Chromosomal aneuploidies and copy number variations in posterior fossa abnormalities diagnosed by prenatal ultrasonography

Role of copy number variation analysis in prenatally diagnosed Blake's pouch cyst

BACKGROUND

Blake's pouch cyst (BPC) is a midline cystic anomaly of the posterior fossa. BPC has been shown to have a risk of aneuploidy prenatally. Copy number variation (CNV) and/or genetic syndromes have been reported in a few prenatal/postnatal cases with BPC. The purpose of this study is to determine the additional value of CNV analysis for prenatal diagnosis and prognosis evaluation of BPC.

METHODS

We reviewed the sonographic findings and genetic results of BPC diagnosed within 6 years at our center. Patients were classified into the isolated and non-isolated groups based on the prenatal and postnatal imaging. We analyzed the chromosomal abnormalities by conventional karyotype analysis combined with chromosomal microarray analysis (CMA) or CNV sequencing (CNV-seq).

RESULTS

We recruited 467 low-risk fetuses as the control group to establish normal references of vermian area and brainstem-vermis (BV) angle. Prenatal/postnatal MRI or neonatal neurosonography was used as diagnostic criteria. 34 patients were diagnosed as BPC, including 21 (61.8%) patients with non-isolated and 13 (38.2%) with isolated. Twenty-two patients underwent CMA/CNV-seq, among them 14 patients were performed both CMA/CNV-seq and karyotype analysis. Seven (7/22, 31.8%) patients with BPC had chromosomal abnormalities, including 3 (3/22, 13.6%) patients with chromosomal aneuploidy - trisomy 21, 18 and 13, and 4 (4/22, 18.2%) patients had pathogenic CNVs located at 3p, 9p, Xp/Xq and 7p. Anomalies in fetal heart (35.3%), central nervous system (CNS) (26.5%) and limb (14.7%) were the three top anomalies accompanying BPC.

CONCLUSIONS

CNV analysis could provide some additional information for prenatal diagnosis and prognosis counseling for patients with non-isolated BPC. And, it adds less value for patients with isolated BPC, however, isolated BPC can be a soft marker for aneuploidy.

Prenatal diagnosis of ultrasound soft markers in a single medical center of mainland China

BACKGROUND

There are a few studies on the chromosomal aberration of Ultrasound soft markers (USMs). The aim of this study was to determine the detection rate of clinically significant chromosomal abnormalities (CSCA) in fetuses with different USMs.

METHODS

This study included fetuses with USMs who underwent invasive prenatal diagnosis for karyotype and/or chromosomal microarray (CMA) by categorizing into two groups: a single USM (SUSM) and multiple USMs (MUSMs).

RESULTS

Of the 358 cases with USMs, CSCA occurred in 3.09% (8/259) and 8.08% (8/99) of the SUSM and MUSM groups, respectively (P < 0.05). Of 16 cases identified with CSCA, theoretically 68.75% (11/16) could be detected by karyotype, while 31.25% (5/16) could be recognized only by CMA. Among CSCA cases, the most frequent USM was an absent or hypoplastic nasal bone (62.5%, 10/16). In cases with negative karyotypes and/or CMA, follow-up results were available in 307 cases, including 292 term deliveries, 6 preterm deliveries, 8 terminations of pregnancy due to USMs, and 1 still birth.

CONCLUSION

MUSMs increased the risk of chromosomal abnormalities. An absent or hypoplastic nasal bone was the most clinically significant marker either alone or in combination with other USMs. Most of SUSM had a good prognosis.

Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges-Systematic Review of the Literature and Meta-Analysis

Fetal malformations occur in 2-3% of pregnancies. They require invasive procedures for cytogenetics and molecular testing. "Structural anomalies" include non-transient anatomic alterations. "Soft markers" are often transient minor ultrasound findings. Anomalies not fitting these definitions are categorized as "dynamic". This meta-analysis aims to evaluate the diagnostic yield and the rates of variants of uncertain significance (VUSs) in fetuses undergoing molecular testing (chromosomal microarray (CMA), exome sequencing (ES), genome sequencing (WGS)) due to ultrasound findings. The CMA diagnostic yield was 2.15% in single soft markers (vs. 0.79% baseline risk), 3.44% in multiple soft markers, 3.66% in single structural anomalies and 8.57% in multiple structural anomalies. Rates for specific subcategories vary significantly. ES showed a diagnostic rate of 19.47%, reaching 27.47% in multiple structural anomalies. WGS data did not allow meta-analysis. In fetal structural anomalies, CMA is a first-tier test, but should be integrated with karyotype and parental segregations. In this class of fetuses, ES presents a very high incremental yield, with a significant VUSs burden, so we encourage its use in selected cases. Soft markers present heterogeneous CMA results from each other, some of them with risks comparable to structural anomalies, and would benefit from molecular analysis. The diagnostic rate of multiple soft markers poses a solid indication to CMA.

Chromosomal Microarray Analysis in Pregnancies With Corpus Callosum or Posterior Fossa Anomalies

OBJECTIVE

We investigated the detection rate of clinically significant chromosomal microarray analysis (CMA) results in pregnancies with sonographic diagnosis of fetal corpus callosum anomalies (CCA) or posterior fossa anomalies (PFA).

METHODS

All CMA tests in pregnancies with CCA or PFA performed between January 2015 and June 2020 were retrospectively evaluated from the Israeli Ministry of Health database. The rate of CMA with clinically significant (pathogenic or likely pathogenic) findings was calculated and compared to a local Israeli cohort of 5,541 pregnancies with normal ultrasound.

RESULTS

One hundred eighty-two pregnancies were enrolled: 102 cases with CCA and 89 with PFA (9 cases had both). Clinically significant CMA results were found in 7/102 of CCA (6.9%) and in 7/89 of PFA (7.9%) cases. The CMA detection rate in pregnancies with isolated CCA (2/57, 3.5%) or PFA (2/50, 4.0%) was lower than in nonisolated cases, including additional CNS and/or extra-CNS sonographic anomalies (CCA-5/45, 11.1%; PFA-5/39, 12.8%), but this was not statistically significant. However, the rate among pregnancies that had extra-CNS anomalies, with or without additional CNS involvement (CCA-5/24, 20.8%; PFA-5/29, 17.2%), was significantly higher compared to all other cases (p = 0.0075 for CCA; p = 0.035 for PFA). Risk of CMA with clinically significant results for all and nonisolated CCA or PFA pregnancies was higher compared to the background risk reported in the control cohort (p < 0.001), but was not significant for isolated cases.

CONCLUSIONS

Our findings suggest that CMA testing is beneficial for the genetic workup of pregnancies with CCA or PFA, and is probably most informative when additional extra-CNS anomalies are observed.

Application of chromosome microarray analysis in prenatal diagnosis

Background

To explore the application value of chromosomal microarray analysis (CMA) in prenatal diagnosis.

Methods

The results of chromosome karyotype analysis and CMA of 477 cases undergoing amniocentesis were analyzed. The results of the no ultrasound abnormality group and the ultrasound abnormality group were compared separately. Within the ultrasound abnormality group, the results of the ultrasound structural malformation group, the ultrasound soft index abnormality group, and other ultrasound abnormality (including abnormal amniotic fluid volume and fetal growth restriction) groups were compared.

Results

Abnormal chromosome and CMA results were found in a total of 71 cases (15.88%, 71/447), which can be broken down into a total of 23 karyotype abnormalities (5.15%, 23/447), consisting of 18 cases of aneuploidy (4.03%, 18/447), 2 cases of unbalanced chromosome rearrangements (0.44%, 2/447), and 3 cases of chimerism (0.67%, 3/447); 17 cases with detection of pathogenic copy number variations (pCNVs) (3.80%, 17/447); and 31 cases of detection of clinical variants of unknown significance (VOUS) (6.93%, 31/447). CMA detected 3.8% more genetic abnormalities than karyotype analysis (in addition to the abnormalities detected simultaneously by karyotype analysis). Between the no ultrasound abnormality group and the ultrasound abnormality group, there was an extremely significant difference in the detection rate of an abnormal chromosomal karyotype (P < 0.01) and of VOUS (P < 0.01), but there was no significant difference in the detection rate of pCNV (P > 0.05). Comparing the ultrasound structural malformation group, the ultrasound soft index abnormality group, and the other ultrasound abnormality group, there were no significant differences in the detection rate of abnormal chromosomal karyotypes (P > 0.05), pCNV (P > 0.05) or VOUS (P > 0.05).

