Evaluating the interpretation ofEvaluating the interpretation of clinical molecular genetic

results

Outi Kämäräinen

Molecular genetic testing

• Examine changes in DNA sequence– Point mutations, deletions, duplications, insertions…

• Wide range of technologies used– One or combination used depending on application

Referrals and interpretation

• Rapidly evolving field• TAT long

Diagnostic testing Mutation scanning

P di ti t tiScreening for known

Predictive testing mutation

A priori / a posteri risk

Carrier testing?

?

A priori / a posteri risk • Affected / carrier• Risk calculations?

EMQN – network at a glance

• Network started in 1997• Accredited to ISO 17043• Over 900 member labs world wide 4367

• 28 disease specific EQA schemes• 2 technique specific EQA schemesq p

2000

1000

1500

0

500

1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010

Year

Participations 26 50 73 149 198 260 432 623 689 832 981 1427 1892 1715

EMQN schemes

• Diseases specific EQA schemes– 3 samples once a year – Assessment of analytical accuracy andAssessment of analytical accuracy and

interpretation of resultsLabs return results via website– Labs return results via website

Sample technical examination

Sample reception

GeneticTesting

Interpretation and reporting

reception

Report content -helpful for genetic

counseling ?

and reporting

Assessment of returns

• Assessment done by expert groupsP d ki it i– Pre agreed marking criteria– Standard scoring of 2

P i t h / ifi– Points are scheme / case specific– Yearly meeting to harmonise marking

Genotype

Interpretation of result

Report stylep y

Assessment of genotyping

• Scored out of 2 marks• Most data qualitative - genotype correct or not?

BRCA2: c 9117G>A p Pro3039Pro– BRCA2: c.9117G>A, p.Pro3039Pro

• Potential deductions– Correct nomenclature used?Correct nomenclature used?

• IVS2-13A/C.bp656• IVS2-13a>g• IVS2-13C>G• c 289 13C>G

• c.293-13C/A>G• c.290-13A/C>G• 655A/C>G• g656C>G

• g.659A/C>G• CYP21A2*9• I2Gnt656• c 97 13A C>G

– Quantitative data – error limits

• c.289-13C>G• c103-13A/C>G

• g656C>G• g.656a>g

• c.97-13A,C>G

Assessment of interpretation

• Scored out of 2 marks• Pre-agreed criteria of elements:

– Answer to clinical question– Answer to clinical question– References– Risk calculations...

Report style

• Comments rather than scores– Accuracy and consistency

Layout– Layout– Spelling errors– Methods referenced

• International guidelinesInternational guidelines– Local practice may differ

Example from Duchenne and Becker Muscular Dystrophy schemeMuscular Dystrophy scheme

• X-linked muscle wasting diseaseg– Deletions and duplications in dystrophin

(65% known mutations)(65% known mutations)– Severity of disease depends on mutation

Example of case

• Clinically diagnosed DMD patient. Genetic testing is t d f i t ti f f l l tirequested for carrier testing for female relatives.

Marking

• GENOTYPE:– Deletion of exons 64-67

(2.0 points)( p )

• INTERPRETATIONINTERPRETATION– The deletion found is out of frame – no functional

protein > confirms diagnosis (1.5 points)protein confirms diagnosis (1.5 points)

– Female relatives maybe carriers and have risk forFemale relatives maybe carriers and have risk for affected children – testing available (0.5 points)

Assessment and ISO17043

• Assessment against pre-agreed criteriag p g• Technical experts used for assessment

T i i– Training– Competency and confidentiality– Harmonisation

• between assessors• between schemes

Genotyping and interpretation scores from HD scheme

2

from HD scheme

1 851.9

1.95

1.751.8

1.85

1 61.651.7

1.551.6

997

998

999

000

001

002

003

004

005

006

007

008

199

199

199

200

200

200

200

200

200

200

200

200

Average genotyping (yellow) and interpretation (purple) scores for Huntington disease

Future directions

Free fetal DNA analysisfor aneuploidyfor aneuploidy

Next generation sequencingmulti-gene disorders

Pharmacogenetics

multi gene disorders

Pharmacogenetics / Molecular Pathology

Acknowledgements

Scheme participants and organisersand organisers

More information:• Website – www.emqn.orgq g

• EMQN OFFICE– support@emqn.org