Application Of Chromosomal Microarray Analysis Research Articles

Guideline for the application of chromosomal microarray analysis in prenatal diagnosis (2023)

After the promulgation of the first edition of expert consensus on the application of chromosomal microarray analysis (CMA) technology in prenatal diagnosis in 2014, after 8 years of clinical and technical development, CMA technology has become a first-line diagnosis technology for fetal chromosome copy number deletion or duplication abnormalities, and is widely used in the field of prenatal diagnosis in China. However, with the development of the industry and the accumulation of experience in case diagnosis, the application of CMA technology in many important aspects of prenatal diagnosis, such as clinical diagnosis testimony, data analysis and genetic counseling before and after testing, needs to be further standardized and improved, so as to make the application of CMA technology more in line with clinical needs. The revision of the guideline was led by the National Prenatal Diagnostic Technical Expert Group, and several prenatal diagnostic institutions such as Peking Union Medical College Hospital were commissioned to write, discuss and revise the first draft, which was discussed and reviewed by all the experts of the National Prenatal Diagnostic Technical Expert Group, and was finally formed after extensive review and revision. This guideline is aimed at the important aspects of the application of CMA technology in prenatal diagnosis and clinical diagnosis, from the clinical application of evidence, test quality control, data analysis and interpretation, diagnosis report writing, genetic counseling before and after testing and other work specifications are elaborated and introduced in detail. It fully reflects the integrated experience, professional thinking and guidance of the current Chinese expert team on the prenatal diagnosis application of CMA technology. The compilation of the guideline for the application of CMA technology in prenatal diagnosis will strive to promote the standardization and advancement of prenatal diagnosis of fetal chromosome diseases in China.

Should Prenatal Chromosomal Microarray Analysis Be Offered for Pulmonary Atresia? A Single-Center Retrospective Study in China.

(1) Objective: To evaluate the application of chromosomal microarray analysis (CMA) in fetuses with pulmonary atresia (PA) and to explore the risk factors for predicting chromosomal imbalances and adverse perinatal outcomes. (2) Methods: This study investigated 428 cases of PA singleton pregnancies that were tested using CMA and quantitative fluorescent polymerase chain reaction (QF-PCR) as first-line genetic testing. The PA cases were divided into two groups: an isolated group and a non-isolated group. (3) Results: CMA revealed clinically relevant copy number variations (CNVs) in 9/139 (6.47%) PA fetuses, i.e., pathogenic copy number variations (pCNVs) in 8/139 (5.76%) fetuses and likely pathogenic CNVs in 1/139 (0.72%) fetuses. Stratified analysis showed that the incidence of clinically significant variants was higher in non-isolated PA fetuses than in isolated PA fetuses (12.50%, 6/48 vs. 3.30%, 3/91, p = 0.036). Regression analysis showed that a combination of other structural abnormalities at diagnosis of PA represented the principal risk factor for chromosomal imbalances (OR = 2.672). A combination of other structural abnormalities and a high maternal age increased the risk of adverse pregnancy outcomes in PA cases, including intrauterine fetal death (IUFD), termination of pregnancy (TOP), and preterm delivery. (4) Conclusions: The value of CMA for locating imbalanced genetic variations in fetuses with PA was highlighted by this study, particularly when combined with additional structural abnormalities.

Concordance of Chromosomal Microarray Analysis in Prenatal Diagnosis of Fetuses with Abnormal Ultrasonographic Soft Markers.

To analyse the effect of chromosomal microarray analysis (CMA) in the prenatal diagnosis of fetuses with abnormal ultrasonographic soft markers. Descriptive study. Place and Duration of the Study: Prenatal Diagnostic Centre, Huizhou Central People's Hospital, from January 2020 to January 2022. A total of 160 pregnant women with abnormal soft markers in the fetuses on prenatal ultrasonography were selected. Amniotic fluid in the second trimester of pregnancy was extracted for CMA. In addition, karyotype analysis of chromosomal G-banding was carried out to analyse the effect of CMA in prenatal diagnosis. The detection rate of copy number variants (CNVs) by CMA was higher than that by karyotype analysis, which was not statistically significant (p=0.059). Compared with karyotype detection, CMA detected five additional cases of pathogenic CNVs, all of which were cases of microdeletion and microduplication. VOUS cases detected by CMA were mostly concentrated in NT thickening, among which cases of uncertain significance were the most. The application of CMA in the prenatal diagnosis of fetuses with abnormal ultrasonographic soft markers can improve the detection rate of pathogenicity. As a prenatal diagnostic method, CMA has high application value and is worthy of clinical promotion. Chromosomal microarray analysis, Abnormal ultrasonographic soft markers, Prenatal diagnosis, Diagnostic efficiency.

