Objective:To explore the application value of chromosome karyotype analysis, chromosomal microarray analysis (CMA) and whole exome sequencing (WES) in prenatal diagnosis of isolated corpus callosum abnormality (CCA) fetus.Methods:Fetuses diagnosed with isolated CCA by ultrasound and MRI and receiving invasive prenatal diagnosis in Guangzhou Women and Children′s Medical Center and Qingyuan People′s Hospital from January 2010 to April 2021 were selected. Karyotype analysis and/or CMA [or copy number variation sequencing (CNV-seq)] were performed on all fetal samples, and WES was performed on fetal samples and their parents whose karyotype analysis and/or CMA (or CNV-seq) results were not abnormal.Results:Among 65 fetuses with isolated CCA, 38 cases underwent karyotype analysis, and 3 cases were detected with abnormal karyotypes, with a detection rate of 8% (3/38). A total of 49 fetuses with isolated CCA underwent CMA (or CNV-seq) detection, and 6 cases of pathogenic CNV were detected, the detection rate was 12% (6/49). Among them, the karyotype analysis results were abnormal, and the detection rate of further CMA detection was 1/1. The karyotype results were normal, and the detection rate of further CMA (or CNV-seq) detection was 14% (3/21). The detection rate of CMA as the first-line detection technique was 7% (2/27). A total of 25 fetuses with isolated CCA with negative results of karyotyping and/or CMA were tested by WES, and 9 cases (36%, 9/25) were detected with pathogenic genes. The gradient genetic diagnosis of chromosomal karyotyping, CMA and WES resulted in a definite genetic diagnosis of 26% (17/65) of isolated CCA fetuses.Conclusions:Prenatal genetic diagnosis of isolated CCA fetuses is of great clinical significance. The detection rate of CMA is higher than that of traditional karyotyping. CMA detection could be used as a first-line detection technique for fetuses with isolated CCA. WES could increase the pathogenicity detection rate of fetuses with isolated CCA when karyotype analysis and/or CMA test results are negative.

OBJECTIVE: To explore the genetic basis for a fetus with structural brain abnormalities. METHODS: The karyotypes of the fetus and its parents were analyzed by conventional G-banding. Chromosome microarray analysis (CMA) was carried out to detect chromosomal microdeletion and microduplication. RESULTS: No kartotypic abnormality was detected in the fetus and its parents. CMA has identified a 194 kb microduplication at Xq25 in the fetus, which encompassed exons 4-35 of the STAG2 gene and was derived from its mother. CONCLUSION The Xq25 duplication encompassing part of the STAG2 gene probably underlay the brain malformation in the fetus.
Chromosome Banding ; Female ; Fetus ; Genetic Testing ; Humans ; Karyotyping ; Pregnancy ; Prenatal Diagnosis

Objective:To evaluate the value of whole exome sequencing (WES) in prenatal clinical application.Methods:A total of 1 152 cases of congenital abnormal [including structural malformation, nuchal translucency (NT) thickening and intrauterine growth restriction] with traditional prenatal diagnosis [including G-band karyotype analysis and chromosome microarray analysis (CMA)] negative were analyzed. The congenital abnormal fetuses were divided into retrospective group and prospective group according to the time of WES detection, that is whether the pregnancy termination or not. According to the specific location of fetal malformation and their family history, the cohort was divided into subgroups. The clinical prognosis of all fetuses were followed up, and the effect of WES test results on pregnancy decision-making and clinical intervention were analyzed. According to the follow-up results, the data of fetuses with new phenotypes in the third trimester or after birth were re-analyzed.Results:Among 1 152 families who received WES, 5 families were excluded because of nonbiological parents. Among the remaining 1 147 families, 152 fetuses obtained positive diagnosis (13.3%,152/1 147), including 74 fetuses in the retrospective group (16.1%,74/460) and 78 fetuses in the prospective group (11.4%,78/687). In fetuses with negative CMA and G-band karyotype analysis results but new phenotypes in the third trimester or after birth, the positive rate by WES data re-analysis was 4.9% (8/163). A total of 34 (21.3%, 34/160) fetuses were directly affected by the corresponding positive molecular diagnosis. Among 68 cases of live births with diagnostic variation grade 4, 29 cases (42.7%, 29/68) received appropriate medical intervention through rapid review of WES results.Conclusions:WES could increase the detection rate of abnormal fetuses with negative G-banding karyotype analysis and CMA by 13.3%. Prenatal WES could guide pregnancy decision-making and early clinical intervention. It might be an effective strategy to pay attention to the special follow-up of the third trimester and postnatal fetus and to re-analyze the WES data.

