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CEQAS is operated by Oxford University Hospitals NHS Foundation Trust

CEQAS is a member of the Consortium

Summary Report for

Acquired microarray EQA 2017

Table of Contents

Section Page

EQA Case Referral and Validated Results 2

Marking Criteria 2
Learning objectives 3
Scoring submissions 3
General Comments and Observations 5
1. Both Cases 5
1.1 Methodologies used
1.2 Analysis and interpretation
1.3 ISCN
2. Clerical accuracy 6
Professional guidelines 6
Scheme Compliance 7
References 7
Assessors 7
EQA in 2018 7
Authorisation/Approval 7

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Scheme Director: Scientific Advisory Board Chair:

Dr. Ros Hastings, Level 1, The Women’s Centre, John Radcliffe Hospital Dr. Lorraine Gaunt, Director of the Genomic Diagnostics Laboratory,
Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU Manchester Centre for Genomic Medicine, Central Manchester University
Tel: 01865 857644, Email: ros.hastings@ouh.nhs.uk Hospitals NHS Foundation Trust, Manchester, M13 9WL, Tel: 0161 276
www.ceqas.org 3269, Fax: 0161 276 6606, Email: lorraine.gaunt@cmft.nhs.uk
 2017 CEQAS External Quality Assessment for Acquired Microarray
The CEQAS EQA for Acquired Microarray provided two DNA samples. The purpose of this EQA was to
assess:
 The correct determination of the genotype of DNA samples from patients referred for acquired
molecular karyotyping (microarrays/arrayCGH)
 The interpretation of the results, in the light of the clinical referral, in a clear and concise format
 The format of the report against ISO151891
2
Laboratories were assessed against ISCN 2016 .

EQA case referral and validated results

Both cases were validated by three assessors independently without prior knowledge of the karyotype (Table
1).

Case 1 was a 69 year old female with a newly diagnosed CLL referred for prognostic indicators. Results
showed an abnormal female profile with a 1.1Mb deletion of 13q14 including the DLEU genes and MIR15A
and MIR16-1.

Case 2 was a 68 year old male referred for a suspicion of MDS at diagnosis, which was later confirmed. The
results of analysis with oligo arrays showed a normal male array profile. The results of analysis with SNP-
based arrays showed an abnormal male array profile with an 85Mb copy neutral homozygous region of almost
the entire long arm of chromosome 7.

Table 1: EQA case validated results

Case Name DoB Referral reason Validated results*
1 Barbara 29/09/1947 Newly diagnosed CLL. arr[GRCh37]
COOK Prognostic indicators? 13q14.2q14.3(50481159_51523194)x1[0.8]
Deletion 13q14.2q14.3 of 1.1 Mb, containing
DLEU1, DLEU2, DLEU7, MIR15A, MIR16-1.
2 John HALL 23/01/1949 Newly diagnosed MDS arr[GRCh37]
7q11.23q36.3(73359124_159126310)x2 hmz*
or
arr(1-22)x2,(X,Y)x1*

85 Mb acquired copy-neutral homozygous region of

chromosome 7q (SNP arrays)

Normal result, no aberration detected (oligo array)

*dependent on platform and cut-off used

Marking criteria
The following marking criteria were used by assessors to score the cases. If a listed criterion was omitted
points were deducted.

Case Category Criteria Marks

deducted if
not
present
1 Analysis correct 2.0 marks
Result is correctly given in ISCN 0.5 marks
The size of the copy number aberrations are given in the report 0.5 marks
Genotyping
Clear written description (marks deducted if written description is 0.5 marks
misleading or incomplete)
Written description of results and the ISCN are concordant 0.5 marks
Interpretation present and correct 2.0 marks
The report should include the prognosis associated with the genetic 0.5 marks
Interpretation findings.
The prognosis provided is correct 0.5 marks
The genome build and platform are given in the report 0.5 marks
The report includes the clinically relevant genes 0.5 marks

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 Correct and sufficient patient details 0.5 marks
Clerical Correct sample type 0.5 marks
accuracy Date of sampling/date of receipt plus date of report given 0.5 marks
Correct referral reason given 0.5 marks
2 Genotyping Analysis correct 2.0 marks
Result is correctly given in ISCN 2.0 marks
The size of the copy number aberrations are given in the report. 0.5 marks
Clear written description (marks deducted if written description is 0.5 marks
misleading or incomplete) 0.5 marks
Written description of results and the ISCN are concordant 0.5 marks
Interpretation Interpretation present and correct 2.0 marks
The prognosis provided is correct 0.5 marks
The report states that the EZH2 gene is within the homozygous region 0.5 marks
Mutation testing should be recommended 0.5 marks
The genome build and platform are given in the report. 0.5 marks
Correct and sufficient patient details 0.5 marks
Clerical Correct sample type 0.5 marks
accuracy Date of sampling/date of receipt plus date of report given 0.5 marks
Correct referral reason given. 0.5 marks

Learning Outcomes
Case 1
 To detect the loss of 13q;
 To recognise that 13q loss is a recurrent abnormality in CLL associated with a favourable prognosis.

