Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies

Self-Reported Access to Specialized Genetics Providers Among Families of Young Children With Birth Defects in Texas

Specialized genetics providers can help families of children with birth defects understand their child's condition and guide their medical treatment. The Birth Defects Epidemiology and Surveillance Branch (BDESB) routinely connects young children from the Texas Birth Defects Registry (TBDR) with select birth defects to agency social workers for assistance. Beginning in November 2022, social workers asked parents they reached: "Has the parent or child met with a geneticist or genetic counselor (or visited a genetics clinic)?". Responses were tabulated, overall and by select characteristics of interest. A chi-square test was used to evaluate if these characteristics were associated (p < 0.05) with self-reported access to a specialized genetics provider. Among the 400 families reached, 261 (65%) did not recall accessing specialized genetics providers. Lower access was observed among children with spina bifida or encephalocele, isolated birth defects, children without medical insurance, children meeting CDC developmental milestones, and younger mothers. Lower access was also observed in certain areas of the state, including the Texas-Mexico border. Our findings suggest that, in Texas, more than half (65%) of families of children with select birth defects are not accessing specialized genetics providers, and additional research is needed to work toward increasing access.

Mainstreaming Diagnostic Genetic Testing and Precision Medicine for Autism Spectrum Disorder: The Role of Child and Adolescent Psychiatrists

Autism Spectrum Disorder (ASD) is a neurodevelopmental psychiatric condition that shares significant clinical and genetic overlap with intellectualdisability (ID) and other neurodevelopmental disorders. Genetic testingin ASD lags far behind that for ID, even though Professional Societiesrecommend genetic testing for all ASD individuals and insurance reimbursement is relatively good. The core competencies for child and adolescent psychiatrists include determining the etiology and diagnosisfor all childhood psychopathology, including ID and ASD. Child psychiatrists should recommend and order genetic testing by exomeor genome sequencing on all children with ASD.

Current and future diagnostics of congenital heart disease (CHD)

Congenital heart defects (CHD) are one of the most common anomalies found among live births and represent a complex multifactorial condition. Given that more than 90 % of cases survive due to improved early treatment options (e.g., catheter intervention, surgical procedure, and improved intensive care), genotype-informed patient follow-up should consider lifelong treatment considering different types of comorbidities. Unfortunately, a thorough genetic workup is only offered to a minority of CHD patients. However, a comprehensive understanding of the genetic underpinnings combined with in-depth phenotyping would strengthen our knowledge regarding the impact of environmental (e.g., pre-gestational diabetes) and genetic causes ranging from aneuploidies to single variants and more complex inheritance patterns on early heart development. Therefore, comprehensive genetic analysis in these patients is an essential way of predicting the prognosis and recurrence risk in families and ultimately improving patients' quality of life due to better therapeutic options. In this review, we examine the different types of variants and genes of different molecular genetics techniques to assess the diagnostic yield in different CHD sub-phenotypes. Given the complex inheritance pattern observed in CHD, we also consider possible future methods and frameworks to improve diagnostics and allow for better genotype-phenotype correlation in this patient group. Predicting recurrence risk and prognosis in CHD patients will ultimately allow for better treatment and lifelong therapeutic outcomes for CHD patients.

New evidence supporting female protective effect in patients with congenital anomalies and neurodevelopmental disorders

The influence of chromosomal sex on human diseases is recognized but underresearched, particularly in diseases with early developmental origins. Copy number variations (CNVs) from sex chromosomes or autosomes, which cause different gene expressions, may influence the disease preferences in females and males. Chromosomal microarray is a standard method for detecting CNVs, with a diagnostic yield of approximately 15 % among patients with congenital anomalies and neurodevelopmental disorders, the primary indications for the analysis. Here, we explore sex disparities in phenotype prevalence and CNV detection rates in patients referred for chromosomal microarray to identify sex-biased traits and CNVs. Our cohort comprises 1412 patients, with a male-to-female ratio of 1.6 to 1. Despite being outnumbered, females are significantly more likely to receive a genetic diagnosis through this type of molecular karyotyping. Most of the patients have neurodevelopmental disorders with other comorbidities. Females have a higher frequency of comorbidities, but the difference in diagnostic yield is significant only in the groups with simpler phenotypes (≤2 comorbidities). Higher diagnostic yield is revealed for congenital heart disease, urogenital anomalies, and the autism spectrum group. All three categories show populational preponderance in males, supporting a higher threshold liability model in females.

Distinct chromosome abnormality patterns for differential diagnosis of hepatocellular carcinoma and cholangiocarcinoma

Hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA) are primary liver cancers with overlapping histopathological features, making accurate diagnosis challenging. This study aimed to identify chromosomal abnormalities that could aid in differentiating these cancers using chromosome microarray analysis (CMA). We analyzed ten frozen tumor tissues each of HCC and CCA, identifying distinct patterns of chromosomal gains and losses. HCC exhibited gains in regions 1p36.32, 1q23.3-q24.1, 3q21.3, 4p16.1, 5q31.1, and 11p15.5, and losses in 2p15, 3p11.1-q11.1, 4q12, 5p12-q11.1, 7q11.23, 14q23.2, 17p11.2, 17p13.3, 22q12.1, 22q12.2-q12.3, and 22q13.2. In contrast, CCA showed gains in 5p13.2, 5p14.1, 8p12-p11.23, 8p22, and 19p13.2, and losses in 1q31.1, 1q42.13, 3p25.3, 6p12.1, 6p25.3, and 17q21.33. Heatmap analysis revealed 17 distinct chromosomal regions between the two groups including 2q14.2, 4p16.3, 5q32, 7p14.3, 7p22.1, 7q11.21, 7q11.23, 7q21.3, 7q22.1, 10q21.3, 18q23, 19p13.2, 19q13.2, 21q21.3, 21q22.13, 22q11.21, and 22q12.2. Among these 1p36.32, 19p13.2, and 19q13.2 emerged as potential biomarkers for differential diagnosis. These findings may aid in confirming cases with overlapping histopathological features contribute to the development of diagnostic tools and improved targeted therapies for HCC and CCA.

Diagnostic Yield of Chromosomal Microarray Analysis in a Cohort of 300 Indian Patients

OBJECTIVES

To present authors' experience of chromosome microarray analysis (CMA) as the first-tier test, which contributed to accumulation and annotation of copy number variations (CNVs) and discovery of novel genetic hot spots in Indian pediatric patients.

METHODS

Karyotyping and CMA (4X180K Agilent) were performed in 300 patients with developmental delay, dysmorphism, autism, intellectual disability or congenital malformations. Various databases such as ClinVar, Clin Gen, OMIM, DECIPHER, etc. were used for interpretation of the results.

RESULTS

The diagnostic yield of clinically significant findings by CMA [16.00% (48/300)] was 9.0% higher than that by karyotyping [7.0% (21/300)]. There were 2.66% (08/300) patients with variations of uncertain significance (VOUS) which were challenging to interpret. Benign variations were considered normal.

CONCLUSIONS

CMA allows increased diagnostic yield of known and new microdeletion/duplication syndromes and molecular characterization of marker chromosomes with gene annotations. There is insufficient data published from India. Every such test done on Indian patients contributes to Indian data accumulation of pathogenic CNVs (pCNVs) and VOUS for future resolution. The benefit of CMA as a first-tier test is that it can improve the understanding towards the associated known and new genetic hot spots, thus providing a better genotype-phenotype correlation. Pre-test and post-test genetic counseling is important.

Toward clinical long-read genome sequencing for rare diseases

Genetic diagnostics is driven by technological advances, forming a tight interface between research, clinic and industry, which enables rapid implementation of new technologies. Short-read genome and exome sequencing, the current state of the art in clinical genetics, can detect a broad spectrum of genetic variants across the genome. However, despite these advancements, more than half of individuals with rare diseases remain undiagnosed after genomic investigations. Long-read whole-genome sequencing (LR-WGS) is a promising technology that identifies previously difficult-to-detect variants while also enabling phasing and methylation analysis and has the potential of generating complete personal assemblies. To pave the way for clinical use of LR-WGS, the clinical genomic community must establish standardized protocols and quality parameters while also developing innovative tools for data analysis and interpretation. In this Perspective, we explore the key challenges and benefits in integrating LR-WGS into routine clinical diagnostics.

Exome Sequencing in the Diagnostic Pathway for Suspected Rare Genetic Diseases: Does the Order of Testing Affect its Cost-Effectiveness?

