Clinical value of screening prenatal ultrasound combined with chromosomal microarrays in prenatal diagnosis of chromosomal abnormalities

OBJECTIVE

To evaluate the clinical value of ultrasound findings in the screening of fetal chromosomal abnormalities and the analysis of risk factors for chromosome microarray analysis (CMA) abnormalities.

METHODS

We retrospectively analyzed the datasets of 15,899 pregnant women who underwent prenatal evaluations at Affiliated Maternity and Child Health Care Hospital of Nantong University between August 2018 and December 2022. Everyone underwent ultrasound screening, and those with abnormal findings underwent CMA to identify chromosomal abnormalities.

RESULTS

The detection rates for isolated ultrasound anomalies and combined ultrasound and CMA anomalies were 11.81% (1877/15,899) and 2.40% (381/15,899), respectively. Among all ultrasound abnormalities, detection rates for isolated ultrasound soft marker anomalies, isolated structural abnormalities, and both ultrasound soft marker anomalies with structural abnormalities were 82.91% (1872/2258), 15.99% (361/2258), and 1.11% (25/2258), respectively. The detection rate of abnormal chromosomes in pregnant women with abnormal ultrasound results was 16.87% (381/2258). The detection rates were 13.33% in cases with two or more ultrasound soft markers anomalies, 47.37% for two or more structural anomalies, and 48.00% for concomitant ultrasound soft marker and structural anomalies.

CONCLUSIONS

Enhanced detection rates of chromosomal anomalies in fetal malformations are achieved with specific ultrasound findings (NT thickening, cardiovascular abnormalities, and multiple soft markers) or when combined with high-risk factors (advanced maternal age, familial history, parental chromosomal anomalies, etc.). When the maternal age is over 35 and with ≥2 ultrasound soft marker anomalies accompanied with any high-risk factors, CMA testing can aid in the diagnosis of prenatal chromosomal abnormalities.

Pathogenic recurrent copy number variants in 7,078 pregnancies via chromosomal microarray analysis

OBJECTIVES

To investigate the incidence of pathogenic recurrent CNVs in fetuses with different referral indications and review the intrauterine phenotypic features of each CNV.

METHODS

A total of 7,078 amniotic fluid samples were collected for chromosome microarray analysis (CMA) and cases carrying pathogenic recurrent CNVs were further studied.

RESULTS

The highest incidence of pathogenic recurrent CNVs was 2.25 % in fetal ultrasound anomalies (FUA) group. Moreover, regardless of other indications, pregnant women with advanced maternal age have a lower incidence compared with whom less than 35 years old (p<0.05). In total 1.17 % (83/7,078) samples carried pathogenic recurrent CNVs: 20 cases with 22q11.2 recurrent region (12 microdeletion and eight microduplication), 11 with 1q21.1 (five microdeletion and six microduplication) and 16p13.11 (four microdeletion and seven microduplication), 10 with 15q11.2 recurrent microdeletion, seven with Xp22.31 recurrent microdeletion and 16p11.2 (three microdeletion and four microduplication), four with 7q11.23 (two microdeletion and two microduplication), three with 17p11.2 (three microdeletion), 17p12 (two microdeletion and one microduplication) and 17q12 (two microdeletion and one microduplication). The rest ones were rare in this study.

CONCLUSIONS

Pathogenic recurrent CNVs are more likely to be identified in FUA group. Pregnant women with advanced maternal age have a lower incidence of pathogenic recurrent CNVs. The profile of pathogenic recurrent CNVs between prenatal and postnatal is different, especially in 22q11.2, 1q21.1, 15q13.3 recurrent region and 15q11.2 deletion.

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.

Chromosome Microarray Analysis for the Investigation of Deletions in Pediatric Movement Disorders: A Systematic Review of the Literature

Background

Chromosome microarray analysis (CMA) can detect copy number variants (CNV) beyond the resolution of standard G-banded karyotyping. De novo or inherited microdeletions may cause autosomal dominant movement disorders.

Objectives

The purpose of this study was to analyze the clinical characteristics, associated features, and genetic information of children with deletions in known genes that cause movement disorders and to make recommendations regarding the diagnostic application of CMA.

Methods

Clinical cases published in English were identified in scientific databases (PubMed, ClinVar, and DECIPHER) from January 1998 to July 2019 following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Cases with deletions or microdeletions greater than 300 kb were selected. Information collected included age, sex, movement disorders, associated features, and the size and location of the deletion. Duplications or microduplications were not included.

Results

A total of 18.097 records were reviewed, and 171 individuals were identified. Ataxia (30.4%), stereotypies (23.9%), and dystonia (21%) were the most common movement disorders. A total of 16% of the patients demonstrated more than one movement disorder. The most common associated features were intellectual disability or developmental delay (78.9%) and facial dysmorphism (57.8%). The majority (77.7%) of microdeletions were smaller than 5 Mb. We find no correlation between movement disorders, their associated features, and the size of microdeletions.

Conclusions

Our results support the use of CMA as an investigational test in children with movement disorders. As the majority of identified articles were case reports and small case series (low quality), future efforts should focus on larger prospective studies to examine the causation of microdeletions in pediatric movement disorders.

