Chromosomal Imbalances Research Articles

MO036: Detection of copy number variations by single-nucleotide-polymorphism array in patients with end-stage renal disease of unknown etiology

Abstract BACKGROUND AND AIMS Establishing the genetic basis of renal disease is pivotal to improve diagnostic and treatment strategies. Pathogenic copy number variations (CNVs) caused by chromosomal imbalances contribute significantly to the pediatric renal disease burden, especially in children with congenital anomalies of the kidney and urinary tract (CAKUT). The role of CNVs in chronic kidney disease of unknown etiology (uCKD) is scarcely investigated, although this group comprises about 20% of adults with end-stage renal disease (ESRD). We screened for causal CNVs in a preliminary sample of patients with ESRD from unknown etiology. METHOD We recruited 94 patients registered with ESRD ≤age 50 from uCKD or hypertension from the Danish Nephrology Registry. Medical records and previous kidney biopsies were initially reviewed, and patients were excluded if a specific cause of kidney disease other than hypertension was identified (n = 35). We performed genome-wide single-nucleotide-polymorphism (SNP) array in 59 patients to identify copy number gains and losses. All CNVs were systematically evaluated as possible causes of kidney disease and broadly classified into three main categories: ‘Normal’, ‘Pathogenic’ or ‘Variant of uncertain significance.’ RESULTS The SNP array results were normal in 57 patients (96.6%). In the remaining two patients (3.4%), we detected pathogenic CNVs with incomplete penetrance in hot spot loci associated with CAKUT: One male patient with ESRD at age 18 was a heterozygous carrier of a 545 kb microdeletion on chromosome 16p11.2 (29.63 Mb to 30.18 Mb). He had left-side renal agenesis and a hypoplastic right kidney at presentation, but no history of developmental delay or dysmorphic features. The microdeletion was considered likely causal, because it included the CAKUT driver gene TBX6 similar to other heterozygous carriers of 16p11.2 microdeletions with isolated renal agenesis or dysplasia. A second patient with ESRD at age 49 had 3.66 Mb duplication on chromosome 1q21.1 (145.43 Mb to 149.09 Mb) in heterozygous form. The patient had no reported CAKUT or other features associated with CNVs in the 1q21.1 loci, and the duplication was therefore deemed unrelated to his renal disease. CONCLUSION Disease-causing CNVs are not frequent in this limited sample of patients with ESRD from unknown etiology. CNV analysis by SNP-array may be most effective in patients with uCKD combined with CAKUT features.

Genome wide noninvasive prenatal testing detects microduplication of the distal end of chromosome 15 in a fetus: a case report

BackgroundNoninvasive prenatal testing (NIPT) is the most recent modality widely used in prenatal diagnostics. Commercially available NIPT has high sensitivity and specificity for the common fetal chromosomal aneuploidies. As future advancements in NIPT sequencing technology are becoming promising and more reliable, the ability to detect beyond aneuploidies and to expand detection of submicroscopic genomic alterations, as well as single-gene disorders might become possible.Case presentationHere we present a case of a 34-year-old pregnant woman, G2P1, who had NIPT screening which detected a terminal microduplication of 10.34 Mb on the long arm of chromosome 15 (15q26.1q26.3). Subsequent prenatal diagnostic testing including karyotype, microarray and fluorescence in situ hybridization (FISH) analyses were performed. Microarray testing confirmed and particularized a copy number gain of 10.66 Mb of the distal end of the long arm of chromosome 15. The G-banding cytogenetic studies yielded results consistent with unbalanced translocation between chromosome 15 and 18. To further characterize the abnormality involving the long arm of chromosome 18 and to map the genomic location of the duplicated 15q more precisely, FISH analysis using specific sub-telomeric probes was performed. FISH analysis confirmed that the extra duplicated segment of chromosome 15 is translocated onto the distal end of the long arm of chromosome 18 at band 18q23. Parental karyotype and FISH studies were performed to see if this unbalanced rearrangement was inherited from a healthy balanced translocation carrier versus being a de novo finding. Parental chromosomal analysis provided no evidence of a rearrangement between chromosome 15 and chromosome 18. The final fetal karyotype was reported as 46,XX,der(18)t(15;18)(q26.2;q23)dn.ConclusionsIn this case study, the microduplication of fetal chromosome 15q26.1q26.3 was accurately detected using NIPT. Our results suggest that further refinements in NIPT have the potential to evolve to a powerful and efficient screening method, which might be used to detect a broad range of chromosomal imbalances. Since microduplications and microdeletions are a potential reportable result with NIPT, this must be included in pre-test counseling. Prenatal diagnostic testing of such findings is strongly recommended.

