Additional value of prenatal genomic array testing in fetuses with isolated structural ultrasound abnormalities and a normal karyotype: a systematic review of the literature M.C. de Wit, M.I. Srebniak, L.C.P. Govaerts, D. Van Opstal, R.J.H. Galjaard and A.T.J.I. Go Link to free access article: http://onlinelibrary.wiley.com/doi/10.1002/uog.12575/abstract

1. UOG Journal Club: February 2014
Additional value of prenatal genomic array testing
in fetuses with isolated structural ultrasound abnormalities and
a normal karyotype: a systematic review of the literature
M.C. de Wit, M.I. Srebniak, L.C.P. Govaerts, D. Van Opstal, R.J.H. Galjaard and
A.T.J.I. Go
Volume 43, Issue 2, Date: February 2014, pages 139-147
Journal Club slides prepared by Dr Leona Poon
(UOG Editor for Trainees)

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Fetuses with multiple congenital abnormalities have a >18% chance
of carrying a microscopic chromosomal abnormality (Nicolaides et al,
1992).
Genomic microarray has been introduced in some prenatal centers as
a diagnostic tool, instead of or in addition to cytogenetic karyotyping.
Genomic microarray achieves a much higher resolution than
cytogenetic karyotyping and reveals copy number variants (CNVs).
Some CNVs can be of etiologic importance in congenital
malformations and syndromes (Cooper et al, 2011).
Clinically significant submicroscopic CNVs are found in 5-10% of
fetuses with multiple ultrasound anomalies and a normal karyotype.
Knowledge about the chances of finding a causative submicroscopic
CNV in a fetus with an isolated ultrasound anomaly is scarce.
Nicolaides KH et al. Lancet 1992;340:704-7.
Cooper GM et al. Nat Genet 2011;43:838-46.

3. Additional value of prenatal genomic array testing in fetuses
with isolated structural ultrasound abnormalities and a normal karyotype:
a systematic review of the literature
De Wit et al., UOG 2014
Objectives
1. To establish the prevalence of genetic CNVs in fetuses
with a structural ultrasound anomaly (restricted to one
anatomical system) and a normal karyotype.
2. To determine the diagnostic and prognostic value of
genomic array testing in these pregnancies.

4. Additional value of prenatal genomic array testing in fetuses
with isolated structural ultrasound abnormalities and a normal karyotype:
a systematic review of the literature
De Wit et al., UOG 2014
Search strategy:
8 May 2013
(Micro)array AND prenatal AND ultrasound anomalies
EX animal, review, case report LIM English
PubMed (n=775)
Embase (n=496)
Exclusion of duplicates (n=169)
Exclusion criteria (title and abstract):
n=1102
Inclusion criteria (full text):
• Selection on normal karyotype or size array abberation
stated
• Description of cohorts composition regarding
ultrasound findings (unsuitable n=18)
• Clear judgment of pathogenicity of CNVs stated
• Known number of pathogenic CNVs per group of
fetuses with an anomaly in a specific anatomical system
(unsuitable n=2)
Criteria for critical appraisal:
 Sample size
 Moment of case recruitment
 Description quality of ultrasound anomalies
 Description quality of array platform and CNVs found
n=38
• Use of technique other than genomic array
• Array performed only for indications other than
ultrasound anomalies
• Non-prenatal setting
• Cohort with only non-structural abnormalities
Web of knowledge: no additional inclusions
Exclusion because of overlapping
cohorts (n=1) and exclusion of
validation studies (n=1)
Included studies (n=18)

5. Additional value of prenatal genomic array testing in fetuses
with isolated structural ultrasound abnormalities and a normal karyotype:
a systematic review of the literature
De Wit et al., UOG 2014
Methodology
Study selection
• Studies reporting on the prevalence of pathogenic submicroscopic CNVs
in fetuses with an ultrasound anomaly were selected. They:
• Described fetuses with a known normal karyotype and described their cohort
in such a manner that fetuses with large genomic aberrations of >10 Mb and/or
chromosome aberrations identified by rapid aneuploidy detection.
• Described the composition of their cohort regarding the number of fetuses
with a structural ultrasound anomaly in a specific anatomical system.
• Reported a clear judgment of the CNVs regarding their presumed nature, for
example, pathogenic or benign.
• Showed the pathogenic CNVs in detail or gave the number of pathogenic
CNVs per group of fetuses with an anomaly in a specific anatomical system.