SOX3 duplication in a boy with 46,XX ovotesticular disorder of sex development and his 46,XX sister with atypical genitalia: Probable germline mosaicism

Ovotesticular disorders of sex development (OT-DSD) are characterized by ovarian follicles and seminiferous tubules in the same individual, with a wide range of atypical genitalia. We report on two sibs with atypical genitalia and SRY-negative 46,XX DSD, OT-DSD was confirmed only in the boy, while the girl had bilateral ovaries. Chromosome microarray analysis (CMA) showed a 737-kb duplication at Xq27.1 including the entire SOX3 gene in both sibs, which was confirmed by quantitative real time PCR. Also, X chromosome inactivation assay showed random inactivation in both sibs. Whole exome sequencing revealed no pathogenic or likely pathogenic variant. CMA of the parents showed normal results for both, suggesting that germline mosaicism could be the reason of recurrence of this duplication in the siblings. Our results support a pathogenic role of SOX3 overexpression in 46,XX subjects leading to variable DSD phenotypes.

A Novel Look at Dosage-Sensitive Sex Locus Xp21.2 in a Case of 46,XY Partial Gonadal Dysgenesis without NR0B1 Duplication

A region of 160 kb at Xp21.2 has been defined as dosage-sensitive sex reversal (DSS) and includes the NR0B1 gene, considered to be the candidate gene involved in XY gonadal dysgenesis if overexpressed. We describe a girl with 46,XY partial gonadal dysgenesis carrying a 297 kb duplication at Xp21.2 upstream of NR0B1 initially detected by chromosomal microarray analysis. Fine mapping of the breakpoints by whole-genome sequencing showed a tandem duplication of TASL (CXorf21), GK and partially TAB3, upstream of NR0B1. This is the first description of an Xp21.2 duplication upstream of NR0B1 associated with 46,XY partial gonadal dysgenesis.

Pathogenic Copy Number Variations Involved in the Genetic Etiology of Syndromic and Non-Syndromic Intellectual Disability-Data from a Romanian Cohort

The investigation of unexplained global developmental delay (GDD)/intellectual disability (ID) is challenging. In low resource settings, patients may not follow a standardized diagnostic process that makes use of the benefits of advanced technologies. Our study aims to explore the contribution of chromosome microarray analysis (CMA) in identifying the genetic etiology of GDD/ID. A total of 371 Romanian patients with syndromic or non-syndromic GDD/ID, without epilepsy, were routinely evaluated in tertiary clinics. A total of 234 males (63.07%) and 137 (36.93%) females, with ages ranging from 6 months to 40 years (median age of 5.5 years), were referred for genetic diagnosis between 2015 and 2022; testing options included CMA and/or karyotyping. Agilent Technologies and Oxford Gene Technology CMA workflows were used. Pathogenic/likely pathogenic copy number variations (pCNVs) were identified in 79 patients (21.29%). Diagnosis yield was comparable between mild ID (17.05%, 22/129) and moderate/severe ID 23.55% (57/242). Higher rates were found in cases where facial dysmorphism (22.97%, 71/309), autism spectrum disorder (ASD) (19.11%, 26/136) and finger anomalies (20%, 27/96) were associated with GDD/ID. GDD/ID plus multiple congenital anomalies (MCA) account for the highest detection rates at 27.42% (17/62). pCNVs represent a significant proportion of the genetic causes of GDD/ID. Our study confirms the utility of CMA in assessing GDD/ID with an uncertain etiology, especially in patients with associated comorbidities.

Prenatal chromosomal microarray analysis in foetuses with isolated absent or hypoplastic nasal bone

OBJECTIVES

To evaluate the efficiency of chromosomal microarray analysis (CMA) in the prenatal diagnosis of foetuses with isolated absent or hypoplastic nasal bone (NB) in the first and second trimester.

METHODS

From January 2015 to April 2021, foetuses with isolated absent or hypoplastic NB who received invasive prenatal diagnosis were enrolled. The results of CMA were analysed.

RESULTS

There were 221 foetuses, including 166 cases with isolated absent NB and 55 cases with isolated hypoplastic NB. Twenty-four foetuses (10.9%, 24/221) had an ultrasonic diagnosis in the first trimester and 197 (89.1%, 197/221) had a ultrasonic diagnosis in the second trimester. The overall diagnostic yield of CMA was 9.0% (20/221). Aneuploidies were detected in 13 (5.9%, 13/221) foetuses, including 10 Down syndrome, 2 Klinefelter's syndrome and 1 trisomy 18. Pathogenic copy number variations (CNVs) were detected in seven foetuses (3.2%, 7/221). In addition, variants of unknown significance (VOUS) were detected in four foetuses. The foetuses with isolated absent NB had a higher detection rate of chromosome abnormality than the isolated hypoplastic NB, but the difference was not significant in the statistical analysis (10.2% vs. 5.5%, χ² =0.642, p = .423). No significant difference was observed in the detection rate between the first trimester and the second trimester (16.6% vs. 8.1%, χ² = 1.002, p = .317, Chi-square test).

CONCLUSION

CMA can increase the diagnostic yield of chromosome abnormality, especially pathogenic CNVs for foetuses with isolated absent or hypoplastic NB. CMA should be recommended when isolated absent or hypoplastic NB is suspected antenatally.7.

A case of prenatal diagnosis of 16q24.3 microdeletion KBG syndrome and review of the literature

Here we report a case of a 16q24.3 microdeletion KBG syndrome (KBGS) in a fetus. The absence of a well‐defined phenotype poses a challenge for genetic diagnosis. This report demonstrated that the high‐risk chromosome 21 trisomy could be the first manifestation of KBGS, as observed in this case.

