Whole exome sequencing improves genetic diagnosis of fetal clubfoot.

OBJECTIVE: This retrospective study aimed to investigate the value of whole exome sequencing (WES) for clubfoot (CF) fetuses with or without other structural abnormalities and to further explore the genetic causes of fetal CF. METHODS: this study included 83 singleton pregnancies diagnosed with fetal CF referred to our center between January 2016 and March 2022; cases were divided into two groups: isolated CF and non-isolated CF. After excluding cases with positive karyotyping and chromosomal microarray analysis results, WES was performed for the eligible fetuses and parents. Monogenic variants detected by WES and perinatal outcomes were recorded and evaluated at postnatal follow-up. RESULTS: overall, clinically significant variations were identified in 12.0% (10/83) of fetuses, and the detection rate was significantly higher in the non-isolated than in the isolated CF group (8/36, 22.2% vs. 2/47, 4.3%, p = 0.031). We additionally detected eight (9.6%) fetuses harboring variants of unknown significance. We identified 11 clinically significant variations correlating with clinical phenotypes in nine genes from ten fetuses, with KLHL40 being the most frequent (n = 2). Furthermore, we observed a significant difference in termination and survival rates between isolated and non-isolated CF cases (27.6 vs. 77.8% and 59.6 vs. 19.4%, p < 0.001 for both). CONCLUSION: our data indicate that WES has a high additional diagnostic yield for the molecular diagnosis of fetal CF, markedly enhancing existing prenatal diagnostic capabilities and expanding our understanding of intrauterine genetic disorders, thus assisting us to better interpret fetal phenotype in the future.

Prenatal diagnosis in the fetal hyperechogenic kidneys: assessment using chromosomal microarray analysis and exome sequencing.

Fetal hyperechogenic kidneys (HEK) is etiologically a heterogeneous disorder. The aim of this study was to identify the genetic causes of HEK using prenatal chromosomal microarray analysis (CMA) and exome sequencing (ES). From June 2014 to September 2022, we identified 92 HEK fetuses detected by ultrasound. We reviewed and documented other ultrasound anomalies, microscopic and submicroscopic chromosomal abnormalities, and single gene disorders. We also analyzed the diagnostic yield of CMA and ES and the clinical impact the diagnosis had on pregnancy management. In our cohort, CMA detected 27 pathogenic copy number variations (CNVs) in 25 (25/92, 27.2%) fetuses, with the most common CNV being 17q12 microdeletion syndrome. Among the 26 fetuses who underwent further ES testing, we identified 7 pathogenic/likely pathogenic variants and 8 variants of uncertain significance in 9 genes in 12 fetuses. Four novel variants were first reported herein, expanding the mutational spectra for HEK-related genes. Following counseling, 52 families chose to continue the pregnancy, and in 23 of them, postnatal ultrasound showed no detectable renal abnormalities. Of these 23 cases, 15 had isolated HEK on prenatal ultrasound. Taken together, our study showed a high rate of detectable genetic etiologies in cases with fetal HEK at the levels of chromosomal (aneuploidy), sub-chromosomal (microdeletions/microduplications), and single gene (point mutations). Therefore, we speculate that combined CMA and ES testing for fetal HEK is feasible and has good clinical utility. When no genetic abnormalities are identified, the findings can be transient, especially in the isolated HEK group.

Prenatal exome sequencing in fetuses with callosal anomalies.

OBJECTIVE: We aimed to investigate the value of exome sequencing (ES) in fetuses with callosal anomalies (CA) with or without other structural anomalies, but with normal findings by karyotyping and chromosome microarray analysis (CMA). METHODS: Cases with CA with or without other structural anomalies were screened for eligibility. Fetuses with abnormal karyotyping or CMA results were excluded. We performed ES on DNA samples from eligible fetus-parental trios and identified diagnostic genetic variants based on the ultrasonographic features. RESULTS: A total of 50 eligible fetus-parental trios were successfully analyzed by ES. We found 17 likely pathogenic or pathogenic variants in 14 genes from 17 fetuses, with a total proportion of diagnostic genetic variants equal to 34.0% (17/50). Of the 17 cases with a diagnosis, 10 (29.4%, 10/35) were isolated and 7 (43.8%, 7/15) were non-isolated. Pregnancy outcome data showed that 70.0% (7/10) of the surviving isolated CA fetuses with negative ES results had a good prognosis in early childhood. CONCLUSIONS: Our study used ES prenatally for CA and showed that ES can be used diagnostically to define the molecular defects that underlie unexplained CA. Most subjects with isolated CA with negative results for genetic causes will have a favorable prognosis in early childhood.

