DOI: 10.1002/pd.

4953

ORIGINAL ARTICLE

Prenatal diagnosis of submicroscopic chromosomal aberrations in

fetuses with ventricular septal defects by chromosomal microarray-
based analysis
Liu Du1, Hong-Ning Xie1*, Lin-Huan Huang2, Ying-Jun Xie2 and Li-Hong Wu1

1
Department of Ultrasonic Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
2
Department of Obstetrics and Gynaecology, Fetal Medical Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
*Correspondence to: Hong-Ning Xie. E-mail: hongning_x@126.com

ABSTRACT
Objectives To evaluate the usefulness of chromosomal microarray analysis in fetuses with ventricular septal defects
(VSDs) with or without associated anomalies and normal karyotype.

Methods Fetuses with VSDs and normal karyotypes were investigated by using an Affymetrix CytoScan HD array. The
cases were classified as isolated or nonisolated VSDs.

Results Among the 52 VSD fetuses, 22 (42.3%) had isolated defects and 30 (57.7%) had additional other ultra-
sound anomalies. Twenty-six CNVs were identified in 18 fetuses (34.6%), 15 benign CNVs were detected in 11
(21.2%) fetuses, and 8 pathogenic CNVs were detected in 6 (11.5%) fetuses. After excluding 2 fetuses with
22q11.2 deletion syndrome, the rate of pathogenic CNVs was 7.7%. The proportion of variants of unknown
significance was 5.8% (3/52). In five cases, additional malformations were detected after birth or abortion, and
one case had a prenatal isolated VSD. The detection rate of pathogenic CNVs in nonisolated VSDs was non-
significantly higher than that in prenatal or postnatal isolated VSDs (4.5%, 1/22 vs 16.7%, 5/30, P = 0.226; 0/21 vs
19.4%, 6/31, P = 0.07).

Conclusions The results demonstrated the value of chromosomal microarray analysis in the prenatal diagnosis of
VSDs. The complexity of other defects enhanced the frequency of pathogenic CNVs, although the results were not
significantly different. © 2016 John Wiley & Sons, Ltd.

Funding sources: This study was supported by funding from the National Natural Science Foundation of China (81571687) and the National Key Technology R&D
Program (2014BAI06B05).
Conflicts of interest: None declared

INTRODUCTION postnatal and prenatal subjects with CHD, which enables

Ventricular septal defects (VSDs) are the most common form of
congenital cardiovascular anomaly, accounting for 30 to 35% of
all congenital heart diseases (CHDs) detected after birth and for
10% of cases in fetal series.1 VSDs have the highest recurrence
rates and are the most common teratogen-associated defects.2
Approximately 20 to 40% of VSDs are attributable to Mendelian
diseases or chromosomal aneuploidies, while the remaining
are attributable to non-Mendelian causes that are poorly
understood.1 A previous study from our center indicated that
the risk of chromosomal abnormalities in cases with compli-
cated extracardiac anomalies or both extracardiac and cardiac
anomalies was significantly higher than that in cases with an
isolated VSD.3 However, most patients with VSDs with good
outcomes undergo spontaneous closure during the intra-
uterine period. In some cases, the prognosis is dominated by
the presence of chromosomal or extracardiac malformations.4
Chromosomal microarray analysis (CMA) has been success-
fully applied to identify copy number variations (CNVs) in
whole-genome screening for chromosomal imbalances at
higher resolution than conventional karyotyping. Reports
detailing the incremental yield in CMA in the prenatal setting
are rapidly emerging.5,6 Most published reports include large
cohorts but describe the incremental yield for a variety of
indications. Subgroup analyses of different types of CHD,
which are the most common structural abnormalities detected
in the prenatal setting, are rarely reported.6,7 The aim of
this study was to evaluate the usefulness of CMA in fetuses
with VSDs with or without associated anomalies and normal
karyotypes and to explore the relationship between sub-
microscopic genetic CNVs and VSDs.
METHODS
Subjects
Between January 2013 and October 2014, 49 singleton preg-
nancies and 3 individual fetuses from twin pregnancies were