Application of chromosomal microarray analysis for fetuses with choroid plexus cysts

To assess the value of chromosomal microarray analysis (CMA) for fetuses with choroid plexus cysts (CPC) detected by prenatal ultrasonography. Amniotic fluid chromosomal karyotype was analyzed in 104 fetuses with CPC, and copy number variations (CNVs) among the fetuses were detected by using CMA. Ten fetuses (9.62%) were found to have an abnormal karyotype, and 14 additional CNVs were detected in those with a normal karyotype. The fetuses were divided into isolated CPC group (n = 87) and non-isolated CPC group (n = 17) based on the presence of additional ultrasonographic abnormalities. The detection rates for karyotypic abnormalities of the two groups were 4.6% and 35.3%, respectively, whilst those for the CMA were 4.6% and 47.1%, respectively. The detection rates for karyotypic abnormalities and CMA of the non-isolated CPC group were significantly higher than those of the isolated CPC group (P < 0.05). The detection rate for CMA in the non-isolated group was significantly higher than chromosomal karyotype abnormalities (P < 0.05). Among the 8 fetuses with abnormal CMA, 4 had single umbilical artery, 3 had abnormal cardiac structure, and 2 had enhanced intestinal echo. CPC is closely associated with chromosomal abnormalities. Chromosome karyotype analysis in combination with CMA can effectively detect fetal chromosomal abnormalities and provide a basis for genetic counseling.

A Three-Year Prospective Study Assessing the Application of Chromosomal Microarray Analysis in 576 High-Risk Pregnant Women.

Background The use of chromosomal microarray analysis (CMA) in prenatal diagnosis of chromosomal and genetic diseases has resulted in a significant improvement in the diagnosis of genetically caused congenital malformations, neurodevelopmental disorders, and congenital anomalies, with a high diagnostic yield in selected prenatal cases. Objective The objective of this study was to evaluate the application of CMA in the prenatal diagnosis of high-risk pregnant women. Method A total of 576 pregnancies were selected from May 2018 to October 2020 in our hospital, including amniotic fluid chromosome, karyotype analysis, and CMA detection. The study group was divided into two groups based on the indications for testing: group A has 88 patients at the age of 35 years or older, and group B patients were in high-risk pregnancies, which consisted of 33 cases of bad pregnancy history, 252 high-risk serological screenings, 70 high-risk non-invasive prenatal testing (NIPT), 65 cases of B-ultrasound indicated fetal development abnormalities or ultrasonic soft marker abnormalities, and 68 other cases of pregnant women or both who have genetic or chromosomal abnormalities. At last, we have an analysis of the detection rate from different testing methods. Results Based on the follow-up test, 576 high-risk pregnant women showed an amniotic fluid chromosome karyotype rate of 18.1% (104/576), and the remaining 472 of these cases suffered a CNV ratio of 14.2% (67/472). 472 women of low clinical relevance are at 4.87% (23/472), 16 people showed a clear cause ratio = 3.39% (16/472), and 28 of the 472 (5.93%) cases showed polymorphism. Conclusions In our study, CMA significantly improved the fetal detection rate and diagnosis rate in high-risk pregnant women, which proved to be a very useful method in the diagnosis of genetically caused neurodevelopmental disorders and congenital anomalies. The use of CMA in high-risk pregnant women is justified, and these women can detect an additional (3.40%, 16/472) of pathogenic microdeletions and microduplications in the cases.

