Submicroscopic Copy Number Variations Research Articles

Submicroscopic copy number variants in Indian children with gene panel negative 46, XY Gonadal Dysgenesis: An exploratory study using comparative genomic hybridization.

46, XY disorders of sex development (DSD) are a group of highly heterogeneous conditions in which the molecular etiology remains unknown in a significant proportion of patients, even with massive parallel sequencing. Clinically significant copy number variants (CNVs) are identified in 20-30% of cases, particularly among those with gonadal dysgenesis (GD) and no molecular diagnosis. Fourteen patients with 46, XY DSD due to GD in whom no pathogenic/likely pathogenic variants were found on next-generation sequencing using a targeted panel of 155 genes were screened for clinically significant CNVs using Affymetrix Comparative Genomic Hybridization (CGH). Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources (DECIPHER) and ClinVar were searched for matching genotypes and phenotypes, and chromosomal regions were screened for genes with known or potential association with GD. Significant CNVs were identified in 6 (43%) of 14 patients with 46, XY GD. A previously unreported 19p13.3 duplication was found in three patients. This CNV was associated with GD based on overlapping CNV regions from previous studies and databases; and the inclusion of CIRBP, a candidate gene implicated in GD. CNVs involving WT1 (11p15) and SOX8 (16p13.3) were also identified. CGH was helpful in pointing toward the molecular etiology in a significant proportion of patients with "idiopathic" 46, XY GD. However, establishing causality will require additional evidence including functional studies.

Pregnancy Outcome of Confined Placental Mosaicism: Meta-analysis of Cohort Studies

ABSTRACT Confined placental mosaicism (CPM) is a condition in which there is chromosomal abnormality in the placenta that is not present in the fetus. Confined placental mosaicism has historically been most often identified following a first-trimester chorionic villus sampling (CVS), in which there are 2 different cell lines in the placenta but a normal karyotype in the fetus based on amniocentesis or neonatal blood. As the outcome for CPM pregnancies is still debated, including the potential for adverse pregnancy and postnatal outcomes, this study aimed to evaluate the rates of adverse neonatal and obstetrical outcomes in CPM-diagnosed pregnancies, as compared with unaffected matched controls. This meta-analysis was performed in accordance with an a priori designed protocol and was registered with the PROSPERO (International Prospective Register of Systematic Reviews) database. A search of EMBASE and MEDLINE databases from 1980 to February 2022 was performed. Included articles were published in the English language and were observational studies including singleton CPM-diagnosed pregnancies (whose controls were unaffected and with normal karyotype). Excluded were all reviews, case reports, and congress abstracts. In addition, high-risk or positive cell-free DNA screening (cfDNA) cases followed by diploid amniotic cells were excluded (because of the different methodology, which may have an effect on the analysis). Because of the paucity of data regarding mosaicism in submicroscopic copy number variants, these abnormalities were also excluded from the analysis. Primary outcomes included the occurrence of the following: termination of pregnancy, major fetal defects (as defined by the Centers for Disease Control and Prevention), small for gestational age (SGA) neonate with birth weight (BW) <10th centile and neonatal SGA with BW less than the third centile, preterm birth (PTB), hypertensive disorders, admission to a neonatal intensive care unit, intrauterine fetal demise at <24 weeks' gestation, and >24 weeks' gestation stillbirth. All other abnormal pregnancy outcomes were searched for, including PTB, obstetrical cholestasis, amniotic infection, gestational diabetes, cesarean delivery, amniotic infection, preterm prelabor rupture of membranes, and neonatal mortality or morbidity. Of 310 retrieved articles, 80 studies were assessed for eligibility, and 8 retrospective matched cohort studies were included. The results of the meta-analysis showed that women with CPM had a higher risk of adverse pregnancy outcomes than those without CPM. The most common adverse outcomes were fetal growth restriction (FGR), PTB, and stillbirth. The risk of FGR was significantly higher in women with CPM, with an odds ratio (OR) of 3.60 (95% confidence interval [CI], 2.40–5.39). Similarly, the risk of PTB was higher in women with CPM, with an OR of 2.64 (95% CI, 1.90–3.67), and the risk of stillbirth was also increased, with an OR of 2.58 (95% CI, 1.51–4.42). Scarcity of reporting for other obstetrical neonatal and obstetrical outcomes hindered further conclusions. In subgroup analysis, the risk of delivering an SGA infant was 3-fold higher for CPM when trisomy 16 was excluded and 11-fold higher for trisomy 16 specifically compared with unaffected controls. The authors acknowledge that the meta-analysis has several limitations, including the heterogeneity of the included studies, the lack of information on the specific type and extent of CPM in each case, and the potential for publication bias. Nevertheless, the study provides valuable insights into the pregnancy outcomes of women with CPM and highlights the need for further research to improve our understanding of this condition. Overall, this meta-analysis suggests that women with CPM are at increased risk of adverse pregnancy outcomes, particularly FGR, PTB, and stillbirth. The findings highlight the importance of early detection of CPM and close monitoring of pregnancies in women with this condition. The study also emphasizes the need for further research to better understand the underlying mechanisms of CPM and to identify effective interventions to improve pregnancy outcomes in affected women.