Prenatal Diagnosis 2016, 36, 1178–1184 © 2016 John Wiley & Sons, Ltd.
Chromosomal microarray analysis of fetal ventricular septal defects 1179

diagnosed with VSDs and normal karyotypes via conventional
G-band karyotype analysis at the Department of Ultrasonic
Medicine and Fetal Medical Center at the First Affiliated
Hospital of Sun Yat-sen University. The fetuses underwent a
routine ultrasound scan, and fetal biometry was assessed at a
median gestational age of 24 + 4 (range 18 + 2–34 + 2) weeks.
Menstrual age was calculated based on the first day of the last
normal menstrual period, defined as regular cyclic menses
without antecedent contraceptive use, and confirmed by either
first or early second trimester sonography. When the heart was
found to be abnormal, echocardiography was performed
(Voluson E6/E8, GE Medical Systems, Zipf, Austria) at our
tertiary referral center and included standard planes with
color Doppler assessment following the guidelines of the
International Society of Ultrasound Obstetrics and Gyne-
cology.8 VSDs were diagnosed by two fetal cardiologists. Based
on the presence of other malformations, the cases were
classified as an isolated or a nonisolated VSD, which
characterized cases with other cardiac anomalies, extracardiac
structural anomalies, or sonographic soft markers. These soft
markers included choroid plexus cysts, echogenic foci in
the heart or bowel, isolated short long bones, thickened
nuchal fold, absent nasal bone, single umbilical artery,
persistent right umbilical vein, sandal gap between the first
and second toes, and fifth finger clinodactyly. Of the included
fetuses, 22 (42.3%) had isolated VSDs and 30 (57.7%) had VSDs
plus other ultrasound anomalies: 14 (26.9%) with other cardiac
anomalies, 11 (21.2%) with extracardiac anomalies, and 5
(9.6%) with other cardiac and extracardiac anomalies (Table 1).
Fetal samples were collected by amniocentesis (n = 17) and
cord blood sampling (n = 32) according to the number of
gestational weeks. For three cases, blood samples were
collected postnatally due to parental refusal of invasive pre-
natal tests. Parental blood samples were collected for every
fetal sample to exclude maternal contamination and to assist
in interpreting the CNVs when necessary and possible. This
study was approved by the ethics committee at the First
Affiliated Hospital of Sun Yat-sen University, and informed
consent was obtained from the parents for invasive prenatal
diagnoses.

Table 1 The sonographic findings of 21 fetuses with nonisolated VSDs with benign or non-CNVs and normal karyotypes

GA at
MA examination
Case (years) (weeks) CMA resulta Cardiac defects Extracardiac anomalies

1 36 31 arr[hg19] 4q32.3(167,619,071-167,591,578) × 4 arr No Thickened nuchal fold, mild

[hg19] 10q21.3(69,099,402-68,510,565) × 1 ventriculomegaly, SUA

2 30 24 arr[hg19] 16p11.2(32,524,764-33,814,547) × 3 DORV SUA

3 37 28 arr[hg19] 16p12.2(21,596,299-21,841,354) × 1 No SUA

4 27 30 arr[hg19] (1-22) × 2 PLSVC FGR

5 33 22 arr[hg19] (1-22) × 2 HLHS, ARSA Duplex kidney

6 28 29 arr[hg19] (1-22) × 2 No Abdominal cyst

7 21 15 arr[hg19] (1-22) × 2 No Omphalocele

8 34 22 arr[hg19] (1-22) × 2 No echogenic bowel, SUA

9 22 33 arr[hg19] (1-22) × 2 CoA Mild ventriculomegaly, enlarged

cisterna magna, encephalodysplasia

10 30 22 arr[hg19] (1-22) × 2 No CPC, micrognathia

11 28 28 arr[hg19] (1-22) × 2 No Umbilical cord cyst

12 37 24 arr[hg19] (1-22) × 2 DORV, PLSVC No

13 37 24 arr[hg19] (1-22) × 2 HRH No

14 33 27 arr[hg19] (1-22) × 2 RAA No

15 34 34 arr[hg19] (1-22) × 2 TGA No

16 31 25 arr[hg19] (1-22) × 2 TGA, PS No

17 31 22 arr[hg19] (1-22) × 2 DORV, PA, anomalous No
origin of right
pulmonary artery

