Contribution of birth defects and genetic diseases to pediatric hospitalizations. A population-based study

Improving the care of children with GENetic Rare disease: Observational Cohort study (GenROC)-a study protocol

INTRODUCTION

Around 2000 children are born in the UK per year with a neurodevelopmental genetic syndrome with significantly increased morbidity and mortality. Often little is known about expected growth and phenotypes in these children. Parents have responded by setting up social media groups to generate data themselves. Given the significant clinical evidence gaps, this research will attempt to identify growth patterns, developmental profiles and phenotypes, providing data on long-term medical and educational outcomes. This will guide clinicians when to investigate, monitor or treat symptoms and when to search for additional or alternative diagnoses.

METHODS AND ANALYSIS

This is an observational, multicentre cohort study recruiting between March 2023 and February 2026. Children aged 6 months up to 16 years with a pathogenic or likely pathogenic variant in a specified gene will be eligible. Children will be identified through the National Health Service and via self-recruitment. Parents or carers will complete a questionnaire at baseline and again 1 year after recruitment. The named clinician (in most cases a clinical geneticist) will complete a clinical proforma which will provide data from their most recent clinical assessment. Qualitative interviews will be undertaken with a subset of parents partway through the study. Growth and developmental milestone curves will be generated through the DECIPHER website (https://deciphergenomics.org) where 5 or more children have the same genetic syndrome (at least 10 groups expected).

ETHICS AND DISSEMINATION

The results will be presented at national and international conferences concerning the care of children with genetic syndromes. Results will also be submitted for peer review and publication.

Current situation and prospect for the diagnosis and treatment of pediatric critical rare diseases in China

The onset of critical rare diseases (RDs) in children is rapid and dangerous, accompanied by a high mortality rate, which brings a heavy burden to both families and society. Multiple malformations, neuromuscular diseases, metabolic diseases, and heart diseases are the most common types of RDs in children of China, often manifesting with multiple organ dysfunction. At present, the diagnosis and treatment of critical RDs in children face challenges such as prolonged diagnosis time, a high misdiagnosis rate, limited treatment modalities, and a significant disease burden. However, with the progress in genetic testing technology, the establishment of multidisciplinary diagnosis and treatment platforms, and the implementation of relevant RD policies in China, children with critical RDs will received enhanced medical services, experience improved prognoses, and reintegrate into social life.

Atypical fetal brain development in fetuses with non-syndromic isolated musculoskeletal birth defects (niMSBDs)

Non-syndromic, isolated musculoskeletal birth defects (niMSBDs) are among the leading causes of pediatric hospitalization. However, little is known about brain development in niMSBDs. Our study aimed to characterize prenatal brain development in fetuses with niMSBDs and identify altered brain regions compared to controls. We retrospectively analyzed in vivo structural T2-weighted MRIs of 99 fetuses (48 controls and 51 niMSBDs cases). For each group (19-31 and >31 gestational weeks (GW)), we conducted repeated-measures regression analysis with relative regional volume (% brain hemisphere) as a dependent variable (adjusted for age, side, and interactions). Between 19 and 31GW, fetuses with niMSBDs had a significantly (P < 0.001) smaller relative volume of the intermediate zone (-22.9 ± 3.2%) and cerebellum (-16.1 ± 3.5%,) and a larger relative volume of proliferative zones (38.3 ± 7.2%), the ganglionic eminence (34.8 ± 7.3%), and the ventricles (35.8 ± 8.0%). Between 32 and 37 GW, compared to the controls, niMSBDs showed significantly smaller volumes of central regions (-9.1 ± 2.1%) and larger volumes of the cortical plate. Our results suggest there is altered brain development in fetuses with niMSBDs compared to controls (13.1 ± 4.2%). Further basic and translational neuroscience research is needed to better visualize these differences and to characterize the altered development in fetuses with specific niMSBDs.