Case 2
 To detect a normal profile when testing with an oligo array;
 To detect a copy neutral loss of heterozygosity of 7q when testing with a SNP based array;
 To recognise that copy neutral loss of heterozygosity can harbour gene mutations of prognostic
significance and further testing should be recommended.

Scoring submissions
Thirty-two laboratories enrolled for this EQA from thirteen different countries. One laboratory withdrew so did
not participate. One laboratory did not offer CLL testing as a diagnostic service using arrays and did not submit
a result for case 1. Five laboratories requested repeat samples, four requested repeats for case 1 & 2 and one
requested a repeat sample for only case 1.
3.
Only two categories of performance in any single EQA are defined: satisfactory and poor Satisfactory
performance is defined as the standard that should be achievable by all laboratories.

A critical error is defined as an error or omission that would have significant disadvantageous clinical
consequences for the patient or family or imply a significant lack of diagnostic skill or scientific knowledge or
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an incorrect analysis. A critical error inevitably results in a poor performance designation . Any critical error is
given a zero score in the relevant category (analytical or interpretation) in which the error occurred and in
some instances leads to zero or low scores in other categories: for example, it is not possible to give a score
for interpretation if the cytogenetic analysis was not correct. The interpretation and clerical accuracy were not
marked if there was a critical analytical error. A non-submission automatically results in a poor performance.

30/31 participating laboratories obtained a satisfactory performance is summarised below in Tables 2 and 3.
There was one critical analytical error in case 2 – see individual cases for further details.

Table 2: Summary of acquired array EQA results

Myeloid Leukaemia EQA assessment. Number of Laboratories
Enrolled 32
Participated 31
Satisfactory performance 30
% satisfactory of those that participated 96.7%

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Table 3: Summary of critical errors
Number of critical errors
Case Total labs
participated
Analysis Interpretation

arr[GRCh37] 13q14.2q14.3(50481159_51523194)x1[0.8] 0 0 31

arr[GRCh37] 7q11.23q36.3(73359124_159126310)x2 hmz*

or 1 0 31
arr(1-22)x2,(X,Y)x1*
*dependent on platform and cut-off used.

The distribution of scores of the submitting laboratories is given in Figures 1 & 2. Participants are encouraged
to refer to the histograms (Figures 1 & 2) showing the performance of all the laboratories and decide through
their own benchmarking whether they consider their performance to be acceptable (maximum score is 12).
The average score for the three categories per case is given in Table 4.

Figure 1: Distribution of EQA scores for all submitting laboratories

16

14

12
Number of laboratories

10

0
5.5 6 9.5 10.5 11 11.5 12
Score

Figure 2: Distribution of average EQA scores for analysis, interpretation and clerical accuracy
35

30

25
Number of laboratories

20

15

10

0
1 1.25 1.5 1.75 2 1.5 1.75 2 1.75 2
Analysis Interpretation Clerical accuracy

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Table 4: Average scores of all participating laboratories (maximum=2)
Category Case 1 Case 2 Maximum mean score that could be obtained
Mean Analysis Score 1.80 1.90 2
Mean Interpretation Score 1.92 1.81 2
Mean Clerical Accuracy Score 1.98 2.00 2
Total Average Score 5.70 5.71 6

General comments and observations

In order to give more positive feedback this year, where there are no deductions in any of the Analysis,
Interpretation and Clerical accuracy categories, the following comments will be given respectively on the
Individual Laboratory Reports (ILRs): ‘Correct result’; ‘All essential interpretive elements given’ and ‘No clerical
errors’.