Application of chromosomal microarray analysis in the diagnosis of genetic etiology of spontaneous abortions

To explore the genetic etiology of spontaneous abortions by using chromosomal microarray analysis (CMA). Fetal tissues derived from 106 spontaneous abortion samples were subjected to CMA assay to detect genome copy number variants (CNVs). The test was successful in 94 cases (88.68%). Fifty four chromosomal abnormalities were detected, which included 44 numerical chromosomal aberrations mainly consisting of aneuploidies, triploidies and mosaicisms. Four pathogenic CNVs were detected, and two of which involved the Cri-du-chat syndrome regions. In addition, 6 chromosomal mosaicism were detected. Numerical chromosomal aberrations and CNVs are the main causes for early spontaneous abortions. CMA can effectively reveal the genetic etiology of spontaneous abortions. Spontaneous abortions at gestational weeks 10 to 11+6 has the highest rate for chromosomal abnormalities, which may provide valuable information for clinical counseling.

Potentials and challenges of chromosomal microarray analysis in prenatal diagnosis.

Introduction: For decades, conventional karyotyping analysis has been the gold standard for detecting chromosomal abnormalities during prenatal diagnosis. With the development of molecular cytogenetic methods, this situation has dramatically changed. Chromosomal microarray analysis (CMA), a method of genome-wide detection with high resolution, has been recommended as a first-tier test for prenatal diagnosis, especially for fetuses with structural abnormalities. Methods: Based on the primary literature, this review provides an updated summary of the application of CMA for prenatal diagnosis. In addition, this review addresses the challenges that CMA faces with the emergence of genome sequencing techniques, such as copy number variation sequencing, genome-wide cell-free DNA testing, and whole exome sequencing. Conclusion: The CMA platform is still suggested as priority testing methodology in the prenatal setting currently. However, pregnant women may benefit from genome sequencing, which enables the simultaneous detection of copy number variations, regions of homozygosity and single-nucleotide variations, in near future.

Comprehensive genetic analysis in first or second trimester pregnancy loss using chromosomal microarray with single nucleotide polymorphism probes

To explore possible genetic causes associated with early pregnancy loss using chromosomal microarray analysis (CMA) with single nucleotide polymorphism (SNP) probes. A retrospective review was performed by the CMA of samples from 961 patients who spontaneously aborted in our hospital before the 20th week of pregnancy. (1) The total chromosome abnormality rate in miscarriage samples was 54.44% (515/946), including single chromosome abnormality (39.53%), two chromosome abnormality (2.22%), multi-chromosome abnormality (0.42%), triploidy or hypertriploidy (4.86%), copy number variants (CNVs) in 41 cases (4.33%), regions of homozygosity (ROH, 0.74%), mosaic (2.22%) and chimera (0.11%). (2) CNV analysis of 41 cases showed that 85.36% were pathogenic and likely pathogenic, 12.20% were classified as clinical significance unknown and 2.44% were interpreted as likely benign; (3) Among the cases of ROH, 2 cases shown whole-genome homozygosity and 1 case had completely homozygous at chromosome 21. The homozygous regions in 2 cases were located at the end of the short arm of chromosome 16, suggesting the mechanism of ROH in such cases could be the result of isodisomy. Chromosome abnormality is an important genetic factor causing pregnancy loss. The application of CMA with SNP probes can indeed improve the detection rate of chromosome abnormalities and evaluate the risk of reproductive fertility in patients with pregnancy loss.

Application of chromosomal microarray analysis in prenatal diagnosis of pregnant women with advanced age