Conclusions

The detection rate of chromosomal karyotype abnormalities in prenatal diagnosis in cases with no ultrasound abnormalities was higher. For cases with fetal ultrasound structural abnormalities, when compared with traditional karyotype analysis, CMA can improve the detection rate of fetal genetic abnormalities. However, the no ultrasound abnormality group also had a high VOUS abnormality detection rate, so it is necessary to strictly define the CMA indications.

Should chromosomal microarray be offered to fetuses with ultrasonographic soft markers in second trimester: A prospective cohort study and meta-analysis

OBJECTIVE

To evaluate whether chromosomal microarray (CMA) should be offered to fetuses with ultrasonographic soft markers (USMs) in the second trimester.

METHODS

A prospective cohort study and meta-analysis were conducted. In the prospective cohort study, 564 fetuses with USMs were enrolled. In the meta-analysis, eligible articles describing copy number variations in fetuses with USMs were included.

RESULTS

In the prospective cohort study, the diagnostic yields of CMA over non-invasive prenatal testing (NIPT) and karyotyping were significantly higher in fetuses with mild ventriculomegaly (MVM) than those in local control cohorts with normal ultrasound. However, the yields of CMA over NIPT and karyotyping in fetuses with other USMs were similar to controls. About ten studies, involving 405 fetuses with MVM and 1412 fetuses with other USMs, were included in the meta-analysis. The pooled diagnostic yields of CMA over NIPT and karyotyping in fetuses with MVM were 4.9% and 3.2%, respectively. In fetuses with other USMs, the yields of CMA over NIPT and karyotyping were 1.2% and 0.4%, respectively.

CONCLUSION

It is reasonable to offer CMA as a first-tier test to fetuses with MVM. However, for fetuses with other USMs, the considerations to perform CMA should not differ from pregnancies with normal ultrasound.

Detection of submicroscopic chromosomal aberrations by chromosomal microarray analysis for the prenatal diagnosis of central nervous system abnormalities

Background

Central nervous system (CNS) abnormalities are a group of serious birth defects associated with high rates of stillbirths, infant death, or abnormal development, and various disease‐causing copy number variations play a much more important role in the etiology of CNS abnormalities. This study intends to present a retrospective study of the prenatal diagnosis and the pregnancy outcome of fetuses diagnosed with CNS abnormalities, and evaluate the clinical value of chromosomal microarray analysis (CMA) in prenatal diagnosis of CNS abnormalities.

Methods

A total of 356 fetuses with CNS abnormalities with or without other ultrasound abnormalities subjected to invasive prenatal diagnosis at the first affiliated hospital of Air Force Medical University from January 2015 to August 2018. All cases have performed both karyotyping and CMA concurrently, but 20 fetuses with chromosome aneuploidy were excluded in the current study.

Results

The CMA identified pathogenic copy number variants (pCNVs) in 27/336 (8.03%) fetuses, likely pCNVs in 8/336 (2.38%) fetuses, and variants of unknown significance (VOUS) in 11/336 (3.27%) fetuses. A total of 222 cases had single CNS abnormalities and the pCNVs detection rate was 5.86% (13/222), the remaining 114 cases including CNS abnormalities plus other structural abnormalities, ultrasonographic soft markers and two or more CNS abnormalities, the pCNVs detection rate was 12.3% (14/114).

