) for parentage discovery and/or microsatellite imputation in order to develop the service to impute microsatellite SNP profiles for parentage verification.

 

Table 1 provides the number of SNP within each group by chromosome. The complete list of SNP include in each group is available on GenoEx.org

 

Table 1: Count of SNP by Chromosome for GenoEx-PSE Service

 

Chromosome

Group A Verification

Group B Discovery

Group C

MS Imputation

 

Total

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

29

11

9

8

9

9

8

11

6

6

9

10

5

6

5

7

5

9

7

8

5

8

7

4

4

4

4

6

6

4

40

42

32

4

33

2

26

31

3

2

27

3

30

1

3

1

2

2

27

5

25

1

2

2

2

2

1

1

2

70

80

110

 

90

 

110

 

40

80

 

40

80

120

80

 

80

121

131

150

13

132

10

37

37

119

11

37

8

36

6

50

86

11

49

115

130

113

8

86

6

6

6

7

7

6

Total

200

354

980

1,534

 
 

 

The list of SNP included in Groups A, B and C have been discussed and recommended by the GenoEx-PSE Expert Group, reporting 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 also recommended file formats for the uploading and downloading of data into the GenoEx-PSE database, which is maintained by the Interbull Centre.

 

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, 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”) is 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 documents which contain information on specific scientific, technical and legal issues and which are made available to (potential) users of these new services:

 

1) ICAR Accreditation of DNA Data Interpretation Centres

 

2) GenoEx-PSE

 

 

 

 

 

 

Useful deadlines
2018-08-20
Useful deadlines for the September 2018 test run Read more...

Official Launch of GenoEx-PSE June 1, 2018
2018-06-01
Information about the launch of GenoEx-PSE, June 1 2018 Read more...

Information about GDPR
2018-05-25
Information about SLU and the new European GDPR Read more...

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

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