To assess the value of chromosomal microarray analysis (CMA) for the detection of fetal anomalies among pregnant women with advanced age. CMA results of 562 cases, in addition with the outcome of pregnancy and neonatal follow-up were reviewed. Among the 562 amniotic fluid samples, 73 cases (12.99%) of fetal chromosomal abnormalities were detected, which included 21 cases (3.73%) of chromosomal aneuploidies and 52 cases (9.25%) of copy number variations (CNVs). The latters included 27 cases of pathological CNVs (4.80%), 4 cases of possible pathogenic CNVs (0.71%) and 42 cases of variants with unknown clinical significance (7.47%). Compared with those under 35, the detection rate of fetal chromosomal aneuploidies for women with advanced age was higher under the indications of voluntary test, abnormal ultrasonic structures, abnormal ultrasonic soft index and risks indicated by non-invasive prenatal testing (NIPT). No significant difference was found in the detection rate of CNVs between those ≥35 and <35 and between those with age factor only and with additional indications (P> 0.05). 552 cases (98.22%) of pregnant women have completed the followed up. Among 31 women with pathological and possible pathogenic fetal CNVs detected by CMA, 25 had terminated the pregnancy, 6 (19.35%) have delivered without obvious abnormality. 41 pregnant women with fetal CNVs of unknown clinical significance have completed the follow up, among whom 3 had terminated the pregnancy, 1 newborn was found with malformation after birth, which yielded an abnormal pregnancy rate of 9.76%. 480 pregnant women with negative CMA results have completed the follow up, among whom 5 (1.04%) had abnormal pregnancy or delivered a child with birth defect. There is a certain difference between the outcome of pregnancy predicted by CMA testing and the actual outcome. The pregnancies with fetal CNVs with unknown clinical significance detected by CMA have a high adverse rate, which should attract clinical attention. CMA testing should be recommended for pregnant women with advanced age regardless of whether they have other symptoms. CMA combined with other detection methods is the trend for prenatal diagnosis.

Clinical Application of Chromosomal Microarray Analysis in Pregnant Women with Advanced Maternal Age and Fetuses with Ultrasonographic Soft Markers.

BackgroundIn pregnant women with advanced maternal age (AMA) and fetuses with ultrasonographic (USG) soft markers it is always challenging to decide whether to implement chromosomal microarray analysis (CMA) or not. It is unclear whether CMA should be used in the fetuses with isolated USG soft markers, and there is still a lack of extensive sample research.Material/MethodsWe enrolled 1521 cases in our research and divided them into 3 groups as follows: pregnant women with isolated AMA (group 1, n=633), pregnant women whose fetuses had isolated USG soft markers (group 2, n=750), and pregnant women with AMA whose fetuses had isolated USG soft markers (group 3, n=138). All pregnant women underwent prenatal ultrasound and amniocentesis, and fetal cells in the amniotic fluid were used for genetic analysis of CMA. All participants signed a written informed consent prior to CMA.ResultsAbnormal findings were detected by CMA in 330 (21.70%) fetuses, including 37 (2.43%) clinically significant copy number variations (CNVs), 52 (3.42%) benign or likely benign CNVs, and 240 (15.78%) variants of unknown significance. The frequency of clinically significant CNVs in group 1 and group 2 were significantly lower than that in group 3 (2.37% and 2.0% vs 5.07%, P<0.01). More than a half (59.46%, 22/37) of the pregnant women decided to continue their pregnancy despite having a fetus diagnosed with clinically significant CNV.ConclusionsCMA can increase the diagnostic yield of fetal chromosomal abnormality for pregnant women with isolated AMA or/and their fetuses had isolated USG soft markers.

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

To explore genetic etiology and prognosis for fetuses with increased nuchal translucency (NT). 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. 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. 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.

Detection of submicroscopic chromosomal aberrations by chromosomal microarray analysis for the prenatal diagnosis of central nervous system abnormalities.

BackgroundCentral nervous system (CNS) abnormalities are a group of serious birth defects associated with high rates of stillbirths, infant death, or abnormal development, and various disease‐causing copy number variations play a much more important role in the etiology of CNS abnormalities. This study intends to present a retrospective study of the prenatal diagnosis and the pregnancy outcome of fetuses diagnosed with CNS abnormalities, and evaluate the clinical value of chromosomal microarray analysis (CMA) in prenatal diagnosis of CNS abnormalities.MethodsA total of 356 fetuses with CNS abnormalities with or without other ultrasound abnormalities subjected to invasive prenatal diagnosis at the first affiliated hospital of Air Force Medical University from January 2015 to August 2018. All cases have performed both karyotyping and CMA concurrently, but 20 fetuses with chromosome aneuploidy were excluded in the current study.ResultsThe CMA identified pathogenic copy number variants (pCNVs) in 27/336 (8.03%) fetuses, likely pCNVs in 8/336 (2.38%) fetuses, and variants of unknown significance (VOUS) in 11/336 (3.27%) fetuses. A total of 222 cases had single CNS abnormalities and the pCNVs detection rate was 5.86% (13/222), the remaining 114 cases including CNS abnormalities plus other structural abnormalities, ultrasonographic soft markers and two or more CNS abnormalities, the pCNVs detection rate was 12.3% (14/114).ConclusionsFetuses with CNS abnormalities have a higher risk of chromosomal abnormalities, our study showed that CNVs play an important role in the etiology of CNS abnormalities. The application of CMA could increase the detection rate of pCNVs causing CNS abnormalities.