Compound heterozygous mutation of the ASXL3 gene causes autosomal recessive congenital heart disease.

To explore mutations in the additional sex combs-like 3 (ASXL3) gene in two Chinese families with congenital heart disease (CHD). Whole-exome sequencing (WES) was used to reveal a novel compound heterozygous mutation in the ASXL3 gene that was associated with CHD. Sanger sequencing of a further 122 CHD patients was used to determine an additional compound heterozygous mutation in the ASXL3 gene. Cell apoptosis was examined by MTS assay and flow cytometry. The cardiac structure was identified via hematoxylin-eosin (HE), Masson's trichrome, and ultrasound scanning. RNA sequencing was performed to identify a series of differentially expressed mRNAs. The mRNA and protein expressions were identified by quantitative real-time PCR and western blotting, respectively. A compound heterozygous mutation c.2168C > G (p.Pro723Arg) and c.5449C > G (p.Pro1817Ala) in the ASXL3 gene associated with CHD was identified. Overexpression of this compound heterozygous mutation in HL-1 cells resulted in increased apoptosis and reduced cell viability. Moreover, it affected cardiac structure and fibrosis in mice. There were 126 downregulated mRNAs and 117 upregulated mRNAs between the ASXL3 compound heterozygous mutation c.2168C > G (p.Pro723Arg) and c.5449C > G (p.Pro1817Ala) mice and wild-type mice. Ezh2, Slc6a4, and Socs3, which could interact with ASXL3 through proteins, were all upregulated. Another compound heterozygous mutation c.3526C > T (p.Arg1176Trp) and c.4643A > G (p.Asp1548Gly) in the ASXL3 gene was identified by screening a further 122 patients with CHD. The ASXL3 gene is important in cardiac development and may exert this influence by affecting the expression of mRNAs associated with cell apoptosis and cell proliferation.

Microarray analysis in fetuses with duodenal obstruction: It is not just trisomy 21.

OBJECTIVE: To explore the copy number variants (CNVs) in case of fetal duodenal obstruction (DO) and assess the associated prenatal findings and postnatal outcomes. MATERIALS AND METHODS: This retrospective study reviewed 51 fetuses with DO and the findings of chromosomal microarray analysis (CMA) used as a first-tier test in our institution between January 2014 and May 2019. RESULTS: The frequency of pathogenic aberrations in fetuses with DO was 15.7% (8/51), including 9.8% (5/51) pathogenic CNVs. Three fetuses with isolated DO each had a deletion on chromosome 13q, one fetus had duplication at 1q43q44, and one had microduplication at 17q12. No significant differences in pathogenic CNVs were observed between isolated DO and DO plus additional anomalies (4/42, 9.5% vs 1/9, 11.1%, P = .89). Of the 51 fetuses with DO, 11 pregnancies were terminated, and eight fetuses had chromosomal abnormalities; one pregnancy ended with intrauterine death, and there were 39 live births. Neonatal outcomes were available for 31 fetuses, and no neonatal deaths occurred after surgery. CONCLUSIONS: Our cohort study demonstrated the value of CMA in fetuses with DO, suggesting that CNVs may underly genetic etiologies that should be considered in the diagnostic evaluation of DO. We think CMA should be recommended in case of DO.

[Application of whole exome sequencing technology in fetuses with congenital structural abnormalities].