BACKGROUND

Patients with suspected rare diseases often experience lengthy and uncertain diagnostic pathways. This study aimed to estimate the cost-effectiveness of exome sequencing (ES) in different positions in the diagnostic pathway for patients suspected of having a rare genetic disease.

METHODS

Data collected retrospectively from 305 patients suspected of having a rare genetic disease (RGD), who received clinical-grade ES and participated in the Canadian multicentre Care4Rare-SOLVE study, informed a discrete event simulation of the diagnostic pathway. We distinguished between tests that can lead to the diagnosis of a specific RGD ('indicator tests') and more routine non-RGD diagnostic tests ('non-indicator tests'). Five strategies were considered: no-ES, and ES as 1st, 2nd, 3rd, or 4th test (Tier 1, Tier 2, Tier 3, and Tier 4, respectively), where ES was the final test in the diagnostic pathway if included. Outcomes included the diagnostic yield, time-to-diagnosis, time on the diagnostic pathway, and test costs for each strategy. The cost-effectiveness analysis from a Canadian healthcare system perspective was conducted with diagnostic yield as the primary outcome of interest. Probabilistic analyses and expert-defined scenario analyses quantified uncertainty.

RESULTS

Implementing ES increases the diagnostic yield by 16 percentage points from 20% with no-ES to 36%. Exome sequencing, as the first test (Tier 1), resulted in the shortest time to a diagnosis and the lowest testing cost. Mean testing costs per patient were CAD4347 (95% CI 3925, 4788) for no-ES, CAD2458 (95% CI 2406, 2512) for Tier 1, CAD3851 (95% CI 3684, 4021) for Tier 2, CAD5246 (95% CI 4956, 5551) for Tier 3 and CAD6422 (95% CI 5954, 6909) for Tier 4, with Tier 1 having the highest diagnostic yield at the lowest cost. The scenario analyses yielded results consistent with those of the base case.

CONCLUSIONS

Implementing ES to diagnose patients suspected of having a RGD can result in a higher diagnostic yield. Although a limitation of our study was that the yield for the non-ES indicator tests was estimated using expert opinion due to a lack of available data, the results underscore the value of ES as a first-line diagnostic test, offering reduced time to diagnosis and lower overall testing costs.

Evaluation of Genomic Proximity Mapping (GPM) for Detecting Genomic and Chromosomal Structural Variants in Constitutional Disorders

Genomic structural variants (SVs) are critical contributors to genetic diversity and disease, yet their detection remains challenging with conventional cytogenetic techniques, such as karyotyping, fluorescence in situ hybridization (FISH), and chromosome microarray analysis (CMA). These methods often lack the resolution and sensitivity needed for comprehensive characterization of chromosomal aberrations. To address these limitations, we implemented genomic proximity mapping (GPM), a genome-wide chromosome conformation capture technology, in a clinical setting. In this study, we applied GPM to a cohort of 123 patients with constitutional disorders, achieving a 100% concordance rate in detecting 411 CNVs and 39 structural rearrangements, in addition to novel findings missed by standard methods. GPM demonstrated unique advantages, such as resolving both balanced and unbalanced chromosomal rearrangements with precise (<5kb) breakpoint resolution, maintaining robust performance with challenging samples, including formalin-fixed, paraffin-embedded (FFPE) tissues, and detecting mosaicism with high sensitivity. Furthermore, GPM reliably provided detailed copy number and loss-of-heterozygosity profiles, streamlining workflows and enhancing diagnostic resolution. GPM represents a transformative tool for genomic diagnostics, offering a high-resolution, comprehensive approach to detecting diverse genomic alterations. Its ability to address limitations of conventional cytogenetics methods positions GPM as a needed advance in the diagnosis, prognosis, and therapeutic management of genetic disorders.

Japanese pediatric neurologist's decision regarding genetic testing for patients with developmental delay/intellectual disability: A nationwide survey

BACKGROUND

Advances in genetic analysis technology are increasing the opportunities for developmental delay/intellectual disability (DD/ID) cases to reach genetic diagnosis. However, the decision to perform genetic testing depends on the physician's decision; furthermore, the accessibility of genetic testing varies by country or region.

METHODS

Japanese certified pediatric neurologists participated in an online survey from February to March 2023 to assess their attitudes toward genetic testing for DD/ID.

RESULTS

The study enrolled 266 pediatric neurologists, including 41 certified clinical geneticists. In Japan, G-banding emerged as the most common first-line genetic testing for DD/ID. For DD/ID without physical and behavioral abnormalities, 30 % of pediatric neurologists indicated that they would not perform genetic testing compared with 15 % of clinical geneticists. 75.6 % of certified clinical geneticists reported experience submitting chromosomal microarray analysis (CMA), while only 39.2 % of pediatric neurologists had experience submitting CMA.

CONCLUSION

Differences in the decision of indication for genetic testing for DD/ID cases were shown to be influenced by specialized genetic training. Improved education and access to genetic specialists may help standardize genetic diagnosis in Japan. On the other hand, a standardized testing policy, especially for non-genetic specialists, is needed to make genetic testing for DD/ID more widely available.

Cytogenomic characterization of mosaic X-ring chromosomes in seventeen patients with Turner syndrome (TS)-42 years of experience at a single-site institution

Individuals with Turner syndrome (TS) phenotypes may exhibit short stature, ovarian dysfunction, and neurocognitive disorders. Their genomes can include ring chromosomes formed from the X chromosome (RCX). Here, we present cytogenomic and clinical findings from seventeen individuals with TS who bore mosaic forms of RCX and frequently presented with short stature and concern for TS. The subjects were retrospectively included and tested at a single-site cytogenetics laboratory for over 42 years. Here, we illustrate each subject's comprehensive cytogenetic workup and phenotypes. The cohort shows comorbidities and sexual characteristics associated with mosaic RCX. These cytogenetic findings and clinical features are distinct from those of individuals with non-mosaic TS. Studying the pattern of X-activation across tissues in this cohort could provide additional data on a postulated source of phenotypic variability. Current guidelines recommend karyotype as the first-line test rather than SNP microarray analysis when aneuploidy is suspected. Conventional cytogenetics is still necessary to understand structural abnormalities, provide genomic context, and detect low-level mosaicism. These cases add to the knowledge of mosaic RCXs and offer new clinical laboratory information that is important for diagnosis and useful for comprehensively caring for and managing TS patients.

Genetic modulation of brain dynamics in neurodevelopmental disorders: the impact of copy number variations on resting-state EEG

Research has shown that many copy number variations (CNVs) increase the risk of neurodevelopmental disorders (e.g., autism, ADHD, schizophrenia). However, little is known about the effects of CNVs on brain development and function. Resting-state electroencephalography (EEG) is a suitable method to study the disturbances of neuronal functioning in CNVs. We aimed to determine whether there are resting-state EEG signatures that are characteristic of children with pathogenic CNVs. EEG resting-state brain activity of 109 CNV carriers (66 deletion carriers, 43 duplication carriers) aged 3 to 17 years was recorded for 4 minutes. To better account for developmental variations, EEG indices (power spectral density and functional connectivity) were corrected with a normative model estimated from 256 Healthy Brain Network controls. Results showed a decreased exponent of the aperiodic activity and a reduced alpha peak frequency in CNV carriers. Additionally, the study showed altered periodic components and connectivity in several frequency bands. Deletion and duplication carriers exhibited a similar overall pattern of deviations in spectral and connectivity measures, although the significance and effect sizes relative to the control group varied across frequency bands. Deletion and duplication carriers can be differentiated by their periodic power in the gamma band and connectivity in the low alpha band, with duplication carriers showing more disrupted alterations than deletion carriers. The distinctive alterations in spectral patterns were found to be most prominent during adolescence. The results suggest that CNV carriers show electrophysiological alterations compared to neurotypical controls, regardless of the gene dosage effect and their affected genomic region. At the same time, while duplications and deletions share common electrophysiological alterations, each exhibits distinct brain alteration signatures that reflect gene dosage-specific effects.