Conclusions

Fetuses with CNS abnormalities have a higher risk of chromosomal abnormalities, our study showed that CNVs play an important role in the etiology of CNS abnormalities. The application of CMA could increase the detection rate of pCNVs causing CNS abnormalities.

Genetic tests aid in counseling of fetuses with cerebellar vermis defects

OBJECTIVE

To assess the value of chromosome microarray analysis (CMA) and whole exome sequencing (WES) in fetuses with cerebellar vermis defects (CVD).

METHODS

From 2013 to 2019, we performed CMA on 43 fetuses with CVD, who were divided into cerebellar vermis hypoplasia (CVH) group and Dandy-Walker malformation (DWM) group according to morphological subtypes. Subsequently, WES was performed on 19 fetuses with normal CMA results to identify diagnostic genetic variants (DGVs).

RESULTS

Chromosome aneuploidies and clinically significant copy number variants were identified in 23.3% (10/43) of fetuses, and a significantly higher positive rate was found in fetuses with multiple compared with isolated malformations (36% vs 5.6%, P = .028). STAG2 genes related to Xq25 duplication syndrome was possibly a novel candidate gene for CVD. WES detected eight DGVs in seven genes among the 19 fetuses tested. Autosomal recessive ciliopathies (4/8) caused by TMEM231, CSPP1, and CEP290 mutations, were the most frequent monogenetic diseases, followed by Opitz GBBB syndrome (2/8) caused by MID1 and SPECC1L variants.

CONCLUSION

The combined use of CMA and WES has the potential to provide genetic diagnoses in 42% (18/43) of fetal CVD. WES should be offered when CMA results are normal.

Prenatal sonographic diagnosis of Dandy-Walker malformation and type III lissencephaly: A novel association

Dandy-Walker malformation (DWM) may occur as part of Mendelian disorders such as Walker-Warburg and Meckel-Gruber syndromes. We report a novel association with type III lissencephaly in a 22-week male fetus. Ultrasound showed fetal akinesia deformation sequence, single umbilical artery, microlissencephaly, hydranencephaly with cerebral lamination, DWM, and pontocerebellar hypoplasia. These abnormalities were confirmed by magnetic resonance imaging and autopsy, which also revealed pulmonary and adrenal hypoplasia, common mesentery and bilateral uretero-pyelo-calyceal dilatation. Neuropathological examination showed brain calcifications and diffuse neuronal degeneration. We conclude that DWM may be a feature of type III lissencephaly and that this association can be easily diagnosed by ultrasound.

Is Cisterna Magna Width a Useful First-Trimester Marker of Aneuploidy?

OBJECTIVE

To assess whether the cisterna magna (CM) width measured in first-trimester fetuses is a useful marker for aneuploidy detection.

METHODS

This was a prospective study in 2 different cohorts in a tertiary referral center. The first cohort comprised 913 fetuses from the general pregnancy population during the period 2012-2016 and was used to construct the CM reference ranges applying the λ-μ-σ (LMS) method. The second cohort included 714 high-risk fetuses undergoing chorionic villus sampling during the period 2012-2016. Mean detection rates using the 95th percentile for CM width observed in chromosomal anomaly groups were compared with those obtained in chromosomally normal fetuses.

RESULTS

The 50th percentile for CM ranged from 1.66 to 2.75 mm when crown-rump length (CRL) increased from 45 to 84 mm. Among high-risk fetuses, the following chromosomal anomalies were diagnosed in 125 (17%) fetuses: trisomy 21 (n = 63), trisomy 18 or 13 (n = 21), monosomy X (n = 9), submicroscopic anomalies (n = 11), and other anomalies (n = 22). The mean CM width for euploid fetuses was 2.4 mm (1.13 multiples of the median, MoM). While CM width was significantly increased in trisomy 21 (mean 2.7 mm; 1.23 MoM; p > 0.05), no differences were found in the other anomaly groups. Among the 63 fetuses with trisomy 21, a CM width above the 99th percentile was observed in 23 fetuses (37%).