WHO grading system for invasive pulmonary lung adenocarcinoma reveals distinct molecular signature: An analysis from the cancer genome atlas database

Lung adenocarcinoma grading has gained interest in the past years. Recently a three-tier tumor grading was proposed showing that it is related to patients' prognosis. Nevertheless, the underlying molecular basis of this morphological grading remains partly unknown.The aim of our work is to take advantage of The Cancer Genome Atlas lung adenocarcinoma (TCGA_LUAD) cohort to describe the molecular data associated to tumor grading.We performed a study on publicly available data of the TCGA database first by assessing a tumor grade on downloadable tumor slides. Secondly we analyzed the molecular features of each tumor grade group.Our work was performed on a study group of 449 patients. We show that aneuploidy score was significantly different between grade 2 and grade 3 groups with different chromosomal imbalance (p < 0.001). SCGB1A1 mRNA expression was higher in grade 2 (p = 0.0179) whereas NUP155, CHFR, POLQ and CDC7 have a higher expression in grade 3 (p = 0.0189, 0.0427, 0.0427 and 0.427 respectively). GZMB and KRT80 have a higher methylation of DNA in grade 2 (p = 0.0201 and 0.0359 respectively). MT1G, CLEC12B and NDUFA7 have a higher methylation of DNA in grade 3 (p < 0.001, 0.0246 and 0.0359 respectively). We showed that the number of activated pathways is different between grade 2 and grade 3 patients (p = 0.004).We showed that differentially expressed genes by mRNA analysis and DNA methylation analysis involve several genes implied in chemoresistance. This could suggest that grade 3 lung adenocarcinoma might be more resistant to chemotherapy.

Introgression of Trifolium ambiguum Into Allotetraploid White Clover (Trifolium repens) Using the Ancestral Parent Trifolium occidentale as a Bridging Species

White clover (Trifolium repens) is an allotetraploid pasture legume widely used in moist temperate climates, but its vulnerability to drought, grazing pressure and pests has restricted its wider use. A related species, Caucasian clover (Trifolium ambiguum), is a potential source of resistances to drought, cold, grazing pressure and pests that could potentially be transferred to white clover by interspecific hybridization. Although direct hybridization has been achieved with difficulty, the hybrids have not been easy to backcross for introgression breeding and no interspecific chromosome recombination has been demonstrated. The present work shows that interspecific recombination can be achieved by using Trifolium occidentale, one of the ancestral parents of T. repens, as a bridging species and that large white clover breeding populations carrying recombinant chromosomes can be generated. A 4x hybrid between T. ambiguum and T. occidentale was crossed with T. repens and then backcrossed for two generations. Five backcross hybrid plants with phenotypes appearing to combine traits from the parent species were selected for FISH-GISH analyses. Recombinant chromosome segments from T. ambiguum were found in all five plants, suggesting that recombination frequencies were significant and sufficient for introgression breeding. Despite early chromosome imbalances, the backcross populations were fertile and produced large numbers of seeds. These hybrids represent a major new resource for the breeding of novel resilient forms of white clover.

Clinical Manifestations of Various Molecular Cytogenetic Variants of Eight Cases of "8p Inverted Duplication/Deletion Syndrome".

Inverted duplication syndrome with an adjacent terminal deletion of the short arm of chromosome 8—inv dup del(8p)—is a rare complex structural chromosomal rearrangement with a wide range of clinical manifestations. Molecular cytogenetic variants of chromosomal imbalance depend on the mechanism of rearrangement formation. We analyzed the clinical–genetic and molecular cytogenetic characteristics of the 8p inverted duplication/deletion syndrome, as well as the genotype–phenotype correlation in eight unrelated cases with the rearrangement of inv dup del(8p). The main clinical manifestations in all cases are psychomotor and language delay, muscle hypotonia, and dysmorphic facial features. Malformations of the central nervous system, such as corpus callosum agenesis, were found in five cases. Seizures were reported in only one case. We found that the cause of the formation of the rearrangement was generally ectopic recombination (seven out of eight cases) and this was due to U-type exchange in only one case. Depending on the mechanism of formation, the characteristics of the genomic imbalance were different, which made it possible to identify two molecular cytogenetic variants in the cases we describe here. No association between molecular cytogenetic variants and clinical manifestations was found.