18 31 23 arr[hg19] (1-22) × 2 CoA No

19 24 18 arr[hg19] (1-22) × 2 DORV No

20 28 32 arr[hg19] (1-22) × 2 TGA No

21 28 23 arr[hg19] (1-22) × 2 TGA No

ARSA, aberrant right subclavian artery; CoA, coarctation of the aorta; CPC, choroid plexus cysts; DORV, double-outlet right ventricle; FGR, fetal growth restriction; GA,
gestational age; HLHS, hypoplastic left heart syndrome; HRH, hypoplastic right heart; MA, maternal age; PA, pulmonary artery atresia; PLSVC, persistent left superior vena cava;
PS, pulmonary artery stenosis; RAA, right aortic arch; SUA, single umbilical artery; TGA, transposition of great artery.
a
The microarray result does not include the fetal gender in compliance with Chinese policy.

Prenatal Diagnosis 2016, 36, 1178–1184 © 2016 John Wiley & Sons, Ltd.
1180
Cytogenetic analysis
Prenatal samples were karyotyped according to standard
procedures for amniotic fluid or blood cells.9 Postnatal
neonate and parental karyotype testing was performed on
peripheral blood lymphocytes. The parental samples were
used to determine whether the rearrangement was de novo
or inherited. Karyotyping analysis was performed by using
conventional G-banding techniques (550-band resolution).
Chromosomal microarray analysis
Fetal DNA was obtained from cultured amniotic fluid or fetal
blood cells, and neonate and parental DNAs were obtained
from cultured peripheral blood cells by using the QIAamp
DNA Mini Kit (Qiagen, Valencia, CA, USA) and subjected to
CMA-single nucleotide polymorphism (SNP) array analysis by
using the Affymetrix CytoScan HD Array (Affymetrix, High
Wycombe, UK). DNA was amplified, labeled, and hybridized
to the CytoScan HD array platform according to the manu-
facturer’s protocol. This array is specifically designed for
cytogenetic research and includes more than 2 million markers
across the genome, including SNP probes and probes for
detecting CNVs (Cyto-arrays). CEL files obtained by scanning
the CytoScan arrays were analyzed with CHROMOSOME ANALYSIS
SUITE software (Affymetrix). The GRCh37 (hg19) genome was
used for annotation. Only probes achieving the manufacturer’s
quality cut-off measures were included in our analysis. Gains
and losses that affected a minimum of 50 markers within a
100-Kb region were initially considered.
The detected copy number gains or losses were system-
atically evaluated for clinical significance by comparing them
with values in the scientific literature and the following publicly
available databases: (1) Database of Genomic Variants (http://
projects.tcag.ca/variation/), (2) Database of Chromosomal
Imbalance and Phenotype in Humans Using Ensembl Resour-
ces (http://decipher.sanger.ac.uk/), (3) International Standards
for Cytogenomic Arrays (https://www.iscaconsortium.org/),
(4) European Cytogeneticists Association Register of Un-
balanced Chromosome Aberrations (http://www.ecaruca.net),
and (5) Online Mendelian Inheritance in Man (OMIM; http://
www.ncbi.nlm.nih.gov/omim). Alterations coinciding with
known polymorphic CNVs were interpreted as benign and not
reported. In contrast, CNVs identified in regions of known
clinical relevance (i.e. involving microdeletion/microdupli-
cation syndrome critical regions) or that comprised genes with
dosage alterations that are associated with congenital defects
were interpreted as pathogenic. A CNV that did not match any
of the criteria mentioned in the preceding texts was considered
a variant of unknown significance (VOUS).10 Microarray
analysis of DNA from maternal and paternal blood samples
was used to determine whether the CNVs detected in the fetal
samples were inherited or de novo.
Statistical analysis
The statistical analysis was performed by using SPSS version 21.
