Prenatal genetic diagnosis of the fetuses with isolated corpus callosum abnormality / 中华妇产科杂志

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.

Molecular studies on parental origin and cell stage of nondisjunction in sex chromosome aneuploidies / 中华预防医学杂志

To study the parental origin and cell stage of nondisjunction in sex chromosome aneuploidies. Retrospectiving and analyzing the results of 385 cases of SCA confirmed by QF-PCR and karyotype analysis in the prenatal diagnosis center of Guangzhou Women and Children Medical Center from January 2015 to December 2020. The types of samples and prenatal diagnosis indications were analyzed. The parental origin and cell stage of nondisjunction in sex chromosome aneuploidies analyzed by comparing the short tandem repeat (STR) peak patterns of samples from fetuses and maternal peripheral blood. The results show that (1) There were 324 cases of nonmosaic SCA, 113 cases (113/324, 34.9%) were 45, XO, 118 cases (118/324, 36.4%) were 47, XXY, 48 cases (48/324, 14.8%) were 47, XXX and 45 cases (45/324, 13.9%) were 47, XYY. 68 (45/324, 60.2%) cases of 45, X were detected in villus samples. The other SCA cases were mainly detected in amniotic fluid samples. There were 61 mosaic SCA samples, 58(58/61, 95.1%) of mosaic SCA samples were mosaic 45, X. (2) The top two indications of 45, X cases are increased nuchal translucency(53/113, 46.9%) and fetal cystic hygroma (41/113, 36.3%), while the most common indication of other types of SCA was high risk of NIPT(170/272, 62.5%). (3) Among 45, X cases, there were 88 cases (88/113, 77.9%) inherit their single X chromosome from their mother and 25 cases (25/119, 22.1%) from their father. In 47, XXY samples, 47 cases (47/118, 39.8%) of chromosome nondisjunction occurred in meiosis stage Ⅰ of oocytes, 51 cases (51/118, 43.2%) occurred in meiosis stage Ⅰ of spermatocytes, and 20 cases (20/118, 16.9%) occurred in meiosis stage Ⅱ of oocytes. Among 47, XXX samples, 29 cases (29/48, 60.4%) of X chromosome nondisjunction occurred in meiosis stage Ⅰof oocytes, 15 cases (15/48, 31.3%) occurred in meiosis stage Ⅱ of oocytes, and 4 cases (4/48, 8.3%) occurred in meiosis stage Ⅱ of spermatocytes. In summary , the cases of 45, X were mainly diagnosed by villous samples for abnormal ultrasound findings. The other cases of SCA were mainly diagnosed by amniocentesis samples for abnormal NIPT results. Different types of SCA, the origin and occurrence period of sex chromosome nondisjunction were different.

Parental origin of prenatally diagnosed pathogenic copy number variation in 56 pedigrees / 中华围产医学杂志

Objective:To investigate the prenatal management for pathogenic copy number variation (CNV) by analyzing the parental origin of CNV and pregnancy outcomes in 56 pedigrees.Methods:This study retrospectively analyzed the information of patients who received interventional prenatal diagnosis and chromosomal microarray analysis (CMA) at Guangzhou Women and Children's Medical Center from January 2015 to December 2020. The cases with pathogenic CNV indicated by CMA and receiving parental CMA for further verification were finally enrolled. Clinical data including prenatal diagnostic indications, chromosomal distribution of the pathogenic fragments and fragment sizes were collected and analyzed using t test. All cases were followed up by telephone and record review. Results:Fifty-six cases were included in this study. Pathogenic CNV in 13 (23.2%, 13/56) fetuses were inherited from one parent (eight from mothers and five from fathers), and mainly located in chromosomes 22 (3/13), 17 (3/11), 16 (2/7), 1 (2/4), and X (3/6) with fragment sizes all less than 3 Mb. The fragment size of inherited pathogenic CNV was significantly smaller than that of de novo CNV [1.69 (1.36-2.22) vs 7.54 (2.11-12.30) Mb, t=3.47, P=0.001]. Among the 43 cases with de novo pathogenic CNV, seven (16.3%) were lost to follow up and 35 (97.2%) terminated the pregnancy. The other one with a 0.58 Mb microruplication at 16p11.2 indicated at 37 gestational weeks gave birth to a baby weighting 2 900 g at 39 gestational weeks and no abnormalities were reported during an eight-month telephone follow-up. Two out of the 13 cases with inherited pathogenic CNV were lost to follow up and six pregnancies were terminated. The other five pregnancies were continued and babies were delivered with no abnormalities during a median follow-up period of 13 (4-15) months. Conclusion:Pathogenic CNV alone should not be the indication for pregnancy termination.