Rare variants in CAPN2 increase risk for isolated hypoplastic left heart syndrome

Hypoplastic left heart syndrome (HLHS) is a severe congenital heart defect (CHD) characterized by hypoplasia of the left ventricle and aorta along with stenosis or atresia of the aortic and mitral valves. HLHS represents only ∼4%-8% of all CHDs but accounts for ∼25% of deaths. HLHS is an isolated defect (i.e., iHLHS) in 70% of families, the vast majority of which are simplex. Despite intense investigation, the genetic basis of iHLHS remains largely unknown. We performed exome sequencing on 331 families with iHLHS aggregated from four independent cohorts. A Mendelian-model-based analysis demonstrated that iHLHS was not due to single, large-effect alleles in genes previously reported to underlie iHLHS or CHD in >90% of families in this cohort. Gene-based association testing identified increased risk for iHLHS associated with variation in CAPN2 (p = 1.8 × 10-5), encoding a protein involved in functional adhesion. Functional validation studies in a vertebrate animal model (Xenopus laevis) confirmed CAPN2 is essential for cardiac ventricle morphogenesis and that in vivo loss of calpain function causes hypoplastic ventricle phenotypes and suggest that human CAPN2707C>T and CAPN21112C>T variants, each found in multiple individuals with iHLHS, are hypomorphic alleles. Collectively, our findings show that iHLHS is typically not a Mendelian condition, demonstrate that CAPN2 variants increase risk of iHLHS, and identify a novel pathway involved in HLHS pathogenesis.

Trends in prenatal diagnosis of congenital anomalies in Western Australia between 1980 and 2020: A population-based study

BACKGROUND

Advances in screening and diagnostics have changed the way in which we identify and diagnose congenital anomalies.

OBJECTIVE

To examine changes in rates of prenatal diagnosis of congenital anomalies over time and by demographic characteristics.

METHODS

We undertook a population-based retrospective cohort study of all children born in Western Australia between 1980 and 2020 and diagnosed with a congenital anomaly. Age at diagnosis (prenatal, neonatal, infancy, early childhood or childhood) prevalence (all-type and type-specific), and prevalence ratios (PR) were calculated. We fit joinpoint regression models to describe the average annual percentage change (APC) in prenatal diagnosis over time, and log-binomial regression models to estimate the association between prenatal diagnosis and demographic characteristics.

RESULTS

Prenatal diagnosis prevalence between the first (1980-1989: 28.3 per 10,000 births) and last (2005-2014: 156.1 per 10,000 births) decades of the study increased 5.5-fold (95% confidence interval [CI] 5.0, 5.9). Substantial increases were observed for cardiovascular (PR 10.7, 95% CI 8.0, 14.6), urogenital (PR 10.5, 95% CI: 8.7, 12.6) and chromosomal anomalies (PR 7.0, 95% CI 5.9, 8.3). Prenatal diagnosis was positively associated with the birth year (adjusted risk ratio [RR] 1.04, 95% CI 1.03, 1.04), advanced maternal age (RR 1.14, 95% CI 1.11, 1.18), multiple anomalies (RR 2.86, 95% CI 2.77, 2.96) and major anomalies (RR 3.75, 95% CI 3.36, 4.19), and inversely associated with remoteness (RR 0.89, 95% CI: 0.83, 0.95) and Aboriginality (RR 0.90, 95% CI 0.83, 0.97).

CONCLUSIONS

Increases in prenatal diagnosis of congenital anomalies were observed in Western Australia from 1980 to 2020, reflecting advances in screening. Prenatal diagnosis was less common in remote regions and in Aboriginal children, strengthening calls for increased provision of antenatal care services for these populations.

Using an experiment among clinical experts to determine the cost and clinical impact of rapid whole exome sequencing in acute pediatric settings

Objective

Evaluate the cost and clinical impacts of rapid whole-exome sequencing (rWES) for managing pediatric patients with unknown etiologies of critical illnesses through an expert elicitation experiment.

Method

Physicians in the intervention group (n = 10) could order rWES to complete three real-world case studies, while physicians in the control group (n = 8) could not. Costs and health outcomes between and within groups were compared.

Results

The cost incurred in the intervention group was consistently higher than the control by 60,000-70,000 THB. Fewer other investigation costs were incurred when rWES could provide a diagnosis. Less cost was incurred when an rWES that could lead to a change in management was ordered earlier. Diagnostic accuracy and the quality of non-pharmaceutical interventions were superior when rWES was available.

Conclusion

In acute pediatric settings, rWES offered clinical benefits at the average cost of 60,000-70,000 THB. Whether this test is cost-effective warrants further investigations. Several challenges, including cost and ethical concerns for assessing high-cost technology for rare diseases in resource-limited settings, were potentially overcome by our study design using expert elicitation methods.

Frequency-based rare diagnoses as a novel and accessible approach for studying rare diseases in large datasets: a cross-sectional study

BACKGROUND

Up to 8% of the general population have a rare disease, however, for lack of ICD-10 codes for many rare diseases, this population cannot be generically identified in large medical datasets. We aimed to explore frequency-based rare diagnoses (FB-RDx) as a novel method exploring rare diseases by comparing characteristics and outcomes of inpatient populations with FB-RDx to those with rare diseases based on a previously published reference list.