OBJECTIVE: To investigate the application value of whole exome sequencing technology in fetuses with congenital structural abnormalities. METHODS: The chromosomal abnormalities of 1147 families were analyzed. According to the follow-up results, the data of fetuses with new phenotypes in late pregnancy or after birth were reanalyzed. Subgroups were divided according to the organs involved and whether single malformation or not. The gene regulatory network map was drawn by using string database and Cytoscape software. Fisher exact probability method was used to compare the difference of the diagnostic rate of pathogenic genes among the groups. RESULTS: A total of 160 fetal cases received positive molecular diagnosed, involving 178 variant sites of 125 pathogenic genes, including 8 cases (4.9%, 8/163) by data reanalysis, and the overall positive diagnosis rate was 13.9%. Diagnostic rate was highest in the group of skeletal malformation (31.5%, 39/124) and lowest in that with thoracic malformation (0, 0/32). The gene clusters of fetal edema and intrauterine growth restriction were independent, and were not associated with the major structural malformations. The probability of each parent carrying the same recessive gene variant was 0.03 (39/1146) and 0.08 (4/53) with positive family history. CONCLUSION: For fetuses with congenital structural abnormalities that are negative for conventional genetic tests, 13.9% of phenotypic associated pathogenic/likely pathogenic genetic variants can be detected by whole exome sequencing technology. Its application value for prenatal diagnosis varies in fetus with different organs involved. Reanalysis of sequencing data for cases with new phenotypes in late pregnancy or after birth can further improve the molecular diagnosis rate. Further investigations are needed to explore the related genetic mechanisms.

All-trans-retinoid acid induces the differentiation of P19 cells into neurons involved in the PI3K/Akt/GSK3ß signaling pathway.

The pluripotent mouse embryonal carcinoma cell line P19 is widely used as a model for research on all-trans-retinoid acid (RA)-induced neuronal differentiation; however, the signaling pathways involved in this process remain unclear. This study aimed to reveal the molecular mechanism underlying the RA-induced neuronal differentiation of P19 cells. Real-time quantitative polymerase chain reaction and Western blot analysis were used to determine the expression of neuronal-specific markers, whereas flow cytometry was used to analyze cell cycle and cell apoptosis. The expression profiles of messenger RNAs (mRNAs) in RA-induced neuronal differentiation of P19 cells were analyzed using high-throughput sequencing, and the functions of differentially expressed mRNAs (DEMs) were determined by bioinformatics analysis. RA induced an increase in both class III ß-tubulin (TUBB3) and neurofilament medium (NEFM) mRNA expression, indicating that RA successfully induces neuronal differentiation of P19 cells. Cell apoptosis was not affected; however, cell proliferation decreased. We found 4117 DEMs, which were enriched in the phosphoinositide 3-kinase/protein kinase B (PI3K/Akt) signaling pathway, Wnt signaling pathway, and cell cycle. Particularly, a few DEMs could be identified in the PI3K/Akt signaling pathway networks, such as PI3K, Akt, glycogen synthase kinase-3ß (GSK3ß), cyclin-dependent kinase 4 (CDK4), P21, and Bax. RA significantly increased the protein expression of PI3K, Akt, phosphorylated Akt, GSK3ß, phosphorylated GSK3ß, CDK4, and P21, but it reduced Bax protein expression. The Akt inhibitor affected the increase of TUBB3 and NEFM mRNA expression in RA-induced P19 cells. The molecular mechanism underlying the RA-induced neuronal differentiation of P19 cells is potentially involved in the PI3K/Akt/GSK3ß signaling pathway. The decreased cell proliferation ability of neuronally differentiated P19 cells could be associated with the expression of cell cycle proteins.

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.

Whole-exome sequencing in the evaluation of fetal congenital anomalies of the kidney and urinary tract detected by ultrasonography.

OBJECTIVE: We aimed to investigate the value of whole-exome sequencing (WES) in fetuses with congenital anomalies of the kidney and urinary tract (CAKUT) with or without other structural anomalies but with normal findings upon karyotyping and chromosome microarray analysis (CMA). METHODS: Cases with CAKUT with or without other structural anomalies were screened for eligibility. Fetuses with abnormal karyotyping or CMA results were excluded. We performed WES on DNA samples from eligible fetus-parental trios and identified diagnostic genetic variants based on ultrasonographic features. RESULTS: A total of 163 eligible fetus-parental trios were successfully analyzed by WES. We found 26 likely pathogenic or pathogenic variants in 18 genes from 20 fetuses, with a total proportion of diagnostic genetic variants of 12.3% (20/163). Genetic variants were significantly more frequently detected in fetuses with multisystem anomalies (27.0%, 10/37), enlarged kidney/echogenic kidney (20%, 4/20), and multicystic dysplastic kidney (11.1%, 4/36). Pregnancy outcome data showed that 88 (94.6%, 88/93) of the surviving cases with negative WES results had a good prognosis in early childhood. CONCLUSIONS: Our study is the largest to use WES prenatally for CAKUT and shows that WES can be used diagnostically to define the molecular defects that underlie unexplained CAKUT.