Evaluating parental satisfaction and empowerment with genetic testing in the Neonatal Intensive Care Unit (NICU)

Genetic disorders are highly represented in the neonatal intensive care unit (NICU). Genetic testing (in particular rapid genome-wide sequencing) has transformed the ability to diagnose and manage these infants. The NICU is a place of stress and overwhelm for parents and implementing genetic testing can pose additional challenges, including anxiety. There is a critical gap in knowledge related to parents' empowerment and satisfaction with the NICU experience for those undergoing genetic testing. The goal of this mixed-methods study was to identify the key contributing factors related to empowerment and areas for improvement in care of parents undergoing genetic testing in the NICU by using validated tools that have not been previously implemented in Canada. A demographic survey and validated online survey tools were distributed to eligible parents. Descriptive statistics and linear regression analysis were performed. We conducted semi-structured interviews to gain insight into the genetic testing experience. The transcribed interviews were analyzed using an interpretive description framework and thematic analysis. A total of 31 surveys and 17 interviews were completed. We have identified self-reported demographic predictors of decreased satisfaction and empowerment for parents, including high income, English-speaking, ethnicity, sex of the parent, prematurity of the newborn, and length of hospital stay. Emerging themes from interviews fall under the broad category of communication and include information, logistics, parental perspective, and support. Subthemes include expectations and delivery of information, attention to timing and organization, comprehensive support, and parental distress and expectations when ordering genetic testing. The findings suggest the need for systematic improvement of the current genetic testing process in NICUs.

Co-occurring non-urinary congenital anomalies among cases with congenital anomalies of the kidney and urinary tract

Cases with congenital anomalies of kidney and urinary tract (CAKUT) often have other associated anomalies. The purpose of this investigation was to assess the prevalence and the types of associated anomalies in CAKUT in a well-characterized population from northeastern France. The associated anomalies in CAKUT were collected in all live births, stillbirths and terminations of pregnancy during 29 years in 387,067 consecutive births of known outcome in the area covered by our population-based registry of congenital anomalies. Of the 1946 cases with CAKUT born during this period (prevalence at birth of 50.3 per 10,000), 653 (33.6%) had associated anomalies. There were 138 (7.1%) patients with chromosomal abnormalities including 39 trisomy 18 (2%), and 195 (10%) syndromic conditions including VA(C)TER(L) association (3.3%), Meckel-Gruber syndrome (2.1%), and prune belly syndrome (1.4%). Three hundred twenty (16.4%) of the cases had multiple congenital anomalies (MCA). Anomalies in the musculoskeletal, the digestive, the cardiovascular and the central nervous systems were the most common other non urinary anomalies. Prenatal diagnosis was obtained in 71.5% of the cases with CAKUT. In conclusion the overall prevalence of associated anomalies, which was one out of three cases, emphasizes the need for a thorough investigation of cases with CAKUT. A routine screening for other non urinary anomalies may be considered in cases with CAKUT. One should be aware that the non urinary anomalies associated with CAKUT can be classified into a recognizable anomaly syndrome or pattern in one out of six cases with CAKUT.

Proband-Only Exome Sequencing for Intellectual Disability in Iran: Diagnostic Yield and Genetic Insights

Intellectual disability (ID) is a leading cause for referral to genetic services, with the most severe cases typically attributed to single genetic defects. This study aimed to evaluate the diagnostic yield of cost-effective proband-only exome sequencing for individuals diagnosed with ID within the Iranian population for the first time where a high rate of parental consanguinity exists. A total of 99 unrelated patients with ID were investigated by exome sequencing during 8 years. As a result, 43 pathogenic/likely pathogenic variants were identified in 40 patients, indicating a molecular diagnostic rate of 40.4% (40/99). The inclusion of five chromosomal copy number variations in the subsequent analysis increased the diagnostic rate of proband-only exome sequencing to 45.4% (45/99). Additionally, parental testing revealed five de novo variants. This contributed to a total diagnostic rate of 50.5% (50/99). In our study, proband-only exome sequencing achieved a remarkable diagnostic rate, identifying nearly half of the ID cases. This rate of diagnosis could be primarily attributed to prevalent consanguineous marriage in the Iranian population and the rare identification of de novo variants. With the ongoing advancements in neurogenetics, proband-only exome sequencing demonstrates significant potential as a future cost-effective diagnostic approach in Iran.

Rare mutations implicate CGE interneurons as a vulnerable axis of cognitive deficits across psychiatric disorders

Neuropsychiatric disorders such as autism spectrum disorder (ASD) and schizophrenia (SCZ) share genetic risk factors, including rare high penetrance single nucleotide variants and copy number variants (CNVs), and exhibit both overlapping and distinct clinical phenotypes. Cognitive deficits and intellectual disability-critical predictors of long-term outcomes-are common to both conditions. To investigate shared and disorder-specific neurobiological impact of highly penetrant rare mutations in ASD and SCZ, we analyzed human single-nucleus whole-brain sequencing data to identify strongly affected brain cell types. Our analysis revealed Caudal Ganglionic Eminence (CGE)-derived GABAergic interneurons as a key nexus for cognitive deficits across these disorders. Notably, genes within 22q11.2 deletions, known to confer a high risk of SCZ, ASD, and cognitive impairment, showed a strong expression bias toward vasoactive intestinal peptide-expressing cells (VIP+) among CGE subtypes. To explore VIP+ GABAergic interneuron perturbations in the 22q11.2 deletion syndrome in vivo , we examined their activity in the Df(16)A +/- mouse model during a spatial navigation task and observed reduced activity along with altered responses to random rewards. At the population level, VIP+ interneurons exhibited impaired spatial encoding and diminished subtype-specific activity suggesting deficient disinhibition in CA1 microcircuits in the hippocampus, a region essential for learning and memory. Overall, these results demonstrate the crucial role of CGE-derived interneurons in mediating cognitive processes that are disrupted across a range of psychiatric and neurodevelopmental disorders.

Distal 1q Duplication and Distal 9p Deletion: A Follow-Up Case Report and Literature Review on Candidate Genes for 9p Deletion Syndrome

Distal 1q duplication and distal 9p deletion are rare chromosomal aberrations associated with developmental delay and mild to moderate congenital malformations. There are inconsistent findings regarding the critical region for trigonocephaly within 9p deletion syndrome. A recent analysis of the largest 9p- cohort to date, however, delineated two critical regions and emphasized the need for replication. We report on a trigonocephalic child with a de novo 46.09 megabases (Mb) terminal duplication of 1q and a 5.31 Mb terminal deletion in 9p, described as 46,XX,der(9)t(1;9)(q32.1;p24.1). The clinical course was predominantly influenced by the 1q duplication. Trigonocephaly, however, was consistent with 9p deletion syndrome. Our findings support the delineation of [GRCh38] 9:3,418,241-5,341,746 as a critical region for trigonocephaly within 9p deletion syndrome. We propose that haploinsufficiency of RFX3, along with complex gene interactions, contributes to the mechanism for disease.

Rapid Whole-Genome Sequencing in Critically Ill Infants and Children with Suspected, Undiagnosed Genetic Diseases: Evolution to a First-Tier Clinical Laboratory Test in the Era of Precision Medicine

The completion of the Human Genome Project in 2003 has led to significant advances in patient care in medicine, particularly in diagnosing and managing genetic diseases and cancer. In the realm of genetic diseases, approximately 15% of critically ill infants born in the U.S.A. are diagnosed with genetic disorders, which comprise a significant cause of mortality in neonatal and pediatric intensive care units. The introduction of rapid whole-genome sequencing (rWGS) as a first-tier test in critically ill children with suspected, undiagnosed genetic diseases is a breakthrough in the diagnosis and subsequent clinical management of such infants and older children in intensive care units. Rapid genome sequencing is currently being used clinically in the USA, the UK, the Netherlands, Sweden, and Australia, among other countries. This review is intended for students and clinical practitioners, including non-experts in genetics, for whom it provides a historical background and a chronological review of the relevant published literature for the progression of pediatric diagnostic genomic sequencing leading to the development of pediatric rWGS in critically ill infants and older children with suspected but undiagnosed genetic diseases. Factors that will help to develop rWGS as a clinical test in critically ill infants and the limitations are briefly discussed, including an evaluation of the clinical utility and accessibility of genetic testing, education for parents and providers, cost-effectiveness, ethical challenges, consent issues, secondary findings, data privacy concerns, false-positive and false-negative results, challenges in variant interpretation, costs and reimbursement, the limited availability of genetic counselors, and the development of evidence-based guidelines, which would all need to be addressed to facilitate the implementation of pediatric genomic sequencing in an effective widespread manner in the era of precision medicine.