METHODS

Retrospective, cross-sectional, nationwide, multicenter study including 830,114 adult inpatients. We used the national inpatient cohort dataset of the year 2018 provided by the Swiss Federal Statistical Office, which routinely collects data from all inpatients treated in any Swiss hospital. Exposure: FB-RDx, according to 10% of inpatients with the least frequent diagnoses (i.e.1.decile) vs. those with more frequent diagnoses (deciles 2-10). Results were compared to patients having 1 of 628 ICD-10 coded rare diseases.

PRIMARY OUTCOME

In-hospital death.

SECONDARY OUTCOMES

30-day readmission, admission to intensive care unit (ICU), length of stay, and ICU length of stay. Multivariable regression analyzed associations of FB-RDx and rare diseases with these outcomes.

RESULTS

464,968 (56%) of patients were female, median age was 59 years (IQR: 40-74). Compared with patients in deciles 2-10, patients in the 1. were at increased risk of in-hospital death (OR 1.44; 95% CI: 1.38, 1.50), 30-day readmission (OR 1.29; 95% CI 1.25, 1.34), ICU admission (OR 1.50; 95% CI 1.46, 1.54), increased length of stay (Exp(B) 1.03; 95% CI 1.03, 1.04) and ICU length of stay (1.15; 95% CI 1.12, 1.18). ICD-10 based rare diseases groups showed similar results: in-hospital death (OR 1.82; 95% CI 1.75, 1.89), 30-day readmission (OR 1.37; 95% CI 1.32, 1.42), ICU admission (OR 1.40; 95% CI 1.36, 1.44) and increased length of stay (OR 1.07; 95% CI 1.07, 1.08) and ICU length of stay (OR 1.19; 95% CI 1.16, 1.22).

CONCLUSION(S)

This study suggests that FB-RDx may not only act as a surrogate for rare diseases but may also help to identify patients with rare disease more comprehensively. FB-RDx associate with in-hospital death, 30-day readmission, intensive care unit admission, and increased length of stay and intensive care unit length of stay, as has been reported for rare diseases.

A holistic approach to maximise diagnostic output in trio exome sequencing

Introduction

Rare genetic diseases are a major cause for severe illness in children. Whole exome sequencing (WES) is a powerful tool for identifying genetic causes of rare diseases. For a better and faster assessment of the vast number of variants that are identified in the index patient in WES, parental sequencing can be applied ("trio WES").

Methods

We assessed the diagnostic rate of routine trio WES including analysis of copy number variants in 224 pediatric patients during an evaluation period of three years.

Results

Trio WES provided a diagnosis in 67 (30%) of all 224 analysed children. The turnaround time of trio WES analysis has been reduced significantly from 41 days in 2019 to 23 days in 2021. Copy number variants could be identified to be causative in 10 cases (4.5%), underlying the importance of copy number variant analysis. Variants in three genes which were previously not associated with a clinical condition (GAD1, TMEM222 and ZNFX1) were identified using the matching tool GeneMatcher and were part of the first description of a new syndrome.

Discussion

Trio WES has proven to have a high diagnostic yield and to shorten the process of identifying the correct diagnosis in paediatric patients. Re-evaluation of all 224 trio WES 1-3 years after initial analysis did not establish new diagnoses. Initiating (trio) WES as a first-tier diagnostics including copy number variant detection should be considered as early as possible, especially for children treated in ICU, if a monogenetic disease is suspected.

A Retrospective Analysis of Clinically Focused Exome Sequencing Results of 372 Infants with Suspected Monogenic Disorders in China

Objective

The context was designed to optimize the diagnostic utility of clinically focused exome sequencing (CFES) and shorten the diagnostic odyssey among pediatric patients suspected of monogenic disorders (MDs).

Methods

Here, we retrospectively analyzed the clinical notes of 372 patients from different areas in the Jiangxi province that were referred for a diagnostic CFES and analysis from June 2018 to March 2022 with symptoms suggestive of MDs. In our study, preliminary tests using the proband-only clinical exome sequencing as a cost-effective first-tier diagnostic test for pediatric patients with unidentified MDs, supplemented by family segregation studies for targeted variants when indicated.