[Application of chromosomal microarray analysis in 815 fetuses with increased nuchal translucency during early pregnancy].

OBJECTIVE: To explore genetic etiology and prognosis for fetuses with increased nuchal translucency (NT). METHODS: A total of 815 fetuses with increased NT (≥ 3.0 mm) were included. The fetuses were grouped by NT thickness and divided into 3.0-3.4 mm, 3.5-4.4 mm, 4.5-5.4 mm, 5.5- 6.4 mm and ≥ 6.5 mm groups. Based on the presence of additional abnormalities, the samples were divided into increased NT alone group and increased NT and other anomalies group. Chromosomal microarray analysis (CMA) was applied as a first-line test to detect pathogenic copy number variations (CNVs). The outcome of the pregnancies was followed up. RESULTS: One hundred seventy-eight (21.8%) fetuses were found to harbor pathogenic CNVs, which included 138 (77.5%) with chromosomal aneuploidies, 14 (7.9%) with microdeletion/microduplication syndromes, and 26 (14.6%) harboring non-syndromic pathogenic CNVs. A significant difference was found in the detection rate of pathogenic CNVs between groups with different NT thickness. The detection rate of pathogenic CNVs also significantly differed between groups with regard to other structural abnormalities or the overall adverse pregnancy outcome. CONCLUSION: CMA can be used as a first-line test for fetuses with increased NT during early pregnancy, with the overall detection rate of pathogenic CNVs being as high as 21.8%. Our results confirmed that NT thickness is correlated with other structural abnormalities and adverse pregnancy outcome, especially for those with NT ≥ 4.5 mm. At the same time, fetuses with other structural abnormalities are at an increased risk for adverse pregnancy outcome.

[Analysis of 26 fetuses with congenital anomalies of the kidney and urinary tract by whole exome sequencing].

OBJECTIVE: To explore the genetic etiology of fetuses with congenital anomalies of the kidney and urinary tract (CAKUT) by whole exome sequencing (WES). METHODS: WES was performed on DNA extracted from cord blood samples of 26 fetuses with unexplained CAKUT with/without other structural anomalies. In the first 19 cases, sequencing was performed on fetal DNA only, and the turnaround time was 11-12 weeks. For the remaining 7 cases, the fetus and its parents were sequenced simultaneously, and the turnaround time was 8-9 weeks. RESULTS: Of the 26 cases, pathogenic variants were identified in 4 (15.4%) cases, which respectively involved UMOD, NEK8, HNF1B, and BBS2 genes, and likely pathogenic variants were identified in 2 (7.7%) cases, which respectively involved HSPD1 and GRIN2B genes. Two of the 4 cases had other anomalies in addition to CAKUT. Thus, the detection rate was only 2/19 (10.5%) for isolated CAKUT and 4/7 (57.1%) for CAKUT with additional anomalies. CONCLUSION: The application of WES as a prenatal diagnostic approach for CAKUT fetuses with or without other anomalies allowed early and accurate diagnosis and improved their clinical management.

Whole-exome sequencing for prenatal diagnosis of fetuses with congenital anomalies of the kidney and urinary tract.

BACKGROUND: In the absence of cytogenetic abnormality, fetuses with congenital anomalies of the kidney and urinary tract (CAKUT) with/without other structural anomalies show a higher likelihood of monogenic causes; however, defining the underlying pathology can be challenging. Here, we investigate the value of whole-exome sequencing (WES) in fetuses with CAKUT but normal findings upon karyotyping and chromosome microarray analysis. METHODS: WES was performed on DNA from the cord blood of 30 fetuses with unexplained CAKUT with/without other structural anomalies. In the first 23 cases, sequencing was initially performed on fetal DNA only; for the remaining seven cases, the trio of fetus, mother and father was sequenced simultaneously. RESULTS: Of the 30 cases, pathogenic variants were identified in 4 (13%) (UMOD, NEK8, HNF1B and BBS2) and incidental variants in 2 (7%) (HSPD1 and GRIN2B). Furthermore, two of the above four cases had other anomalies in addition to CAKUT. Thus, the detection rate was only 2/22 (9.1%) for isolated CAKUT and 2/8 (25%) for CAKUT with other abnormalities. CONCLUSIONS: Applying WES to the prenatal diagnostic approach in CAKUT fetuses with or without other anomalies allows for an accurate and early etiology-based diagnosis and improved clinical management. To expedite interpretation of the results, trio sequencing should be employed; however, interpretation may nevertheless be compromised by incomplete coverage of all relevant genes.