Prenatal diagnosis of fetuses with Emanuel syndrome: Results of ultrasound examination and invasive genetic testing.

To investigate prenatal manifestations of Emanuel syndrome (ES) by retrospectively analyzing the results of prenatal diagnosis. Thirteen fetuses were collected from five hospitals, of which six were confirmed with 47,der(22)t(11;22; ES) by karyotype and chromosomal microarray analysis (CMA). Seven were diagnosed with 46,t(11;22) balanced translocations by karyotype, including one de novo mosaic 46,XX,t(11;22). In 3/7, CMA was performed but did not identify chromosomal imbalances. The results of prenatal diagnoses were reviewed, including ultrasound examinations and genetic testing. In ES fetuses, the derivative 22 was consistently inherited from the mother, while in the balanced translocation group, the t(11;22) chromosome was of paternal origin in 3/6 cases, All ES fetuses presented with multiple abnormalities by ultrasound examinations. Diaphragm hernia (3/6), Dandy-Walker complex (3/6), and kidney aplasia (3/6), were the most common ultrasound findings. Sonographic soft markers such as increased nuchal translucency, increased nuchal fold thickness appeared in 3 cases and all of these were associated with other anomalies. However, none of the ultrasound findings differentiated ES from other genetic syndromes during fetal period. In this series, in fetuses with a der(22), the derivative chromosome was consistently of maternal origin. In contrast, 46,t(11;22) balanced translocations were of maternal or paternal origin. The results contribute to the literature regarding the fetal phenotype of ES. Due to the absence of specific features distinguishing ES from other genetic syndromes, confirming the diagnosis through invasive genetic testing is necessary.

Chromosomal imbalances detected via RNA-sequencing in 28 cancers.

MotivationRNA-sequencing (RNA-seq) of tumor tissue is typically only used to measure gene expression. Here, we present a statistical approach that leverages existing RNA-seq data to also detect somatic copy number alterations (SCNAs), a pervasive phenomenon in human cancers, without a need to sequence the corresponding DNA.ResultsWe present an analysis of 4942 participant samples from 28 cancers in The Cancer Genome Atlas (TCGA), demonstrating robust detection of SCNAs from RNA-seq. Using genotype imputation and haplotype information, our RNA-based method had a median sensitivity of 85% to detect SCNAs defined by DNA analysis, at high specificity (∼95%). As an example of translational potential, we successfully replicated SCNA features associated with breast cancer subtypes. Our results credential haplotype-based inference based on RNA-seq to detect SCNAs in clinical and population-based settings.Availability and implementationThe analyses presented use the data publicly available from TCGA Research Network (http://cancergenome.nih.gov/). See Methods for details regarding data downloads. hapLOHseq software is freely available under The MIT license and can be downloaded from http://scheet.org/software.html.Supplementary information Supplementary data are available at Bioinformatics online.

Role of Chromosomal Imbalances in the Pathogenesis of DSD: A Retrospective Analysis of 4657 Prenatal Samples

Role of Chromosomal Imbalances in the Pathogenesis of DSD: A Retrospective Analysis of 4657 Prenatal Samples

De novo 22q11.2 deletions and auricular findings in two Chinese patients with microtia.

BackgroundCongenital microtia is a common craniofacial malformation resulting from both environmental and genetic factors. Recurrent chromosomal imbalances were observed in patients with microtia. The 22q11.2 deletion is one of the most common microdeletions in human beings. The cell division cycle 45 gene (CDC45) embedded in the proximal 22q11.2 deleted region is involved in craniofacial development. However, only a few studies have focused on the 22q11.2 deletion as genetic etiology in microtia patients and studied its associated external ear deformity characteristics in detail.MethodsIn this research, a total of 65 patients from north China with sporadic microtia were studied. Copy number variations of CDC45 were screened using AccuCopy assay. The 22q11.2 deletion harboring CDC45 was identified by whole‐genome sequencing and targeted next‐generation sequencing. A parental test was carried out to determine the origin of the deletion.Results CDC45 copy number loss was identified in two patients with microtia. A set of qPCR assays demonstrated two patients carried a typical proximal 22q11.2 deletion between the low‐copy repeats on chromosome 22q11.2 (LCR22A and LCR22D), encompassing CDC45. The 22q11.2 deletions were de novo in each patient. In‐depth auricular phenotype assessment showed these two patients have a distinct concha‐type ear malformation while other microtia patients have lobule‐type microtia among the 65 microtia patient cohort in this study.ConclusionHere we present two additional Chinese microtia patients with de novo 22q11.2 proximal deletion harboring CDC45 and further report these patients’ distinct ear malformation.