Results

Probands with confirmed diagnostic (CD) or likely diagnostic (LD) genetic influences accounted for 12% of all cases, whereas those with an uncertain diagnosis accounted for 48%. We also found that systemic primary carnitine deficiency (CDSP) (SLC22A5 gene) and phenylketonuria (PAH gene) were relatively more prevalent, and these patients with CDSP had the most frequent c.1400C > G variant (p.S467C) and c.51C > G variant (p. F17L) in this study. In addition, statistical analysis revealed that the estimates of diagnostic yields varied across certain phenotypic features of patients, and patients with specific phenotypic traits tended to benefit more from CFES.

Conclusion

The CFES may be a first-line genetic test for diagnosing young children with suspected genetic conditions, as it validates the identification of molecular genetics alterations and facilitates comprehensive medical management. Moreover, we found that infants exhibiting metabolism/homeostasis abnormalities, craniofacial /otolaryngology/ ophthalmologic abnormalities, and/or the integument were significantly more likely to receive a genetic diagnosis via CFES than infants without such features. However, due to the current study's low diagnostic yield and inherent limitations, high-quality clinical studies with larger sample sizes are still needed to provide more likely results and confirm our findings.

The incorporation of next-generation sequencing into pediatric care

Genetic condition is one of the major etiologies causing morbidity and mortality in infants and children. More and more etiologies can be solved using next-generation sequencing (NGS) as it develops. Currently, whole-exome sequencing (WES) and whole-genome sequencing (WGS) have been highly integrated into clinical practice. The average diagnostic yield of WES/WGS in pediatric patients with genetic condition was around 40% (range: 21%-80%), with acceptable turnaround time and cost. The higher diagnostic yield categories are deafness, ophthalmic, neurological, skeletal conditions, and inborn error of metabolism. Positive results provide benefit with those for actionable diseases, next pregnancy planning, and family members. For those in critical condition, with the emergence of sequencing technology and bioinformatics analysis tools, provisional diagnosis can be made as short as 13.5 h using ultrarapid WGS. We believe this powerful tool has changed pediatric daily practice.

The DevTox Germ Layer Reporter Platform: An Assay Adaptation of the Human Pluripotent Stem Cell Test

Environmental chemical exposures are a contributing factor to birth defects affecting infant morbidity and mortality. The USA EPA is committed to developing new approach methods (NAMs) to detect chemical risks to susceptible populations, including pregnant women. NAM-based coverage for cellular mechanisms associated with early human development could enhance identification of potential developmental toxicants (DevTox) for new and existing data-poor chemicals. The human pluripotent stem cell test (hPST) is an in vitro test method for rapidly identifying potential human developmental toxicants that employs directed differentiation of embryonic stem cells to measure reductions in SOX17 biomarker expression and nuclear localization. The objective of this study was to expand on the hPST principles to develop a model platform (DevTox GLR) that utilizes the transgenic RUES2-GLR cell line expressing fluorescent reporter fusion protein biomarkers for SOX17 (endoderm marker), BRA (mesoderm marker), and SOX2 (ectoderm and pluripotency marker). Initial assay adaption to definitive endoderm (DevTox GLR-Endo) was performed to emulate the hPST SOX17 endpoint and enable comparative evaluation of concordant chemical effects. Assay duration was reduced to two days and screening throughput scaled to 384-well format for enhanced speed and efficiency. Assay performance for 66 chemicals derived from reference and training set data resulted in a balanced accuracy of 72% (79% sensitivity and 65% specificity). The DevTox GLR-Endo assay demonstrates successful adaptation of the hPST concept with increased throughput, shorter assay duration, and minimal endpoint processing. The DevTox GLR model platform expands the in vitro NAM toolbox to rapidly identify potential developmental hazards and mechanistically characterize toxicant effects on pathways and processes associated with early human development.

Healthcare Burden of Rare Diseases: A Population-Based Study in Tuscany (Italy)

Patients with rare diseases (RDs) need tailored, continuous, and multidisciplinary hospital care. This retrospective cohort study aimed to analyse the healthcare burden of RD patients using a multi-database approach, by linking the data of the Rare Diseases Registry of Tuscany with the regional hospital discharge database. The study population included 21,354 patients diagnosed with a RD between 1 January 2000 and 31 December 2017. The healthcare burden was evaluated for all the RDs during 2009–2018 period. The hospitalisation rate (per 1000) decreased over the years, ranging from 606.9 in 2009 (95% CI: 589.2–625.0) to 443.0 in 2018 (95% CI: 433.2–453.0). A decrease in the average length of stay (LOS) was observed in the earlier years, followed by an increase up to a steady trend (8.3 days in 2018). The patients with RDs of metabolism and the genitourinary system showed the highest hospitalisation rate (903.3 and 644.0 per 1000, respectively). The patients with rare immune system disorders and diseases of the skin and subcutaneous tissue showed the highest LOS (9.7 and 9.5 days, respectively). The methodological approach presented in this population-based study makes it possible to estimate the healthcare burden of RDs, which is crucial in the decision-making and planning aimed at improving patient care.