CONCLUSIONS

The new reference range for CM width at 11-13 weeks of gestation did not differ from previous studies. In first-trimester fetuses with trisomy 21, CM width appears to be increased, although its value as an ultrasound marker is limited, because of its detection rate of 37%.

Fetal and perinatal outcome associated with small cerebellar diameter based on second- or third-trimester ultrasonography

OBJECTIVE

To examine the outcome of pregnancy with fetal transverse cerebellar diameter (TCD) below the fifth percentile based on routine second- or third-trimester ultrasonography.

METHODS

We retrospectively analyzed the outcomes of 12 344 women according to TCD Z scores based on systematic second- or third-trimester ultrasound examination between 2007 and 2015. Information on major malformations, chromosomal anomalies, intrauterine or neonatal demise, and other abnormal findings were collected.

RESULTS

In total, 408 fetuses with small prenatal TCD underwent clinical investigation; 160 major malformations were noted, consisting mainly of neurological or cardiac anomalies (39,2%%). Chromosomal anomalies were reported in 39 (9.5%) and intrauterine or neonatal demise in 41 cases (10%). Major malformations and chromosomal anomalies were found in 46.4% and 10% of fetuses with extremely small TCD (Z score < -2.5), respectively, 31.3% and 12.7% of fetuses with small TCD (Z score between -2.0 and -1.645), and 39.6 % and 7.7% of fetuses with subnormal TCD (Z score between -2.0 and -1.645). Intrauterine or neonatal demise was noted in 22%, 8.8%, and 4.8% of fetuses with extremely small, small, and subnormal TCD, respectively (P < .05). Among intrauterine growth-restricted fetuses, fetal demise or neonatal adverse outcome was reported in 75%, 81.8%, and 18.5%, respectively. Of all the fetuses, 2.2% were lost to follow-up.

CONCLUSION

A small cerebellar diameter below the fifth percentile is a relevant marker to detect associated anomalies during routine ultrasound examination in the second or third trimester. This is related to a high rate of fetal malformations, chromosomal anomalies, and genetic disorders, regardless of the severity of the cerebellar small size. Small TCD seems to be a prognostic factor for fetal growth restriction. Therefore, when facing a TCD below the fifth percentile, patients should be referred for further sonography and fetal karyotyping.

Impact of introduction of noninvasive prenatal testing on uptake of genetic testing in fetuses with central nervous system anomalies

OBJECTIVE

To evaluate the impact of introduction of noninvasive prenatal testing (NIPT) on the uptake of invasive testing in pregnancies complicated by fetal central nervous system (CNS) anomalies.

METHODS

Retrospective review of all singleton pregnancies complicated by fetal CNS anomalies seen at a single tertiary center between 2010 and 2017. Cases who had undergone invasive testing or NIPT prior to the diagnosis of the CNS anomaly were excluded. Cases were segregated according to whether they were seen prior to introduction of NIPT (group A, 2010-2013) or thereafter (group B, 2014-2017). We examined the rate of invasive and noninvasive genetic testing in each group.

RESULTS

We retrieved 500 cases: 308 (62%) were isolated CNS anomalies, and 192 (38%) had additional structural anomalies. In the total cohort, 165 women (33%) underwent expectant management with no further prenatal genetic testing, 166 (33%) had invasive testing, 52 (10%) had NIPT, and 117 pregnancies (23%) were terminated without further prenatal investigations. The introduction of NIPT significantly decreased the number of pregnancies having no testing (44% group A vs 22% in group B, p < .0001), particularly in the group presenting with isolated ventriculomegaly, but did not affect the uptake of invasive testing (34% vs 32%, respectively; p = .61). NIPT would have missed 4% of pathogenic copy number variants (CNVs) in the group of cases with isolated brain anomalies and 11% of CNVs in cases with complex anomalies.

CONCLUSIONS

Uptake of invasive prenatal testing in fetuses with brain anomalies was not affected by NIPT. However, the incidence of no genetic testing was significantly reduced. NIPT was a suboptimal testing strategy in this population as it missed a significant number of subchromosomal genetic anomalies.