SNP-Based Chromosomal Microarray Analysis for Detecting DNA Copy Number Variations in Fetuses with a Thickened Nuchal Fold

The aim of the study was to assess the diagnostic potential of SNP-based chromosomal microarray analysis for detecting pathogenic copies number variations (CNVs) in fetuses with a normal karyotype, in which an increase in the nuchal translucence of >2.5 mm was detected by ultrasound at a gestational age of 11 weeks to 13 weeks 6 days.Materials and MethodsThe study included 225 pregnant women who underwent invasive prenatal diagnostic procedures following the detection of an isolated thickening of the fetal nuchal fold. The fetal material obtained was examined using a cytogenetic test; if a normal karyotype was confirmed, chromosomal microarray analysis was performed as a second-line test.ResultsPathogenic CNVs were detected in 22 of 225 fetuses (9.8%) with a normal karyotype. Of these 22 fetuses, pathogenic CNVs not classified as syndromes were detected in 14 cases (63.6%), and those previously described as syndromes — in 8 cases (36.4%). In 9 fetuses (41%), CNVs in two non-homologous chromosomes were determined; these findings indicated a high likelihood of carrying balanced translocations in the parents. Indeed, when analyzing the parent’s karyotype, in 8 out of 9 couples, balanced translocations were found in one of the parents.ConclusionUsing chromosomal microarray analysis in fetuses with a thickened nuchal fold makes it possible to increase the ability to detect chromosomal imbalances, including those caused by pathological meiotic segregation of parental reciprocal translocation.

Whole-genome analysis of a putative rare and complex interchromosomal reciprocal insertion: thorough investigations for a straightforward interpretation

Research questionShould whole-genome investigations be considered systematically before a complex chromosomal abnormality preimplantation genetic testing for structural chromosomal rearrangements (PGT-SR) management is carried out using conventional cytogenetic techniques? DesignA male carrying a putative rare interchromosomal reciprocal insertion (IRI) 46,XY,ins(14;?)(q11;?).ish der(14)ins(14;22)(q11.2;q11.2q11.2)(xcp14+,xcp22+,N25+,3’TRA/D+),der(22)ins(22;14)(q11.2;q11.2q11.2)(xcp22+,xcp14+,N25-,5’TRA/D+), and his partner were referred to our centre for preimplantation genetic testing analysis after three spontaneous miscarriages. Whole-genome sequencing was used to distinguish between the proposed IRI and an alternative explanation of reciprocal translocation. Fluorescence in-situ hybridization was used to detect all chromosome segments involved in this chromosomal rearrangement, to identify transferable normal and balanced embryos. ResultsWhole-genome sequencing allowed the determination of the number of chromosomal breakpoints involved in chromosomal rearrangement between chromosomes 14 and 22. Finally, only two breakpoints were identified instead of four in IRI rearrangements, which suggests a reciprocal translocation rearrangement. A probe strategy was established to highlight all chromosomal imbalances, whether IRI or reciprocal translocation, and preimplantation genetic testing cycles were achieved. ConclusionConventional cytogenetic techniques are not capable of identifying all complex chromosomal rearrangements, especially those involving centromeric regions and short arms of acrocentric chromosomes. The advent of new sequencing technologies has allowed for a better appreciation of genome complexity. In this study, whole-genome analysis provided additional information to explain the occurrence of genomic events and confirmed that the initial diagnosis of IRI identified by conventional cytogenetic techniques was, in fact, a simple reciprocal translocation. A reliable PGT-SR strategy was proposed for this couple to achieve their parental project.

Chromosome Imbalances in Neuroblastoma-Recent Molecular Insight into Chromosome 1p-deletion, 2p-gain, and 11q-deletion Identifies New Friends and Foes for the Future.