Application of chromosomal microarray analysis in prenatal diagnosis of fetuses with increased nuchal translucency

To determine the frequency of chromosomal abnormalities and outcome of pregnancy for fetuses with increased nuchal translucency (NT). Between July 2014 and February 2018, 247 fetuses with increased NT (>95th centile)were analyzed by chromosome microarray analysis (CMA). The fetuses were divided into ones with isolated increased NT (168 cases), increased NT with cystic hygroma (20 cases), increased NT with edema (12 cases) or increased NT with other abnormalities (47 cases). All couples were followed up by telephone calls. The rate of chromosomal abnormalities was 31.6% (78/247), which included 66 cases with chromosomal aneuploidies and 12 with copy number variants (CNVs). CNVs accounted for 31.4% (11/35) of total abnormalities among fetuses with isolated increased NT, whilst only 2.3% (1/43) of the total abnormalities among fetuses with non-isolated increased NT. Three fetuses with a normal CMA result had mental and physical retardation. Two of them were diagnosed with single gene disorders by whole exome sequencing. CMA can detect more chromosomal microdeletion/microduplications among fetuses with isolated increased NT. Furthermore, fetuses with increased NT and anegative CMA result during pregnancy cannot exclude all adverse outcomes.

Application of chromosome microarray analysis in neonatal birth defects

Objective To explore the application of chromosomal microarray analysis (CMA) in neonatal birth defects and further determine the frequency of chromosome imbalances in neonates with birth defects. Methods Retrospective analysis was performed in 121 neonates with specific features, such as distinctive facial features, congenital heart disease, congenital malformation, neonatal decreased responsive, hypotonia, seizures and others at the Department of Neonatology, Guangdong Women and Children Hospital from May 2016 to November 2017.All the cases were analyzed by using chromosomal microarray analysis (CMA). Results A total of 23 (19.0%) patients were identified with pathogenic CNVs, 3 patients (2.5%) with uncertain clinical significant CNVs.There were 5 patients (4.1%)with chromosome numerical abnormalities, 12 patients (9.9%)with microdeletion/microduplication syndrome, 6 patients (5.0%) with chromosome deletion or duplication.All groups whose incidence was sorted from high to low were facial characters(30.3%), congenital malformation(21.6%), neonatal decreased responsive(9.1%) and other indications(6.7%). Conclusions CMA is a valuable clinical diagnostic tool that allows precise identification of chromosome imbalances as the cause of birth defects in neonates.CMA can detect many more clinically relevant genomic abnormalities than conventional cytogenetic study and assist the clinician in diagnosis, early neonatal intervention, and genetic counseling. Key words: Birth defect; Chromosome microarray analysis; Chromosome disorder

Application of chromosomal microarray analysis and next-generation sequencing for the analysis of abortic tissues

To assess the value of chromosomal microarray analysis (CMA) and next-generation sequencing (NGS) for the analysis of abortic tissues. A total of 242 samples of spontaneous abortion were collected and tested by CMA or NGS. The detection was successfully in 238 cases (98.35%). In total 143 cases of chromosomal abnormalities were detected, which accounted for 60.08% of all cases. Numerical chromosomal abnormalities were found in 133 cases(93.01%), structural abnormalities were found in 9 cases (6.29%), and uniparental disomy was found in 1 case(0.70%). Both CMA and NGS have the advantages of high-throughput, good coverage, high resolution and rapid analysis. They can be used for the detection of the causes of spontaneous abortions. CMA is more useful for the detection of aneuploidies and uniparental disomy, while NGS has advantages in its throughput, capacity in detecting low percentage chimerism and cost, which can provide more options for clinicians.