Phenotypic and mutational spectrum of ROR2-related Robinow syndrome

Robinow syndrome is characterized by a triad of craniofacial dysmorphisms, disproportionate-limb short stature and genital hypoplasia. A significant degree of phenotypic variability seems to correlate with different genes/loci. Disturbances of the non-canonical WNT-pathway have been identified as the main cause of the syndrome. Biallelic variants in ROR2 cause an autosomal recessive form of the syndrome with distinctive skeletal findings. Twenty-two patients with a clinical diagnosis of autosomal recessive Robinow syndrome were screened for variants in ROR2 using multiple molecular approaches. We identified 25 putatively pathogenic ROR2 variants, 16 novel, including single nucleotide variants and exonic deletions. Detailed phenotypic analyses revealed that all subjects presented with a prominent forehead, hypertelorism, short nose, abnormality of the nasal tip, brachydactyly, mesomelic limb shortening, short stature and genital hypoplasia in male patients. A total of 19 clinical features were present in more than 75% of the subjects, thus pointing to an overall uniformity of the phenotype. Disease-causing variants in ROR2, contribute to a clinically recognizable AR trait phenotype with multiple skeletal defects. A comprehensive quantitative clinical evaluation this cohort delineated the phenotypic spectrum of ROR2-related Robinow syndrome. The identification of exonic deletion variant alleles further supports the contention of a loss-of-function mechanism in the etiology of the syndrome. This article is protected by copyright. All rights reserved.

Progress in Methods for Copy Number Variation Profiling

Copy number variations (CNVs) are the predominant class of structural genomic variations involved in the processes of evolutionary adaptation, genomic disorders, and disease progression. Compared with single-nucleotide variants, there have been challenges associated with the detection of CNVs owing to their diverse sizes. However, the field has seen significant progress in the past 20–30 years. This has been made possible due to the rapid development of molecular diagnostic methods which ensure a more detailed view of the genome structure, further complemented by recent advances in computational methods. Here, we review the major approaches that have been used to routinely detect CNVs, ranging from cytogenetics to the latest sequencing technologies, and then cover their specific features.

Prenatal ultrasound phenotypic and genetic etiology of the 17q12 microduplication syndrome

BACKGROUND

Several studies have reported on the clinical phenotype of the 17q12 microduplication syndrome, a rare autosomal dominant genetic disorder, in children and adults, but few have reported on its prenatal diagnosis. This study analyzed the prenatal ultrasound phenotypes of the 17q12 microduplication syndrome to improve the understanding, diagnosis, and monitoring of this disease in fetuses.

METHODS

A retrospective analysis of 8,200 pregnant women who had received an invasive antenatal diagnosis at tertiary referral hospitals between January 2016 and August 2021 was performed. Amniotic fluid or cord blood was sampled from the pregnant women for karyotyping and chromosome microarray analysis (CMA).

RESULTS

The CMA revealed microduplication in the 17q12 region of the genome in five fetuses, involving fragments of about 1.5-1.9 Mb. Five fetuses with the 17q12 microduplication syndrome had different prenatal ultrasound phenotypes, including duodenal obstruction (two fetuses); mild ventriculomegaly, dysplasia of the septum pellucidum, agenesis of the corpus callosum (one fetus); and a strong echo in the left ventricle only (one fetus). The ultrasound phenotype of one fetus was normal. Among the five fetuses with the 17q12 microduplication syndrome, the parents of three refused CNV segregation analysis, while CNV segregation analysis was performed for the remaining two fetuses to confirm whether the disorder was inherited maternally or paternally, with normal phenotypes. After genetic counseling, the parents of those two fetuses chose to terminate the pregnancy, while the parents of the three unverified fetuses continued the pregnancy, with normal follow-up after birth.

CONCLUSION

Although prenatal ultrasound phenotypes in fetuses with the 17q12 microduplication syndrome are highly variable, our study has highlighted the distinct association between duodenal obstruction and the 17q12 microduplication syndrome. Understanding the relationship between the pathogenesis of the 17q12 microduplication in prenatal ultrasound phenotypes and its long-term prognosis will contribute to better genetic counseling concerning the 17q12 microduplication syndrome, which is still a challenge.

Autosomal chromosome microdeletions in three adolescent girls with premature ovarian insufficiency: a case report

BACKGROUND

Premature ovarian insufficiency (POI) in the pediatric age group is most commonly related to X chromosome abnormalities such as Turner syndrome. Autosomal chromosome microdeletions in ovarian failure are relatively rare. The present study identified new autosomal deletions in three girls with POI.

CASE

We present three adolescent girls aged 14-15 years who had not attained menarche. Upon physical examination, there was a lack of breast tissue and no prominent secondary sexual characteristics. Clinical evaluation, hormonal tests, abdominal ultrasonography, and chromosome karyotyping were performed. Chromosome microarray analysis (CMA) was also performed to detect DNA copy number changes. Luteinizing hormone level was significantly increased, while follicular stimulating hormone level was > 25 IU/L with low estradiol levels. Autosomal deletions were detected in all three cases by CMA. The first patient had 0.454 Mb deletion on 15q25.2, the second patient had 1.337 Mb deletion on 19p13.3, and the third patient had 0.163 Mb deletion on 16p11.2.

CONCLUSIONS

POI is rare in children and is most commonly associated with X chromosome abnormalities. However, normal karyotype does not exclude the presence of chromosomal abnormality. CMA should be considered in cases with POI to detect microdeletions in autosomal chromosomes.