Clinical application of SNP array analysis in fetuses with ventricular septal defects and normal karyotypes.

PURPOSE: The present study aims to evaluate the utility of high-resolution single-nucleotide polymorphism (SNP) arrays in fetuses with ventricular septal defects (VSDs) with or without other structural anomalies but with normal karyotypes and to investigate the outcomes of cases of prenatal VSDs via clinical follow-up. METHODS: We analyzed 144 fetuses with VSDs and normal karyotypes using Affymetrix CytoScan HD arrays and the analyses were carried out a year after birth. RESULTS: Clinically significant CNVs were detected in 12 fetuses (8.3%). The most common pathogenic CNV was a 22q11.2 deletion with a detection rate of 2.8% (4/144). Well-known microdeletion or microduplication syndromes, including Smith-Magenis, Miller-Dieker, 9q subtelomeric deletion, 1p36 microdeletion, 1q21.1 microduplication, and terminal 4q deletion syndrome, were identified in six cases. Three regions of chromosomal imbalance were also identified: microduplication at 12q24.32q24.33, microdeletion at 16p13.13p13.12 and microdeletion at Xp21.1. The genes TBX1, SKI, GJA5, EHMT1, NOTCH1 were identified as established genes and LZTR1, PRDM26, YWHAE, FAT1, AKAP10, ERCC4, and ULK1 were identified as potential candidate genes of fetal VSDs. There was no significant difference in pathogenic CNVs between isolated VSDs and VSDs with additional structural abnormalities. Ninety-five (74.8%) pregnant women with fetuses with benign CNVs chose to continue the pregnancy and had a favorable prognosis, while nine (75%) pregnant women with fetuses with pathogenic CNVs chose to terminate the pregnancy. CONCLUSIONS: High-resolution SNP arrays are valuable tools for identifying submicroscopic chromosomal abnormalities in the prenatal diagnosis of VSDs. An excellent outcome can be expected for VSD fetuses that are negative for chromosomal anomalies and other severe anatomic abnormalities.

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.

[Application of chromosome microarray analysis in 489 children with developmental delay/intellectual disability].

OBJECTIVE: To assess the value of chromosome microarray analysis (CMA) for identifying the etiology of developmental delay/intellectual disability (DD/ID). METHODS: A total of 489 children referred for DD/ID with or without other abnormalities were recruited. All patients showed a normal karyotype. DNA was extracted and hybridized with Affymetrix CytoScan 750K array by following the manufacturer's protocol. The data was analyzed with CHAS v2.0 software. RESULTS: The children were classified as with isolated DD/ID (n=358), DD/ID with epilepsy (n=49), and DD/ID with other structural anomalies (n=82). Pathogenic copy number variants (CNVs) were identified in 126 cases (25.8%), which included 89 (24.9%, 89/358) of whose with isolated DD/ID, 13 (26.5%, 13/49) of those with DD/ID and epilepsy, and 24 (29.3%, 24/82) of whose with DD/ID and other structural anomalies [P=0.064 (24.9% vs. 26.5%), P=0.679 (24.9% vs. 29.3%), and P=0.113 (26.5% vs. 29.3%), respectively]. Among the 126 cases, 79 were identified as microdeletion/microduplication syndromes, which included 15q24 microdeletion syndrome, Xq28 microduplication syndrome, and Lowe syndrome. Forty-seven cases had de novo pathogenic CNVs. ABAT, PMM2, FTSJ1, DYNC1H1 and SETBP1 were considered as candidate genes for DD/ID. CONCLUSION: CMA is an effective method for identifying the etiology of DD/ID and is capable of identifying microdeletion/microduplication syndromes as well as de novo pathogenic CNVs which may be missed by conventional karyotyping. Based on the results, candidate genes for DD/ID may be identified.

[Application of chromosomal microarray analysis for fetuses with ventricular septal defects].