Gene-Interaction-Sensitive enrichment analysis in congenital heart disease

Background

Gene set enrichment analysis (GSEA) uses gene-level univariate associations to identify gene set-phenotype associations for hypothesis generation and interpretation. We propose that GSEA can be adapted to incorporate SNP and gene-level interactions. To this end, gene scores are derived by Relief-based feature importance algorithms that efficiently detect both univariate and interaction effects (MultiSURF) or exclusively interaction effects (MultiSURF*). We compare these interaction-sensitive GSEA approaches to traditional χ² rankings in simulated genome-wide array data, and in a target and replication cohort of congenital heart disease patients with conotruncal defects (CTDs).

Results

In the simulation study and for both CTD datasets, both Relief-based approaches to GSEA captured more relevant and significant gene ontology terms compared to the univariate GSEA. Key terms and themes of interest include cell adhesion, migration, and signaling. A leading edge analysis highlighted semaphorins and their receptors, the Slit-Robo pathway, and other genes with roles in the secondary heart field and outflow tract development.

Conclusions

Our results indicate that interaction-sensitive approaches to enrichment analysis can improve upon traditional univariate GSEA. This approach replicated univariate findings and identified additional and more robust support for the role of the secondary heart field and cardiac neural crest cell migration in the development of CTDs.

Supplementary Information

The online version contains supplementary material available at (10.1186/s13040-022-00287-w).

Risk factors for hospitalisation in Welsh infants with a congenital anomaly

OBJECTIVES

To investigate risk factor associated with hospitalisation of infants with a congenital anomaly in Wales, UK.

DESIGN

A population-based cohort study.

SETTING

Data from the Welsh Congenital Anomaly Register and Information Service linked to the Patient Episode Database for Wales and livebirths and deaths from the Office for National Statistics.

PATIENTS

All livebirths between 1999 and 2015 with a diagnosis of a congenital anomaly, which was defined as a structural, metabolic, endocrine or genetic defect, as well as rare diseases of hereditary origin.

MAIN OUTCOME MEASURES

Adjusted OR (aOR) associated with 1 or 2+ hospital admissions in infancy versus no admissions were estimated for sociodemographic, maternal and infant factors using multinomial logistic regression for the subgroups of all, isolated, multiple and cardiovascular anomalies.

RESULTS

25 523 infants affected by congenital anomalies experienced a total of 50 705 admissions in infancy. Risk factors for ≥2 admissions were younger maternal age ≤24 years (aOR: 1.17; 95% CI 1.06 to 1.30), maternal smoking (aOR: 1.20; 1.10 to 1.31), preterm birth (aOR: 2.52; 2.25 to 2.83) and moderately severe congenital heart defects (aOR: 6.25; 4.47 to 8.74). Girls had an overall decreased risk of 2+ admissions (aOR: 0.84; 0.78 to 0.91). Preterm birth was a significant risk factor for admissions in all anomaly subgroups but the effect of the other characteristics varied according to anomaly subgroup.

CONCLUSIONS

Over two-thirds of infants with an anomaly are admitted to hospital during infancy. Our findings identified sociodemographic and clinical characteristics contributing to an increased risk of hospitalisation of infants with congenital anomalies.

