Implementation of high-resolution SNP arrays in the investigation of fetuses with ultrasound malformations: 5 years of clinical experience

Chromosome Microarray Analysis and Exome Sequencing: Implementation in Prenatal Diagnosis of Fetuses with Digestive System Malformations

(1) Purpose: Retrospective back-to-back comparisons were performed to evaluate the accuracy, effectiveness, and incremental yield of chromosome microarray analysis (CMA) and exome sequencing (ES) analysis in fetuses with digestive system malformations (DSMs). (2) Methods: In total, 595 women with fetal DSMs who underwent prenatal diagnosis were enrolled. We analyzed the diagnostic yields of CMA and ES and evaluated pregnancy outcomes. Copy number variants (CNVs) were classified according to the American College of Medical Genetics and Genomics guidelines. (3) Results: Pathogenic CNVs were detected in 11/517 (2.12%) fetuses, and variants of unknown significance (VUS) were identified in 69 (13.35%) fetuses using CMA. ES detected 29 pathogenic/likely pathogenic variants in 23/143 (16.08%) fetuses and 26/143 (18.2%) VUS. In those with other ultrasound abnormalities, the detection rate of multiple system structural malformations was 41.2%, followed by skeletal (33.3%), cardiovascular (25.4%), and central nervous system (18.6%) malformations. Of the 391 surviving children, 40 (10.2%) exhibited varying degrees of mental retardation. (4) Conclusion: A correlation exists between DSMs and chromosomal abnormalities. When combined with other systemic abnormalities, the incidence of chromosomal abnormalities increases significantly. Patients with congenital DSM are at risk of developing neurodevelopmental disorders. Combined CMA and ES detection of fetal DSM has good clinical application potential.

Prenatal Diagnosis of Talipes Equinovarus by Ultrasound and Chromosomal Microarray Analysis: A Chinese Single-Center Retrospective Study

Background: There are few studies on the detection rate by chromosomal microarray analysis (CMA) of the prenatal diagnosis of talipes equinovarus (TE) compared to conventional karyotyping. We aimed to explore the molecular etiology of fetal TE and examine the detection rate by CMA, which provides more information for the clinical screening and genetic counseling of TE. Methods: In this retrospective study, pregnancies diagnosed with fetal TE were enrolled and clinical data for all cases were retrieved from our medical record database, including demographic data for pregnancies, ultrasound findings, karyotype/CMA results, and pregnant and perinatal outcomes. Results: Among the 164 patients, 17 (10.4%) clinically significant variants were detected by CMA. In 148 singleton pregnancies, the diagnostic rate of clinically significant variants was significantly higher in the non-isolated TE group than in the isolated TE group (10/37, 27.0% vs. 6/111, 5.4%, P < 0.001). In twin pregnancies, 1 (6.3%) pathogenic copy number variant was present in the other 16 twin pregnancies. Conclusions: This study demonstrates that CMA is useful for the prenatal genetic diagnosis of fetal TE. Fetal TE with the associated structural malformation correlates with a higher probability of clinically significant variants. This data may aid prenatal diagnosis and genetic counseling for fetal TE.

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.

Application of Single Nucleotide Polymorphism Microarray in Prenatal Diagnosis of Fetuses with Central Nervous System Abnormalities

Background

The current gold standard of karyotype analysis for prenatal diagnosis of fetuses with central nervous system (CNS) abnormalities has some limitations. Here, we assessed the value of single nucleotide polymorphism (SNP) arrays as a diagnostic tool.

Methods

The results of prenatal diagnosis of 344 fetuses with CNS abnormalities as determined by ultrasonographic screening were retrospectively analyzed. All fetuses underwent chromosomal karyotype analysis and genome-wide SNP array analysis simultaneously. The resultant rates and frequencies of genomic abnormalities were compared.

Results

Karyotype analysis found 45 (13.2%) abnormal CNS cases, while SNP array found 60 (17.4%) cases. SNP array detected 23 (6.7%) cases of submicroscopic abnormalities that karyotype analysis did not find. The detection rate of karyotype analysis was 8.1% in the group with isolated CNS anomalies, but 16.5% in the group with CNS abnormalities plus extra ultrasound anomalies. Detection rates of SNP array were 12.4% and 20.8% in these two groups, respectively. Statistical analysis showed that the detection rates of both methods were significantly higher in the group with CNS malformations and other ultrasound anomalies than in the group with isolated CNS anomalies. Abnormal chromosomes were detected most frequently in fetuses with holoprosencephaly.

