1. Ensuring high quality genomic testing
Dr Katrina Rack
GenQA, John Radcliffe Hospital, Oxford

2. GenQA Self funding, not for profit organisation
External Quality Assessment scheme
Self funding, not for profit organisation
ISO accredited EQA schemes
Member of the UK NEQAS consortium
Participants worldwide

3. What is EQA
Process that assesses laboratories analytical and interpretive skills compared to other laboratories by testing the accuracy and quality of their results.

4. External verification of quality of service Improve quality of care
Aim Educational
External verification of quality of service
Improve quality of care
Not
To judge centres 4 4

5. Why EQA is important Ensure quality across national borders
Harmonise the quality of genetic diagnostic services
Ensure quality across national borders
Establish continuous quality improvement
Helps centres to stay up-to-date
Identifies imperfect practice and improves quality
Patient safety 5 5

6. Principles of EQA
Same samples/data set sent to all participating laboratories
Samples either ‘real’ or mimic real cases
Independent validation using range of methods
Assessed for - genotyping/analytical accuracy
- interpretation of the result
- clerical accuracy of the report
Continual performance monitoring
Provides feedback on any potential issues

7. From 1st January 2018 78 Hosted by NHS Lothian
within Laboratory Medicine, Royal Infirmary, Edinburgh 78
Hosted by OUH NHS Foundation Trust
in Women’s Centre, John Radcliffe Hospital,
Oxford

8. Why the new partnership
Historically the 2 schemes provided either cytogenetic or molecular genetic EQAs.
Progressively new technologies replacing traditional techniques
Traditional cytogenetic/molecular genetic boundaries have disappeared in laboratories
EQA providers needed to respond to this change.
Development of joint EQAs

9. GenQA - Aim Join forces to offer a comprehensive genetic EQA Scheme
EQA to assess laboratories analytical and interpretation skills
Tool for Individual training and competency assessment
Educational EQAs

10. End to end testing

11. Benefits for Participants
Single access point to website to streamline EQA management
Access to more EQA schemes through one provider
Reduced costs
Assurance of delivery of high quality EQAs through UK NEQAS Consortium membership

12. Benefits for GenQA
Aids development of EQAs that are open to different technologies
Draw on expertise of both EQA schemes and have access to a large number of expert advisors (approximately 200)
Reduce website development costs
Long term stability to enable developments and meet needs of participants

13. Offers 78 EQAs for genetic/genomic testing More EQAs planned for 2019

14. Offers 74 EQAs for genetic testing
Institution competency
Offers 74 EQAs for genetic testing
Reflect analytical and interpretation processes
Reflect training policies
Individual competency
Offers 4 Educational EQAs for Clinical Genetics
Offers – a training and competency tool for laboratory staff 14 14

15. Tumour Assessment Training/ Competency Clinical Genetics Educational
Newborn screening
Pre-implantation Genetic Testing
DNA extraction and quality measurement
Haematology
Next Generation Sequencing
Rapid Prenatal testing/screening inc. NIPT/D
Molecular Genetics core diseases
Constitutional - postnatal
Molecular Pathology
Constitutional - prenatal
Tumour Assessment
Training/
Competency
Clinical Genetics
Educational

16. Types of EQA
Sample
Distribution of samples for analysis (DNA, amplified DNA, fixed cells, FFPE slides)
Online datasets
Analysis of G-band and FISH images online
Serial EQA for Clinical Genetics
Educational case scenarios

17. Types of EQA Analytical and interpretation Interpretation only
Analytical only
Analytical and interpretation
Interpretation only
Variety of EQA types required as they assess different parts of the testing process

18. EQA Techniques assessed
Chromosome banding analysis
FISH
QF-PCR
MLPA
Arrays/NGS
Gene mutation analysis - single genes/gene panels/NGS
RT-PCR for cancer fusion genes

19. How are EQAs run Each EQA marked by a group of assessors
Experienced clinical scientists, clinicians or pathologists with necessary competency in relevant genetic testing field
>200 Assessors from 18 countries
Agreed Marking and Performance Criteria
Two EQA performance designations:
Satisfactory
Poor