A satisfactory report will give details of analytical results, a clear written description and an interpretation of the
significance of the result, including the likely outcome, an assessment of recurrence risk as appropriate, and
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recommendations for clinical or laboratory follow up . If the participating laboratory itself does not routinely
offer interpretative reports, CEQAS requests that the Clinical Geneticist making the final interpretation should
be involved in the EQA submission. The purpose of the assessment is to examine the service provided to the
patient, not just the technical ability of the laboratory. Significant penalties are applied if an abnormal array
report does not include any interpretation of the results.
4
A single page report is recommended where practical. European Reporting Guidelines requires the referral
reason to be included in the report. It is good practice to include the patient details in the report. ISO15189
1
requires all reports to include the patient details including the date of sampling and date of reporting .

Participants are encouraged to use the comments section below the report (on the website) for feedback to
the assessors and also to inform the assessors of any National policies that might affect the content of their
report.

There was a marked improvement in the quality of the reports. The majority were of a good standard with
laboratories providing a comprehensive interpretation.

There were some recurrent observations from the submitted reports. While these observations may not have
been applicable to your laboratory submission, some of them are listed below for general information.
 Incorrect use of ISCN 2016;
 Benign CNVs should not be included in the ISCN and should not be described in the report
 The limitations of the technique were not always complete; some of the following limitations were
sometimes omitted.

1. Both cases
1.1. Methodologies used
The methodologies used by the 31 participants were either an oligo array (11 laboratories) or a SNP-based
oligo array (20 laboratories). The platforms used varied in probe density. The EQA was not prescriptive as to
the technique used to perform this exercise as long as the limitations of the methodology were fully
understood and stated on the clinical report. One laboratory was unable to obtain a result from the DNA
supplied for case 2.

1.2. Analysis and interpretation

1.2.1 Case 1
 Case 1 was a 69 year old female with a newly diagnosed CLL referred for prognostic indicators.
Validated results showed an abnormal female profile with a 1.1Mb deletion of 13q14 including the
DLEU genes, MIR15A and MIR16-1;
 All laboratories correctly identified the 13q14 deletion and there were no critical analytical or
interpretation errors;
 All laboratories stated at least one of the genes located within the deleted region : 29 laboratories
stated that the deleted region contained the DLEU gene(s) and 16 laboratories either stated that the
RB1 gene was not deleted or that it was a type I deletion;
 13 laboratories included a statement on the TP53 deletion status. Assessors recommend that a
statement regarding the status of clinically relevant genes should be included in the report as clinicians

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 may not be aware that these genes have been explicitly tested and showed no aberrations e.g. No
deletion of TP53 detected;
 In addition to TP53 deletion testing, for complete prognostication TP53 mutation screening should be
5
undertaken ;
 Deletions of 13q14 are associated with a favorable prognosis. All laboratories provided prognostic
information on their report.

1.2.2 Case 2
 Case 2 was a 68 year old male referred for a suspicion of MDS at diagnosis, which was later
confirmed;
 Validation of analysis results by oligo arrays showed a normal male array profile while analysis by
SNP based arrays showed an abnormal male array profile with an 85Mb acquired copy-neutral loss of
heterozygosity (aCN-LOH) of almost the entire long arm of chromosome 7;
 11 laboratories used an oligo array without SNP probes and reported a normal male array profile;
 20 laboratories used a SNP based array and all reported an aCN-LOH of 7q;
 There was one critical analytical error which resulted from the identification of a much smaller 12Mb
interstitial aCN-LOH of 7q;
 aCN-LOH of 7q is a recurrent abnormality in MDS;
 The detection of 7q aCN-LOH may suggest the presence of mutations in MDS-related genes located
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in the affected region. Therefore mutation analysis should be recommended ;
 The region of 7q aCN-LOH in this case includes, amongst others, the EZH2 gene which is associated
with a poor prognosis when mutated. Subsequent mutation analysis performed on this EQA sample
detected an EZH2 mutation;
 This case highlights the benefit of performing SNP arrays in haematological malignancies;
 The IPSS-R score is related to cytogenetically visible abnormalities although it can also be used for
copy number gains and losses detected by any platform which can be expected to be seen by
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chromosome analysis . It is also appropriate to use IPSS-R when
o No copy number alterations are detected by oligo arrays
o No copy number alterations and no aCN-LOH are detected by SNP based arrays
 If aCN-LOH is the sole abnormality (i.e. no associated copy number gains or losses), the IPSS-R
score is not applicable as aCN-LOH is not included in the scoring system;
 In addition there is recommendation for FISH to exclude a MECOM rearrangement ;
8

 There were no interpretation errors.

1.3 ISCN
Recurrent ISCN errors included:
 The results should be given according to ISCN 2016 . Six laboratories used ISCN 2013 in this EQA;
2

 Omitting a comma between sex chromosomes in a normal male profile (i.e. (X,Y)x1) for array results;
 The inclusion of benign CNVs in the ISCN. It is not recommended to include benign/likely benign
CNVs in the ISCN.

