Parallel Tests of Whole Exome Sequencing and Copy Number Variant Sequencing Increase the Diagnosis Yields of Rare Pediatric Disorders

Postnatal Outcomes of Fetal Variants of Unknown Significance in Prenatal Chromosomal Microarray Analysis: A Single-Center Study

INTRODUCTION

Chromosomal microarray analysis (CMA) can identify clinically significant microdeletions and microduplications, providing valuable insights into the genetic basis of various disorders. Our study was to evaluate clinical management and prognosis of fetuses with prenatal variants of unknown significance (VOUS) and determine diagnostic approaches for subsequent pregnancies.

METHODS

This study included 2,953 fetuses undergoing CMA at the Prenatal Diagnostic Center of Changzhou Maternal and Child Health Care Hospital from January 2018 to December 2022, identifying 162 cases with VOUS. Parent-of-origin testing determined the origin of copy number variations. Prenatal genetic counseling was provided, and outcomes were followed for 3-36 months post-birth.

RESULTS

All 162 VOUS cases received prenatal genetic counseling. Among these, 123 continued the pregnancy; 22 chose termination, and 17 were lost to follow-up. Of the continuations, 116 delivered at term and 7 preterm. Post-birth follow-up showed 5/123 live-born fetuses developed relevant clinical phenotypes. Parent-of-origin testing in 21 cases identified 18 hereditary and 3 de novo variants. Additionally, five subsequent pregnancies were monitored, with two undergoing amniocentesis and three receiving low-risk noninvasive prenatal testing, all with positive outcomes.

CONCLUSION

VOUS, occurring in approximately 5% of cases, require comprehensive prenatal genetic counseling and show generally favorable outcomes. Despite low association with adverse clinical phenotypes, the importance of postnatal follow-up and regular report updates is emphasized to detect potential clinical associations early.

Whole-Exome Sequencing Improves Understanding of Inherited Retinal Dystrophies in Korean Patients

Retinitis pigmentosa (RP) encompasses a diverse range of hereditary, degenerative retinal ailments, presenting notable obstacles to molecular genetic diagnoses due to the intricate array of variants in different genes involved. This study enrolled 21 probands and their families who have been diagnosed with nonsyndromic RP but without a previous molecular diagnosis. We employed whole-exome sequencing (WES) to detect possible harmful gene variations in individuals with unknown-cause RP at the molecular level. WES allowed the identification of ten potential disease-causing variants in eight different genes. In 8 out of the total 21 patients, this method successfully identified the underlying molecular causes, such as putative pathogenic variants in genes including CRB1, KLHL7, PDE6B, RDH12, RP1, RPE65, USH2A, and RHO. A novel variant was identified in one of these genes, specifically PDE6B, providing valuable information on prospective targets for future enhanced gene therapeutic approaches.

A systematic review of the assessment of the clinical utility of genomic sequencing: Implications of the lack of standard definitions and measures of clinical utility

PURPOSE

Exome sequencing (ES) and genome sequencing (GS) are diagnostic tests for rare genetic diseases. Studies report clinical utility of ES/GS. The goal of this systematic review is to establish how clinical utility is defined and measured in studies evaluating the impacts of ES/GS results for pediatric patients.

METHODS

Relevant articles were identified in PubMed, Medline, Embase, and Web of Science. Eligible studies assessed clinical utility of ES/GS for pediatric patients published before 2021. Other relevant articles were added based on articles' references. Articles were coded to assess definitions and measures of clinical utility.

RESULTS

Of 1346 articles, 83 articles met eligibility criteria. Clinical utility was not clearly defined in 19% of studies and 92% did not use an explicit measure of clinical utility. When present, definitions of clinical utility diverged from recommended definitions and varied greatly, from narrow (diagnostic yield of ES/GS) to broad (including decisions about withdrawal of care/palliative care and/or impacts on other family members).

CONCLUSION

Clinical utility is used to guide policy and practice decisions about test use. The lack of a standard definition of clinical utility of ES/GS may lead to under- or overestimations of clinical utility, complicating policymaking and raising ethical issues.

Exome sequencing improves the molecular diagnostics of paediatric unexplained neurodevelopmental disorders

BACKGROUND

Neurodevelopmental disorders (NDDs) and/or associated multiple congenital abnormalities (MCAs) represent a genetically heterogeneous group of conditions with an adverse prognosis for the quality of intellectual and social abilities and common daily functioning. The rapid development of exome sequencing (ES) techniques, together with trio-based analysis, nowadays leads to up to 50% diagnostic yield. Therefore, it is considered as the state-of-the-art approach in these diagnoses.

RESULTS

In our study, we present the results of ES in a cohort of 85 families with 90 children with severe NDDs and MCAs. The interconnection of the in-house bioinformatic pipeline and a unique algorithm for variant prioritization resulted in a diagnostic yield of up to 48.9% (44/90), including rare and novel causative variants (41/90) and intragenic copy-number variations (CNVs) (3/90). Of the total number of 47 causative variants, 53.2% (25/47) were novel, highlighting the clinical benefit of ES for unexplained NDDs. Moreover, trio-based ES was verified as a reliable tool for the detection of rare CNVs, ranging from intragenic exon deletions (GRIN2A, ZC4H2 genes) to a 6-Mb duplication. The functional analysis using PANTHER Gene Ontology confirmed the involvement of genes with causative variants in a wide spectrum of developmental processes and molecular pathways, which form essential structural and functional components of the central nervous system.