The frequency of CNVs was compared between isolated VSDs
and VSDs associated with other anomalies in both prenatal
and postnatal cases by using Fisher’s exact test. A value of
P < 0.05 was considered to indicate statistical significance.
Prenatal Diagnosis 2016, 36, 1178–1184
L. Du et al.
RESULTS
Twenty-six CNVs were identified in 18 fetuses (34.6%, 18/52)
and ranged in size from 27 Kb to 7.86 Mb. Six of the fetuses
(11.5%) had more than one CNV, with an average of 1.4 CNVs
per case. Fifteen CNVs from 11 fetuses were interpreted as
likely benign and of no clinical significance, were listed in
Database of Genomic Variants, or included no known gene.
Eight clinically significant CNVs were detected in six fetuses
(11.5%, 6/52); these CNVs overlapped with a known syndrome
or with a Database of Chromosomal Imbalance and Phenotype
in Humans Using Ensembl Resources entry and were
determined to be pathogenic or within important OMIM
genes. Two fetuses (cases 23 and 24) had two clinically
significant CNVs. We detected the known 22q11.2 deletion
syndrome in two fetuses; after excluding these fetuses,
the detection rate was 7.7% (4/52). Case 22 was a
monochorionic–diamniotic twin with discordant ultrasound
phenotypes; one fetus had a VSD and stenosis of the main
pulmonary artery, and the other was normal. SNP-based array
analysis showed that these were monozygotic twins that
harbored no gene variations related to abnormal cardiac
development. Both twins suffered intrauterine death at
34 weeks and 3 days of gestation. CNVs of uncertain clinical
significance were detected in three (5.8%, 3/52) fetuses.
The results from nine cases with pathogenic CNVs or
VOUS are shown in Table 2. Five fetuses were born, and three
fetuses whose parents refused to undergo invasive prenatal
testing were found to have abnormal phenotypes after birth
and displayed clinically significant CNVs. Three patients
terminated their pregnancy, while one case resulted in
intrauterine death. Additionally, in five (9.6%) cases, more
malformations were detected after birth or abortion that were
either difficult to detect or not considered detectable by
prenatal ultrasound, such as broad thumbs and first toes,
polydactylism, and the absence of the left ear. Pathogenic
CNVs were identified in one fetus with a prenatal diagnosis of
an isolated VSD (case 23). Five fetuses with VSDs had other
associated abnormalities. No differences were observed in the
frequency of chromosomal aberrations between the isolated
VSDs and the VSDs associated with other anomalies for either
the prenatal or postnatal cases (4.5%, 1/22 vs 16.7%, 5/30,
P = 0.226; 0/21 vs 19.4%, 6/31, P = 0.07).
Discussion
Recent studies have suggested that detecting CNVs by array
analysis could be more informative than chromosomal
analysis.11,12 Recently, array analysis has become a standard
procedure for prenatal genetic analysis, and it is commonly
preceded by rapid aneuploidy detection to exclude common
aneuploidies.13,14 The prevalence of clinically significant CNVs
in prenatal CHDs has been described in several cohorts.15–17
Most published reports include large cohorts but generally
describe an incremental yield in CHDs. As the diagnostic
accuracy of prenatal ultrasound increases, targeted infor-
mation regarding specific diagnoses will also need to be
determined. Subgroup analysis of CHDs at the level of specific
defects in the prenatal setting is rarely reported. Moreover,
categorizations of CHDs are not consistent among different
© 2016 John Wiley & Sons, Ltd.
 Table 2 Characteristics of fetuses with pathogenic CNVs (cases 22–27) or VOUS (cases 28–30) detected by CMA among the 52 fetuses with VSDs with normal karyotypes