Congenital anomalies and genetic disorders in neonates and infants: a single-center observational cohort study

Neonates with genetic disorders or congenital anomalies (CA) contribute considerably to morbidity and mortality in neonatal intensive care units (NICUs). The objective of this study is to study the prevalence of genetic disorders in an academic level IV NICU. We retrospective collected and analyzed both clinical and genetic data of all 1444 infants admitted to the NICU of the Radboudumc (October 2013 to October 2015). Data were collected until infants reached at least 2 years of age. A total of 13% (194/1444) of the patients were genetically tested, and 32% (461/1444) had a CA. A total of 37% (72/194) had a laboratory-confirmed genetic diagnosis. In 53%, the diagnosis was made post-neonatally (median age = 209 days) using assays including exome sequencing. Exactly 63% (291/461) of the patients with CA, however, never received genetic testing, despite being clinically similar those who did.Conclusions: Genetic disorders were suspected in 13% of the cohort, but only confirmed in 5%. Most received their genetic diagnosis in the post-neonatal period. Extrapolation of the diagnostic yield suggests that up to 6% of our cohort may have remained genetically undiagnosed. Our data show the need to improve genetic care in the NICU for more inclusive, earlier, and faster genetic diagnosis to enable tailored management. What is Known: • Genetic disorders are suspected in many neonates but only genetically confirmed in a minority. • The presence of a genetic disorder can be easily missed and will often lead to a diagnostic odyssey requiring extensive evaluations, both clinically and genetically. What is New: • Different aspects of the clinical features and uptake of genetic test in a NICU cohort. • The need to improve genetic care in the NICU for more inclusive, earlier, and faster genetic diagnosis to enable tailored management.

Zebrafish models of fetal alcohol spectrum disorders

Fetal alcohol spectrum disorder (FASD) describes a wide range of structural deficits and cognitive impairments. FASD impacts up to 5% of children born in the United States each year, making ethanol one of the most common teratogens. Due to limitations and ethical concerns, studies in humans are limited in their ability to study FASD. Animal models have proven critical in identifying and characterizing the mechanisms underlying FASD. In this review, we will focus on the attributes of zebrafish that make it a strong model in which to study ethanol-induced developmental defects. Zebrafish have several attributes that make it an ideal model in which to study FASD. Zebrafish produced large numbers of externally fertilized, translucent embryos. With a high degree of genetic amenability, zebrafish are at the forefront of identifying and characterizing the gene-ethanol interactions that underlie FASD. Work from multiple labs has shown that embryonic ethanol exposures result in defects in craniofacial, cardiac, ocular, and neural development. In addition to structural defects, ethanol-induced cognitive and behavioral impairments have been studied in zebrafish. Building upon these studies, work has identified ethanol-sensitive loci that underlie the developmental defects. However, analyses show there is still much to be learned of these gene-ethanol interactions. The zebrafish is ideally suited to expand our understanding of gene-ethanol interactions and their impact on FASD. Because of the conservation of gene function between zebrafish and humans, these studies will directly translate to studies of candidate genes in human populations and allow for better diagnosis and treatment of FASD.

Exome first approach to reduce diagnostic costs and time - retrospective analysis of 111 individuals with rare neurodevelopmental disorders

This single-center study aims to determine the time, diagnostic procedure, and cost saving potential of early exome sequencing in a cohort of 111 individuals with genetically confirmed neurodevelopmental disorders. We retrospectively collected data regarding diagnostic time points and procedures from the individuals' medical histories and developed criteria for classifying diagnostic procedures in terms of requirement, followed by a cost allocation. All genetic variants were re-evaluated according to ACMG recommendations and considering the individuals' phenotype. Individuals who developed first symptoms of their underlying genetic disorder when Next Generation Sequencing (NGS) diagnostics were already available received a diagnosis significantly faster than individuals with first symptoms before this cutoff. The largest amount of potentially dispensable diagnostics was found in genetic, metabolic, and cranial magnetic resonance imaging examinations. Out of 407 performed genetic examinations, 296 (72.7%) were classified as potentially dispensable. The same applied to 36 (27.9%) of 129 cranial magnetic resonance imaging and 111 (31.8%) of 349 metabolic examinations. Dispensable genetic examinations accounted 302,947.07€ (90.2%) of the total 335,837.49€ in potentially savable costs in this cohort. The remaining 32,890.42€ (9.8%) are related to non-required metabolic and cranial magnetic resonance imaging diagnostics. On average, the total potentially savable costs in our study amount to €3,025.56 per individual. Cost savings by first tier exome sequencing lie primarily in genetic, metabolic, and cMRI testing in this German cohort, underscoring the utility of performing exome sequencing at the beginning of the diagnostic pathway and the potential for saving diagnostic costs and time.