Conclusion

Genome-wide SNP array technology can significantly improve the positive detection rate of fetuses with CNS abnormalities. Combining karyotype analysis and SNP array technology is recommended for detecting the development of fetuses with abnormal CNS.

REDBot: Natural language process methods for clinical copy number variation reporting in prenatal and products of conception diagnosis

Background

Current copy number variation (CNV) identification methods have rapidly become mature. However, the postdetection processes such as variant interpretation or reporting are inefficient. To overcome this situation, we developed REDBot as an automated software package for accurate and direct generation of clinical diagnostic reports for prenatal and products of conception (POC) samples.

Methods

We applied natural language process (NLP) methods for analyzing 30,235 in‐house historical clinical reports through active learning, and then, developed clinical knowledge bases, evidence‐based interpretation methods and reporting criteria to support the whole postdetection pipeline.

Results

Of the 30,235 reports, we obtained 37,175 CNV‐paragraph pairs. For these pairs, the active learning approaches achieved a 0.9466 average F1‐score in sentence classification. The overall accuracy for variant classification was 95.7%, 95.2%, and 100.0% in retrospective, prospective, and clinical utility experiments, respectively.

Conclusion

By integrating NLP methods in CNVs postdetection pipeline, REDBot is a robust and rapid tool with clinical utility for prenatal and POC diagnosis.

Nonimmune hydrops fetalis: Genetic analysis and clinical outcome

OBJECTIVE

To investigate the genetic causes and clinical outcomes of nonimmune hydrops fetalis (NIHF).

METHODS

Cohort of cases of NIHF between July 2013 and December 2018. Initial genetic testing included quantitative fluorescence polymerase chain reaction for aneuploidies, karyotyping and chromosomal microarray analysis (CMA). In negative results, whole exome sequencing (WES) of the fetuses and parents was performed. Clinical post-natal follow-up assessments were conducted.

RESULTS

One hundred and nine patients fulfilled the study inclusion criteria and were sequentially genetically assessed by karyotype, CMA and WES. Among them, 24.8% (27/109) had a clinically significant genetic abnormality: 21 (19%) had abnormal karyotypes; 3/72 had pathogenic/likely pathogenic copy number variants (additional yield = 4.2%); and 3 had single gene disorders. The pregnancy termination and live birth rates of the cases with positive genetic testing results were significantly different from those with negative results (92.6% vs 53.7% and 3.7% vs 31.7%, respectively, P < .05 for both). During clinical follow-up of the survivors, 3/23 (13.0%) children developed an additional phenotype.

CONCLUSION

This study improves our understanding of the diagnostic yield of CMA and WES for NIHF. A genetic diagnosis of NIHF can help determine the fetal prognosis and recurrence risk and influence pregnancy decision-making.

Chromosomal abnormalities detected by karyotyping and microarray analysis in twins with structural anomalies

OBJECTIVES

To evaluate the incidence and types of chromosomal abnormalities detected in twins with structural anomalies and compare their distribution according to chorionicity and amnionicity and by structural-anomaly type. The added value of chromosomal microarray analysis (CMA) over conventional karyotyping in twins was also estimated.

METHODS

This was a single-center, retrospective analysis of 534 twin pregnancies seen over an 11-year period, in which one or both fetuses were diagnosed with congenital structural anomalies on ultrasound. The ultrasound findings and invasive prenatal diagnostic results were reviewed. Twin pregnancies were categorized as monochorionic monoamniotic (MCMA), monochorionic diamniotic (MCDA) or dichorionic diamniotic (DCDA). Chromosomal abnormalities detected by G-banding karyotyping and/or CMA were analyzed by chorionicity and amnionicity and by structural-anomaly type.

RESULTS

The 534 twin pairs analyzed comprised 25 pairs of MCMA, 112 pairs of MCDA and 397 pairs of DCDA twins. Of the 549 fetuses affected by structural anomalies, 432 (78.7%) underwent invasive prenatal testing and cytogenetic results were obtained. The incidence of overall chromosomal abnormalities in the DCDA fetuses (25.4%) was higher than that in the MCMA (3.7%) and MCDA (15.3%) fetuses. The incidence of aneuploidy was significantly higher in the DCDA group (22.8%) than in the MCMA (0.0%) and MCDA (12.4%) groups. The incidence of chromosomal abnormalities detected in fetuses, with anomalies of the cardiovascular, faciocervical, musculoskeletal, genitourinary and gastrointestinal systems, was higher in the DCDA group than in the MCDA group. In both the DCDA and MCDA groups, hydrops fetalis was associated with the highest incidence of chromosomal abnormality; of these fetuses, 67.6% had Turner syndrome (45,X). Pathogenic copy-number variations (CNVs) undetectable by karyotyping were identified by CMA in five (2.0%; 95% CI, 0.3-3.7%) DCDA fetuses. No pathogenic CNVs were found in MCMA and MCDA twins.