Clinical application of chromosomal microarray analysis in fetuses with increased nuchal translucency and normal karyotype.

BackgroundSubmicroscopic chromosomal imbalance is associated with an increased nuchal translucency (NT). Most previous research has recommended the use of chromosomal microarray analysis (CMA) for prenatal diagnosis if the NT ≥ 3.5 mm. However, there is no current global consensus on the cutoff value for CMA. In this study, we aimed to discuss the fetuses with smaller increased NT which was between cutoff value of NT for karyotype analysis (NT of 2.5 mm in China) and the recommended cutoff value for CMA (NT of 3.5 mm) whether should be excluded from CMA test.MethodsSingleton pregnant women (N = 192) who had undergone invasive procedures owing to an increased NT (NT ≥ 2.5 mm) were enrolled. Fetal cells were collected and subjected to single nucleotide polymorphism array and karyotype analyses simultaneously. Cases were excluded if the karyotype analysis indicated aneuploidy and apparent structural aberrations.ResultsFourteen cases of aneuploidy and four cases of structural abnormalities were excluded. Of the remaining 174 cases, 119 fetuses had NTs of 2.5–3.4 mm, and 55 fetuses with NT ≥ 3.5 mm. Eleven copy number variants (CNVs) were identified. In fetuses with smaller NTs, six (6/119, 5.9%) variations were detected, including two (2/119, 1.6%) clinically significant CNVs (pathogenic or likely pathogenic CNV), one likely benign CNV, two variants unknown significance, and one incidental CNV. Five (5/55, 9.1%) variations were found in fetuses with NT ≥ 3.5 mm. Among these CNVs, three (3/55, 5.5%) cases had clinically significant CNVs, and two had likely benign CNV. There were no statistically significant differences in the incidence of all CNVs and clinically significant CNVs in the two groups (p > 0.05).ConclusionCMA improved the diagnostic yield of chromosomal aberrations for fetuses with NTs of 2.5–3.4 mm and apparently normal karyotype, regardless of whether other ultrasonic abnormalities were observed.

The application of chromosomal microarray analysis to the prenatal diagnosis of isolated mild ventriculomegaly

ObjectiveTo investigate the clinical value of chromosomal microarray analysis (CMA) in the prenatal diagnosis of genetic abnormalities in fetal isolated mild ventriculomegaly. Materials and methodsThis retrospective study reviewed 101 fetuses with isolated mild ventriculomegaly who had undergone invasive prenatal diagnosis at our hospital. CMA was performed in all cases to detect chromosomal aneuploidy as well as copy number variations (CNVs) that are too small to be detected by conventional karyotyping. Real time quantitative PCR (qPCR) or multiplex ligation dependent probe amplification (MLPA) was used to confirm all fetal CNVs <400 Kb. ResultsExcept for three cases of chromosomal aneuploidy, CMA revealed pathogenic copy number variations (CNVs) in 3.0% (3/101) of the fetuses; these cases demonstrated involvement in the chromosomal regions 15q11.2, 1q21.1 and Xq27.3q28. Furthermore, we detected three likely pathogenic (3.0%) and two variants of uncertain significance (2.0%) among 101 fetuses diagnosed as isolated mild ventriculomegaly on ultrasound examination. ConclusionOur study suggests that CNVs could aid in the risk assessment and genetic counseling in fetuses with isolated ventriculomegaly.

Chromosomal Microarray Analysis as a First-Tier Clinical Diagnostic Test in Patients With Developmental Delay/Intellectual Disability, Autism Spectrum Disorders, and Multiple Congenital Anomalies: A Prospective Multicenter Study in Korea.

