ECA 2019 Participants meeting - GenQA · 2019-07-12 · Chromosome breakage scheme ... MRA –mosaic trisomy 13 - not realising it could be CPM. Blood ... 1 Delayed puberty, short

Collaboration between CEQAS and UK NEQAS for Molecular Genetics

Member of consortium

Participants Meeting 2019

Oxford University Hospitals

NHS Foundation Trust NHS Lothian, Edinburgh

Agenda

1. Welcome

2. Overview of GenQA

3. GenQA Updates

4. Is there evidence of fading competency of cytogenetics from EQA?

5. Spring EQA results

6. Questions and answer session

7. A.O.B




Overview of GenQA

Ros HastingsGenQA

94

68 Countries

94

68 Countries

79 Countries

2019

Delivering 94 EQAs across 14 specialities

Molecular Genetics

core diseasesHaematology

Newbornscreening

Pre-implantation

Genetic Testing

Non-invasive prenatal testing

Molecular Rapid

Aneuploidy testing

DNA extraction and quality

measurement

Next Generation Sequencing

Molecular Pathology

Constitutional - prenatal

Constitutional -postnatal

Tumour

Assessment

Training/

CompetencyClinical

Genetics

Educational

EQAs

Complete genomic testing pathway

Ensuring quality from end to end

End to End testing

DNA extraction

DNA quality

DNA quantity

Genotyping accuracyInterpretation Reporting

Sample

collectionConsultation

Pre-test referral

Pre-test

consultation/

Referral

Sample Analysis Interpretation Reporting ConsultationMDT

Karyotyping FISH Array BoBs MLPA QF-PCR

Sens/spec

+ + + + + +TAT

- ± - + + +Workload

- - - ± ± +Automation

- - ± ± ± ±Reagent

costs + + - + + +Partial

+ - + ± ± ±Mosaicism

+ + + 30% ± +

Advantages and disadvantages of techniques

GenQA

➢ ISO 17043 Accredited EQAs

➢ Operated from Oxford & Edinburgh

➢ Part of the Consortium

➢ Not-for-profit organisation

➢ Offers 90 EQAs for genetic laboratory testing

➢ Offers 4 Educational EQAs for Clinical Genetics

Format of EQAs

➢ Images/DNA/fixed cells/FFPE sent to laboratories

➢ Technique used not prescriptive

➢ Referral information based on real patient referrals

➢ Submit reports including results & interpretation online

➢ Individual Laboratory Report (ILR)

➢ EQA Summary Report

- Feedback from assessors

- Recommendations

➢ Appeals

➢ Final EQA Summary report

➢ Review of findings by laboratory

Education / Internal review / Quality Improvement

MRA participation 2004-2019

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2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019

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2009

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2008: CPA accredited Scheme

2012: UKAS ISO17043 accredited EQAs

2004-2006: Pilot EQAs

MRA Techniques used 2004 - 2018

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2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018

BoBs

MLPA

QF-PCR

Marking EQAs

Stages split into 3 categories

✓Analysis/Genotyping

✓ Interpretation

✓Clerical accuracy

Agreed marking criteria and the assigned deductions

The total score for each category is 2.0 points

❖ Errors or omissions incur deductions e.g. 0, -0.5, -1.0 or -2.0.

❖ Genetic experts review the marking criteria.

❖ Essential answers incur deductions if omitted.

❖ Recommended answers either a minor deduction or comment




GenQA updates

Ros HastingsGenQA

➢Chromosome breakage scheme – Full EQA in 2019

Online – plus sample if available in 2020

➢G-TACT extension of modules to include CNVs and ISCN

➢GenQA Scheme Director – Dr Sandi Deans

➢GenQA Consultant (part-time) – Ros Hastings

➢New staff – Mark Sales, Fiona Morgan, Becky Treacy, Gillian Holland

New pilot s

➢ 2020 TP53 mutation analysis and IGHV mutation status in CLL

➢ New pilot - Disorders of sexual development (DSD) this Autumn

➢ Sex chimerism

Accreditation – ISO17043 – extension to scope

➢PGT-A, PGT-SR, PGT-PB, Sarcoma, Lymphoma

GenQA updates




Evidence of fading competence from

EQA?