Simple SummaryNeuroblastoma is a pediatric cancer that arises in the sympathetic nervous system. High-risk neuroblastoma is clinically challenging and identification of novel therapies, particularly those that offer a reduction in morbidity for these patients, is a high priority. Combining genetic analyses with investigation of molecular mechanisms, while considering recent advances in our understanding of key developmental events, provides avenues for future treatment. Here we review and highlight several recently published articles that address novel molecular mechanisms arising from chromosome 1p, 2p, and 11q aberrations, which likely contribute to high-risk neuroblastoma, and discusses their potential impact on treatment options. Neuroblastoma is the most common extracranial solid pediatric tumor, with around 15% childhood cancer-related mortality. High-risk neuroblastomas exhibit a range of genetic, morphological, and clinical heterogeneities, which add complexity to diagnosis and treatment with existing modalities. Identification of novel therapies is a high priority in high-risk neuroblastoma, and the combination of genetic analysis with increased mechanistic understanding—including identification of key signaling and developmental events—provides optimism for the future. This focused review highlights several recent findings concerning chromosomes 1p, 2p, and 11q, which link genetic aberrations with aberrant molecular signaling output. These novel molecular insights contribute important knowledge towards more effective treatment strategies for neuroblastoma.

Evolutionary patterns of chromosomal instability and mismatch repair deficiency in proximal and distal colorectal cancer.

Colorectal carcinomas (CRCs) progress through heterogeneous pathways. The aim of this study was to analyse whether or not the cytogenetic evolution of CRC is linked to tumour site, level of chromosomal imbalance and metastasis. A set of therapy-naïve pT3 CRCs comprising 26 proximal and 49 distal pT3 CRCs was studied by combining immunohistochemistry of mismatch repair (MMR) proteins, microsatellite analyses and molecular karyotyping as well as clinical parameters. A MMR deficient/microsatellite-unstable (dMMR/MSI-H) status was associated with location of the primary tumour proximal to the splenic flexure, and dMMR/MSI-H tumours presented with significantly lower levels of chromosomal imbalances compared with MMR proficient/microsatellite-stable (pMMR/MSS) tumours. Oncogenetic tree modelling suggested two evolutionary clusters characterized by dMMR/MSI-H and chromosomal instability (CIN), respectively, for both proximal and distal CRCs. In CIN cases, +13q, -18q and +20q were predicted as preferentially early events, and -1p, -4 -and -5q as late events. Separate oncogenetic tree models of proximal and distal cases indicated similar early events independent of tumour site. However, in cases with high CIN defined by more than 10 copy number aberrations, loss of 17p occurred earlier in cytogenetic evolution than in cases showing low to moderate CIN. Differences in the oncogenetic trees were observed for CRCs with lymph node and distant metastasis. Loss of 8p was modelled as an early event in node-positive CRC, while +7p and +8q comprised early events in CRC with distant metastasis. CRCs characterized by CIN follow multiple, interconnected genetic pathways in line with the basic 'Vogelgram' concept proposed for the progression of CRC that places the accumulation of genetic changes at centre of tumour evolution. However, the timing of specific genetic events may favour metastatic potential.

17q12 Recurrent Deletions and Duplications: Description of a Case Series with Neuropsychiatric Phenotype.

Syndromic neurodevelopmental disorders are usually investigated through genetics technologies, within which array comparative genomic hybridization (Array-CGH) is still considered the first-tier clinical diagnostic test. Among recurrent syndromic imbalances, 17q12 deletions and duplications are characterized by neurodevelopmental disorders associated with visceral developmental disorders, although expressive variability is common. Here we describe a case series of 12 patients with 17q12 chromosomal imbalances, in order to expand the phenotypic characterization of these recurrent syndromes whose diagnosis is often underestimated, especially if only mild traits are present. Gene content and genotype-phenotype correlations have been discussed, with special regard to neuropsychiatric features, whose impact often requires etiologic analysis.