OBJECTIVE: To assess the value of chromosomal microarray analysis (CMA) for fetal duodenal obstruction (DO). METHODS: Fifty-one fetuses with DO identified by prenatal ultrasound were divided into DO only group and DO with other anomaly group. CMA was carried out on amniotic fluid or umbilical blood samples, and the outcome of pregnancy of all cases were followed up. RESULTS: Eight fetuses (15.7%) were found with genomic abnormalities, which included 3 chromosomal aneuploidies and 5 copy number variations (CNVs), including one 17q12 microduplication syndrome, one 13q21.33q31.1 microdeletion, one 13q21.32q22.3 deletion, one 13q21.2q31.1 deletion and one 1q43q44 duplication. EDNRB from 13q and HNF1B from 17q12 are candidate genes for fetal DO. No significant difference was found in the detection rate of pathogenic CNVs between the DO only and DO with other anomaly groups (9.5% vs.11.1%, P> 0.05). There were 39 live borns, 1 stillbirth, and 11 artificial abortions (8 with abnormal CMA results). CONCLUSION There is a correlation between fetal DO and abnormal copy number of the genome, for which prenatal diagnosis is necessary. CMA not only can detect microdeletions/microduplications, but also identify pathogenic genes, which can facilitate prenatal diagnosis, genetic counseling and prognosis for the fetus.
Chromosome Aberrations ; DNA Copy Number Variations ; Duodenal Obstruction/genetics* ; Female ; Fetus ; Humans ; Microarray Analysis ; Pregnancy ; Prenatal Diagnosis

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.
Female ; Fetal Diseases ; Fetus/diagnostic imaging* ; Humans ; Pregnancy ; Prenatal Diagnosis ; Technology ; Ultrasonography, Prenatal ; Whole Exome Sequencing

OBJECTIVE: To explore the genetic basis for three patients with development delay and to correlate their clinical phenotypes with genetic findings. METHODS: The karyotypes of the probands and their parents were analyzed by conventional G-banding. Chromosomal microarray analysis (CMA) was used to detect microdeletion and microduplication. RESULTS: No kartotypic abnormality was detected in the patients and their parents. CMA analysis identified a de novo 3.10 Mb deletion on chromosome 15q24.1q24.2 in case 1, a de novo 3.14 Mb deletion at 15q24.1q24.2 in case 2, and a 3.13 Mb deletion at 15q24.1q24.2 in case 3. All deletions have encompassed the CPLX3,SEMA7A and SIN3A genes. CONCLUSION The three patients were diagnosed with 15q24 microdeletion syndrome. CPLX3,SEMA7A and SIN3A may be the key genes responsible for this syndrome.
Adaptor Proteins, Signal Transducing ; genetics ; Antigens, CD ; genetics ; Child ; Chromosome Deletion ; Chromosome Disorders ; genetics ; Chromosomes, Human, Pair 15 ; genetics ; GPI-Linked Proteins ; genetics ; Humans ; Intellectual Disability ; genetics ; Repressor Proteins ; genetics ; Semaphorins ; genetics

OBJECTIVE: To explore the genetic etiology for a child with ocular dysplasia. METHODS: Clinical examination was carried out. Medical history of the child was collected. Genomic DNA was extracted from peripheral blood samples. Chromosomal microarray analysis (CMA) was used to detect potential genomic copy number variations. RESULTS: Ultrasonography revealed cataracts in both eyes of the child. MRI showed increased extracranial space, supratentorial ventricular dilatation, reduced white matter volume, increased T2WI signal and a large occipital cisterna. CMA showed that the patient carried a 249 kb microdeletion at Xq25q26.1 region, namely [hg19]arrXq25q26.1 (128 652 372 - 128 901 629)×0. CONCLUSION The child was diagnosed with Lowe syndrome, for which the 249 kb microdeletion at Xq25q26.1 is probably accountable.
Child ; Chromosome Aberrations ; DNA Copy Number Variations ; Humans ; Microarray Analysis ; Oculocerebrorenal Syndrome

OBJECTIVETo identify pathogenic mutations of ANTXR2 gene in a patient with juvenile hyaline fibromatosis.