Microdeletion 12p12.1 involving SRY-related HMG-box 5 gene with developmental delay and autistic behavior

The estimated prevalence of intellectual disability (ID) is 10.37/1000 population. One of the major causes of ID is a chromosomal abnormality. SRY-related HMG-box 5 (SOX5) gene encodes a member of the SOX family of transcription factors, which may act as a transcriptional regulator involved in the regulation of chondrogenesis and the development of the nervous system by regulation of the production of subcortical projection neurons. Array-comparative genomic hybridization (array-CGH) is a molecular-cytogenetic method used to detect submicroscopic copy number variants within the genome, which is not visible by conventional karyotyping. We describe the extensive application of array-CGH in a 4-year-old male child who presented with global developmental delay (DD), behavioral abnormality, microcephaly, mild dysmorphic facial features, and constriction ring around prepuce with 12p12.1 microdeletion (166 kb deletion) involving SOX5 gene. The patient is under follow-up with a pediatrician, geneticist, speech therapist, and physiotherapist. A high index of suspicion for cytogenetic abnormalities should be present in a pediatric patient presenting with DD, genitourinary abnormalities, and associated with or without facial dysmorphism.

Prenatal detection of chromosomal abnormalities and copy number variants in fetuses with corpus callosum agenesis.

The corpus callosum is the main pathway that connects interhemispheric communication. Agenesis of corpus callosum (ACC) have not consistently detected replicate genetic risk factors, potentially due to Etiological heterogeneity of this trait. This study aimed to retrospectively analyze the molecular basis for the ACC and the potential genotyping-phenotyping association and provide the basis for genetic counselling. Karyotyping and chromosomal microarray analysis were performed for copy number variants. Three cases had 1p36 deletions, two cases had 2q31.2 and 2p16.3 microdeletions, one case had microdeletion of Xq26.3q27.1, five cases involved derived chromosomes due to unbalanced translocations. These cases had variable deletions and duplications with partial overlapping. Phenotypically, besides agenesis of corpus callosum and other brain morphological abnormalities as well as heart abnormalities. ACC may occur alone or be related to other abnormal clinical phenotypes, and its genetic mechanism is very complicated. These results revealed ACC is associated with a variety of chromosomal abnormalities. The findings of the present study expand the genotypes associated with ACC, and further delineation of the genotype-phenotype correlations for ACC. With current applications of chromosome microarray analysis, congenital submicroscopic copy-number variations in fetuses can be detected more effectively.