20. Tumour Assessment Training/ Competency Clinical Genetics Educational
Newborn screening
Pre-implantation Genetic Testing
DNA extraction and quality measurement
Haematology
Next Generation Sequencing
Rapid Prenatal testing/screening inc. NIPT/D
Molecular Genetics core diseases
Constitutional - postnatal
Molecular Pathology
Constitutional - prenatal
Tumour Assessment
Training/
Competency
Clinical Genetics
Educational

21. Going forward, What’s planned?
Continuation of existing schemes
Develop new EQAs and evolve existing EQAs, where appropriate, to respond to genetic service requirements
Diversify into individual-based assessments e.g. G-TACT and Tissue-i
Extend repertoire of educational EQAs
Increased staffing means that we will be able to provide a better service

22. Going forward, What’s planned?
Continuation of existing schemes
Develop new EQAs and evolve existing EQAs, where appropriate, to respond to genetic service requirements
Diversify into individual-based assessments e.g. G-TACT and Tissue-i
Extend repertoire of educational EQAs
Increased staffing means that we will be able to provide a better service

23. National test directory - need for new EQAs Principles of the National Genomic Testing Strategy
Creation of a national network of genomic laboratories to ensure equity and consistent availability of testing
All genetic and genomic testing for cancer and constitutional set out and specified in a single national test directory – mandated in standard NHS contract
Outlines the appropriate genetic tests for different indications
Directory specifies technology, targets, scope, indication with any qualifiers with aim/utility of testing – most cancer is for large panels
Peer reviewed and updated annually to keep up with technological advance – expect scope of WGS to extend

24. National Genomic Testing Directory
Clinical Indication
Setting
Test Scope
Target/Gene
Technology
Non-squamous
non-small cell lung cancer
Prognostic/
Predictive
Small variant detection
EGFR
Small panel
Opportunity to scope, develop and implement future EQAs

25. Going forward, What’s new?
Continuation of existing schemes
Develop new EQAs and evolve existing EQAs, where appropriate, to respond to genetic service requirements
Diversify into individual-based assessments e.g. G-TACT and Tissue-i
Extend repertoire of educational EQAs

26. Individual training assessment and competency tool
Genomics Training Assessment & Competency Tool

27. ISO 15189:2012

28. G-TACT virtual laboratory
GenQA website access
Individual participation
Comprises different modules
Task scenarios randomly generated
Automated assessment
Complete at your own pace (12 mths)
Sample Reception
Duty Scientist
Tumour content assessment
Test data analysis
Sequence variant interpretation
Report authorisation
Sample Reception
Duty Scientist
Tumour content assessment
Test data analysis
Sequence variant interpretation
Report authorisation
Sample Reception
Duty Scientist
Tumour content assessment
Test data analysis
Sequence variant interpretation
Report authorisation

29. Process of variant classification 
In development
In development
In development
Chromosome analysis
CNV classification  
Trial mode  
Process of variant classification
BRCA variant classification in
ovarian cancer
Including CNVs

30. How is it assessed? Performance not monitored by GenQA
Monitored by Institution
Automatic responses can be over ridden by Institution
Training and performance reviews

31. Going forward, What’s planned?
Continuation of existing schemes
Develop new EQAs and evolve existing EQAs, where appropriate, to respond to genetic service requirements
Diversify into individual-based assessments e.g. G- TACT and Tissue-i
Extend repertoire of educational EQAs

32. Clinical genetics
Currently running 4 educational EQAs for Clinical Genetics
Cardio genetics
Dysmorphology
Monogenic disorders
Oncogenetics
Comprised of case scenarios based on sequential consultations including
Family history
Test requests and test results
Counselling
EQA for genetic counsellors planned for 2019

33. Laboratories Acknowledgements GenQA Staff Assessors SAG members
____________________________________________________________________________________________________________
Acknowledgements
GenQA Staff
Assessors
SAG members
but most of all the
Laboratories