Associated Size of Other postnatal Parental material

Case anomalies Sample CMA result CNV CNV type OMIM or corresponding disorder Classification Outcome findings available
22 PS UCB arr[hg19] 17p11.2 3.7 Mb Loss Smith–Magenis syndrome Pathogenic Intrauterine No No
(16,727,264- fetal death
20,433,502) × 1

23 No Postnatal arr[hg19] 10q22.3 124 Kb; Gain; loss SFTPA1 (178630), SFTPA2 (178642); Pathogenic; Born Broad thumbs No
blood (81,298,315- 205 Kb Rubinstein–Taybi syndrome pathogenic and first toes,
sample 81,422,268) × 3; arr polydactylism,

Prenatal Diagnosis 2016, 36, 1178–1184

[hg19] 16p13.3 pulmonary
(3,793,680- fibrosis
3,998,261) × 1

24 Pulmonary UCB arr[hg19] 11p15.5p15.4 3.16 Mb; Gain; gain Silver–Russell syndrome; MKRN3 (603856), UBE3A Pathogenic; TOP No Yes, not
hypoplasia; FGR (230,615- 7.86 Mb (601623), GABRB3 (137192), 0CA2 (611409), pathogenic inherited
3,398,117) × 3; arr MAGEL2 (605283), HERC2 (605837), NDN
[hg19] 15q11.2q13.2 (602117), SNRPN (182279), NIPA1 (608145)
(22,770,421-
31,073,669) × 3
Chromosomal microarray analysis of fetal ventricular septal defects

25 Thickened nuchal UCB arr[hg19] 16p13.3 23.5 Kb Loss HBA1 (141800), HBA2 (141850) Pathogenic TOP Polydactylism No
fold, long bone (85,880-320,729) × 1
dysplasia,
micrognathia,
prenatal thickness

26 IAA Postnatal arr[hg19] 22q11.21 3.15 Mb Loss 22q11.2 deletion syndrome Pathogenic Born PDA, ASD No
blood (18,644,790-
sample 21,800,797) × 1

27 IAA Postnatal arr[hg19] 22q11.21 3.15 Mb Loss 22q11.2 deletion syndrome Pathogenic Born Peculiar facies, No
blood (18,644,790- ASD, thymus
sample 21,800,797) × 1 absence
28 No UCB arr[hg19] 3.6 Mb Gain PEX10 (602859), SMIM1 (615242), PRDM16 VOUS Born No Yes, not
1p36.33p36.32 (605557), CEP104 (616690), TMEM240 inherited
(849,466- (616101), GABRD (137163), SKI (164780),
41,56,277) × 2 ~ 3 ISG15 (147571), TNFRSF4 (600315), AGRN
(103320), B3GALT6 (615291), DVL1 (601365)

29 PS UCB arr[hg19] 1p21.2 150 Kb Gain AGL (610860), SLC35A3 (605632), SASS6 VOUS Born No No
(100,202,842- (609321), DBT (248610)
100,952,789) × 3

30 DORV, DA absent UCB arr[hg19] 16p13.3 273 Kb Gain AXIN1 (603816) VOUS TOP Absence of No
(272,913-546,267) × 3 left ear

ASD, atrial septal defect; DA, ductus arteriosus; DORV, double outlet right ventricle; FGR, fetal growth restriction; IAA, interruption of aortic arch; PDA, patent ductus arteriosus; PS, pulmonary artery stenosis; SUA, single umbilical artery; TOP,
termination of pregnancy; UCB, umbilical cord blood.

© 2016 John Wiley & Sons, Ltd.