Difficulties of Prenatal Genetic Counseling for a Subsequent Child in a Family With Multiple Genetic Variations

Many parents with a disabled child caused by a genetic condition appreciate the option of prenatal genetic diagnosis to understand the chance of recurrence in a future pregnancy. Genome-wide tests, such as chromosomal microarray analysis and whole-exome sequencing, have been increasingly used for prenatal diagnosis, but prenatal counseling can be challenging due to the complexity of genomic data. This situation is further complicated by incidental findings of additional genetic variations in subsequent pregnancies. Here, we report the prenatal identification of a baby with a MECP2 missense variant and 15q11.2 microduplication in a family that has had a child with developmental and epileptic encephalopathy caused by a de novo KCNQ2 variant. An extended segregation analysis including extended relatives, in addition to the parents, was carried out to provide further information for genetic counseling. This case illustrates the challenges of prenatal counseling and highlights the need to understand the clinical and ethical implications of genome-wide tests.

Chromosomal Microarray Analysis as First-Tier Genetic Test for Schizophrenia

Schizophrenia is a chronic, devastating mental disorder with complex genetic components. Given the advancements in the molecular genetic research of schizophrenia in recent years, there is still a lack of genetic tests that can be used in clinical settings. Chromosomal microarray analysis (CMA) has been used as first-tier genetic testing for congenital abnormalities, developmental delay, and autism spectrum disorders. This study attempted to gain some experience in applying chromosomal microarray analysis as a first-tier genetic test for patients with schizophrenia. We consecutively enrolled patients with schizophrenia spectrum disorder from a clinical setting and conducted genome-wide copy number variation (CNV) analysis using a chromosomal microarray platform. We followed the 2020 “Technical Standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen)” to interpret the clinical significance of CNVs detected from patients. We recruited a total of 60 patients (36 females and 24 males) into this study. We detected three pathogenic CNVs and one likely pathogenic CNV in four patients, respectively. The detection rate was 6.7% (4/60, 95% CI: 0.004–0.13), comparable with previous studies in the literature. Also, we detected thirteen CNVs classified as uncertain clinical significance in nine patients. Detecting these CNVs can help establish the molecular genetic diagnosis of schizophrenia patients and provide helpful information for genetic counseling and clinical management. Also, it can increase our understanding of the pathogenesis of schizophrenia. Hence, we suggest CMA is a valuable genetic tool and considered first-tier genetic testing for schizophrenia spectrum disorders in clinical settings.

Genetic Evaluation of Inpatient Neonatal and Infantile Congenital Heart Defects: New Findings and Review of the Literature

The use of clinical genetics evaluations and testing for infants with congenital heart defects (CHDs) is subject to practice variation. This single-institution cross-sectional study of all inpatient infants with severe CHDs evaluated 440 patients using a cardiovascular genetics service (2014–2019). In total, 376 (85.5%) had chromosome microarray (CMA), of which 55 (14.6%) were diagnostic in syndromic (N = 35) or isolated (N = 20) presentations. Genetic diagnoses were made in all CHD classes. Diagnostic yield was higher in syndromic appearing infants, but geneticists’ dysmorphology exams lacked complete sensitivity and 6.5% of isolated CHD cases had diagnostic CMA. Interestingly, diagnostic results (15.8%) in left ventricular outflow tract obstruction (LVOTO) defects occurred most often in patients with isolated CHD. Geneticists’ evaluations were particularly important for second-tier molecular testing (10.5% test-specific yield), bringing the overall genetic testing yield to 17%. We assess these results in the context of previous studies. Cumulative evidence provides a rationale for comprehensive, standardized genetic evaluation in infants with severe CHDs regardless of lesion or extracardiac anomalies because genetic diagnoses that impact care are easily missed. These findings support routine CMA testing in infants with severe CHDs and underscore the importance of copy-number analysis with newer testing strategies such as exome and genome sequencing.

Prenatal Diagnosis of True Fetal Mosaicism with Small Supernumerary Marker Chromosome Derived from Chromosome 16 by Funipuncture and Molecular Cytogenetics Including Chromosome Microarray

This study examined the molecular characterization of a prenatal case with true fetal mosaicism of small supernumerary marker chromosome 16 (sSMC(16)). A 41-year-old female underwent amniocentesis at 19 weeks of gestation due to advanced maternal age. Chromosomal analysis for cultured amniocytes revealed a karyotype of 47,XY,+mar[4]/46,XY[16]. Spectral karyotyping and metaphase fluorescence in situ hybridization (FISH) demonstrated that the sSMC was derived from chromosome 16 (47,XY,+mar.ish der(16)(D16Z1+)[13/20]). Confined placental mosaicism was initially suspected because the prenatal ultrasound revealed a normal structure and the pregnancy was uneventful. However, interphase FISH of cord blood performed at 28 weeks of gestation showed 20% mosaicism of trisomy chromosome 16 (nuc ish(D16Z2×3)[40/200]). Chromosome microarray analysis further demonstrated 55% mosaicism of an 8.02 Mb segmental duplication at the subcentromeric region of 16p12.1p11.1 (arr[GRCh37] 16p12.1p11.1(27021975_35045499)×3[0.55]). The results demonstrated a true fetal mosaicism of sSMC(16) involving chromosome16p12.1p11.1 that is associated with chromosome 16p11.2 duplication syndrome (OMIM #614671). After non-directive genetic counseling, the couple opted for late termination of pregnancy. This case illustrated the use of multiple molecular cytogenetic tools to elucidate the origin and structure of sSMC, which is crucial for prenatal counseling, decision making, and clinical management.