Prenatal diagnosis and pregnancy outcome of increased nuchal translucency with or without nuchal cystic hygroma in fetuses during first trimester / 中华围产医学杂志

Objective:To compare the prenatal diagnosis and pregnancy outcome of increased nuchal translucency (NT) with or without nuchal cystic hygroma (CH) in fetuses with first-trimester NT ≥5 mm.Methods:Data from 131 fetuses with NT ≥5 mm who received invasive prenatal diagnosis at Guangzhou Women and Children's Medical Center from July 2017 to December 2020 were retrospectively collected and analyzed. Those with a septum in the cyst were grouped as NT with CH group ( n=57), and those without as increased NT without CH group ( n=74). Genetic test results, incidence of structural malformations, survival rate after birth were compared using Chi-square test or Fisher's exact test and non-parametric test. Results:There was no significant difference in the incidence of fetal genetic abnormalities[67.6%(50/74) vs 61.4%(35/57), χ 2=0.54, P=0.464], ultrasonic structural malformations [21.6%(16/74) vs 33.3%(19/57), χ 2=2.26, P=0.133], or in the survival rate (12/14 vs 3/8, P=0.053) between increased NT without CH group and NT with CH group. Conclusions:For increased NT with or without CH, although the two groups had different spectrum of disease, they had a high incidence of chromosomal abnormalities and structural malformations, and both groups had a certain healthy survival rate after birth.

Genetic analysis and prenatal diagnosis of a fetus with Xq25 microduplication / 中华医学遗传学杂志

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.

Analysis of families with fetal congenital abnormalities but negative prenatal diagnosis by whole exome sequencing / 中华妇产科杂志

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.

Application of whole exome sequencing technology in fetuses with congenital structural abnormalities / 中华医学遗传学杂志

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.

Value of chromosomal microarray analysis for fetuses with duodenal obstruction / 中华医学遗传学杂志

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.

Application of chromosomal microarray analysis in 815 fetuses with increased nuchal translucency during early pregnancy / 中华医学遗传学杂志

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.

Consistency between quantitative fluorescent-polymerase chain reaction and karyotyping in prenatal diagnosis / 中华围产医学杂志

Objective:To analyze the consistency between karyotyping and quantitative fluorescent- polymerase chain reaction (QF-PCR) in prenatal diagnosis.Methods:This study retrospectively analyzed the clinical data of 10 967 patients undergoing karyotyping and QF-PCR for prenatal diagnosis in Guangzhou Women and Children's Hospital from January 2010 to December 2017. The failure rate, results, and diagnosis of common chromosomal disorders of the two methods were compared. The sensitivity and specificity of QF-PCR in detecting chromosomal mosaicism were evaluated using the receiver operative characteristic (ROC) curve.Results:(1) The failure rates of karyotyping and QF-PCR were 0.99% (109/10 967) and 0.10% (11/10 967), respectively. (2) The karyotypes of 9 960 out of the 10 858 successfully cultured samples were normal, and 99.89% (9 949/9 960) results were consistent between the two methods. The other 898 cases included 694 (77.28%) with common chromosomal abnormalities (trisomy 21, 18 and 13 and sex chromosomal abnormality) and 204 (22.72%) with other chromosomal abnormalities. The consistency between the two methods in detecting common chromosomal abnormalities was 95.68% (664/694). (3) The consistency in the detection of trisomy 21, 18 and 13 and sex chromosomal abnormality between karyotyping and QF-PCR were 99.74% (382/383), 100.00% (125/125), 100.00% (33/33) and 81.05% (124/153). However, the common chromosomal mosaicism was only noted for 44.44% (24/54). (4) Among cases with a mosaic ratio over 18.5%, the sensitivity and specificity of QF-PCR were 0.958 (95% CI: 0.789-0.999) and 0.600 (95% CI: 0.406-0.773) with the area under the ROC curve (AUC) of 0.811 (95% CI: 0.696-0.926, P<0.001). (5) Thirty cases with negative QF-PCR results but positive mosaic chromosomal aberrations were followed up. Ten (33.3%) pregnant women terminated their pregnancies, and two (6.7%) were lost to follow-up. The other 18 cases delivered healthy neonates that all survived after birth. Conclusions:In prenatal diagnosis, QF-PCR and karyotyping were highly consistent in the detection of trisomy 21, 13, and 18, but have significant discordance in the diagnosis of sex chromosomal abnormality.

Clinical and genetic analysis of three pediatric patients with 15q24 microdeletion syndrome / 中华医学遗传学杂志

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.

Analysis of 26 fetuses with congenital anomalies of the kidney and urinary tract by whole exome sequencing / 中华医学遗传学杂志

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.

Chorionic villus cell culture and karyotype analysis in 1983 cases of spontaneous miscarriage / 中华妇产科杂志