OBJECTIVE: To explore the genetic etiology of fetuses with ventricular septal defects (VSD) using chromosomal microarray analysis (CMA). METHODS: A total of 248 fetuses were divided into isolated VSD group, VSD with other cardiac and/or great vessels malformation group, VSD with extra-cardiac anomalies group (including malformation and sonographic soft markers), and VSD with both cardiac and extra-cardiac anomalies group. Standard karyotyping was carried out for all fetuses, and CMA was performed for 6 fetuses with an abnormal karyotype and a proportion of fetuses with a normal karyotype. All cases were followed up, and neonates were followed up until 1 year of age. RESULTS: Chromosomal abnormalities were identified in 60 (24.2%) of the 248 fetuses. For 6 of the fetuses subjected to further CMA analysis, the origin of abnormal chromosomes were clarified, among which 2 have overlapped with the critical region of Wolf-Hirschhorn syndrome. Candidate genes for VSD included WHSC1, LBX1, LDB3 and BBS10. For 143 fetuses with a normal karyotype, CMA has identified pathogenic copy number variations (CNVs) in 11 cases (7.7%). These included 9 well-known microdeletion or microduplication syndromes, including 22q11.2 microdeletion, 17p11.2 microdeletion (Smith-Magenis syndrome), 17p13.3 microdeletion (Miller-Dieker syndrome), 1p36 microdeletion, 1q21.1 microduplication and 4q deletion. Candidate genes for VSD included TBX1, LZTR1, FAT1, AKAP10, SKI, PRDM26, GJA5, ERCC4 and YWHAE. For 48.7% of the fetuses with benign CNVs, spontaneously closure has occurred within the first year of life. CONCLUSION: CMA may increase the detection rate of submicroscopic imbalances by 7.7%. No significant correlation between different groups of VSD and the pathogenic CNVs was observed. Whole-genome CMA should be recommended to the fetuses with VSD but a normal karyotype. Nearly half of VSDs with benign CNVs may close spontaneously within the first year of life.

[Application of chromosome microarray analysis for the delineation of pathogenesis for fetal ventriculomegaly].

OBJECTIVE: To assess the value of genome-wide high-resolution chromosomal microarray analysis (CMA) for the delineation of pathogenesis for fetal ventriculomegaly diagnosed by ultrasound or magnetic resonance imaging (MRI). METHODS: Three hundred and forty-one cases of fetal ventriculomegaly were collected. The samples were grouped based on the extent of lateral ventricular dilatation, presence of additional features, site of occurrence, and the maternal age. All samples were subjected to karyotyping analysis. For those with a normal karyotype, DNA was extracted and hybridized with an Affymetrix CytoScan HD array. All cases were followed up. RESULTS: Among the 341 fetuses, 21 (6.2%) were detected with an abnormal karyotype. For the 320 cases with a normal karyotype, 179 (55.9%) have accepted CMA analysis. Potentially pathogenic CNVs were identified in 12 (6.7%) of the 179 cases, whose sizes ranged from 198 kb to 8.71 Mb. These included a 1q21.3q23.1 deletion, a 2q37.3 deletion, a 3p14.1p13 deletion, a 6q25.3 deletion, a 8q11.23 duplication, a 10q21.1 deletion, a 15q11.2 deletion and a 16p13.11p12.3 duplication, a 22q13.33 duplication, a 22q11.21 duplication and a Xp21.1 duplication (Duchenne muscular dystrophy). Pathogenic CNVs were detected respectively in 7.5% and 3.1% of those with mild and severe ventriculomegaly (P=0.615), in 6.1% and 7.4% of those with isolated and non-isolated ventriculomegaly (P=0.732), in 5.6% and 7.9% of those with unilateral and bilateral ventriculomegaly (P=0.511), and in 6.7% of both elderly and non-elderly groups (P=1.000). CONCLUSION: The detection rate for abnormal karyotypes among fetuses with ventriculomegaly was 6.2%. CMA can increase the detection rate by approximately 6.7%. There was no significant correlation between ventriculomegaly and presence of pathogenic CNVs. In clinical practice, fetuses with ventriculomegaly and a normal karyotype should be considered for CMA analysis.

[Application of chromosome microarray analysis for fetuses with multicystic dysplastic kidney].