Comprehensive Evaluation of Non-invasive Prenatal Screening to Detect Fetal Copy Number Variations

Objective

To evaluate the effectiveness of non-invasive prenatal screening (NIPS) in prenatal screening of fetal pathogenic copy number variants (CNVs).

Materials and Methods

We evaluated the prenatal screening capacity using traditional and retrospective approaches. For the traditional method, we evaluated 24,613 pregnant women who underwent NIPS; cases which fetal CNVs were suggested underwent prenatal diagnosis with chromosomal microarray analysis (CMA). For the retrospective method, we retrospectively evaluated 47 cases with fetal pathogenic CNVs by NIPS. A systematic literature search was performed to compare the evaluation efficiency.

Results

Among the 24,613 pregnant women who received NIPS, 124 (0.50%) were suspected to have fetal CNVs. Of these, 66 women underwent prenatal diagnosis with CMA and 13 had true-positive results. The positive predictive value (PPV) of NIPS for fetal CNVs was 19.7%. Among 1,161 women who did not receive NIPS and underwent prenatal diagnosis by CMA, 47 were confirmed to have fetal pathogenic CNVs. Retesting with NIPS indicated that 24 of these 47 cases could also be detected by NIPS, representing a detection rate (DR) of 51.1%. In total, 10 publications, namely, six retrospective studies and four prospective studies, met our criteria and were selected for a detailed full-text review. The reported DRs were 61.10–97.70% and the PPVs were 36.11–80.56%. The sizes of CNVs were closely related to the accuracy of NIPS detection. The DR was 41.9% (13/31) in fetuses with CNVs ≤ 3 Mb, but was 55.0% (11/20) in fetuses with CNVs > 3 Mb. Finally, to intuitively show the CNVs accurately detected by NIPS, we mapped all CNVs to chromosomes according to their location, size, and characteristics. NIPS detected fetal CNVs in 2q13 and 4q35.

Conclusion

The DR and PPV of NIPS for fetal CNVs were approximately 51.1% and 19.7%, respectively. Follow-up molecular prenatal diagnosis is recommended in cases where NIPS suggests fetal CNVs.

Molecular characterization of small supernumerary marker chromosomes derived from chromosome 14/22 detected in adult women with fertility problems: Three case reports and literature review

RATIONALE

Small supernumerary marker chromosomes (sSMC) are structurally abnormal chromosomes, which can be detected in patients with developmental retardation, infertile problems, and prenatal fetus. We report 3 adult female with fertility problems carrying sSMC(14/22) and aim to explore the correlation between sSMC(14/22) and fertility problems in women.

PATIENT CONCERNS

Three Chinese female patients were referred for infertility consultation in our hospital.

DIAGNOSES

The karyotype of these 3 patients were 47, XX, +mar. The chromosome microarray analysis (CMA) detected various chromosomal duplications and deletions in the 3 cases: a 0.49Mb gain of 5q32 for case 1; a 0.54Mb gain of 14q32.33 and a 1.83Mb gain of 16p11.2 for case 2; a 0.37Mb loss of 13q21.2q21.31 and a 0.12Mb gain of Xp11.2 for case 3. Fluorescence in situ hybridization (FISH) using the specific probes for chromosomes 13/21, 14/22, and 15 was applied to identify the origination of these sSMC, which were all finally identified as sSMC(14/22).

INTERVENTIONS

Case 1 underwent the artificial reproductive technology to get her offspring and finally delivered a healthy male infant at 39 weeks. Case 2 did not plan to choose in vitro fertilization (IVF) to get offspring. Case 3 refused to do assisted reproductive technology.

OUTCOMES

The genotype-phenotype correlation of sSMC(14/22) remain unclear. However, the existence of sSMC(14/22) might negatively affect the fertility ability in sSMC female carriers.

LESSONS

The combined application of traditional banding technique and molecular cytogenetic techniques can better identify more details of sSMC. For sSMC carriers with fertility problems, they could get their offsprings through assisted reproductive technologies after comprehensive fertility assessment.

The prevalence of genetic diagnoses in fetuses with severe congenital heart defects

Purpose

Congenital heart defects (CHD) are associated with genetic syndromes. Rapid aneuploidy testing and chromosome microarray analysis (CMA) are standard care in fetal CHD. Many genetic syndromes remain undetected with these tests. This cohort study aims to estimate the frequency of causal genetic variants, in particular structural chromosome abnormalities and sequence variants, in fetuses with severe CHD at mid-gestation, to aid prenatal counselling.

Methods

Fetuses with severe CHD were extracted from the PRECOR registry (2012–2016). We evaluated pre- and postnatal genetic testing results retrospectively to estimate the frequency of genetic diagnoses in general, as well as for specific CHDs.

Results

919 fetuses with severe CHD were identified. After exclusion of 211 cases with aneuploidy, a genetic diagnosis was found in 15.7% (111/708). These comprised copy number variants in 9.9% (70/708). In 4.5% (41/708) sequence variants were found that would have remained undetected with CMA. Interrupted aortic arch, pulmonary atresia with ventricular septal defect and atrioventricular septal defect were most commonly associated with a genetic diagnosis.

Conclusion

In case of normal CMA results, parents should be offered exome sequencing sequentially, if time allows for it, especially if the CHD is accompanied by other structural malformations due to the large variety in genetic syndromes.