Identifying characteristics associated with genetic testing in the NICU

Genetic testing is an integral part of Neonatal Intensive Care Unit (NICU) care. There are reported disparities in both NICU care and genetic testing related to race and language spoken. Identifying characteristics associated with genetic testing in NICUs could help detect patients who may benefit from genetic testing, as well as any current disparities. We sought to analyze characteristics of NICU admits who had genetic testing in general and specific test categories. Characteristics were requested from the Children's Hospital Neonatal Consortium database for patients admitted to Primary Children's Hospital's NICU in 2022. Statistical analysis was performed to determine if characteristics were more likely to result in genetic testing and if differences between those with genetic testing and those without were significant. All genetic test types were more likely ordered with genetic consultations. Cytogenetic testing was more likely in patients with a cardiology consult or who were Spanish-speaking. Patients who were of Hispanic origin were more likely to have molecular testing ordered. The average number of specialty consults for a patient was higher for those with genetic testing. Premature and low birthweight infants had longer time to genetic test ordering. No disparities were identified, which could be due to a small, homogenous sample. The differences with Spanish-speaking patients and those with mothers of Hispanic origin could be due to many factors, including consenting practices. It may be difficult to identify infants who might need genetic testing when they are low birthweight and/or premature. It is important to continue monitoring for differences in ordering practice for this vulnerable population.

Identification of Long Noncoding RNA Candidate Disease Genes Associated With Clinically Reported Copy Number Variants in Congenital Heart Disease

BACKGROUND

Copy number variants (CNVs) contribute to 3% to 10% of isolated congenital heart disease (CHD) cases, yet their pathogenic roles remain unclear. Diagnostic efforts have focused on protein-coding genes, largely overlooking long noncoding RNAs (lncRNAs), which play key roles in development and disease.

METHODS AND RESULTS

We systematically analyzed lncRNAs overlapping clinically validated CNVs in 743 patients with CHD from the Cytogenomics of Cardiovascular Malformations Consortium. We identified heart-expressed lncRNAs, constructed a gene regulatory network using weighted gene coexpression network analysis, and identified gene modules associated with heart development. Functional enrichment and network analyses were used to identify lncRNAs that may be involved in heart development and potentially contribute to CHD. The code is stably archived at https://doi.org/10.5281/zenodo.13799779. We identified 18 lncRNA candidate genes within modules significantly correlated with heart tissue, highlighting their potential involvement in CHD pathogenesis. Notably, lncRNAs such as lnc-STK32C-3, lnc-TBX20-1, and CRMA demonstrated strong associations with known CHD genes. Strikingly, although only 7.6% of known CHD genes were affected by a CNV, 68.8% of the CNVs contained a lncRNA expressed in the heart.

CONCLUSIONS

Using weighted gene coexpression network analysis, we identified CNV-associated lncRNAs with potential relevance to CHD, underscoring the complexities of noncoding regions in disease pathogenesis. These findings suggest that lncRNAs may play a greater role in CHD than previously recognized, highlighting the need for broader genomic analyses that extend beyond protein-coding genes. This study provides a foundation for further exploration of lncRNAs in CHD, with potential implications for improved genetic characterization and diagnosis.

Whole exome sequencing as a screening tool in dogs: A pilot study

Background

Whole-exome sequencing (WES) is used to selectively sequence all exons of protein-coding genes. WES is considered as a cost-effective and direct approach for identifying phenotype-associated variants in protein-coding regions and is as such situated between the traditional Sanger sequencing and whole genome sequencing (WGS). While WES is already widely used as a clinical tool in human and medical genetics, its use in veterinary medicine is currently restricted to research purposes. In this article, we aimed to provide baseline performance characteristics of a WES design to assess its suitability with future applications in veterinary clinical genetics in mind.

Methods

To assess the potential of WES in a clinical setting for dogs, 49 canine samples underwent capture, sequencing and analysis for the presence of 352 known phenotype-associated variants. The sequencing performance was compared for three types of variants, based on their size and location: single nucleotide variants (SNVs) inside exons, larger indel variants (≤20 bp) inside exons and intronic variants.

Results

On average, 85 % and 82 % of the exonic SNPs and larger variants were sequenced at a sequencing depth of ≥ 10x in the 49 samples, respectively. In the best performing sample, 94 % of the exonic SNPs were covered at least 10x, whereas in the worst performing sample, still 71 % of the exonic SNPs had an average sequencing depth of more than 10x.

Conclusion

To our knowledge, this is the first report that describes the performance of a research-intended WES design if it would be used in clinical genetics. This study found that WES demonstrated high efficacy in detecting variants located within target regions, including those that were not initially included in the design. However, the performance varied across different variants. The next steps would be the development of improved designs and settings to ameliorate the results.

Paired copy number variation analysis in siblings discordant for familial Parkinson's disease

ObjectivesNumerous studies on the genetic pathogenesis of familial Parkinson's Disease (PD) have explained the etiology of only a limited percentage of cases. In this study, we aimed to identify copy number variations (CNVs) in patients with familial PD compared to their healthy siblings.MethodsGenomic microarray analysis was performed using the CytoScan HD array platform, and paired copy number variation analysis was performed using Partek Genomics Suite.ResultsA total of 211 CNVs were detected in patients (genomic markers per CNV >10, markers per base pair >0.0005). Genes localized in CNV regions were enriched in the "Metabolism of xenobiotics by cytochrome P450" pathway. Subsequently, CNVs located in regions with segmental duplication, large genomic gap or "dosage sensitivity unlikely," with a frequency higher than 0.01%, and found to be "both amplified and deleted" in patients were excluded. Genes potentially affected by exonic copy number losses were HPGDS, TUBB8, ZMYND11, FLI-1, THADA, FAM47E, FAM47E-STBD1, AGMO, CYRIB, and MIR5194, while the detected copy number gains included the exons of the PCSK6, MIR4522, WSB1, C8orf44-SGK3, SGK3, and MCMDC2. No copy number variations were detected on chromosomes 13 and 18.ConclusionsHere, we report the results of the first paired CNV analysis in siblings discordant for Familial Parkinson's Disease. Validation and frequency determination of rare and novel CNVs identified in larger familial PD cohorts may reveal novel PD risk genes. The metabolism of xenobiotics by cytochrome P450 pathway deserves further functional and translational studies in familial Parkinson's disease.

Diagnostic Utility of Trio-Exome Sequencing for Children With Neurodevelopmental Disorders

Importance

Copy number variants (CNVs) and single-nucleotide variations (SNVs) or insertions and deletions are key genetic contributors to neurodevelopmental disorders (NDDs). Traditionally, chromosome microarray and exome sequencing (ES) have been used to detect CNVs and single gene variants, respectively.

Objective

To identify genetic variants causing NDDs and evaluate the diagnostic yield and clinical utility of ES by simultaneously analyzing CNVs and SNVs in patients with NDDs and their biologic parents (trios).

Design, Setting, and Participants

This retrospective cohort study included pediatric patients with suspected NDDs who visited Shanghai Children's Hospital between January 1, 2018, and December 31, 2023. ES was used to investigate trios (trio-ES) including patients with NDDs who remained undiagnosed after phenotype identification and underwent gene panel testing, multiplex ligation-dependent probe amplification, or karyotyping. Comprehensive clinical and laboratory data were collected. Data were analyzed from July 2022 to December 2023.

Exposure

NDDs, characterized by global developmental delay or intellectual disability.

Main Outcomes and Measures

The study measured the overall diagnostic yield of SNVs and CNVs in the NDD cohort as well as within NDD syndromic subtypes.

Results

Of the 1106 patients with NDDs, 731 (66.1%) were male. The mean (SD) age of patients at diagnosis was 3.80 (2.82) years. The overall diagnostic yield of trio-ES was 46.1% (510 diagnoses among 1106 patients), with 149 CNVs (13.5%), 355 SNVs (32.1%), and 4 cases of uniparental disomy (0.4%). Codiagnosis of SNVs and CNVs occurred in 2 cases (0.2%). Among the trios, 812 candidate germline variants were identified, including 634 SNVs (78.1%), 174 CNVs (21.4%), and 4 cases of uniparental disomy (0.5%). Of these, 423 SNVs (66.7%) and 157 CNVs (90.2%) were diagnostic variants, while 211 SNVs (33.3%) and 17 CNVs (9.8%) were variants of uncertain significance. Sixteen CNVs smaller than 20 kilobase were detected using ES.