Objective To investigate the relationship between spontaneous miscarriage and embryonic chromosome abnormalities,and to evaluate the clinical application of karyotype analysis by chorionic villus cell culture. Methods The chorionic villus karyotype of 1983 cases of miscarriage from January 2010 to July 2016 in Guangzhou Women and Children′ s Mecical Center were analyzed retrospectively. The miscarried chorionic villi were obtained by curettage under sterilized condition. The chromosome specimens were prepared after chorionic villus cell culture. Karyotype analysis was performed by G-banding technique. Results In the 1983 samples, successful karyotype analysis was performed in 1770 cases, with the successful rate of 89.98%. Chromosomal abnormalities were found in 1038 cases (58.64%,1038/1770). Chromosomal structural abnormalities were found in 37 cases. The numeral abnormalities were more common than structural abnormalities, and most of the numeral abnormalities were aneupoidies. In turn, they were trisomy 16, 45,X, trisomy 22, trisomy 2, trisomy 21, trisomy 15. The most common structural abnormality was balanced translocation, including Robersonian translocation. Female embryoes accounted for 61.02%(1080/1770) miscarriages and for 57.4%(596/1770) of chromosomal abnormalities, while male embroyes acoounted for 61.02%(1080/1770),57.4%(596/1770)respectively. The proportion of female embryoes was higher than male embryoes. The median age of the patients was 30 years old(16-46 years old). As the maternal age increased, the proportion chromosomal abnormalities increased. The incidence of chromosomal abnormalities in the advanced age group (≥35 years) was 68.38%(240/351), which was significantly higher than that in the younger group (56.24% ,798/1419; χ2=17.10, P<0.01). Conclusions Embryonic chromosomal abnormalities are the most common cause of early spontaneous miscarriage. The abnormalities centralize in some karyotypes. There is certain relationship between maternal age and the incidence of miscarriage, as well as the embryonic gender. Chorionic villus cell culture and karyotype analysis are helpful in finding the cause of miscarriage and counsel the patients.

Application of chromosomal microarray analysis for fetuses with ventricular septal defects / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To explore the genetic etiology of fetuses with ventricular septal defects (VSD) using chromosomal microarray analysis (CMA).</p><p><b>METHODS</b>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.</p><p><b>RESULTS</b>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.</p><p><b>CONCLUSION</b>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.</p>

Identification of novel compound heterozygous mutations in the ANTXR2 gene in a Chinese patient with juvenile hyaline fibromatosis / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To identify pathogenic mutations of ANTXR2 gene in a patient with juvenile hyaline fibromatosis.</p><p><b>METHODS</b>Genomic 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.</p><p><b>RESULTS</b>A 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.</p><p><b>CONCLUSION</b>The 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.</p>

Application of chromosome microarray analysis in 489 children with developmental delay/intellectual disability / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To assess the value of chromosome microarray analysis (CMA) for identifying the etiology of developmental delay/intellectual disability (DD/ID).</p><p><b>METHODS</b>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.</p><p><b>RESULTS</b>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.</p><p><b>CONCLUSION</b>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.</p>

Application of chromosome microarray analysis for the delineation of pathogenesis for fetal ventriculomegaly / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>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).</p><p><b>METHODS</b>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.</p><p><b>RESULTS</b>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).</p><p><b>CONCLUSION</b>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.</p>

Chromosome microarray analysis of patients with 18q deletion syndrome / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To analyze the correlation between the genotype and phenotype of 18q deletion syndrome with chromosome microarray analysis (CMA).</p><p><b>METHODS</b>Eight 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.</p><p><b>RESULTS</b>CMA 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.</p><p><b>CONCLUSION</b>CMA can precisely locate the breakpoints of 18q and facilitate definition of the genotype-phenotype correlations, which is useful for prognosis.</p>

Application of chromosome microarray analysis for patients with skeletal anomalies and a normal karyotype / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To analyze patients with skeletal anomalies (SA) but a normal karyotype using chromosome microarray analysis (CMA).</p><p><b>METHODS</b>From 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.</p><p><b>RESULTS</b>Two 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.</p><p><b>CONCLUSION</b>Whole-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.</p>

Application of chromosomal microarray analysis for fetuses with talipes equinovarus / 中华妇产科杂志

Objective To investigate the application of fetuses with talipes equinovarus (TE) using chromosomal microarray analysis (CMA) technology. Methods From May 2012 to June 2015, 54 fetuses were found with TE and with or without other structural anomalies by prenatal ultrasound. Karyotyping was taking for them all, and the fetuses with normal karyotypes took another CMA test. The data were analyzed with CHAS software. Finally all the cases were followed up to know about their pregnancy outcomes. Results One of the 54 cases was detected with abnormal karyotype which was trisomy 18 (2%, 1/54). CMA was undertaken to the remaining fetuses, they were divided into 2 groups, including isolated TE group (n=38) and complex TE group (n=15). The detection rate of clinical significant copy number variations (CNV) by CMA was 11% (6/53), while isolated and complex TE group were 5% (2/38) and 4/15, respectively (P=0.047). Of the 53 cases, 51 cases were successfully followed up. Eleven cases were found without TE after birth, and the false positive rate (FPR) of TE was 22%(11/51). Conclusions Whole-genome high-resolution CMA increased the detection rate by 11% in fetuses with TE. With the FPR and the detection rate of the clinical significant CNV of 2 groups, whole-genome CMA could be recommended to the fetuses with complex TE group but normal karyotypes. A series of ultrasonic tests should be suggested to the isolate TE group, while with the abnormal ultrasound, fetuses would be suggested to have CMA test for decreasing the rates of invasive prenatal diagnosis and FPR.