Clinical value of genetic analysis in prenatal diagnosis of short femur

Background

Fetal femur length (FL) is an important biometric index in prenatal screening. The etiology of short femur is diverse, with some pathogenic causes leading to adverse outcomes. To improve the accuracy and practicability of diagnosis, we investigated the value of genetic analysis in prenatal diagnosis of short femur.

Methods

We examined chromosomal microarray analysis (CMA) (64 fetuses) and karyotyping (59 fetuses) data retrospectively for short femur without fetal growth restriction (FGR). Genetic testing was conducted for 15 fetuses.

Results

Karyotyping and CMA detected chromosomal aberrations at rates of 13.6% and 27.2%, respectively. Among fetuses with other abnormalities, detection rates were 21.0% higher with CMA than karyotyping. CMA identified chromosomal abnormalities in 36.4% of cases with a FL 2–4 standard deviations (SDs) below the gestational age (GA) mean. Abnormality detection by CMA reached 38.5% in the second trimester. Duplication of 12p, 16p13.1 deletion, and uniparental disomy 16 were identified by CMA in three cases of short femur. Gene sequencing detected clinically notable mutations in 12/15 fetuses, among which 9/12 fetuses had FLs >4 SDs below the GA mean.

Conclusions

CMA yielded a higher detection value than karyotyping in fetuses with other abnormalities or a FL 2–4 SDs below the GA mean during the second trimester. Gene sequencing should be performed when FL is >4 SDs below the mean.

Paternal Low-Level Mosaicism-Caused SATB2-Associated Syndrome

Mutations of SATB2 (OMIM#608148) gene at 2q33.1 have been associated with the autosomal dominant SATB2-associated syndrome (SAS), which is still short of comprehensive diagnosis technologies for small deletions and low-level mosaicism. In this Chinese Han family, single nucleotide polymorphism array identified a 4.9-kb deletion in the SATB2 gene in two consecutive siblings exhibiting obvious developmental delay and dental abnormalities but failed to find so in their parents. Prenatal diagnosis revealed that their third child carried the same deletion in SATB2 and the pregnancy was terminated. To determine the genetic causes behind the inheritance of SATB2 deletion, gap-PCR was performed on peripheral blood-derived genomic DNA of the family and semen-derived DNA from the father. Gap-PCR that revealed the deletions in the two affected siblings were inherited from the father, while the less intense mutant band indicated the mosaicism of this mutation in the father. The deletion was 3,013 bp in size, spanning from chr2: 200,191,313-200,194,324 (hg19), and covering the entire exon 9 and part of intron 8 and 9 sequences. Droplet digital PCR demonstrated mosaicism percentage of 13.2% and 16.7% in peripheral blood-derived genomic DNA and semen-derived DNA of the father, respectively. Hereby, we describe a family of special AT-rich sequence-binding protein 2-associated syndrome caused by paternal low-level mosaicism and provide effective diagnostic technologies for intragenic deletions.

Prenatal diagnosis of de novo monosomy 18p deletion syndrome by chromosome microarray analysis: Three case reports

RATIONALE

Monosomy 18p deletion syndrome refers to a rare chromosomal disorder resulting from the part deletion of the short arm of chromosome 18. Prenatal diagnosis of de novo 18p deletion syndrome is a challenge due to its low incidence and untypical prenatal clinical presentation.

PATIENT CONCERNS

Three cases received amniocentesis due to increased nuchal translucency (INT), high risk for Down syndrome, and INT combined intrauterine growth retardation (IUGR), respectively.

DIAGNOSIS

The 3 cases were diagnosed with de novo monosomy 18p deletion syndrome by amniocentesis and chromosome microarray analysis (CMA).

INTERVENTIONS

Karyotype analysis and CMA were used to analyze the abnormal chromosome.

OUTCOMES

Case 1 and case 2 revealed 13.87 and 12.68 Mb deletions by array-CGH analysis, respectively. Case 3 revealed 6.9 Mb deletions in 18p11.32p11.31 and 7.5 Mb deletions in 18p11.23p11.21 by single nucleotide polymorphism array. All of the pregnancies were terminated due to the abnormal chromosome.

LESSONS

The fetal phenotype of monosomy 18p deletion syndrome shows great variability and may not be evident during the pregnancy. CMA may be served as an effective tool for the diagnosis of prenatal monosomy 18p deletion syndrome diagnosis.

Chromosomal Microarray Analysis versus Karyotyping in Fetuses with Increased Nuchal Translucency

We have carried out a retrospective study of chromosome anomalies associated with increased nuchal translucency (NT) in order to compare yield rates of karyotype, chromosome microarray analysis (CMA), and non-invasive prenatal testing (NIPT) in this condition. Presenting with increased NT or cystic hygroma ≥3.5 mm as an isolated sign, 249 fetuses underwent karyotype and/or CMA from 11 to 18 gestational weeks. Karyotype and fluorescence in situ hybridization (FISH) analyses detected 103 chromosomal anomalies including 95 aneuploidies and eight chromosomal rearrangements or derivatives. Further, seven pathogenic copy number variants (CNV), five likely pathogenic CNVs, and 15 variants of unknown significance (VOUS) were detected by CMA in fetuses with normal karyotype. Genetic testing is now facing new challenges due to results with uncertain clinical impacts. Additional investigations will be necessary to interpret these findings. More than 15% of the anomalies that we have diagnosed with invasive techniques could not be detected by NIPT. It is therefore definitely not recommended in the case of ultrasound anomalies. These results, while corroborating the use of CMA in fetuses with increased NT as a second tier after rapid aneuploidy testing, do not suggest a dismissal of karyotype analysis.