Conclusions and Relevance

In this cohort study, trio-ES, by simultaneously detecting SNVs and CNVs, achieved a diagnostic yield of 46.1%. Trio-ES may be particularly applicable for identifying small CNVs and recessive genetic diseases involving both SNVs and CNVs. These findings suggest that in clinical practice, simultaneously analyzing SNVs and CNVs using trio-ES data has a favorable genetic diagnostic yield for children with NDDs.

Navigating Genetic Testing in Nephrology: Options and Decision-Making Strategies

Technological advances such as next-generation sequencing (NGS) have enabled high-throughput assessment of the human genome, supporting the usage of genetic testing as a first-line tool across clinical medicine. Although individually rare, genetic causes account for end-stage renal disease in 10% to 15% of adults and 70% of children, and in many of these individuals, genetic testing can identify a specific etiology and meaningfully impact management. However, with numerous options for genetic testing available, nephrologists may feel uncomfortable integrating genetics into their clinical practice. Here, we aim to demystify the process of genetic test selection and highlight the opportunities for interdisciplinary collaboration between nephrologists and genetics professionals, thereby supporting precision medicine for patients with kidney disease. We first detail the various clinical genetic testing modalities, highlighting their technical advantages and limitations, and then discuss indications for their usage. Next, we provide a generalized workflow for genetic test selection among individuals with kidney disease and illustrate how this workflow can be applied to genetic test selection across diverse clinical contexts. We then discuss key areas related to the usage of genetic testing in clinical nephrology that merit further research and approaches to investigate them.

The impact of genetic counselor involvement in genetic and genomic test order review: A scoping review

PURPOSE

The increasing complexity of genetic technologies paired with more genetic tests being ordered by nongenetic health care providers, has resulted in an increase in the number of inappropriately ordered tests. Genetic counselors (GCs) are ideally suited to assess the appropriateness of a genetic test.

METHODS

We performed a scoping review of GC involvement in utilization management initiatives in order to describe the impact of having GCs involved in this process. Five databases (MEDLINE, EMBASE, CINHAL, EBM reviews, and Web of Science Core Collection) and gray literature were searched. We considered literature published in English since 2010.

RESULTS

A total of 51 studies were included. The most commonly evaluated outcomes included cancellation rate, economic efficiencies, impact on medical management, diagnostic rate, and time or triage efficiencies. Several studies also described GC impact on nongenetic health care providers.

CONCLUSION

Employment of GCs in the laboratory has been implemented widely as a solution to test misordering. These studies describe ways in which GCs can be integrated into testing workflows to reduce the number of inappropriate tests and have wider impacts on nongenetic health care providers' ordering practices and the patient experience.

Clinical and genetic findings in autism spectrum disorders analyzed using exome sequencing

Autism spectrum disorder (ASD) refers to a group of complex neurodevelopmental disorders and is characterized by impaired reciprocal social interaction and communication, as well as the presence of restricted interests and stereotyped and repetitive behaviors. As a complex neurodevelopmental disorder, the phenotype and severity of autism are extremely heterogeneous, with differences from one patient to another. Chromosome microarray (CMA) and fragile X syndrome analyses has been used as a powerful tool to identify new candidate genes for ASD.

METHODS

In the present study, CMA was first used to scan for genome-wide copy number variants in the patient, and no clinically significant copy number variants were found. Exome sequencing (ES) was used for further genetic testing.

RESULTS

ES was performed on 20 subjects. Eighty percent of our sample presented intellectual disability. Other co-occurring clinical conditions included speech disorders, psychomotor delay, the presence of dysmorphic features and medical co-morbidities. A pathogenic variant was identified in 10 patients (ADNP, FBN1, WAC, ASXL3, NR4A2, ALX4, ANKRD1, POGZ, SHANK3 and BPTF). Patients with a positive finding in ES were more likely to present a dysmorphic trunk, more than three dysmorphic features, hypotonia, psychomotor delay and strabismus.

CONCLUSIONS

ES offers expanded diagnostic options for patients with ASD who are negative on CMA. However, further studies are needed for a better understanding of ASD etiology and also the different phenotypes.

Copy number variant analysis improves diagnostic yield in a diverse pediatric exome sequencing cohort

Exome sequencing is the current standard for diagnosing Mendelian disorders; however, it is generally not considered the first-line test for detecting copy number variants (CNVs). We retrospectively investigated the additional diagnostic yield by performing concurrent CNV analysis using exome data in a large and diverse pediatric cohort. Patients were referred from various sources with variable phenotypes. Human Phenotype Ontology terms were used to prioritize variants for analysis. Ancestry and CNV analyses were performed using Somalier and NxClinical, respectively. A total of 1538 patients were tested, with the majority being Admixed Americans. Diagnostic CNVs were identified in 70 patients (4.6%), ranging from exonic deletions to large, unbalanced rearrangements, aneuploidies, and mosaic findings. While no significant differences were identified in diagnostic yield, or rates of negative or uncertain diagnoses, between ancestries, our study demonstrates the feasibility and increased yield of CNV analysis of exome data, across multiple phenotypes, referral sources, and ancestries.

Identification of cryptic breakpoints through single-tube long fragment read whole genome sequencing based on preimplantation genetic testing

This study utilized single-tube long fragment read whole genome sequencing (stLFR WGS) to identify cryptic chromosomally balanced translocations in preimplantation genetic testing (PGT), aiming to improve outcomes for couples experiencing recurrent pregnancy loss (RPL). G-banded karyotyping initially revealed normal results for Family 1 and a reciprocal translocation for Family 2. However, PGT's low-coverage WGS uncovered recurrent copy number variations (CNVs) that contradicted the initial findings. Further analysis using stLFR WGS and Sanger sequencing precisely located the breakpoints, revealing a balanced translocation between chromosomes 7 and 13 in Family 1's male and a complex translocation involving chromosomes 9, 10, and 11 in Family 2's female. By selecting non-carrier embryos for transfer, the study resulted in successful births of healthy infants. These findings highlight the critical role of PGT in detecting concealed chromosomal rearrangements and demonstrate stLFR WGS as an effective diagnostic tool for breakpoint identification, significantly impacting reproductive decisions for couples with cryptic balanced translocations and RPL.

OMKar: optical map based automated karyotyping of genomes to identify constitutional abnormalities

The whole genome karyotype refers to the sequence of large chromosomal segments that make up an individual's genotype. karyotype analysis, which includes descriptions of aneuploidies and other rearrangements is crucial for understanding genetic risk factors, for diagnosis, treatment decisions, and genetic counseling linked to constitutional disorders. The current karyotyping standard is based on microscopic examination of chromosomes, a complex process that requires high expertise and offers Mb scale resolution. Optical Genome Mapping (OGM) technology can identify large DNA lesions in a cost-effective manner. In this paper, we developed OMKar, a method that uses OGM data to create a virtual karyotype. OMKar processes Structural (SV) and Copy Number (CN) Variants as inputs and encodes them into a compact breakpoint graph. It recomputes copy numbers using Integer Linear Programming to maintain CN balance and then identifies constrained Eulerian paths representing entire donor chromosomes. In tests using 38 whole genome simulations of constitutional disorders, OMKar reconstructed the karyotype with 88% precision and 95% recall on SV concordance and 95% Jaccard score on CN concordance. We applied OMKar to 50 prenatal, 41 postnatal, and 63 parental samples from ten different sites. OMKar reconstructed the correct karyotype in 144 out of 154 samples, covering 25 of 25 aneuploidies, 32 of 32 balanced translocations, and 72 of 82 unbalanced variations. Detected constitutional disorders included Cri-du-chat, Wolf-Hirschhorn, Prader-Willi deletions, Down, and Turner syndromes. Importantly, it identified a plausible genetic mechanism for five cases of constitutional disorder that were not detected by other technologies. Together, these results demonstrate the robustness of OMKar for OGM-based karyotyping. OMKar is publicly available at https://github.com/siavashre/OMKar .