CONCLUSION

Taken together, we present one of the first ES studies of this scale from the central European region. Based on the high diagnostic yield for paediatric NDDs in this study, 48.9%, we confirm trio-based ES as an effective and reliable first-tier diagnostic test in the genetic evaluation of children with NDDs.

Biallelic variants in genes previously associated with dominant inheritance: CACNA1A, RET and SLC20A2

A subset of families with co-dominant or recessive inheritance has been described in several genes previously associated with dominant inheritance. Those recessive families displayed similar, more severe, or even completely different phenotypes to their dominant counterparts. We report the first patients harboring homozygous disease-related variants in three genes that were previously associated with dominant inheritance: a loss-of-function variant in the CACNA1A gene and two missense variants in the RET and SLC20A2 genes, respectively. All patients presented with a more severe clinical phenotype than the corresponding typical dominant form. We suggest that co-dominant or recessive inheritance for these three genes could explain the phenotypic differences from those documented in their cognate dominant phenotypes. Our results reinforce that geneticists should be aware of the possible different forms of inheritance in genes when WES variant interpretation is performed. We also evidence the need to refine phenotypes and inheritance patterns associated with genes in order to avoid failures during WES analysis and thus, raising the WES diagnostic capacity in the benefit of patients.

Clinical Application of Whole Exome Sequencing for Monogenic Disorders in PICU of China

Objectives

Whole exome sequencing (WES) has been widely used to detect genetic disorders in critically ill children. Relevant data are lacking in pediatric intensive care units (PICUs) of China. This study aimed to investigate the spectrum of monogenic disorders, the diagnostic yield and clinical utility of WES from a PICU in a large children's hospital of China.

Methods

From July 2017 to February 2020, WES was performed in 169 critically ill children with suspected monogenic diseases in the PICU of Beijing Children's Hospital. The clinical features, human phenotype ontology (HPO) terms, and assessment of clinical impact were analyzed.

Results

The media age of the enrolled children was 10.5 months (range, 1 month to 14.8 years). After WES, a total of 43 patients (25%) were diagnosed with monogenic disorders. The most common categories of diseases were metabolic disease (33%), neuromuscular disease (19%), and multiple deformities (14%). The diagnosis yield of children with "metabolism/homeostasis disorder" and "growth delay" or "ocular anomalies" was higher than that of children without these features. In addition, the diagnosis rate increased when more features were observed in children. The results of WES had an impact on the treatment for 30 cases (70%): (1) change of treatment (n = 11), (2) disease monitoring initiation (n = 18), (3) other systemic evaluation (n = 3), (4) family intervention (n = 2), and (5) rehabilitation and redirection of care toward palliative care (n = 12).

Conclusion

WES can be used as an effective diagnostic tool in the PICU of China and has an important impact on the treatment of patients with suspected monogenic conditions.

Genetic evaluation in children with short stature

PURPOSE OF REVIEW

Short stature is a common clinical manifestation in children. Yet, a cause is often unidentifiable in the majority of children with short stature by a routine screening approach. The purpose of this review is to describe the optimal genetic approach for evaluating short stature, challenges of genetic testing, and recent advances in genetic testing for short stature.

RECENT FINDINGS

Genetic testing, such as karyotype, chromosomal microarray, targeted gene sequencing, or exome sequencing, has served to identify the underlying genetic causes of short stature. When determining which short stature patient would benefit from genetic evaluation, it is important to consider whether the patient would have a single identifiable genetic cause. Specific diagnoses permit clinicians to predict responses to growth hormone treatment, to understand the phenotypic spectrum, and to understand any associated co-morbidities.

SUMMARY

The continued progress in the field of genetics and enhanced capabilities provided by genetic testing methods expands the ability of physicians to evaluate children with short stature for underlying genetic defects. Continued effort is needed to elaborate new genetic causes of linear growth disorders, therefore, we expand the list of known genes for short stature, which will subsequently increase the rate of genetic diagnosis for children with short stature.

Exome sequencing as the first-tier test for pediatric respiratory diseases: A single-center study

The high clinical and genetic heterogeneity makes it difficult to reach a confirmative diagnosis of suspected pediatric respiratory inherited diseases. Many patients with monogenic respiratory disorders could be missed without genetic testing. We performed a single-center study in Beijing Children's Hospital to demonstrate the clinical utility of exome sequencing (ES) as a first-tier test by evaluating the diagnostic yields of ES for inherited diseases with respiratory symptoms. A total of 107 patients were recruited in this study. We identified 51 pathogenic or likely pathogenic variants in 37 patients by ES (with or without copy number variants sequencing). The overall diagnostic yield was 34.6% (37/107). The most frequent disorders in our cohort were primary immunodeficiency disease (PIDs) (18/37, 48.6%) and primary ciliary dyskinesia (PCD) (9/37, 24.3%). We further reviewed the directive outcomes of genetic testing on the 37 positive cases. Our study demonstrated the effectiveness of ES as a first-tier test in China for diagnosing monogenic diseases of the respiratory system. In the era of precision medicine, ES as a first-tier test can rapidly make a molecular diagnosis and direct the intervention of the positive cases in pediatric respiratory medicine.