Strategies to Uplift Novel Mendelian Gene Discovery for Improved Clinical Outcomes

Rare genetic disorders, while individually rare, are collectively common. They represent some of the most severe disorders affecting patients worldwide with significant morbidity and mortality. Over the last decade, advances in genomic methods have significantly uplifted diagnostic rates for patients and facilitated novel and targeted therapies. However, many patients with rare genetic disorders still remain undiagnosed as the genetic etiology of only a proportion of Mendelian conditions has been discovered to date. This article explores existing strategies to identify novel Mendelian genes and how these discoveries impact clinical care and therapeutics. We discuss the importance of data sharing, phenotype-driven approaches, patient-led approaches, utilization of large-scale genomic sequencing projects, constraint-based methods, integration of multi-omics data, and gene-to-patient methods. We further consider the health economic advantages of novel gene discovery and speculate on potential future methods for improved clinical outcomes.

Xenopus as a platform for discovery of genes relevant to human disease

Congenital birth defects result from an abnormal development of an embryo and have detrimental effects on children's health. Specifically, congenital heart malformations are a leading cause of death among pediatric patients and often require surgical interventions within the first year of life. Increased efforts to navigate the human genome provide an opportunity to discover multiple candidate genes in patients suffering from birth defects. These efforts, however, fail to provide an explanation regarding the mechanisms of disease pathogenesis and emphasize the need for an efficient platform to screen candidate genes. Xenopus is a rapid, cost effective, high-throughput vertebrate organism to model the mechanisms behind human disease. This review provides numerous examples describing the successful use of Xenopus to investigate the contribution of patient mutations to complex phenotypes including congenital heart disease and heterotaxy. Moreover, we describe a variety of unique methods that allow us to rapidly recapitulate patients' phenotypes in frogs: gene knockout and knockdown strategies, the use of fate maps for targeted manipulations, and novel imaging modalities. The combination of patient genomics data and the functional studies in Xenopus will provide necessary answers to the patients suffering from birth defects. Furthermore, it will allow for the development of better diagnostic methods to ensure early detection and intervention. Finally, with better understanding of disease pathogenesis, new treatment methods can be tailored specifically to address patient's phenotype and genotype.

Preferences and values for rapid genomic testing in critically ill infants and children: a discrete choice experiment

Healthcare systems are increasingly considering widespread implementation of rapid genomic testing of critically ill children, but evidence on the value of the benefits generated is lacking. This information is key for an optimal implementation into healthcare systems. A discrete choice experiment survey was designed to elicit preferences and values for rapid genomic testing in critically ill children. The survey was administered to members of the Australian public and families with lived experience of rapid genomic testing. A Bayesian D-efficient explicit partial profiles design was used, and data were analysed using a panel error component mixed logit model. Preference heterogeneity was explored using a latent class model and fractional logistic regressions. The public (n = 522) and families with lived experiences (n = 25) demonstrated strong preferences for higher diagnostic yield and clinical utility, faster result turnaround times, and lower cost. Society on average would be willing to pay an additional AU$9510 (US$6657) for rapid (2 weeks results turnaround time) and AU$11,000 (US$7700) for ultra-rapid genomic testing (2 days turnaround time) relative to standard diagnostic care. Corresponding estimates among those with lived experiences were AU$10,225 (US$7158) and AU$11,500 (US$8050), respectively. Our work provides further evidence that rapid genomic testing for critically ill children with rare conditions generates substantial utility. The findings can be used to inform cost-benefit analyses as part of broader healthcare system implementation.

Effect of Genetic Testing on Diagnosing Gastrointestinal Pediatric Patients with Previously Undiagnosed Diseases

Purpose

Four consanguineous Jordanian families with affected members of unknown gastrointestinal related diseases were recruited to assess the utility and efficiency of whole exome sequencing (WES) in reaching the definitive diagnosis.

Patients and Methods

Members from four consanguineous Jordanian families were recruited in this study. Laboratory and imaging tests were used for initial diagnosis, followed by performing WES to test all affected members for the detection of causative variants. Sanger sequencing was used for validation.

Results

We had a 100% success rate identifying each case presented in this study.

Conclusion

This is the first study applying a WES testing approach in the diagnosis of pediatric diseases in Jordan. Our results strongly suggest the need to implement WES as an evident diagnostic tool in the clinical setting, as it will subsequently allow for proper disease management and genetic counseling.

Genetics and pediatric hospital admissions, 1985 to 2017

PURPOSE

To determine the prevalence and sociodemographic and hospitalization history of genetic conditions in a sample of inpatients in a pediatric hospital in 2017, and to compare results with unpublished studies from 1985, 1995, and 2007.

METHODS

Two weeks of admissions were classified according to a pre-existing categorization, based on genetic etiology, encompassing chromosomal and monogenic conditions, multifactorial (MF) conditions, and no known genetic cause.