1181
1182
reports, which hinder the calculation of the yield per specific
CHD. VSDs associated with the most prevalent CHDs occur
either in isolation or in combination with other defects.
Approximately 20 to 40% of VSDs are attributable to Mendelian
diseases or chromosomal aneuploidies, while the remaining
are attributable to non-Mendelian causes that are poorly
understood.1 However, little is known about the involvement
of CNVs in either isolated or nonisolated VSDs. Therefore, we
speculate that CNVs could be a contributing factor in VSD
etiology that will potentially have important implications for
planning treatment strategies and be helpful for counseling
parents about the risks of recurrence.
Regarding the relationship between VSDs and CNVs in
prenatal cases, only one study analyzed CHD subgroups and
found that 10.6% (14/132) of fetuses with VSDs had pathogenic
submicroscopic CNVs.7 Our findings are consistent with those
of this previous report, and we further compared the incidence
of pathogenic submicroscopic CNVs in fetuses with isolated
VSDs and in those with VSDs associated with other abnor-
malities. In our study, the detection rate of VSDs plus other
ultrasound anomalies was nonsignificantly higher than that
of isolated VSDs. We are currently unaware of any other
published reports that address this issue. This outcome is
consistent with prenatal reports that describe CHDs in
general.6,15,16 It has also been observed that fetuses with CHDs
and additional structural abnormalities demonstrate a
nonsignificantly higher number of pathogenic CNVs than
fetuses with isolated CHDs. However, this finding is incon-
sistent with multiple postnatal studies that showed that
children with CHDs and other anomalies, particularly
neurologic abnormalities or developmental delays, had signi-
ficantly more CNVs than those with isolated disease. A
potential reason for this discrepancy is that many of the
subjects in the current study were followed up for less than
2 years after birth, which many not be sufficient for the
accurate documentation of neurologic deficits.18
The detection of VSDs before birth has greatly increased over
the past few years due to the use of higher-quality equipment
and the incorporation of expert guidelines for CHD screening
during pregnancy.19,20 However, prenatal ultrasound cannot
identify all signs of syndromes, such as dysmorphic features,
nor can it predict mental retardation. We showed that the
false-negative rate for the prenatal detection of extracardiac
malformations associated with VSDs was low: only 5 of 52
(9.6%) of the neonates presented with unexpected mal-
formations, the majority of which were considered uniden-
tifiable or difficult to identify during pregnancy. Only one of
these cases appeared to be an isolated VSD by prenatal
screening and had a pathogenic CNV. The diagnosis of isolated
VSDs is considered reliable in the majority of cases, and the
rate of postnatally detected malformations is low. This could
lead to an overestimation of the detection rate of pathogenic
CNVs in isolated cases, although the rate was not significantly
different from that of isolated VSDs and VSDs with other
abnormalities that were confirmed postnatally.
Excluding the 22q11.2 deletions, the pathogenic CNVs in
four cases may be related to abnormal cardiac development.
Case 22 harbored a 3.7-Mb deletion in chromosome 17p11.2
Prenatal Diagnosis 2016, 36, 1178–1184
L. Du et al.
linked to Smith–Magenis syndrome, which exhibits wide
phenotypic variability. This patient showed mild-to-moderate
mental retardation, while other patients with this syndrome
exhibit atypical facial features and cardiac, renal, and
otolaryngologic abnormalities.21,22 However, a high-resolution
array analysis of a monochorionic–diamniotic twin with a
discordant phenotype did not explain why only one member
of the twin pair was affected with features associated with
Smith–Magenis syndrome. Multiple possible explanations
exist, including the presence of a regulatory factor that affects
gene expression or a coding region CNV, the presence of
mutations only in the affected individual, or mutations in a
region that may not have been revealed by current CNV
analysis methods. Additionally, it is possible that the cause of
these congenital malformations may not be directly related
to genetics and may involve a currently unidentified
environmental factor.23 Case 23 had a 205-Kb deletion in
chromosome 16p13.3 detected by postnatal CMA that was
linked to Rubinstein–Taybi syndrome, a condition charac-
terized by short stature, moderate-to-severe intellectual
disability, distinctive facial features, and broad thumbs and
first toes.24,25 Additional features of this disorder can include
eye abnormalities, heart and kidney defects, dental problems,
and obesity.25–27 These signs and symptoms vary among
affected individuals, and approximately 25% are associated
with CHDs, such as patent ductus arteriosus, atrial septal
defects, and VSDs.27,28 Case 24 harbored a 3.16-Mb duplication
in chromosome 11p15.5 and a 7.86-Mb duplication in 15q11.2.
The parental samples were tested and confirmed a maternal
disomy duplication in chromosome 11p15.5 that was linked
to Russell–Silver syndrome, which is characterized by prenatal
and postnatal growth retardation, relative macrocephaly,
triangular face, and body asymmetry; approximately 10 to