6. Additional value of prenatal genomic array testing in fetuses
with isolated structural ultrasound abnormalities and a normal karyotype:
a systematic review of the literature
De Wit et al., UOG 2014
Methodology
Data extraction
• Four reviewers independently extracted data.
• The appraisal included features of validated quality-assessment tools and
used sample size, cohort selection, study perspective, the description
quality of ultrasound findings and CNV classification as the parameters for
assessment.
• An array result was assumed to be causative and pathogenic if the
reporting author classified it as such.
• For every group of fetuses with an ultrasound anomaly restricted to one
particular anatomical system, the prevalence of pathogenic CNVs and its
95% CI was calculated.

7. Additional value of prenatal genomic array testing in fetuses
with isolated structural ultrasound abnormalities and a normal karyotype:
a systematic review of the literature
De Wit et al., UOG 2014
Results
Pooled prevalence of pathogenic submicroscopic CNVs
in a specific anatomical system
Isolated anomalies
Resp
CNS
Facial
5/81
35/563
6/113
6.2%
6.2%
5.3%
(0.9-11.4)
(4.2-8.2) (1.2-9.4)
Pooled
prevalence
(95% CI)
Cardiac
22/476
4.6%
(2.7-6.5)
Pooled
prevalence
(95% CI)
Isolated anomalies
NT
Cystic
GIT
Urogenital
>3.5 mm hygroma
7/105
9/153
5/162
12/262
6.7%
5.9%
3.1%
4.6%
(1.9-11.4)
(2.2-9.6) (0.4-5.7)
(2.0-7.1)
MSK
24/305
7.9%
(4.8-10.9)
Total
125/2220
5.6%
(4.7-6.6)

8. Additional value of prenatal genomic array testing in fetuses
with isolated structural ultrasound abnormalities and a normal karyotype:
a systematic review of the literature
De Wit et al., UOG 2014
Results
Multiple
All
anomalies anomalies
Tyreman (2009)
6/24
9/82 (11.1)
Vialard (2009)
3/36
3/36 (8.3)
Coppinger WG (2009)
1/62
5/122 (4.1)
Coppinger TA (2009)
7
0/15
Kleeman (2009)
1
0/43
Evangelidou (2010)
0/8
Leung (2011)
2/10
4/48 (8.5)
D’ Amours (2012)
2/24
4/47 (8.5)
Lee (2012)
3/36
15/136 (11.0)
Shaffer (2012)
77/808
159/2184 (7.3)
Faas (2012)
1/40
2/90 (2.2)
Ganesamoorthy (2013)
3/25
4/70 (5.7)
Mademont-Soler (2013)
1/23
1/51 (2.0)
Rooryck (2013)
2/56 (3.6)
Schmid (2013)
4/10
5/45 (11.1)
Hillman (2013)
11
6/187 (3.2)
Scott (2013)
2/62 (3.2)
Vestergaard (2013)
1/22
8/77 (10.3)
Reference
Prevalence of pathogenic
submicroscopic CNVs
in multiple / all anomalies
Pooled
prevalence
(95% CI)
Multiple
All
anomalies anomalies
104/1139 229/3359
9.1%
6.8%
(7.5-10.8) (6.0-7.7)

9. Additional value of prenatal genomic array testing in fetuses
with isolated structural ultrasound abnormalities and a normal karyotype:
a systematic review of the literature
De Wit et al., UOG 2014
Limitations
The prevalence of pathogenic submicroscopic CNVs between the
reviewed studies varied between 0 to 11.1%.
The most prevalent discrepancies can be:
• Most probably explained by the predominantly small sample sizes:
only four studies described cohorts of > 100 fetuses.
• Partially explained by
• Differences in cohort selection: ranging from ‘major ultrasound anomalies’ to
‘any abnormality detected by ultrasound’.
• Some cases of non-structural anomalies or unspecified ultrasound findings
were difficult for exclusion.
• Enormous variety and resolution in the array platforms used (e.g. single
nucleotide polymorphisms [SNPs] and bacterial artificial chromosomes [BACs]).