METHODSGenomic DNA was extracted from peripheral venous blood sample from the patient. All coding exons (exons 1-17) and splicing sites of the ANTXR2 gene were amplified with PCR. Potential mutations were detected with direct sequencing of the PCR products. 100 unrelated healthy subjects were used as the controls. CLUSTALX (1.81) was employed to analyze cross-species conservation of the mutant amino acid. Impact of the mutations was analyzed with software including SIFT, PolyPhen-2 and MutationTaster.

RESULTSA compound heterozygous mutation c.1074delT/c.1153G>C, was identified, among which c.1153G>C has not been reported previously and was predicted to be probably damaging. Both mutations were not found among the 100 healthy controls.

CONCLUSIONThe patient's condition may be attributed to the compound heterozygous mutations of c.1074delT and c.1153G>C of the ANTXR2 gene. Above results has facilitated molecular diagnosis for this patient.

Child, Preschool ; Female ; Heterozygote ; Humans ; Hyalinosis, Systemic ; diagnosis ; genetics ; Mutation ; Receptors, Peptide ; genetics

OBJECTIVETo analyze patients with skeletal anomalies (SA) but a normal karyotype using chromosome microarray analysis (CMA).

METHODSFrom June 2012 to May 2015, 43 children found to have skeletal anomalies with or without other abnormalities were subjected to karyotyping analysis. For those with a normal karyotype, DNA was extracted and hybridized with Affymetrix CytoScan 750 kb arrays following the manufacturer's protocol. The results were analyzed with CHAS v2.0 software.

RESULTSTwo patients (4.65%) were detected with an abnormal karyotype. The remaining 41 patients with a normal karyotype were classified into 3 groups: isolated SA (n=17), SA with mental retardation (n=6), and SA with other structural anomalies (n=18). Clinically significant copy number variations (CNVs) were found in 21.95% (9/41) of the cases, which included 17.65% (3/17) with isolated SA, 33.33% (2/6) with SA and mental retardation, and 22.22% (4/18) of SA with other structural deformities.

CONCLUSIONWhole-genome CMA can detect clinically significant CNVs which may not be found by conventional karyotyping analysis and increase the detection rate by approximately 21.95%. It may be recommended for patients with SA but a normal karyotype.

Bone and Bones ; abnormalities ; Child ; Child, Preschool ; Chromosome Aberrations ; DNA Copy Number Variations ; Humans ; Infant ; Infant, Newborn ; Karyotype ; Oligonucleotide Array Sequence Analysis

OBJECTIVETo analyze the correlation between the genotype and phenotype of 18q deletion syndrome with chromosome microarray analysis (CMA).

METHODSEight cases with 18q deletion syndrome were selected, including two affected fetuses and six children patients. DNA was extracted and hybridized with Affymetrix CytoScan TM 750K arrays following the manufacturer's standard protocol. The data was analyzed with a special software package.

RESULTSCMA analysis identified pathogenic copy number variations (CNVs) on 18q in all cases, which ranged from 6.612 Mb to 22.973 Mb. NFATC1, GALR1, MBP, SALL3 and TSHZ1 are likely to be causative genes for congenital heart disease, psychological, growth retardation, and cleft palate.

CONCLUSIONCMA can precisely locate the breakpoints of 18q and facilitate definition of the genotype-phenotype correlations, which is useful for prognosis.

Child, Preschool ; Chromosome Deletion ; Chromosome Disorders ; genetics ; Chromosomes, Human, Pair 18 ; genetics ; DNA Copy Number Variations ; Female ; Humans ; Infant ; Male ; Microarray Analysis