Preliminary Findings on the Use of Array Comparative Genomic Hybridization in Youth with Autism Spectrum Disorder in Qatar: A Case Series Study

Autism Spectrum Disorder (ASD) is a neurodevelopmental condition with rising prevalence. Traditional diagnostic approaches often lack biological markers, making precision in diagnosis challenging. This study explores the role of array Comparative Genomic Hybridization (aCGH) in improving diagnostic accuracy for ASD. Five clinical vignettes of children diagnosed with ASD via DSM-5 or ADOS-2 were evaluated at a child and adolescent psychiatry clinic. Genome-wide oligonucleotide aCGH analysis was conducted using the Human Genome CGH Microarray kit (OGT), containing approximately 180,000 probes with 30-37 kb spacing based on the GRCh37 build. Fragile X syndrome was excluded using the Asuragen Amplidex PCR/CE FMR1 kit. The case series included boys aged 8-11 from diverse ethnic backgrounds (Asian, African, and Qatari), all presenting with varying degrees of ASD. Genetic analyses revealed significant chromosomal changes affecting eight genes, SHOX, HNF1B, COH1, AHNAK, DOCK8, TIAM1, TBL1XR1, and ALKBH8, highlighting diverse genetic contributions to ASD. These findings encompassed both chromosomal gains and losses, as well as variants of uncertain significance (VUS). The aCGH analyses provided valuable genetic insights, refining the diagnostic process and informing personalized management strategies for ASD. This suggests that aCGH is a useful tool in identifying clinically relevant genetic variations, particularly in settings with limited resources, where other diagnostic modalities may be less accessible.

Genomics-informed neuropsychiatric care for neurodevelopmental disorders: Results from a multidisciplinary clinic

PURPOSE

Patients with neurodevelopmental disorders (NDDs) have high rates of neuropsychiatric comorbidities. Genomic medicine may help guide care because pathogenic variants are identified in up to 50% of patients with NDDs. We evaluate the impact of a genomics-informed, multidisciplinary, neuropsychiatric specialty clinic on the diagnosis and management of patients with NDDs.

METHODS

We performed a retrospective study of 316 patients from the University of California, Los Angeles Care and Research in Neurogenetics Clinic, a genomics-informed multidisciplinary clinic.

RESULTS

Among the 246 patients who underwent genetic testing, 41.8% had a pathogenic or likely pathogenic variant. Patients had 62 different genetic diagnoses, with 12 diagnoses shared by 2 or more patients, whereas 50 diagnoses were found in only single patients. Genetic diagnosis resulted in direct changes to clinical management in all patients with a pathogenic or likely pathogenic variant, including cascade testing (30.6%), family counseling (22.2%), medication changes (13.9%), clinical trial referral (2.8%), medical surveillance (30.6%), and specialty referrals (69.4%).

CONCLUSIONS

A genomics-informed model can provide significant clinical benefits to patients with NDDs, directly affecting management across multiple domains for most diagnosed patients. As precision treatments advance, establishing a genetic diagnosis will be critical for proper management. With the growing number of rare neurogenetic disorders, clinician training should emphasize core principles of genomic medicine over individual syndromes.

Clinical Utility of Proband Only Clinical Exome Sequencing in Neurodevelopmental Disorders

Chromosomal microarray is recommended as the first line of investigation in neurodevelopmental disorders (NDDs). However, advances in next-generation sequencing have unraveled more than 900 genes associated with NDDs, thus improving the genetic diagnosis. Therefore, this study was conducted to explore the utility of clinical exome sequencing (CES) in NDDs from a tertiary care centre in India. A retrospective observational analysis of 78 children with NDDs for whom CES was performed between 2017 and 2021 was conducted. The American College of Medical Genetics and Genomics (ACMG) criteria were used to classify the variants. The mean age was 5.8 ± 3.6 y, and 42 (53%) were male. Pathogenic, likely pathogenic, and variants of uncertain significance (VUS) were observed in 22 (28.2%), 10 (12.8%), and 26 (33.3%) patients, respectively, which included five copy number variants. The diagnostic yield for pathogenic and likely pathogenic variants in NDDs by CES was 41%, which was reasonably high.

Comprehensive analysis of chromosome abnormalities by chromosome conformation based karyotyping (C-MoKa) in patients with conception failure and pregnancy loss

BACKGROUND

Chromosome abnormalities are a leading cause of conception failure and pregnancy loss. While traditional cytogenetics technologies like karyotyping have been helpful in identifying structural variations (SVs), they face challenges in detecting complex rearrangements and cryptic structures. In this study, we developed a new method called chromosome conformation based karyotyping (C-MoKa) to comprehensively detect different types of chromosomal abnormalities in patients with conception failure and pregnancy loss.

METHODS

A total of 70 clinical samples exhibiting known results of SVs, mosaic aneuploidies, copy number variations （CNVs） and uniparental disomy (UPD) were included in our cohort and underwent C-MoKa analysis. The results obtained from different techniques, including karyotyping, CNV-seq, and CMA were compared and analyzed.

RESULTS

Distinct chromosomal conformation patterns of various variations were observed and analyzed in clinical samples. Our C-MoKa method not only validated all the findings of karyotyping, CNV-seq and CMA, but also provided more detailed results. It demonstrated superior fragment resolution (<500 Kb) and more precise breakpoints (>100 kb). Moreover, C-MoKa showed higher sensitivity in decoding intricate rearrangements in a single test.

CONCLUSIONS

Our results highlight the potential utility of C-MoKa in precisely unraveling SVs, mosaic aneuploidies, CNVs, and UPD in clinical settings, which can significantly impact further clinical decision-making.

Associated Anomalies in Radial Ray Deficiency

Radial ray deficiency (RRD) may be isolated, without other congenital anomalies or co-occurring with other, non-RRD, congenital anomalies. The prevalence and the types of co-occurring anomalies are variable in the reported studies. The aim of this study was to obtain the prevalence and the types of co-occurring congenital anomalies among cases with RRD in a geographically well-characterized population of 387,067 consecutive births in northeastern France from 1979 to 2007 including live births, stillbirths and terminations of pregnancy. During the study period 83 cases with RRD were ascertained (prevalence of 2.14 per 10,000 births), 63 cases (75.9%) had co-occurring anomalies. Cases with co-occurring anomalies were divided into chromosomal anomalies (18 cases, 22%), syndromic conditions (syndromes and associations, 23 cases, 28%), and multiple congenital anomalies (MCA) (22 cases, 26%). Trisomies 18 and autosomal deletions were the most common chromosomal abnormalities. Thrombocytopenia absent radii syndrome, VACTERL association, Fanconi anemia, Roberts syndrome, and Holt-Oram syndrome were the most common syndromic conditions. Anomalies in the musculoskeletal, the cardiovascular, the urinary, and the orofacial system were the most common co-occurring anomalies in cases with MCA. As cases with RRD have often co-occurring congenital anomalies, a multidisciplinary checkup of these cases is recommended.

Utility of Optical Genome Mapping in Repeat Disorders

Genomic repeat sequences are patterns of nucleic acids that exist in multiple copies throughout the genome. More than 60 Mendelian disorders are caused by the expansion or contraction of these repeats. Various specific methods for determining tandem repeat variations have been developed. However, these methods are highly specific to the genomic region being studied and sometimes require specialized tools. In this study, we have investigated the use of Optical Genome Mapping (OGM) as a diagnostic tool for detecting repeat disorders. We evaluated 19 patients with a prediagnosis of repeat disorders and explained the molecular etiology of 9 of them with OGM (5 patients with Facioscapulohumeral Muscular Dystrophy (FSHD), 2 patients with Friedreich's Ataxia (FA), 1 patient with Fragile X Syndrome (FXS), and 1 patient with Progressive Myoclonic Epilepsy 1A (EPM1A)). We confirmed OGM results with more widely used fragment analysis techniques. This study highlights the utility of OGM as a diagnostic tool for repeat expansion and contraction diseases such as FA, FXS, EPM1A, and FSHD.

Best Practice & Research clinical obstetrics & gynaecology

Screening for fetal genetic disorders is a focus of prenatal care. Cell free DNA (cfDNA) screening for aneuploidies became available in 2011. Initially available only to high-risk individuals, this test is now standard of care in many settings. cfDNA screening has expanded to include sex chromosomal aneuploidies, copy number variants, and rare autosomal trisomies. However, the positive predictive value for rarer conditions is significantly lower, the number of conditions tested for is small, and abnormal results may occur due to maternal genetic findings. The field is changing quickly, and national recommendations for the use of cfDNA in screening for fetal and maternal diseases varies internationally. Research on the performance of screening for many different genetic disorders using cfDNA is ongoing, and suggests that this methodology may allow for testing of a much greater number of genetic conditions. Additionally, improved understanding of the cfDNA molecules themselves may provide additional insights: both high and low fetal fractions may suggest adverse pregnancy outcomes, and characteristics of the fragments themselves may help distinguish tissue of origin.