CONCLUSIONS

Dichorionic twins with structural anomalies have a higher risk of chromosomal abnormalities, especially aneuploidies, than do monochorionic twins. The incremental diagnostic yield of CMA over karyotyping seems to be lower (2.0%) in twins than that reported in singleton pregnancy. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.

Prenatal diagnosis of submicroscopic chromosomal aberrations in fetuses with congenital cystic adenomatoid malformation by chromosomal microarray analysis

OBJECTIVES

To explore the copy number variations (CNVs) of fetal congenital cystic adenomatoid malformation (CCAM).

METHODS

Fetuses with CCAM were investigated by karyotypes and chromosomal microarray analysis (CMA). The cases were classified as isolated or CCAM with additional structural anomalies. The pregnancy outcome and neonatal prognosis were reported after the follow-up investigation.

RESULTS

The karyotypes of 43 fetuses were analyzed and no abnormal karyotype was detected. Thirty-seven cases were further tested using CMA. The CMA identified pathogenic CNVs in three fetuses with a pathogenic detection rate of 8.1%. Well-known microdeletion or microduplication syndromes, including RCAD syndrome, HNPP, and CMT1A were identified, among which HNPP and CMT1A were incidental findings. After excluding two incidental findings, there were no pathogenic CNVs in isolated CCAM. There were no significant differences in pathogenic CNVs between isolated CCAM and CCAM with additional structural anomalies (0%, 0/31 versus 16.7%, 1/6, p=.162). Nearly half of the patients (53.8%, 14/26) underwent surgery after birth with good postoperative recoveries while the remaining half patients were spontaneous regression or asymptomatic.

CONCLUSIONS

The results demonstrated the value of CMA in the prenatal diagnosis of CCAM. CCAM associated with other structural defects enhanced the frequency of pathogenic CNVs while isolated CCAM may not be associated with an increase in the prevalence of pathogenic CNVs. CCAMs have an overall good prognosis.

Chromosomal microarray analysis in pregnancies at risk for a molecular disorder

Objective: The aim of this study was to evaluate the utility of chromosomal microarray (CMA) in patients who were solely referred for molecular diagnosis.Methods: During a 2-year period, CMA was the patients' choice, whether to opt for it or not, for those at risk for fetal hemoglobin Bart's disease or β-thalassemia major who were referred for invasive prenatal diagnosis and had a normal fetal genotype. CytoScan 750 K array (Affymetrix Inc., Santa Clara, CA) was used for CMA. The CMA testing results were collected.Results: There were 184 patients, who had a normal genotypic result, opting CMA testing without an obvious indication for fetal karyotyping. The median maternal age was 29 years (range, 17-34); the median gestational age was 13 weeks (range, 11-20). In two out of 184 (1.1%) cases unexpected de novo pathogenic microdeletions were found: a 3.2 Mb 22q11.21 microdeletion and a 0.8 Mb 16p11.2 microdeletion.Conclusions: Pregnancies at risk for thalassemia can also benefit from performing CMA. This information might be a part of the contents in comprehensive pretest counseling for those who are referred for diagnostic testing due to a molecular disorder.

Chromosomal microarray analysis in the prenatal diagnosis of orofacial clefts: Experience from a single medical center in mainland China

The aim of this study was to investigate the value of chromosomal microarray analysis (CMA) for the prenatal diagnosis of orofacial clefts.A total of 143 fetuses with oral clefts were detected by ultrasound during prenatal exam between 2012 and 2017 in our center. We categorized the cases into 4 groups: isolated cleft lip (CL) (CL only), isolated cleft palate (CP only), isolated cleft lip and palate (CLP) (CLP only), and syndromic CLP (combined with other malformations). The CMA was performed in all cases, while 139 fetuses were referred for G-banded chromosome analysis.There were 42 male and 10 female fetuses were born, with a sex ratio of 4.2:1. The isolated CLP group accounted for 74.1% (106/143) of cases, while the isolated CL, isolated CP, and syndromic CP groups accounted for 13.9% (20/143), 2% (3/143), and 10% (14/143), respectively. A total of 11 fetuses had pathogenic copy number variants (CNVs, 7.7%), including isolated CP (1/143, 0.7%), isolated CLP (5/143, 3.5%), and syndromic CLP (5/143, 3.5%). Compared with the CMA results, 5 fetuses were found to have an abnormal karyotype (5/139, 3.6%). However, no abnormalities were found in either karyotype analysis or CMA in the isolated CL group.CMA is a valuable tool for identifying submicroscopic chromosomal abnormalities in the prenatal diagnosis of oral clefts. An excellent outcome can be expected for fetuses with isolated CL that are negative for chromosomal abnormalities.