Ros HastingsGenQA

Fading competence?➢Etiology/Mechanisms of formation not understood

➢Segregation patterns

➢Errors in analysis (blood and haematology)

➢Blood – 46,X,i(Y)(p10)[17]/45,X[13]

➢Blood – der(15)t(3;15)(q29;q11.1) classifying as the wrong centromere for the ‘der’ chromosome and not understanding the inheritance pattern segregation

➢Myeloid – Missing a recurrent translocation

➢POC – Mother has a balanced t(4;17)(q31;q24) . Fetus male but evidence of maternal cell contamination (MCC).

➢PGT – demonstrating interpretation of abnormal profiles relating to parental karyotypes

➢MRA – mosaic trisomy 13 - not realising it could be CPM

Blood➢Blood - 46,X,i(Y)(p10)[17]/45,X[13].ish i(Y)(SRY++)

46,XY - i(Y)(p10) not identified – classic abnormality

Different patient management if i(Y)(p10) identified

46,X,i(Y)(p10)[17]/45,X[13].ish i(Y)(SRY++)

Blood - 2➢Blood – Mother a carrier of a 46,XX,t(3;15)(q29;q11.1).

Array shows gain of 3q29 in child. Karyotype 47,XY,+der(15)t(3;15)(q29;q11.1)

der(3)t(3;15)(q29;q11.1) is a different product and not viable

given the wrong centromere for the ‘der’ chromosome.

not understood the inheritance segregation pattern of the maternal balanced t(3;15)

Myeloid➢Myeloid – 48,XX,+8,t(9;11)(p21;q23),+14[15]

47,XX,t(9;11)(p21;q23),+14[15]

- +8 missed

48,XX,+8,+14[15].nuc ish(KMT2Ax2)(5’KMT2A sep 3’KMT2Ax1)[100]

- t(9;11) missed

Recurrent translocations should be known – check text books or French Atlas of Haematology for images

48,XX,+8,t(9;11)(p21;q23),+14

FISH : KMT2A rearranged

POC➢POC – Mother has a balanced, 46,XX,t(4;17)(q31;q24) translocation.

Fetus - 46,XY and 46,XX,t(4;17)(q31;q24) metaphases

Likely evidence of maternal cell contamination (MCC) – QF-PCR would confirm.

mos 46,XX,t(4;17)(q31;q24)[4]/46,XY[6]

Did not suspect MCC. ‘mos’ incorrectly given.

MCC is not reported in ISCN but maybe put in the report text.

Fetus – 46,XY

➢PGT – not demonstrating interpretation of abnormal profiles relating to parental karyotypes

Mother carrier of an inv(21), 46,XX,inv(21)(p13q22.12)

11MB loss of chromosome 21q22.12q22.3 not interpreted as a recombinant (21)

PGT

MRA EQASome centres did not recognise or interpret the profiles correctly for:

→ Mosaicism

→ CPM

→ MCC

2018 MRA EQA

Mosaic trisomy 13 in CVS [60% trisomy 13]. No ultrasound anomalies.

21/110 centres did not recognise the sample was mosaic

19/110 centres did not consider this could be CPM and the fetus could

be normal for chromosome 13

Hence a workshop was arranged at the ESHG 2019 for participants to:

¤ recognise the different abnormal profiles for mosaics, CPM and MCC

¤ understand the underlying mechanism of post-zygotic non-disjunction and

post-zygotic meiotic correction or trisomy rescue

¤ facilitate the interpretation of the abnormal results

¤ request the appropriate follow up samples.

Embryological Origins

Gardner & Sutherland 3rd Edition 2004

26

27

CPM

How can GenQA help address any potential fading competency?

➢Aim of EQA is to educational

➢GenQA is developing an individual training and competency tool – please sign up to use it

To include representative images of most recurrent, or types, of chromosome abnormalities found in:-

▪ Haematological neoplasms

▪ Chromosome sex disorders

▪ Infertility

▪ Also normal variants

➢ Workshops e.g. MRA workshop at ESHG




Training and Competency Modules for

CNVs

G-TACTRos Hastings

GenQA

Genomics Training Assessment & Competency ToolVariant classification module

Variant Assessment Module

➢ List of variants provided

➢ Clinical details available

➢ Enter evidence and

classify variant

BRCA1/BRCA2 variant classification EQA run 1

BRCA1/BRCA2 variant classification EQA run 1

Change in clinical management/treatment options

Treatment

given

Classification affects patient management

New G-TACT modules in development for

cytogenomics

• Chromosome banding analysis – beginners

Metaphase and Karyotype available for analysis

Correct? Yes or No – provide reasons

• Chromosome banding analysis - haematology

Metaphase and Karyotype available for analysis

Normal? Yes or no

Provide ISCN

• CNV analysis – Prenatal and post natal

Format similar to previous online survey

Clinical details

CNV provided with genomic co-ordinates

Inheritance pattern if appropriate

Classification variant, classification given clinical information and supporting documentation