Application of chromosome microarray analysis in patients with unexplained developmental delay/intellectual disability in South China

BACKGROUND AND METHODS

Chromosome microarray analysis (CMA) is currently the first-tier diagnostic assay for the evaluation of developmental delay (DD) and intellectual disability (ID) with unknown etiology. Here, we present our clinical experience in implementing whole-genome high-resolution single nucleotide polymorphism (SNP) arrays to investigate 489 patients with unexplained DD/ID in whom standard karyotyping analyses showed normal karyotypes. This study aimed to assess the usefulness of CMA for clinical diagnostic testing in the Chinese population.

RESULTS

A total of 489 children were classified into three groups: isolated DD/ID (n = 358), DD/ID with epilepsy (n = 49), and DD/ID with other structural anomalies (n = 82). We identified 126 cases (25.8%, 126/489) of pathogenic copy number variants (CNVs) by CMA, including 89 (24.9%, 89/358) with isolated DD/ID, 13 (26.5%, 13/49) with DD/ID with epilepsy, and 24 (29.3%, 24/82) with DD/ID with other structural anomalies. Among the 126 cases of pathogenic CNVs, 79 cases were identified as microdeletion/microduplication syndromes, among which 76 cases were classified as common syndromes, and 3 cases were classified as rare syndromes, including 15q24 microdeletion syndrome, Xq28 microduplication syndrome and Lowe syndrome. Additionally, there were forty-seven cases of non-syndromic pathogenic CNVs. The ABAT, FTSJ1, DYNC1H1, and SETBP1 genes were identified as DD/ID candidate genes.

CONCLUSION

Our findings suggest the necessity of CMA as a routine diagnostic test for unexplained DD/ID in South China.

UPD16 itself is not a cause of intrauterine growth restriction

BACKGROUND

The clinical relevance of uniparental disomy (UPD16) for chromosome 16 is currently unclear.

METHODS AND RESULT

We performed chromosome microarray analysis on two fetus and their placentas, fluorescence in situ hybridization (FISH) to exclude the hidden chr16 trisomy mosaicism in the fetuses, and clinical whole-exome sequencing to assess for homozygosity mutations of autosomal-recessive diseases.

RESULTS

Microarray analysis of two fetuses had UPD16. The membranous placenta of the case 1 had confined placental mosaicism (CPM) for trisomy 16. Clinical whole-exome sequencing on chromosome 16 revealed three potentially pathogenic single nucleotide polymorphisms (SNPs). Gap-polymerase chain reaction (PCR) and MLPA for a-thal deletions demonstrated that case 2 was homozygous for the -SEA deletion.

CONCLUSIONS

The poor outcome in these fetuses may be attributed to other factors, the membranous placenta and the -SEA deletion, respectively. Fetal UPD16 itself might be not correlated with intrauterine growth restriction (IUGR) and thus is not the basic cause of IUGR.

Cutis laxa in a patient with 1p36 deletion syndrome

Chromosome 1p36 deletion is the most common subtelomeric deletion syndrome characterized by variable features including unique facial appearance, intellectual disability, developmental delay, cardiac defects, seizures and hypotonia. Here, we report a patient with developmental delay, dilated cardiomyopathy, seizures, hirsutism and cutis laxa who was diagnosed with 1p36 deletion syndrome by chromosome microarray analysis. This patient is the first reported case of 1p36 deletion syndrome associated with cutis laxa and our results suggest that the 1p36 region contains one or more genes relevant to cutis laxa. This case also indicates the importance of considering chromosome abnormalities (microdeletion/microduplication syndromes) in patients presenting skin disorders combined with unexplained developmental delay, intellectual disability or multiple congenital abnormalities.

Congenital cataract with LSS gene mutations: a new case report

BACKGROUND

Congenital cataract is one of the major causes of blindness and amblyopia in children. About one-third of the cases are inherited.

CASE PRESENTATION

We applied whole exome sequencing for a pediatric patient with congenital cataract, small penis, baldness and absence of eyebrows and detected a compound heterozygous mutation in the lanosterol synthase (LSS) gene. These two mutations were inherited from the patient's parents. Both mutations altered the amino acid coding, at highly conserved amino acid residues.

CONCLUSIONS

We concluded that the mutations affect the structural stability of the protein to some extent.

De Novo 1.77-Mb Microdeletion of 10q22.2q22.3 in a Girl With Developmental Delay, Speech Delay, Congenital Cleft Palate, and Bilateral Hearing Impairment

Interstitial deletions of chromosome band 10q22.1q22.3 are rare. We here report a 2.5-year-old female patient with developmental delay, speech delay, congenital cleft palate, and bilateral hearing impairment. The girl's karyotype was normal. Chromosome microarray analysis (CMA) revealed a 1.77-Mb de novo interstitial deletion in 10q22.2q22.3. The deletion harbors 9 genes, including KAT6B, DUPD1, DUSP13, SAMD8, VDAC2, COMTD1, ZNF503, NCRNA00245, and C10orf11. This is the first patient with a deletion of the smallest size in 10q22.2q22.3 as detected using single nucleotide polymorphism (SNP) arrays. Comparisons with patients with overlapping deletions and in neighboring regions demonstrate the clinical impact of each deletion and in the context of other deletions within the 10q22q23 region. Additionally, KAT6B and C10orf11 could represent disease-associated genes that contribute to developmental delay, speech and language delay, and congenital cleft palate.