2. Clerical accuracy
Marks were deducted for the incorrect sample type, incorrect patient name or date of birth, no date of sample
receipt (or date of sampling) or date of report or omitting to give a minimum of two patient identifiers. EQA
1
submissions were marked against ISO15189 .
 Two laboratories omitted to include the limitations of the technique on their report.
 Limitations should include :
o Non detection of balanced rearrangements;
o Non detection of point mutations;
o Non detection of low level mosaicism;
o Non detection of aCN-LOH (if using oligo-based platforms without SNPs).
 There was noticeable improvement in the completeness of the limitations of the technique when
compared to 2016. However, for oligo arrays several laboratories omitted to state that copy neutral
loss of heterozygosity would not be detected;
 30/31 participating laboratories gave the array platform and manufacturer used in their report;
 All participating laboratories gave the genome build to ascertain the gene content.

Professional guidelines
Guidelines used in the assessment of laboratory reports include, as appropriate:-
 2
ISCN 2016 ;
 9 4
European Cytogenetic Guidelines and European Reporting Guidelines ;

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CEQAS Acquired array summary report 2017_V1 website Page 6 of 7
 8
Guidelines for Genomic array analysis in acquired haematological neoplastic disorders ;
 1
ISO15189: 2012 Medical laboratories – Requirements for quality and competence ;
 10 11,12
WHO 2008 , WHO 2016 updates

Scheme compliance
All laboratories anonymised their reports.

Participants are encouraged to use the comments section below the report (on the website), for comments to
the assessors and also to inform the assessors of any national or local policies that might affect the content of
the report.

References
1. ISO15189:2012. Medical laboratories – requirements for quality and competence.
2. McGowan-Jordan, J., Simons, A., Schmid, M. (2016), ISCN 2016: An International System for Human Cytogenomic
Nomenclature. S. Karger, Basel.
3. CEQAS Haematology Performance criteria 2016v1 http://www.ceqas.org/performance-criteria
4. Claustres M, et al., (2013). Recommendations for reporting results of diagnostic genetic testing (Biochemical, Cytogenetic and
Molecular Genetic). On behalf of the ESHG Quality Committee. Eur. J. Hum. Genet., 22:160-170
5. Pospisilova, S., et al (2012) ERIC recommendations on TP53 mutation analysis in chronic lymphocytic leukemia. Leukemia
26;1458-61
6. Tiu R.V., et al. Prognostic impact of SNP array karyotyping in myelodysplastic syndromes and related myeloid
malignancies.Blood 117; 4552-4562
7. Greenberg, P., et al. (2010), Revised International Prognostic Scoring System for Myelodysplastic Syndromes. Blood, 120:
2454–2465.
8. Schoumans, J., et al. (2016), Guidelines for Genomic array analysis in acquired haematological neoplastic disorders. Genes,
Chromosomes & Cancer. 55:480-491
9. General Guidelines and Quality Assurance for Cytogenetic Guidelines (2012),ECA Newsletter, Jan 2012 and http://www.e-c-
a.eu/files/downloads/Guidelines/E.C.A._General_Guidelines_Version-2.0.pdf
10. Swerdlow R.H., et al, editors. WHO classification of tumours of haematopoietic and lymphoid tissues. World Health
Organization.Lyon: IARC, 2008.
11. Arber, D.A., et al (2016). The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute
leukemia. Blood 127: 2391-2405.
12. Swerdlow,S.H., ,Campo,E.,et al (2016) The 2016 revision of the World Health Organization classification of lymphoid
neoplasms. Blood, 127:2375- 2390

Assessors
A specialist group of assessors undertook the analysis of the returns.
Assessor Panel Location
Eva van den Berg-de Ruiter Groningen, the Netherlands
Berna Beverloo Rotterdam, the Netherlands
Jacqueline Schoumans CHUV, Lausanne, Switzerland
Javier Suela Madrid, Spain

EQA in 2018
If you have any comments on how this EQA might be improved in the future or you require any further
information please email the Scheme Director at the address on page 1.

Thank you for participating in this EQA. We hope you found participation useful and will continue to participate
in future.

On behalf of: CEQAS.

Katrina Rack Ros Hastings,

Scheme Deputy Director Scheme Director

Authorisation/Approval
This document has been authorised/approved on behalf of CEQAS by: Ros Hastings on 30/10/2017

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