OBJECTIVE: To explore the genetic etiology of fetuses with multicystic dysplastic kidney (MCDK) by chromosome microarray analysis (CMA). METHODS: Seventy-two fetuses with MCDK were analyzed with conventional cytogenetic technique, among which 30 fetuses with a normal karyotype were subjected to CMA analysis with Affymetrix CytoScan HD arrays by following the manufacturer's protocol. The data was analyzed with ChAS software. RESULTS: Conventional cytogenetic technique has revealed three fetuses (4.2%) with identifiable chromosomal aberrations. CMA analysis has detected pathogenic CNVs in 5 fetuses (16.7%), which included two well-known microdeletion or microduplication syndromes, i.e., 17q12 microdeletion syndrome and Williams-Beuren syndrome (WBS) and three submicroscopic imbalances at 4q35.2, 22q13.33, and 1p33. PEX26, FKBP6, TUBGCP6, ALG12, and CYP4A11 are likely the causative genes. CONCLUSION: CMA can identify the submicroscopic imbalances unidentifiable by conventional cytogenetic technique, and therefore has a significant role in prenatal diagnosis and genetic counseling. The detection rate of pathogenic CNVs in fetuses with MCDK was 16.7% by CMA. 17q12 microdeletion syndrome and WBS are associated with MCDK. Mutations of PEX26, FKBP6, TUBGCP6, ALG12, and CYP4A11 genes may be the causes for MCDK.

[Analysis of 22 patients with congenital cleft lip and palate using high-resolution chromosome microarray].

OBJECTIVE: To assess the value of chromosome microarray analysis (CMA) for identifying the etiology of patients with congenital cleft lip and palate. METHODS: Twenty-two patients with no identifiable chromosomal aberrations by conventional cytogenetic technique were selected. DNA was extracted and hybridized with Affymetrix CytoScan(TM) HD arrays following the manufacturer's protocol. The data were analyzed with a CHAS v2.0 software. RESULTS: CMA analysis has identified submicroscopic copy number variants (CNVs) in all of the cases, which have ranged from 100 kb to 1.8 Mb. Potential pathogenic CNVs were identified in 5 patients (22.7%), which involved microdeletions and microduplications on 8p23.1, 10q22.2-q22.3, 6q26, 20p12.1 and 18q12.3. MYST4, MACROD2 and SOX7 genes are likely the causative genes. CONCLUSION: CMA is an effective method for identification of etiology in patients with cleft lip and palate. CMA should be provided for patients with cleft lip and palate but a normal karyotype. Especially for those with additional structural abnormalities, there is a high risk for submicroscopic chromosomal aberrations.

Single-cell RNA sequencing reveals cellular and molecular landscape of fetal cystic hygroma.

BACKGROUND: The molecular mechanism of fetal cystic hygroma (CH) is still unclear, and no study has previously reported the transcriptome changes of single cells in CH. In this study, single-cell transcriptome sequencing (scRNA-seq) was used to investigate the characteristics of cell subsets in the lesion tissues of CH patients. METHODS: Lymphoid tissue collected from CH patients and control donors for scRNA-seq analysis. Differentially expressed gene enrichment in major cell subpopulations as well as cell-cell communication were analyzed. At the same time, the expression and interactions of important VEGF signaling pathway molecules were analyzed, and potential transcription factors that could bind to KDR (VEGFR2) were predicted. RESULTS: The results of scRNA-seq showed that fibroblasts accounted for the largest proportion in the lymphatic lesions of CH patients. There was a significant increase in the proportion of lymphatic endothelial cell subsets between the cases and controls. The VEGF signaling pathway is enriched in lymphatic endothelial cells and participates in the regulation of cell-cell communication between lymphatic endothelial cells and other cells. The key regulatory gene KDR in the VEGF signaling pathway is highly expressed in CH patients and interacts with other differentially expressed EDN1, TAGLN, and CLDN5 Finally, we found that STAT1 could bind to the KDR promoter region, which may play an important role in promoting KDR up-regulation. CONCLUSION: Our comprehensive delineation of the cellular composition in tumor tissues of CH patients using single-cell RNA-sequencing identified the enrichment of lymphatic endothelial cells in CH and highlighted the activation of the VEGF signaling pathway in lymphoid endothelial cells as a potential modulator. The molecular and cellular pathogenesis of fetal cystic hygroma (CH) remains largely unknown. This study examined the distribution and gene expression signature of each cell subpopulation and the possible role of VEGF signaling in lymphatic endothelial cells in regulating the progression of CH by single-cell transcriptome sequencing. The enrichment of lymphatic endothelial cells in CH and the activation of the VEGF signaling pathway in lymphatic endothelial cells provide some clues to the pathogenesis of CH from the perspective of cell subpopulations.