Genome-wide identification of disease-causing copy number variations in 450 individuals with anorectal malformations

Anorectal malformations (ARM) represent a spectrum of rare malformations originating from a perturbated development of the embryonic hindgut. Approximately 60% occur as a part of a defined genetic syndrome or within the spectrum of additional congenital anomalies. Rare copy number variations (CNVs) have been associated with both syndromic and non-syndromic forms. The present study represents the largest study to date to explore the contribution of CNVs to the expression of ARMs. SNP-array-based molecular karyotyping was applied in 450 individuals with ARM and 4392 healthy controls. CNVs were identified from raw intensity data using PennCNV. Overlapping CNVs between cases and controls were discarded. Remaining CNVs were filtered using a stringent filter algorithm of nine filter steps. Prioritized CNVs were confirmed using qPCR. Filtering prioritized and qPCR confirmed four microscopic chromosomal anomalies and nine submicroscopic CNVs comprising seven microdeletions (del2p13.2, del4p16.2, del7q31.33, del9p24.1, del16q12.1, del18q32, del22q11.21) and two microduplications (dup2p13.2, dup17q12) in 14 individuals (12 singletons and one affected sib-pair). Within these CNVs, based on their embryonic expression data and function, we suggest FOXK2, LPP, and SALL3 as putative candidate genes. Overall, our CNV analysis identified putative microscopic and submicroscopic chromosomal rearrangements in 3% of cases. Functional characterization and re-sequencing of suggested candidate genes is warranted.

Abnormal chromosomes identification using chromosomal microarray

In this study, we presented a case series to highlight the chromosomal microarray (CMA) in identifying chromosomal abnormalities which is undetectable by conventional karyotyping or known abnormal chromosomes without clear diagnosis. Extensive studies showed that CMA was gradually accepted as a prenatal invasive testing during pregnancy. The aim of this study was to evaluate the diagnostic effect of CMA for foetuses with abnormal chromosomes unrecognised by conventional karyotyping. Pregnant women who need prenatal diagnosis with all indications were enrolled in this study. For aberrant cytogenetic findings that cannot be defined by routine karyotyping, single nucleotide polymorphism array (SNP-array) was used. Six cases with abnormal karyotype were included in the study. With higher resolution of translocation breakpoints, CMA could detect smaller chromosomal imbalances that were undetectable by karyotyping. This study highlights the value of CMA for the detection of submicroscopic abnormalities in foetuses that cannot be detected by conventional karyotyping. Impact Statement What is already known on this subject? Chromosomal microarray (CMA) offers additional diagnostic benefits by revealing submicroscopic imbalances or copy number variations (CNVs) that are too small to be identified on a standard G-banded chromosome preparation. What do the results of this study add? We added a case series to highlight the CMA in identifying chromosomal abnormalities not detectable by conventional karyotyping or known abnormal chromosomes without clear diagnosis. What are the implications of these findings for clinical practice and/or further research? This study highlights the value of CMA in the case of associated foetuses with submicroscopic abnormalities that cannot detect by conventional karyotyping.

Comparative Genomic Hybridization to Microarrays in Fetuses with High-Risk Prenatal Indications: Polish Experience with 7400 Pregnancies.

The aim of this study was to determine the suitability of the comparative genomic hybridization to microarray (aCGH) technique for prenatal diagnosis, but also to assess the frequency of chromosomal aberrations that may lead to fetal malformations but are not included in the diagnostic report. We present the results of the aCGH in a cohort of 7400 prenatal cases, indicated for invasive testing due to ultrasound abnormalities, high-risk for serum screening, thickened nuchal translucency, family history of genetic abnormalities or congenital abnormalities, and advanced maternal age (AMA). The overall chromosomal aberration detection rate was 27.2% (2010/7400), including 71.2% (1431/2010) of numerical aberrations and 28.8% (579/2010) of structural aberrations. Additionally, the detection rate of clinically significant copy number variants (CNVs) was 6.8% (505/7400) and 0.7% (57/7400) for variants of unknown clinical significance. The detection rate of clinically significant submicroscopic CNVs was 7.9% (334/4204) for fetuses with structural anomalies, 5.4% (18/336) in AMA, 3.1% (22/713) in the group of abnormal serum screening and 6.1% (131/2147) in other indications. Using the aCGH method, it was possible to assess the frequency of pathogenic chromosomal aberrations, of likely pathogenic and of uncertain clinical significance, in the groups of cases with different indications for an invasive test.