• ISCN

Examples Correct? Yes or No




Spring EQA results

Katrina Rack & Mark SalesGenQA

Myeloid G-band

1 AML 48,XX,+8,t(9;11)(p21.3;q23.3),+14[10]

KMT2A rearrangement detected

BCR-ABL rearrangement NOT detected

RARA gene rearrangement NOT detected

2 AML 45,XX,-7[10]

B&T G-band

1 Increased WBC - CLL 46,XX[20]

Deletion of 13q14 detected (D13S319/DLEU)

No deletion of MYB, ATM or TP53 or trisomy 12 detected

2 Enlarged lymph nodes.

Night sweats and Fatigue -

Lymphoma

46,XX,del(10)(q23q25),t(14;18)(q32;q21)[6]/46,XX[7].

Presence of an IGH-BCL2 gene rearrangement

No evidence of a BCL6 gene or MYC gene

rearrangement

B&T FISH

1 New diagnosis of CLL No deletion of ATM or TP53 or 13q14 detected or

evidence of trisomy 12

2 Known chronic lymphocytic leukaemia (CLL).

Disease progressing – treatment now

required.

Deletion of ATM.

No deletion of TP53 or 13q14 detected or evidence of

trisomy 12

Lymphoma

1 High grade large cell lymphoma, the

differential diagnosis includes Burkitt

lymphoma. Urgent FISH testing required for

definitive diagnosis and classification

MYC/IGH no rearrangement, 3 copies MYC

MYC rearranged

IGH-BCL2 not rearranged

BCL2 and BCL6 not rearranged

2 Extra-nodal marginal zone lymphoma

–prognostic testing required.

MALT1 rearranged

BCL2 not rearranged

Acquired array

1 New diagnosis of MDS Trisomy 14

Loss of homozygosity in 7q35q36.3 (20 Mb)

2 CLL Bi-allelic 13q deletion

5Mb 13q14.2 q14.3 deletion

1.2Mb 13q 14.2q14.3 deletion (homozygous region)

Amniotic fluid

1 Mosaic trisomy 21 on CVS.

No scan abnormalities at 16 weeks.

mos 47,XX,+21[13]/46,XX[17]

2Mother known to have del(X)(p11.4p22.2)

mos 46,X,del(X)(p11.4p22.2)mat[23]/47,X,del(X)(p11.4p22.2)mat,+21[10]

POC- G-band

1 Spontaneous loss following high risk serum screening (risk 1:45) 46,XY,+21,der(21;21)(q10;q10)

2 Mother has a t(4;17)(q31;q24) translocation. Products of conception following

multiple miscarriages. Spontaneous pregnancy loss. Consultant has requested

examination of the products.

46,XY

maternal contamination present (~40%)

POC-M

1 Intrauterine death (IUD) at 13 weeks. Male fetus at

autopsy. Ultrasound had shown increased nuchal

translucency, fetal hydrops and abnormal heart.

arr[GRCh37] 5p15.33p13.3(22149_30457696)x1 (30.4MB loss)

2 Fetal loss at 22 weeks following 3 weeks of reduced

fetal movement. An ultrasound scan had shown IUGR

and a 10mm nuchal fold. Female fetus.

arr[GRCh37] 18p11.32p11.21(155478_14773575)x1 (14.6MB loss)

Blood G-band

1 Delayed puberty, short stature, signs of Turner syndrome mos 47,XXX[22]/45,X[20]

2 Bilateral undescended testes. Normal penis and scrotum. No dysmorphism on

examination by consultant paediatrician. Array analysis showed a 3q29 gain.

47,XY,+der(15)t(3;15)(q29;q11.1)




Q & A





AOB


➢ EQA samples sourcing laboratories and assessors

➢ EQA Scientific advisory groups (SAG)

➢ GenQA EQA team

➢ Expert Advisors/Assessors

Acknowledgements

The participants

Contact us on [email protected]

mailto:[email protected]

Documents

ECA 2019 Participants meeting - GenQA · 2019-07-12 · Chromosome breakage scheme ... MRA –mosaic trisomy 13 - not realising it could be CPM. Blood ... 1 Delayed puberty, short