10. Additional value of prenatal genomic array testing in fetuses
with isolated structural ultrasound abnormalities and a normal karyotype:
a systematic review of the literature
De Wit et al., UOG 2014
Discussion
• 5.6% (95% CI 4.7-6.6) chance of finding a causal submicroscopic CNV
in fetuses with a structural ultrasound anomaly restricted to one
anatomical system and a normal karyotype
• The group with NT>3.5 mm has the lowest prevalence of pathogenic
submicroscopic CNVs (3.1%, 95% CI 0.4-5.7)
• Pathogenic genomic micro-imbalances are most frequently found in polymalformed fetuses (9.1%, 95% CI 7.5-10.8).
• Clinically relevant submicroscopic CNVs are spread through the whole
genome, therefore, screening for sub-telomeric abnormalities before array
testing is not advised.

11. Additional value of prenatal genomic array testing in fetuses
with isolated structural ultrasound abnormalities and a normal karyotype:
a systematic review of the literature
De Wit et al., UOG 2014
Discussion
• Screening with FISH for the 22q11 microdeletion before array testing
appears to be of limited value.
• The application of an internationally recognized fetal phenotype coding
system would be of great value because such a system:
• Would allow better comparison of cases
• More reliable calculation of the prevalence of pathogenic
submicroscopic CNVs in specific structural fetal defects
• Discovery of new / novel pathogenic CNVs
• The International Standards for Cystogenomic Arrays phenotype form (
https://www.iscaconsortium.org) is a good instrument that uses Human
Phenotype Ontology terms.

12. Additional value of prenatal genomic array testing in fetuses
with isolated structural ultrasound abnormalities and a normal karyotype:
a systematic review of the literature
De Wit et al., UOG 2014
Discussion
• To allow the discovery of new pathogenic CNVs, whole-genome array
platforms should be recommended in prenatal setting.
• If local policy does not allow genome-wide analysis, 2-step analysis
could be performed: targeted analysis with a lower backbone resolution
• Both pathogenic CNVs and variants of unknown clinical significance
(VOUS) should be published and human genome build should be stated.
• A clear definition for the term ‘incidental finding’ should be established.
• Postnatal follow-up in cases with specific malformations on ultrasound is
essential in drawing conclusions on microarray tests in prenatal diagnosis.

13. Additional value of prenatal genomic array testing in fetuses
with isolated structural ultrasound abnormalities and a normal karyotype:
a systematic review of the literature
De Wit et al., UOG 2014
Conclusions
• Genomic microarray should be performed in fetuses with
both isolated and multiple ultrasound anomalies.
• Causative submicroscopic CNVs are found in 5.6% of
fetuses with isolated anomalies and in 9.1% of fetuses with
multiple anomalies.
• Implementation of an international uniform classification
system for ultrasound abnormalities is necessary to contribute
to the comparability of cohorts.

14. Additional value of prenatal genomic array testing in fetuses
with isolated structural ultrasound abnormalities and a normal karyotype:
a systematic review of the literature
De Wit et al., UOG 2014
Discussion points
• Should genomic array replace traditional cytogenetic karyotyping in the prenatal diagnosis of fetuses with
both isolated and multiple ultrasound anomalies?
• Do we have enough evidence to support the use of genomic array in clinical settings?
• If yes,
• How should fetal medicine subspecialists and geneticists counsel women prior to invasive testing?
• How will it impact on the current system of cytogenetic services?
• If no,
• How can we rapidly collate as much information on CNVs and VOUS?