EP256: Intrafamilial variability in chromosome 2q13 microdeletion: Case report and review of the literature

Chromosome microarray technology has disclosed an increasing number of submicroscopic copy number variants for which interpretation of pathogenicity can be difficult. One useful approach is comparison of phenotypic findings among individuals with similar genotypes, both within families and in unrelated individuals. Delineation of pathogenicity can pose a difficult challenge when information on a given submicroscopic copy number variant is scarce, or conflicting. Certain cytogenetic locations appear prone to copy number variation, considered to be mediated by flanking highly homologous duplicated regions.

Increased Diagnostic Yield of Array Comparative Genomic Hybridization for Autism Spectrum Disorder in One Institution in Taiwan.

Background and Objectives: Chromosomal microarray offers superior sensitivity for identification of submicroscopic copy number variants (CNVs) and is recommended for the initial genetic testing of patients with autism spectrum disorder (ASD). This study aims to determine the diagnostic yield of array comparative genomic hybridization (array-CGH) in ASD patients from a cohort of Chinese patients in Taiwan. Materials and Methods: Enrolled in this study were 80 ASD children (49 males and 31 females; 2–16 years old) followed up at Taipei MacKay Memorial Hospital between January 2010 and December 2020. The genomic DNA extracted from blood samples was analyzed by array-CGH via the Affymetrix GeneChip Genome-Wide Human single nucleotide polymorphism (SNP) and NimbleGen International Standards for Cytogenomic Arrays (ISCA) Plus Cytogenetic Arrays. The CNVs were classified into five groups: pathogenic (pathologic variant), likely pathogenic (potential pathologic variant), likely benign (potential normal genomic variant), benign (normal genomic variant), and uncertain clinical significance (variance of uncertain significance), according to the American College of Medical Genetics (ACMG) guidelines. Results: We identified 47 CNVs, 31 of which in 27 patients were clinically significant. The overall diagnostic yield was 33.8%. The most frequently clinically significant CNV was 15q11.2 deletion, which was present in 4 (5.0%) patients. Conclusions: In this study, a satisfactory diagnostic yield of array-CGH was demonstrated in a Taiwanese ASD patient cohort, supporting the clinical usefulness of array-CGH as the first-line testing of ASD in Taiwan.

53. Re-analysis of reported constitutional copy number variants using the newly published 2019 ACMG/ClinGen Technical Standards reveals few significant interpretation changes

Cytogenomic microarray analysis (CMA) is a powerful tool to identify submicroscopic copy number variants (CNVs) in patients with developmental delay and/or congenital anomalies, detecting CNVs in roughly 20% of this population. It is challenging to establish many CNVs as definitively pathogenic or benign, leading to a significant proportion of CNVs reported as variants of uncertain significance (VOUS). In a 6 year period, our laboratory reported a CNV in 20% of approximately 5,000 patients. Of these CNVs, 40% were interpreted as VOUS, with limited benefit to the patient.

D-karyo-A New Prenatal Rapid Screening Test Detecting Submicroscopic CNVs and Mosaicism.

Chromosomal microarray analysis (CMA), recently introduced following conventional cytogenetic technology, can detect submicroscopic copy-number variations (CNVs) in cases previously diagnosed as “cytogenetically benign”. At present, rapid and accurate chromosomal analysis is required in prenatal diagnostics, but prenatal CMA is not widely used due to its high price and long turnaround time. We introduced a new prenatal screening method named digital karyotyping (D-karyo), which utilizes a preimplantation genetic test for the aneuploidy (PGT-A) platform. First, we conducted a preliminary experiment to compare the original PGT-A method to our modified method. Based on the preliminary results, we decided to implement the modified strategy without whole-genome amplification (WGA) and combined it with three analytical software packages. Next, we conducted a prospective study with 824 samples. According to the indication for invasive tests, the D-karyo positive rates were 2.5% and 5.0%, respectively, in the screening positive group with NT ≥ 3.5 mm and the group with fetal abnormalities by ultrasound. D-karyo is a breakthrough modality that can detect submicroscopic CNVs ≥ 1.0 Mb accurately in only 10.5 h for 24 samples at a low cost. Implementing D-karyo as a prenatal rapid screening test will reduce unnecessary CMA and achieve more accurate prenatal genetic testing than G-banding.