Whole exome sequencing as a diagnostic adjunct to clinical testing in fetuses with structural abnormalities

OBJECTIVES

To evaluate the diagnostic yield of prenatal whole exome sequencing (WES) for monogenic disorders in fetuses with structural malformations and normal results on cytogenetic testing, and to describe information on pathogenic variants that is provided by WES.

METHODS

Karyotyping, chromosomal microarray analysis (CMA) and WES were performed sequentially on stored samples from a cohort of 3949 pregnancies with fetal structural abnormalities detected on ultrasound and/or magnetic resonance imaging, referred between January 2011 and December 2015. Diagnostic rates of the three techniques were investigated overall, for phenotypic subgroups and for proband-only vs fetus-mother-father samples. Information on pathogenic variants was identified by WES.

RESULTS

Overall, 18.2% (720/3949) of fetuses had an abnormal karyotype. Pathogenic copy number variants were detected on CMA in 8.2% (138/1680) of fetuses that had a normal karyotype result. WES performed on a subgroup of 196 fetuses with normal CMA and karyotype results revealed the putative genetic variants responsible for the abnormal phenotypes in 47 cases (24%). The molecular diagnosis rates for fetus-mother-father and proband-only samples were 26.5% (13/49) and 23.1% (34/147), respectively. Variants of uncertain significance were detected in 12.8% (25/196) of fetuses, of which 22 were identified in the fetal proband-only group (15%; 22/147) and three in the fetus-mother-father group (6.1%; 3/49). The incidental finding rate was 6.1% (12/196).

CONCLUSIONS

WES is a promising method for the identification of genetic variants that cause structural abnormalities in fetuses with normal results on karyotyping and CMA. This enhanced diagnostic yield has the potential to improve the clinical management of pregnancies and to inform better the reproductive decisions of affected families. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.

Prenatal homozygosity mapping detects a novel mutation in CHST3 in a fetus with skeletal dysplasia and joint dislocations

In selected cases, homozygosity mapping followed by direct sequencing of one or a few carefully selected candidate genes in a prenatal setting can be beneficial to obtain diagnosis in consanguineous families.

Microarrays in prenatal diagnosis

In prenatal diagnosis, chromosomal microarray (CMA) has not yet fully replaced conventional karyotyping but has rapidly become the recommended test in pregnancies with ultrasound abnormalities. In this review, we provide an overview of the published data concerning this technology and the controversies concerning its use in the prenatal setting. There is abundant evidence indicating the added detection of pathogenic abnormalities with CMA in comparison to the traditional karyotyping, especially in fetuses with multiple or isolated ultrasound abnormalities such as congenital heart disease, increased nuchal translucency, or oral cleft. On the other hand, there is also a risk to detect variants of unknown significance, late-onset disorders, and variants in susceptibility loci. However, it has been shown that pregnant couples tend to prefer a maximum of information about the health of their unborn child. Taken together, CMA has considerable diagnostic and prognostic values during pregnancy and should therefore be the test of choice.

Chromosomal Microarray Testing in NEC: A Case Report

Necrotizing enterocolitis (NEC) remains the most common reason for emergent surgery in the neonatal intensive care unit. The common pathophysiology in all NEC involves alteration in gut microflora, abnormal blood supply to the intestine, and uncontrolled cytokine release. We report a full-term neonate who developed NEC. The neonate had surgical resection of approximately 120cms of bowel. After an initial proximal jejunostomy she underwent a successful jejuno-ileal anastomosis with preservation of her ileocolic valve at 6 weeks of age. A little more than one year of age, she is being weaned off her parenteral nutrition (PN) as her bowel adaptation continues. A chromosomal microarray analysis (CMA) resulted in the identification of a 15q13.3 microdeletion.