20% of Russell–Silver syndrome cases are associated with
CHDs, such as atrial septal defects, VSDs, tetralogy of Fallot,
and pulmonary artery stenosis.29,30 The duplication in chro-
mosome 15q11.2 included many OMIM genes associated with
immunological diseases, congenital heart defects, neuro-
developmental impairment, and metabolic diseases. Campos
et al. reported a newborn with severe coarctation of the aorta,
patent ductus arteriosus, an atrial septal defect, and several
VSDs identified by echocardiography, duodenal atresia, left
appendix, constipation, feeding difficulties, failure to thrive,
hypertonia, and neuropsychomotor development delay; this
child died at the age of 4 months.31 Case 25 had a 23.5-Kb
deletion in chromosome 16p13.3 that contained two OMIM
genes, HBA1 and HBA2, which are associated with Hemoglobin
H disease.32
We observed three (5.8%) cases of VOUS. Case 28 had a
mosaic 3.6-Mb duplication of 1p36.33p36.32. The parents’
array comparative genomic hybridization results were normal.
Thus, the fetal CNV was de novo, and its clinical significance
was uncertain. Case 29 harbored a 150-Kb duplication in
chromosome 1p21.2 involving two OMIM genes, AGL and
DBT, which are associated with glycogen storage disease III
and maple syrup urine disease, respectively.33,34 The parental
samples were unavailable, and the clinical significance of the
fetal CNV was uncertain. Case 30 had a 273-Kb duplication in
© 2016 John Wiley & Sons, Ltd.
Chromosomal microarray analysis of fetal ventricular septal defects
chromosome 16p13.3 that involved one OMIM gene, AXIN1,
which is associated with a caudal duplication anomaly and
hepatocellular carcinoma.35,36 The parental samples were
unavailable; thus, the clinical significance of this fetal CNV
was uncertain. Due to the complex cardiac abnormalities, the
parents opted to terminate the pregnancy, and the absence
of the left ear was observed at autopsy after not being detected
by prenatal ultrasound.
Microarray analysis not only provides copy number infor-
mation but also identifies low mosaicism.16 In our study,
CMA revealed a mosaic 3.6-Mb duplication of 1p36.33p36.32
with 23% coverage. However, few cases of isolated terminal
duplications of 1p36 have been reported, perhaps due to either
under ascertainment or a proportionately higher incidence
of more complex rearrangements.37 Giannikou et al. first
reported two cases with isolated terminal duplications of
1p36; both of these patients displayed developmental retar-
dation and psychomotor delays. Echocardiography in one
patient revealed left ventricle hypertrophy.38 Zhu et al.
reported a fetus with a partial duplication of 1p36.33p36.32
(23%) and uniparental disomy of chromosome 6.39 Postpartum
pathology revealed a square head, rocker bottom feet, long
bone dysplasias, ectopic thyroids around the thymus, and
cystic structures in the adrenal cortex.39 In contrast, our case
had a 2.6-mm prenatal isolated VSD, and the parents’ CMA
results were normal. Therefore, we believe this duplication to
be a VOUS. At the last follow-up, the baby was more than
2 years old with normal growth and development, and the size
of the defect had decreased to 1 mm.
In conclusion, our data show that CMA is a valuable tool for
identifying unbalanced submicroscopic chromosomal abnor-
malities and low mosaicism in the prenatal diagnosis of VSDs.
The data also confirm that fetal ultrasound misses certain
additional lesions, although the false-negative rate of extra-
cardiac malformations associated with VSDs is low. It is
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Prenatal Diagnosis 2016, 36, 1178–1184
1183
difficult to provide a link between a CNV or a candidate gene
and the observed phenotype due to complex mechanisms,
such as incomplete penetrance, the effect of imprinted genes
or modifiers, mutations in recessive genes, and position
effects. The complexity of additional defects enhanced the
frequency of pathogenic CNVs, although the results were not
significantly different. CMA coreliably aids in clinical molecular
diagnosis and prenatal genetic counseling.
Ethics approval
The procedures were performed in accordance with the
ethical standards of the responsible committee on human
experimentation.
WHAT’S ALREADY KNOWN ABOUT THIS TOPIC?
• Ventricular septal defects are the most common form of congenital
cardiovascular anomaly; approximately 20 to 40% of ventricular
septal defects are attributable to Mendelian diseases or
chromosomal aneuploidies, while the remaining are attributable to
non-Mendelian causes that are poorly understood. Chromosomal
microarray analysis has been successfully applied to identify copy
number variations in postnatal and prenatal subjects with congenital
heart disease and has enabled whole-genome screening for
chromosomal imbalances at higher resolution than conventional
karyotyping. Subgroup analyses of different types of congenital
heart disease and associated copy number variation are rare.
WHAT DOES THIS STUDY ADD?
• In this study, our data show that chromosomal microarray analysis is
a valuable tool for identifying unbalanced submicroscopic
chromosome abnormalities in the prenatal diagnosis of ventricular
septal defects (VSDs). The detection rate of copy number variations
in VSDs with other ultrasound anomalies was nonsignificantly higher
than that in isolated VSDs.
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