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

BACKGROUND

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.

METHODS

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.

RESULTS

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.

CONCLUSIONS

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.

Expanding the clinical spectrum of 19p13.3 microduplication syndrome: a case report highlighting nephrotic syndrome and literature review

BACKGROUND

Common clinical findings in patients with 19p13.3 duplication include intrauterine growth restriction, intellectual disability, developmental delay, microcephaly, and distinctive facial features. In this study, we report the case of a patient with 19p13.3 microduplication and novel clinical findings, specifically nephrotic syndrome.

CASE PRESENTATIONS

A 4-year-old girl was admitted to our hospital in December 2020 with a fever and cough that had persisted for 3 days. A series of treatments, chromosomal microarray analysis (CMA) and whole exome sequencing (WES) were performed. Relevant literature was reviewed using the search terms "19p13.3" and "19p13.3 microduplication syndrome" in the China Knowledge Network, Wanfang Database, Weipu Journal Service Platform, and PubMed (date range: database establishment to September 2023). In addition to common symptoms, such as developmental delay, microcephaly, distinctive facial features, and congenital heart defects, the patient also had nephrotic syndrome, a previously unreported phenomenon. CMA results showed a 3.6 Mb fragment duplication (copy number: 3) in the chr19p13.3 region, containing 127 protein-coding genes (including CELF5, NFIC, SMIM24, PIAS4, ATCAY, MAP2K2, and ZBTB7A). WES revealed a filamin C mutation (p.Glu309Valfs × 11). The mutation status of the patient and her father was heterozygous, whereas the mutation was not detected in the mother.

CONCLUSION

Microduplication in the 19p13.3 region could be one of the genetic factors contributing to the observed clinical phenotypes. However, patients with developmental delay, microcephaly, distinctive facial features, congenital heart defects, and urogenital system disorders may exhibit these manifestations due to various genetic syndromes; therefore, simply considering the possibility of 19p13.3 microduplication syndrome based on these non-specific features is not sufficient. Further comprehensive evaluations, including CMA, should be conducted in conjunction with other genetic tests and detailed clinical examinations to accurately determine the underlying genetic causes.

Advances in chromosomal microarray analysis: Transforming neurology and neurosurgery

Over the past two decades, genomics has transformed our understanding of various clinical conditions, with Chromosomal Microarray Analysis (CMA) standing out as a key technique. Offering unparalleled sensitivity, CMA detects submicroscopic chromosomal imbalances, enabling the examination of DNA for copy number variations, deletions, duplications, and other structural differences. In neurology, CMA has revolutionised diagnoses, personalised treatment plans, and patient outcomes. By identifying genetic anomalies linked to neurological conditions, CMA allows clinicians to tailor treatments based on individual genetic profiles, enhancing precision medicine. CMA's clinical utility spans numerous neurological conditions, providing crucial insights into neurodevelopmental disorders, CNS tumours, neurodegenerative diseases, cerebrovascular diseases, and epilepsy. In neurodevelopmental disorders, CMA aids in diagnosing autism and intellectual disabilities, facilitating early interventions that improve long-term outcomes. In epilepsy, CMA helps identify genetic causes of drug-resistant seizures, enabling more targeted therapies and reducing adverse reactions. CMA also aids in stratifying risk for cerebrovascular diseases, enabling preventive interventions that improve patient prognosis. Despite its potential, challenges remain, such as interpreting variants of uncertain significance (VOUS), the lack of standardised testing guidelines, and issues of cost and accessibility. Addressing these challenges will optimise CMA's impact, advancing personalised medicine and reshaping neurology. This review discusses CMA's pivotal role in bridging the gap between genomics and clinical practice, underscoring its potential to transform neurogenetics and ultimately improve patient care.

Diversity and consequences of structural variation in the human genome

The biomedical community is increasingly invested in capturing all genetic variants across human genomes, interpreting their functional consequences and translating these findings to the clinic. A crucial component of this endeavour is the discovery and characterization of structural variants (SVs), which are ubiquitous in the human population, heterogeneous in their mutational processes, key substrates for evolution and adaptation, and profound drivers of human disease. The recent emergence of new technologies and the remarkable scale of sequence-based population studies have begun to crystalize our understanding of SVs as a mutational class and their widespread influence across phenotypes. In this Review, we summarize recent discoveries and new insights into SVs in the human genome in terms of their mutational patterns, population genetics, functional consequences, and impact on human traits and disease. We conclude by outlining three frontiers to be explored by the field over the next decade.

Detection of Clinically Relevant Monogenic Copy-Number Variants by a Comprehensive Genome-Wide Microarray with Exonic Coverage

BACKGROUND

Disease-causing copy-number variants (CNVs) often encompass contiguous genes and can be detected using chromosomal microarray analysis (CMA). Conversely, CNVs affecting single disease-causing genes have historically been challenging to detect due to their small sizes.

METHODS

A custom comprehensive CMA (Baylor College of Medicine - BCM v11.2) containing 400k probes and featuring exonic coverage for >4200 known or candidate disease-causing genes was utilized for the detection of CNVs at single-exon resolution. CMA results across a consecutive clinical cohort of more than 13 000 patients referred for genetic investigation at Baylor Genetics were examined. The genomic characteristics of CNVs impacting single protein-coding genes were investigated.

RESULTS

Pathogenic or likely pathogenic (P/LP) CNVs (n = 190) affecting single protein-coding genes were detected in 188 patients, accounting for 9.9% (188/1894) of patients with P/LP CMA findings. The P/LP monogenic CNVs accounted for 9.2% (190/2058) of all P/LP nuclear CNVs detected by CMA. A total of 57.9% (110/190) of P/LP monogenic CNVs were smaller than 50 kb in size. Single exons were affected by 26.3% (50/190) of P/LP monogenic CNVs while 13.2% (25/190) affected 2 exons. CNVs were detected across 107 unique genes associated with predominantly autosomal dominant (AD) and X-linked (XL) conditions but also contributed to autosomal recessive (AR) conditions.

CONCLUSIONS

CMA with exon-targeted coverage of disease-associated genes facilitated the detection of small CNVs affecting single protein-coding genes, adding substantial clinical sensitivity to comprehensive CNV investigation. This approach resolved monogenic CNVs associated with autosomal and X-linked monogenic etiologies and yielded multiple significant findings. Monogenic CNVs represent an underrecognized subset of disease-causing alleles for Mendelian disorders.

Genomic insights from a deeply phenotyped highly consanguineous neurodevelopmental disorders cohort

PURPOSE

The genetic underpinning of neurodevelopmental disorders (NDDs) in diverse ethnic populations, especially those with high rates of consanguinity, remains largely unexplored. Here, we aim to elucidate genomic insight from 576 well-phenotyped and highly consanguineous (16%) NDD cohort.

METHODS

We used chromosomal microarray (CMA; N:247), exome sequencing (ES; N:127), combined CMA and ES (N:202), and long-read genome sequencing to identify genetic etiology. Deep clinical multivariate data were coupled with genomic variants for stratification analysis.

RESULTS

Genetic diagnosis rates were 17% with CMA, 29.92% with ES, and 37.13% with combined CMA and ES. Notably, children of consanguineous parents showed a significantly higher diagnostic yield (P < .01) compared to those from nonconsanguineous parents. Among the ES-identified pathogenic variants, 36.19% (38/105) were novel, implicating 35 unique genes. Long-read sequencing of seizure participants unresolved by combined test identified expanded FMR1 trinucleotide repeats. Additionally, we identified 2 recurrent X-linked variants in the G6PD in 3.65% (12/329) of NDD participants. These variants were absent in large-population control cohorts and cohort comprising neurodevelopmental and neuropsychiatric populations of European descendants, indicating a possible associated risk factor potentially resulting from ancient genetic drift.

CONCLUSION

This study unveils unique clinical and genomic insights from a consanguinity rich Bangladeshi NDD cohort.

Editors' Best of 2024

There is, in the content of the Journal, an embarrassment of riches, and picking a "best" seems to demand a certain qualification: is the "best" the most interesting, most surprising, most educational, most important, most provocative, most enjoyable? How to choose? We are hardly unbiased and can admit to a special affection for the ones that we and the authors worked hardest on, modifying version after version into shape. Acknowledging these biases, here are the 2024 articles that we think deserve your attention or at least a second read.