BackgroundTo validate the clinical application of chromosomal microarray analysis (CMA) as a first-tier clinical diagnostic test and to determine the impact of CMA results on patient clinical management, we conducted a multicenter prospective study in Korean patients diagnosed as having developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), and multiple congenital anomalies (MCA).MethodsWe performed both CMA and G-banding cytogenetics as the first-tier tests in 617 patients. To determine whether the CMA results directly influenced treatment recommendations, the referring clinicians were asked to complete a 39-item questionnaire for each patient separately after receiving the CMA results.ResultsA total of 122 patients (19.8%) had abnormal CMA results, with either pathogenic variants (N=65) or variants of possible significance (VPS, N=57). Thirty-five well-known diseases were detected: 16p11.2 microdeletion syndrome was the most common, followed by Prader-Willi syndrome, 15q11-q13 duplication, Down syndrome, and Duchenne muscular dystrophy. Variants of unknown significance (VUS) were discovered in 51 patients (8.3%). VUS of genes putatively associated with developmental disorders were found in five patients: IMMP2L deletion, PTCH1 duplication, and ATRNL1 deletion. CMA results influenced clinical management, such as imaging studies, specialist referral, and laboratory testing in 71.4% of patients overall, and in 86.0%, 83.3%, 75.0%, and 67.3% of patients with VPS, pathogenic variants, VUS, and benign variants, respectively.ConclusionsClinical application of CMA as a first-tier test improves diagnostic yields and the quality of clinical management in patients with DD/ID, ASD, and MCA.

Clinical application of chromosomal microarray analysis for the diagnosis of Williams-Beuren syndrome in Chinese Han patients.

BackgroundWilliams–Beuren syndrome (WBS; OMIM #194,050) is a rare multisystem disorder of a variable phenotypic spectrum caused by a heterozygous microdeletion in the WBS chromosome region (WBSCR) in 7q11.23.MethodsWe screened 38 Chinese Han patients with suspected WBS using chromosomal microarray analysis (CMA).ResultsPathogenic CNVs were identified in 34 of the patients, including 29 cases with a typical 7q11.23 microdeletion, three cases with atypical copy number variations (CNVs) within the WBS chromosome region and two cases with CNVs associated with other known syndromes. All 29 WBS patients with a typical microdeletion exhibited distinctive facial dysmorphisms and developmental delay. We observed that the incidence of pulmonary abnormalities was slightly higher than that of aortic abnormalities. We also found long philtrum and prominent lips with a thick lip that may warrant suspicion of WBS in the Chinese Han patients.ConclusionCMA facilitates diagnosis in individuals with classic/nonclassic features of WBS and demonstrated that when Chinese Han patients present with a less classical phenotype, such as pulmonary abnormalities, this may raise suspicion for a WBS diagnosis and suggest a referral for a genetics evaluation for a differential diagnosis.

Application of chromosomal microarray analysis for a cohort of 2600 Chinese patients with miscarriage

Chromosomal microarray analysis (CMA) is a technique for screening numerical and structural abnormalities of chromosomes at the whole genome level. It is a routine tool for pediatric and prenatal genetic diagnoses. It has also been applied to investigate the genetic etiologies of miscarriages. In our study, we used the CMA technology to analyze the chromosomal variations of fetuses from miscarriages at the whole genome level, and to evaluate its clinical applications in studies of miscarriages. The CMA analyses were performed on 2600 miscarriage specimens, of which 2505 specimens (96.35%) were successfully analyzed. Among them, 1021 specimens were analyzed with CytoScan Optima chip; 1211 specimens were analyzed with CytoScan 750K chip; and 273 cases were analyzed with CytoScan HD chip. Chromosomal abnormalities were identified in 967 specimens (38.6%) by these 3 kinds of chips, of which 506 specimens (50.00%) were detected with CytoScan Optima chip; 388 specimens were detected by CytoScan 750K chip (32.00%); and 73 cases (26.74%) were detected in CytoScan HD chip. Among the 967 cases of chromosomal abnormalities, 801 cases (82.83%) were numerical chromosomal abnormalities; 94 cases (9.72%) were structural abnormalities; 56 cases (5.79%) were mosaicisms; and 16 (1.65%) were regions of homozygosity. Our research suggests that CMA is a reliable, robust, and high-resolution technology for genetic diagnosis of miscarriage in clinical practice, which can also provide results as guidance for the risk assessment of assisted fertility.