Characterization of Copy-Number Variations and Possible Candidate Genes in Recurrent Pregnancy Losses.

It is well established that embryonic chromosomal abnormalities (both in the number of chromosomes and the structure) account for 50% of early pregnancy losses. However, little is known regarding the potential differences in the incidence and distribution of chromosomal abnormalities between patients with sporadic abortion (SA) and recurrent pregnancy loss (RPL), let alone the role of submicroscopic copy-number variations (CNVs) in these cases. The aim of the present study was to systematically evaluate the role of embryonic chromosomal abnormalities and CNVs in the etiology of RPL compared with SA. Over a 3-year period, 1556 fresh products of conception (POCs) from miscarriage specimens were investigated using single nucleotide polymorphism array (SNP-array) and CNV sequencing (CNV-seq) in this study, along with further functional enrichment analysis. Chromosomal abnormalities were identified in 57.52% (895/1556) of all cases. Comparisons of the incidence and distributions of chromosomal abnormalities within the SA group and RPL group and within the different age groups were performed. Moreover, 346 CNVs in 173 cases were identified, including 272 duplications, 2 deletions and 72 duplications along with deletions. Duplications in 16q24.3 and 16p13.3 were significantly more frequent in RPL cases, and thereby considered to be associated with RPL. There were 213 genes and 131 signaling pathways identified as potential RPL candidate genes and signaling pathways, respectively, which were centered primarily on six functional categories. The results of the present study may improve our understanding of the etiologies of RPL and assist in the establishment of a population-based diagnostic panel of genetic markers for screening RPL amongst Chinese women.

Confined placental mosaicism of Duchenne muscular dystrophy: a case report

BackgroundSmall copy number variations confined to the placenta are extremely rare findings in chorionic villus sampling, nonetheless of great clinical importance. To the best of our knowledge, this is the first reported case of confined placental mosaicism for an intragenic Duchenne muscular dystrophy (DMD) gene deletion.Case presentationWe describe a pregnant woman where confined placental mosaicism for an intragenic DMD deletion was detected. She was referred for a chorionic villus sampling due to an increased risk of trisomy 21 derived from combined first trimester screening. Rapid aneuploidy detection showed a male fetus with normal results for chromosomes 13, 18 and 21. A chromosomal microarray demonstrated a deletion of exons 61–62 in the DMD gene in approximately 50% of the cells. A follow-up analysis on amniotic cells showed a normal result for the DMD gene. Hence, confined placental mosaicism was confirmed.ConclusionsWe propose tissue specific fragile sites as a possible theoretical mechanism for the formation of submicroscopic copy number variations and highlight that the finding of DMD deletion mosaicism in a chorionic villus sample might be isolated to the placenta. Therefore, confirmation by amniocentesis is of crucial clinical importance to avoid misdiagnosis of the fetus.

Clinical Utility of SNP Array Analysis in Prenatal Diagnosis: A Cohort Study of 5000 Pregnancies.