Prenatal Diagnosis of Walker-Warburg Syndrome Using Single Nucleotide Polymorphism Array: A Clinical Experience from Three Related Palestinian Families with Congenital Hydrocephalus

Background Congenital hydrocephalus is a common and often disabling disorder. Various syndromic forms of hydrocephalus have been reported in the Palestinian population including Walker-Warburg syndrome (WWS), Carpenter syndrome, and Meckel syndrome. Aim In this report we discuss the antenatal diagnosis of congenital hydrocephalus in three related Palestinian families. Method Single nucleotide polymorphism (SNP) array was performed prenatally for the third affected fetus. Results A diagnosis of WWS was found and molecular testing revealed a known pathogenic mutation in the POMT2 gene. An affected fetus from the other family was diagnosed and tested postnatally in light of this finding. Testing of another affected stillborn offspring was performed and revealed the same mutation. Conclusions Here, we show that the use of prenatal SNP array testing can be helpful in elucidating the etiology of congenital hydrocephalus and in guiding appropriate perinatal care. Also, testing for this specific POMT2 mutation should be considered in cases of prenatally detected hydrocephalus in Palestinian families.

Subtelomeric multiplex ligation-dependent probe amplification as a supplement for rapid prenatal detection of fetal chromosomal aberrations

Background

Pregnant women with high-risk indications are highly suspected of fetal chromosomal aberrations. To determine whether Multiplex Ligation-dependent Probe Amplification (MLPA) using subtelomeric probe mixes (P036-E2 and P070-B2) is a reliable method for rapid detection of fetal chromosomal aberrations. The subtelomeric MLPA probe mixes were used to evaluate 50 blood samples from healthy individuals. 168 amniocytes and 182 umbilical cord blood samples from high-risk fetuses were analyzed using the same subtelomeric MLPA probe sets. Karyotyping was also performed in all cases of high-risk pregnancies, and single nucleotide polymorphism array analysis was used to confirm submicroscopic and ambiguous results from MLPA/karyotyping.

Results

Subtelomeric MLPA analysis of normal samples showed normal result in all cases by use of P036-E2 probe mix, while P070-B2 probe mix gave normal results for all but one case. In one normal control case P070-B2 produced a duplicated signal of probe for 13q34. In the high-risk group, totally 44 chromosomal abnormalities were found by karyotyping and MLPA, including 23 aneuploidies and 21 rearrangements or mosaics. MLPA detected all 23 aneuploidies, 12 rearrangements and 1 mosaic. Importantly, MLPA revealed 4 chromosomal translocations, 2 small supernumerary marker chromosomes (sSMCs), and 3 subtelomeric imbalances that were not well characterized or not detectable by karyotyping. However, MLPA showed negetive results for the remaining 8 rearrangements or mosaics, including 3 low mosaic aneuploidies, 1 inherited sSMC, and 4 paracentric inversions.

Conclusions

Results suggest that combined use of subtelomeric MLPA and karyotyping may be an alternative method for using karyotype analyses alone in rapid detection of aneuploidies, rearrangements, and sSMCs.

Electronic supplementary material

The online version of this article (doi:10.1186/s13039-014-0096-1) contains supplementary material, which is available to authorized users.

Microarray Technology for the Diagnosis of Fetal Chromosomal Aberrations: Which Platform Should We Use?

The advantage of microarray (array) over conventional karyotype for the diagnosis of fetal pathogenic chromosomal anomalies has prompted the use of microarrays in prenatal diagnostics. In this review we compare the performance of different array platforms (BAC, oligonucleotide CGH, SNP) and designs (targeted, whole genome, whole genome, and targeted, custom) and discuss their advantages and disadvantages in relation to prenatal testing. We also discuss the factors to consider when implementing a microarray testing service for the diagnosis of fetal chromosomal aberrations.

A new direction for prenatal chromosome microarray testing: software-targeting for detection of clinically significant chromosome imbalance without equivocal findings

Purpose. To design and validate a prenatal chromosomal microarray testing strategy that moves away from size-based detection thresholds, towards a more clinically relevant analysis, providing higher resolution than G-banded chromosomes but avoiding the detection of copy number variants (CNVs) of unclear prognosis that cause parental anxiety.

Methods. All prenatal samples fulfilling our criteria for karyotype analysis (n = 342) were tested by chromosomal microarray and only CNVs of established deletion/duplication syndrome regions and any other CNV >3 Mb were detected and reported. A retrospective full-resolution analysis of 249 of these samples was carried out to ascertain the performance of this testing strategy.

Results. Using our prenatal analysis, 23/342 (6.7%) samples were found to be abnormal. Of the remaining samples, 249 were anonymized and reanalyzed at full-resolution; a further 46 CNVs were detected in 44 of these cases (17.7%). None of these additional CNVs were of clear clinical significance.

Conclusion. This prenatal chromosomal microarray strategy detected all CNVs of clear prognostic value and did not miss any CNVs of clear clinical significance. This strategy avoided both the problems associated with interpreting CNVs of uncertain prognosis and the parental anxiety that are a result of such findings.