Diagnostic yields of genetic testing and related benefits in infantile epileptic spasms syndrome: A systematic review and meta-analysis

BACKGROUND

Diagnostic yields for infantile epileptic spasms syndrome (IESS) are notably heterogeneous across different testing modalities and studies. To investigate the proportion of individuals with IESS harboring causative/pathogenic genetic variants identified using whole-exome sequencing (WES), multi-gene panels (MGPs), and chromosomal microarray (CMA), thereby providing evidence to inform guidelines for genetic testing strategies.

METHODS

The study team searched PubMed, Embase, and Cochrane Central Register of Controlled Trials between January 2012- October2023. Data were extracted and synthesized by two investigators following the preferred reporting items for systematic reviews and meta-analyses guideline. The primary outcome was the pooled diagnostic rate of individual WES, MGPs, and CMA across studies. Subgroup analyses were performed based on the inclusion of cases with tuberous sclerosis complex and the number of genes included on MGPs.

RESULTS

Our study included 30 studies, involving 2 738 participants. The diagnostic rates in IESS for WES (13 studies, n = 799), MGPs (13 studies, n = 1 117), and CMA (13 studies, n = 629) were 26 % (95 % CI = 21 %-31 %), 20 % (95 % CI = 15 %-27 %), and 14 % (95 % CI = 11 %-16 %), respectively. WES and MGPs showed comparable diagnostic yields (P = 0.34). Our results indicated that 61.6 % of individuals with genetic IESS may potentially benefit from genetic diagnosis in terms of clinical management.

CONCLUSIONS

Our results showed that WES and MGPs exhibited comparable genetic diagnostic yields. Therefore, either method could be equally recommended as a first-tier testing approach for IESS cases with suspected genetic or unknown etiologies, especially considering the potential clinical benefits derived from genetic diagnosis.

Expanding Upon Genomics in Rare Diseases: Epigenomic Insights

DNA methylation is an essential epigenetic modification that plays a crucial role in regulating gene expression and maintaining genomic stability. With the advancement in sequencing technology, methylation studies have provided valuable insights into the diagnosis of rare diseases through the various identification of episignatures, epivariation, epioutliers, and allele-specific methylation. However, current methylation studies are not without limitations. This mini-review explores the current understanding of DNA methylation in rare diseases, highlighting the key mechanisms and diagnostic potential, and emphasizing the need for advanced methodologies and integrative approaches to enhance the understanding of disease progression and design more personable treatment for patients, given the nature of rare diseases.

CRISPR Diagnostics for Quantification and Rapid Diagnosis of Myotonic Dystrophy Type 1 Repeat Expansion Disorders

Repeat expansion disorders, exemplified by myotonic dystrophy type 1 (DM1), present challenges in diagnostic quantification because of the variability and complexity of repeat lengths. Traditional diagnostic methods, including PCR and Southern blotting, exhibit limitations in sensitivity and specificity, necessitating the development of innovative approaches for precise and rapid diagnosis. Here, we introduce a CRISPR-based diagnostic method, REPLICA (repeat-primed locating of inherited disease by Cas3), for the quantification and rapid diagnosis of DM1. This method, using in vitro-assembled CRISPR-Cas3, demonstrates superior sensitivity and specificity in quantifying CTG repeat expansion lengths, correlated with disease severity. We also validate the robustness and accuracy of CRISPR diagnostics in quantitatively diagnosing DM1 using patient genomes. Furthermore, we optimize a REPLICA-based assay for point-of-care-testing using lateral flow test strips, facilitating rapid screening and detection. In summary, REPLICA-based CRISPR diagnostics offer precise and rapid detection of repeat expansion disorders, promising personalized treatment strategies.

Effects of gene dosage on cognitive ability: A function-based association study across brain and non-brain processes

Copy-number variants (CNVs) that increase the risk for neurodevelopmental disorders also affect cognitive ability. However, such CNVs remain challenging to study due to their scarcity, limiting our understanding of gene-dosage-sensitive biological processes linked to cognitive ability. We performed a genome-wide association study (GWAS) in 258,292 individuals, which identified-for the first time-a duplication at 2q12.3 associated with higher cognitive performance. We developed a functional-burden analysis, which tested the association between cognition and CNVs disrupting 6,502 gene sets biologically defined across tissues, cell types, and ontologies. Among those, 864 gene sets were associated with cognition, and effect sizes of deletion and duplication were negatively correlated. The latter suggested that functions across all biological processes were sensitive to either deletions (e.g., subcortical regions, postsynaptic) or duplications (e.g., cerebral cortex, presynaptic). Associations between non-brain tissues and cognition were driven partly by constrained genes, which may shed light on medical comorbidities in neurodevelopmental disorders.

High-resolution genetic analysis of whole APC gene deletions: a report of two cases and patient characteristics

Familial adenomatous polyposis (FAP) is an autosomal dominant syndrome caused by germline variants in the APC gene, leading to the development of numerous colorectal polyps and significantly increases the risk of colorectal cancer. A diagnosis is typically made using colonoscopy, and genetic testing can assist in patient surveillance and carrier identification. Recent advances include the use of whole-genome array comparative genomic hybridization (a-CGH), which provides better resolution of genetic imbalances. We aimed to explore the specific features of FAP patients with whole APC gene deletions using high-resolution a-CGH and to compare patient characteristics. Two polyposis patients with whole APC deletions were identified, and the lost genetic sizes ranged from 0.3-1.1 Mb. Nervous abnormalities were a characteristic symptom in a patient with a 1.1 Mb loss. A patient with an approximately 0.3 Mb loss, which included the entire APC gene, presented a polyposis phenotype without intellectual disability. The comparison of genetic losses, with or without intellectual disability, revealed 7 genetic changes. Consequently, EPB41L4A is a candidate gene associated with the neurogenic phenotype.

Should newborn genetic testing for autism be introduced?

This manuscript provides a review of the potential role of newborn genetic testing for autism, and whether the state has an inherent responsibility to facilitate and subsidise this. This is situated within the broader construct of benefits and limitations of genetic testing currently. Potential benefits of such presymptomatic genetic testing include facilitating earlier diagnosis and access to appropriate intervention which can improve the treatment outcome for the child and indirectly benefit caregivers and society by reducing the care needs of the child and adult in future. However, there are several limitations to newborn genetic testing including the variable penetrance of 'autism-risk' genes, marked phenotypic heterogeneity of autism, real-world limitations in access to treatment, potential psychological harm to caregivers and financial considerations. We hence argue for facilitation of diagnostic genetic testing instead, especially for parents who seek to have greater understanding of recurrence likelihoods, related to reproductive decision-making. Facilitation of such testing can be in the form of both financial subsidies and infrastructural elements including availability of testing facilities and trained healthcare personnel for individualised pregenetic and postgenetic test counselling.

Optical genome mapping with genome sequencing identifies subtelomeric Xq28 deletion and inserted 7p22.3 duplication in a male with multisystem developmental disorder

We report a 17-year-old male with supravalvular stenosis, initial failure to thrive and delayed early development, short stature, acromelia, dysmorphic facial features, hypertelorism, macrocephaly, syringomyelia, hypertension, and anxiety disorder. Fluorescent in situ hybridization (FISH), chromosomal microarray analysis (CMA), and exome sequencing (ES) were nondiagnostic. Combined optical genome mapping (OGM) and genome sequencing (GS) showed a complex rearrangement including an X chromosome with a 22.5 kb deletion in band Xq28 replaced by a 61.4 kb insertion of duplicated chromosome 7p22.3 material. The deletion removes the distal 3' untranslated region (UTR) of FUNDC2, the entire CMC4 and MTCP1, and the first five exons of BRCC3. Transcriptome analysis revealed absent expression of CMC4 and MTCP1 and BRCC3 with normal transcript level of FUNDC2. The inserted duplication includes only one known gene: UNCX. Similar overlapping Xq28 deletions have been reported to be associated with Moyamoya disease (MMD), short stature, hypergonadotropic hypogonadism (HH), and facial dysmorphism. Although he has short stature, our patient does not have signs of Moyamoya arteriopathy or hypogonadism. The structurally abnormal X chromosome was present in his mother, but not in his unaffected brother, maternal uncle, or maternal grandparents. We propose that the combination of his absent Xq28 and duplicated 7p22.3 genomic material is responsible for his phenotype. This case highlights the potential of combined OGM and GS for detecting complex structural variants compared with standard of care genetic testing such as CMA and ES.