BackgroundSingle nucleotide polymorphism array (SNP-array) has been introduced for prenatal diagnosis. We aimed to evaluate the clinical value of SNP-array in the diagnosis of fetal chromosomal anomalies.MethodsA retrospective study was conducted on 5000 cases tested by SNP-array, and the results of 4022 cases analyzed by both karyotyping and SNP-array were compared.ResultsSNP-array analysis of 5000 samples revealed that the overall abnormality detection rate by SNP-array was 12.3%, and the overall detection rate of clinically significant copy number variations (CNVs) by SNP-array was 2.6%. SNP-array identified clinically significant submicroscopic CNVs in 4.5% fetuses with anomaly on ultrasonography, in 1.6% of fetuses with advanced maternal age (AMA), in 2.5% of fetuses with abnormal result on maternal serum screening, in 2.9% of fetuses with abnormal non-invasive prenatal testing (NIPT) results and in 3.0% of fetuses with other indications. Of the 4022 samples analyzed by both karyotyping and SNP-array, SNP-array could identify all the aneuploidy and triploidy detected by karyotyping but did not identify balanced structural chromosomal abnormalities and low-level mosaicism detected by karyotyping.ConclusionSNP-array could additionally identify clinically significant submicroscopic CNVs, and we recommend the combination of SNP-array analysis and karyotyping in prenatal diagnosis.

PREIMPLANTATION GENETIC TESTING: Non-invasive prenatal testing for aneuploidy, copy-number variants and single-gene disorders.

The discovery of cell-free fetal DNA (cffDNA) in maternal plasma has enabled a paradigm shift in prenatal testing, allowing for safer, earlier detection of genetic conditions of the fetus. Non-invasive prenatal testing (NIPT) for fetal aneuploidies has provided an alternative, highly efficient approach to first-trimester aneuploidy screening, and since its inception has been rapidly adopted worldwide. Due to the genome-wide nature of some NIPT protocols, the commercial sector has widened the scope of cell-free DNA (cfDNA) screening to include sex chromosome aneuploidies, rare autosomal trisomies and sub-microscopic copy-number variants. These developments may be marketed as 'expanded NIPT' or 'NIPT Plus' and bring with them a plethora of ethical and practical considerations. Concurrently, cfDNA tests for single-gene disorders, termed non-invasive prenatal diagnosis (NIPD), have been developed for an increasing array of conditions but are less widely available. Despite the fact that all these tests utilise the same biomarker, cfDNA, there is considerable variation in key parameters such as sensitivity, specificity and positive predictive value depending on what the test is for. The distinction between diagnostics and screening has become blurred, and there is a clear need for the education of physicians and patients regarding the technical capabilities and limitations of these different forms of testing. Furthermore, there is a requirement for consistent guidelines that apply across health sectors, both public and commercial, to ensure that tests are validated and robust and that careful and appropriate pre-test and post-test counselling is provided by professionals who understand the tests offered.

Systematic Analysis of Copy-Number Variations Associated With Early Pregnancy Loss

(Abstracted from Ultrasound Obstet Gynecol 2020;55:96–104) Early pregnancy loss is most commonly caused by embryonic numerical and structural chromosomal abnormalities, which explain more than 50% of miscarriages. In more recent years, submicroscopic copy-number variations (CNVs) have also been identified in some early miscarriage specimens.

Systematic analysis of copy-number variations associated with early pregnancy loss.

Embryonic numerical and structural chromosomal abnormalities are the most common cause of early pregnancy loss. However, the role of submicroscopic copy-number variations (CNVs) in early pregnancy loss is unclear, and little is known about the critical regions and candidate genes for miscarriage, because of the large size of structural chromosomal abnormalities. The aim of this study was to identify potential miscarriage-associated submicroscopic CNVs and critical regions of large CNVs as well as candidate genes for miscarriage. Over a 5-year period, 5180 fresh miscarriage specimens were investigated using quantitative fluorescent polymerase chain reaction/CNV sequencing or chromosomal microarray analysis. Statistically significant submicroscopic CNVs were identified by comparing the frequency of recurrent submicroscopic CNVs between cases and a published control cohort. Furthermore, genes within critical regions of miscarriage-associated CNVs were prioritized by integrating the Residual Variation Intolerance Score and the human gene expression dataset for identification of potential miscarriage candidate genes. Results without significant maternal-cell contamination were obtained in 5003 of the 5180 (96.6%) cases. Clinically significant chromosomal abnormalities were identified in 59.1% (2955/5003) of these cases. Three recurrent submicroscopic CNVs (microdeletions in 22q11.21, 2q37.3 and 9p24.3p24.2) were significantly more frequent in miscarriage cases, and were considered to be associated with miscarriage. Moreover, 44 critical regions of large CNVs were observed, including 14 deletions and 30 duplications. There were 309 genes identified as potential miscarriage candidate genes through gene-prioritization analysis. We identified potential miscarriage candidate CNVs and genes. These data demonstrate the importance of CNVs in the etiology of miscarriage and highlight the importance of ongoing analysis of CNVs in the study of miscarriage. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.