Genetic and epigenetic characterization of posterior pituitary tumors

Pituicytoma (PITUI), granular cell tumor (GCT), and spindle cell oncocytoma (SCO) are rare tumors of the posterior pituitary. Histologically, they may be challenging to distinguish and have been proposed to represent a histological spectrum of a single entity. We performed targeted next-generation sequencing, DNA methylation profiling, and copy number analysis on 47 tumors (14 PITUI; 12 GCT; 21 SCO) to investigate molecular features and explore possibilities of clinically meaningful tumor subclassification. We detected two main epigenomic subgroups by unsupervised clustering of DNA methylation data, though the overall methylation differences were subtle. The largest group (n = 23) contained most PITUIs and a subset of SCOs and was enriched for pathogenic mutations within genes in the MAPK/PI3K pathways (12/17 [71%] of sequenced tumors: FGFR1 (3), HRAS (3), BRAF (2), NF1 (2), CBL (1), MAP2K2 (1), PTEN (1)) and two with accompanying TERT promoter mutation. The second group (n = 16) contained most GCTs and a subset of SCOs, all of which mostly lacked identifiable genetic drivers. Outcome analysis demonstrated that the presence of chromosomal imbalances was significantly associated with reduced progression-free survival especially within the combined PITUI and SCO group (p = 0.031). In summary, we observed only subtle DNA methylation differences between posterior pituitary tumors, indicating that these tumors may be best classified as subtypes of a single entity. Nevertheless, our data indicate differences in mutation patterns and clinical outcome. For a clinically meaningful subclassification, we propose a combined histo-molecular approach into three subtypes: one subtype is defined by granular cell histology, scarcity of identifiable oncogenic mutations, and favorable outcome. The other two subtypes have either SCO or PITUI histology but are segregated by chromosomal copy number profile into a favorable group (no copy number changes) and a less favorable group (copy number imbalances present). Both of the latter groups have recurrent MAPK/PI3K genetic alterations that represent potential therapeutic targets.

Clinical and molecular cytogenetic description of a female patient with de novo 18q inversion duplication/deletion

The genetic causes of global developmental delay (GDD) and intellectual disability (ID) are heterogeneous. Chromosomal imbalance has been recognized as the most frequent cause of ID for years. We describe the report of a female patient aged 1 year and 5 months at presentation who had GDD, prenatal growth retardation, failure to thrive, microcephaly, dysmorphic facial features including: broad forehead, high anterior hair line with sparse scalp hair, wide palpebral fissures, long eye lashes, blue sclera, sparse arched eye brows, prominent and wide nasal root, hypertelorism, micrognathia and dysplastic low set ears in addition to widely spaced nipples, bilateral clenched fists, camptodactyly, rocker bottom feet and brittle nails.. Her karyotype revealed 46,XX,add (18)(q23). Comprehensive cytogenomic analysis was performed using multiplex ligation-dependent probe amplification (MLPA), fluorescence in situ hybridization (FISH), and aCGH techniques to determine the parental origin and the possible mechanism responsible for this abnormal karyotype. Both parents had normal karyotypes. MLPA and FISH analysis for the patient revealed deletion of 18q subtelomere, and whole chromosome paint (WCP) associated with inverted DAPI indicated that all the duplicated segments originated from chromosome 18 and there was inversion of 18q segment. Array CGH identified 55.8-Mb duplicated segment and 614-kb deleted terminal 18q. Single nucleotide polymorphism (SNP) analysis for the patient and the parents revealed that the duplicated and deleted 18q regions originated from paternal chromosome 18. These findings suggested that the event occurred during paternal meiosis or early postzygotic stage. The suggested mechanism responsible for this type of rearrangement is nonhomologous end point recombination and U-type exchange.

VP28.09: Genome‐wide cell‐free DNA test for fetal chromosomal abnormalities: unrestricted versus restricted reporting

In our centre, when self-financed genome-wide cell free (cf)DNA testing was launched, in addition to risk results on trisomies 21, 18 and 13, sex chromosome aneuploidies (SCAs) and seven microdeletion syndromes, additional findings of genome-wide chromosomal aberrations at a resolution of three Mb or above were also reported. In 2018, we changed our policy and additional findings were no longer reported. This study aimed to compare the screening performance of genome-wide cfDNA testing for chromosomal aneuploidies and genomic imbalances between two periods where additional findings were reported and not reported. Data were obtained from 3981 consecutive pregnant women who requested for cfDNA testing during 2015-2019. Those that had positive results had diagnostic confirmatory procedures. The performance of screening of the cfDNA test was determined by calculating concordance rate (CoR), detection (DR) or confirmation rate (CR) and combined-discordant rate. The no-result rates were similar between the two reporting periods (2.04% vs 2.08%). CoR for Trisomy 21 and 18 were 100% and 100%, respectively. There were two cases tested high-risk for Trisomy 13, with CoR of 0%. 12 cases were high-risk for any sex chromosome aneuploidies (SCA) with an overall concordance of 75%; specifically, 45,X had 0% concordance, while SCAs involving the Y-chromosome had 83.3% concordance. There were 15 cases that tested high-risk for any rare autosomal trisomy, with CoR of 13.3%. For the two reporting periods, the combined-discordant rates were 0.93% and 0.17%, which were significantly different (P = 0.002). Restricting the reporting of additional findings from genome-wide cfDNA analysis has reduced the combined-discordant rate, but there is no reduction in the no-result rate.