Recurrent copy number variations as risk factors for autism spectrum disorders: analysis of the clinical implications

Chromosomal microarray analysis (CMA) is currently considered a first-tier diagnostic assay for the investigation of autism spectrum disorders (ASD), developmental delay and intellectual disability of unknown etiology. High-resolution arrays were utilized for the identification of copy number variations (CNVs) in 195 ASD patients of Greek origin (126 males, 69 females). CMA resulted in the detection of 65 CNVs, excluding the known polymorphic copy number polymorphisms also found in the Database of Genomic Variants, for 51/195 patients (26.1%). Parental DNA testing in 20/51 patients revealed that 17 CNVs were de novo, 6 paternal and 3 of maternal origin. The majority of the 65 CNVs were deletions (66.1%), of which 5 on the X-chromosome while the duplications, of which 7 on the X-chromosome, were rarer (22/65, 33.8%). Fifty-one CNVs from a total of 65, reported for our cohort of ASD patients, were of diagnostic significance and well described in the literature while 14 CNVs (8 losses, 6 gains) were characterized as variants of unknown significance and need further investigation. Among the 51 patients, 39 carried one CNV, 10 carried two CNVs and 2 carried three CNVs. The use of CMA, its clinical validity and utility was assessed.

Dysmorphology services: a snapshot of current practices and a vision for the future

Dysmorphology concerns the recognition and management of rare, multiple anomaly syndromes. Genomic technologies and software for gestalt recognition will re-shape dysmorphology services. In order to reflect on a model of the service in the post-genomic era, we compared the utility of dysmorphology consultations in two Mediterranean cities, Athens, Greece and Afula, Israel (MDS), the Manchester Centre for Genomic Medicine, a UK service with dysmorphology expertise (UKDS) and the DYSCERNE, digital service (DDS). We show that it is more likely that chromosome microarray analysis will be performed if suggested in the UKDS rather than in the MDS; this, most probably reflects the difference of access to genetic testing following funding limitations in the MDS. We also show that in terms of achieved diagnosis, the first visit to a dysmorphology clinic is more significant than a follow-up. We show that a confirmed syndrome diagnosis significantly decreases the requests for other, non-genetic, laboratory investigations. Conversely, it increases the requests for reviews by other specialists and, most significantly (t-test: 8.244), it increases further requests for screening for possible associated complications. This is the first demonstration of the demands, on a health service, following the diagnosis of a dysmorphic condition.

22q11.2 Microduplication in a patient with 19p13.12-13.13 deletion

BACKGROUND

The chromosome 22q11.2 region microduplication has been described in patients with variable phenotypes. Here we present a 3-month-old girl with both 22q11.2 microduplication and 19p13.12-13.13 deletion. The presence of both genomic imbalances in one patient has not been previously reported in literature.

METHODS

A routine G-banding karyotype analysis was performed using peripheral lymphocytes. Chromosome microarray analysis (CMA) was done using Affymetrix CytoScan™ HD array.

RESULTS

The result of karyotyping showed that the patient is 46,XX,t(12;19)(q24.3;p13.1), but CMA detected a 2.8Mb microduplication within the region 22q11.2 (chr22: 18,648,866-21,465,659) and a 1.2Mb deletion on the chromosome 19at band p13.12-p13.13 (chr19: 13,107,938-14,337,347) in her genome, while no abnormalities were identified on 12q24.3. The 3-month-old girl presented with microcephaly, cleft palate, low set and retroverted ears, and facial dysmorphism which consisted of the following: a long narrow face, widely spaced eyes, downslanting palpebral fissures, broad nasal base, short philtrum, thin upper lip, and micro/retrognathia. She also had a congenital right pulmonary artery sling and tracheal stenosis and suffered from significant hypotonia and partial bilateral mixed hearing loss.

CONCLUSIONS

We report a case of 22q11.2 duplication syndrome with 19p13.12-13.13 deletion. Synergistic effect from the two genomic imbalances is likely responsible for the complicated clinical features observed in this patient.

Copy neutral loss of heterozygosity in 20q in chronic lymphocytic leukemia/small lymphocytic lymphoma

Single nucleotide polymorphism (SNP)-based chromosome microarray analysis was used to uncover copy neutral loss of heterozygosity (LOH) in the long arm of chromosome 20 in blood or bone marrow specimens from three patients with chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL). All three patients presented with lymph node enlargement. Whereas one of the patients has had a complicated clinical course, the other two have a more indolent disease. Sequence analysis of the tumor suppressor gene ASXL1, which is located in 20q and is commonly mutated in malignant myeloid diseases and occasionally in CLL/SLL specimens, revealed no mutations in our three patients with copy neutral LOH in 20q. The possible contribution of other imprinted microRNAs and antisense genes residing in 20q to the pathogenesis of a subset of CLL/SLL patients is discussed. These findings illustrate the value of SNP arrays for the detection of novel recurrent genomic alterations that may contribute to CLL/SLL onset or progression.

Chromothripsis in a Case of TP53-Deficient Chronic Lymphocytic Leukemia

We describe genomic findings in a case of CLL with del(17p13.1) by FISH, in which SNP array analysis revealed chromothripsis, a phenomenon by which regions of the cancer genome are shattered and recombined to generate frequent oscillations between two DNA copy number states. The findings illustrate the value of SNP arrays for precise whole genome profiling in CLL and for the detection of alterations that would be overlooked with a standard FISH panel. This second report of chromothripsis in CLL indicates that this phenomenon is a recurrent change in this disease.