Prevalence of mosaicism in uncultured chorionic villus samples after chromosomal microarray and clinical outcome in pregnancies affected by confined placental mosaicism.

To evaluate the prevalence of mosaicism in chorionic villus sampling (CVS) samples after chromosomal microarray (CMA) and clinical outcome of pregnancies affected by confined placental mosaicism. We retrieved all results from CMA, array-based comparative genomic hybridization, on CVS samples from January 2011 to November 2017 from Central and North Denmark Regions. Mosaic results from uncultured chorionic villi, cytotrophoblasts and mesenchymal cells, after CVS and follow-up on amniocytes, fetal tissue, or postnatal blood were studied and matched with clinical data from The Danish Fetal Medicine Database. Prevalence of mosaicism was 93 out of 2,288 (4.1%) CVS samples of which 17 (18.3%) concerned submicroscopic copy number variations (CNVs) <10 Mb. Follow-up analyses were performed in 62 cases. True fetal mosaicism (TFM) was confirmed in 18.4% (7/38) when mosaicism involved whole chromosome aneuploidy and in 25.0% (6/24), when involving a CNV (P = .59). Median birth weight z-score was higher in cases of confined placental mosaicism for a CNV (0.21) than cases involving whole chromosomes (-0.74) (P = .02). Prevalence of mosaicism in CVS samples is higher after CMA on uncultured tissue than after conventional karyotyping on cultured tissue. The risk of TFM is equally high in cases of mosaicism for CNVs and whole chromosomes.

Developmental retardation due to paternal 5q/11q translocation in a Chinese infant: clinical, chromosomal and microarray characterization

Although it is known that the parental carriers of chromosomal translocation are considered to be at high risk for spontaneous abortion and embryonic death, normal gestation and delivery remain possible. This study aims to investigate the genetic factors of a Chinese infant with multiple malformations and severe postnatal development retardation. In this study, the routine cytogenetic analysis, chromosomal microarray analysis (CMA) and fluorescence in situ hybridization (FISH) analysis were performed. Conventional karyotype analyses revealed normal karyotypes of all family members. CMA of the DNA of the proband revealed a 8.3 Mb duplication of 5q35.1-qter and a 6.9 Mb deletion of 11q24.3-qter. FISH analyses verified a paternal tiny translocation between the long arm of chromosomes 5 and 11. Our investigation serves to provide important information on genetic counselling for the patient and future pregnancies in this family. Moreover, the combined use of CMA and FISH is effective for clarifying pathogenically submicroscopic copy number variants.

Application of copy number variation sequencing for prenatal diagnosis in women at an advanced maternal age

To assess the value of copy number variation analysis based on next generation sequencing (CNV-seq) in prenatal diagnosis for women at advanced maternal age. A prospective analysis was carried out for women who underwent amniocentesis at 18~36 weeks of gestation for fetal CNV-seq for advanced maternal age. For 1461 unrelated Chinese women with a singleton pregnancy, CNV-seq was performed for all samples successfully. The proportion of chromosomal abnormalities was 2.3% (34/1461), of which 44.12% were submicroscopic copy number variations (<5 Mb). Pregnant women at an advanced maternal age should be informed for not only common trisomies but all pathogenic chromosomal aberrations. NGS was a sensitive and accurate approach for detecting CNVs.