Chromosomal microarray analysis, including constitutional and neoplastic disease applications, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG)

Chromosomal microarray technologies, including array comparative genomic hybridization and single-nucleotide polymorphism array, are widely applied in the diagnostic evaluation for both constitutional and neoplastic disorders. In a constitutional setting, this technology is accepted as the first-tier test for the evaluation of chromosomal imbalances associated with intellectual disability, autism, and/or multiple congenital anomalies. Furthermore, chromosomal microarray analysis is recommended for patients undergoing invasive prenatal diagnosis with one or more major fetal structural abnormalities identified by ultrasonographic examination, and in the evaluation of intrauterine fetal demise or stillbirth when further cytogenetic analysis is desired. This technology also provides important genomic data in the diagnosis, prognosis, and therapy of neoplastic disorders, including both hematologic malignancies and solid tumors. To assist clinical laboratories in the validation of chromosomal microarray methodologies for constitutional and neoplastic applications, the American College of Medical Genetics and Genomics (ACMG) Laboratory Quality Assurance Committee has developed these updated technical laboratory standards, which replace the ACMG technical standards and guidelines for microarray analysis in constitutional and neoplastic disorders previously published in 2013.

Reply

We thank Drs Jing and Li for their thoughtful comments on our study1 and their reflections on prenatal screening for 22q11.2 deletion. They raise important points on which we would like to comment further and provide clarification. Drs Jing and Li suggest that ultrasound is more sensitive than cell-free DNA (cfDNA) testing in screening for 22q11.2 deletion, citing a study by Schindewolf et al.2. However, that study was intended to document the ultrasound findings seen most frequently in pregnancies with a 22q11.2 deletion in the second and third trimesters, not to determine the sensitivity of ultrasound for fetal 22q11.2 deletion. To our knowledge, this has not been evaluated in any study. Nonetheless, we agree that prenatal ultrasound findings have been well described by Schindewolf et al. and others and suggest that cfDNA screening in the first trimester can complement, not replace, second-trimester ultrasound as a screening tool for 22q11.2 deletion. As Drs Jing and Li note, the collective prevalence of other fetal microduplications and microdeletions is not insignificant, even when ultrasound is normal, and there is broad consensus that chorionic villus sampling or amniocentesis with microarray analysis should be offered whenever evaluation of a pregnancy for submicroscopic genomic alterations is desired. Similar to Drs Jing and Li, we would also welcome a method for accurate, genome-wide non-invasive prenatal screening with demonstrated clinical utility for detecting chromosomal imbalances at a resolution comparable to that of microarray, but currently available technologies fall short of this goal. In a prospective head-to-head comparison of genome-wide cfDNA testing and chromosomal microarray testing in 198 pregnancies, Guseh and colleagues showed that expanded non-invasive genome-wide screening has a lower detection rate for clinically significant chromosomal abnormalities when compared with that of chromosomal microarray analysis, and that pathogenic subchromosomal imbalances (< 7 Mb) contribute substantially to the missed abnormalities3. A clinical trial from The Eunice Kennedy Shriver National Institute of Child Health and Human Development showed that > 50% of (likely) pathogenic subchromosomal imbalances identified by chromosomal microarray analysis in anatomically normal fetuses are < 5 Mb in size4. We would also like to clarify a minor point. The cfDNA test evaluated in our study is described as ‘targeted’ in order to differentiate it from ‘genome-wide’ cfDNA testing because of the different technological design of the two approaches. It is not a standalone test for 22q11.2 deletion, as might have been misinterpreted from the phrasing. The Harmony® test screens for trisomy 21, trisomy 18 and trisomy 13, with the option of screening for sex chromosome aneuploidy and/or 22q11.2 deletion from the same blood collection. In many respects, we agree with Drs Jing and Li and support an approach to prenatal screening in which the benefits of cfDNA testing, ultrasound and diagnostic testing are incorporated to guide pregnancy management and improve outcome in 22q11.2 deletion syndrome and other prenatally diagnosable conditions.

OC05.05: Observed chromosomal imbalances and performance of cell‐free DNA testing in pregnancies with fetal cardiac abnormalities

OC05.05: Observed chromosomal imbalances and performance of cell‐free DNA testing in pregnancies with fetal cardiac abnormalities