RESULTS

In 2017, 299 (16%) patients had chromosomal or monogenic conditions, 6-7% more than 2007 and 1995, but similar to 1985. Autosomal dominant (AD) conditions increased from <2% previously to 6% in 2017 (p < 0.001). MF conditions comprised the majority throughout, increasing from 45% to 54%. Age at admission was highest in autosomal recessive (AR) and X-linked categories in 1995, 2007, and 2017, reflected in their high number of previous admissions, while the AD, MF, and nongenetic categories were the youngest with similar lengths of stay and previous admissions.

CONCLUSION

Conditions with a genetic contribution account for over half of pediatric inpatients. Since 1985, there have been many changes in age at admission and length of stay, but it is the increasing prevalence of AR, AD, and MF conditions that is important when considering future service provision.

Diagnosis of genetic diseases in seriously ill children by rapid whole-genome sequencing and automated phenotyping and interpretation

By informing timely targeted treatments, rapid whole-genome sequencing can improve the outcomes of seriously ill children with genetic diseases, particularly infants in neonatal and pediatric intensive care units (ICUs). The need for highly qualified professionals to decipher results, however, precludes widespread implementation. We describe a platform for population-scale, provisional diagnosis of genetic diseases with automated phenotyping and interpretation. Genome sequencing was expedited by bead-based genome library preparation directly from blood samples and sequencing of paired 100-nt reads in 15.5 hours. Clinical natural language processing (CNLP) automatically extracted children's deep phenomes from electronic health records with 80% precision and 93% recall. In 101 children with 105 genetic diseases, a mean of 4.3 CNLP-extracted phenotypic features matched the expected phenotypic features of those diseases, compared with a match of 0.9 phenotypic features used in manual interpretation. We automated provisional diagnosis by combining the ranking of the similarity of a patient's CNLP phenome with respect to the expected phenotypic features of all genetic diseases, together with the ranking of the pathogenicity of all of the patient's genomic variants. Automated, retrospective diagnoses concurred well with expert manual interpretation (97% recall and 99% precision in 95 children with 97 genetic diseases). Prospectively, our platform correctly diagnosed three of seven seriously ill ICU infants (100% precision and recall) with a mean time saving of 22:19 hours. In each case, the diagnosis affected treatment. Genome sequencing with automated phenotyping and interpretation in a median of 20:10 hours may increase adoption in ICUs and, thereby, timely implementation of precise treatments.

The Financial Impact of Genetic Diseases in a Pediatric Accountable Care Organization

Background: Previous studies revealed patients with genetic disease have more frequent and longer hospitalizations and therefore higher healthcare costs. To understand the financial impact of genetic disease on a pediatric accountable care organization (ACO), we analyzed medical claims from 2014 provided by Partners for Kids, an ACO in partnership with Nationwide Children's Hospital (NCH; Columbus, OH, USA). Methods: Study population included insurance claims from 258,399 children. We assigned patients to four different categories (1-A, 1-B, 2, & 3) based on the strength of genetic basis of disease. Results: We identified 22.7% of patients as category 1A or 1B- having a disease with a "strong genetic basis" (e.g., single gene diseases, chromosomal abnormalities). Total ACO paid claims in 2014 were $379M, of which $161M (42.5%) was attributed to category 1 patients. Furthermore, we identified 23.3% of patients as category 2- having a disease with a suspected genetic component or predisposition (e.g., asthma, type 1 diabetes)- whom accounted for an additional 28.6% of 2014 costs. Category 1 patients were more likely to experience at least one hospitalization compared to category 3 patients- those without genetic disease [odds ratio [OR] = 4.12; 95% confidence interval [CI] = 3.86-4.39; p < 0.0001]. Overall, category 1 patients experienced nearly five times the number of inpatient (IP) admissions and twice the number of outpatient (OP) visits compared to category 3 patients (p < 0.0001). Conclusion: Nearly half (42.5%) of healthcare paid claims cost in 2014 for this study population were accounted for by patients with single-gene diseases or chromosomal abnormalities. These findings precede and support a need for an ACO to plan for effective healthcare strategies and capitation models for children with genetic disease.

Impacts of genomics on the health and social costs of intellectual disability

BACKGROUND

This study provides an integrated assessment of the economic and social impacts of genomic sequencing for the detection of monogenic disorders resulting in intellectual disability (ID).

METHODS

Multiple knowledge bases were cross-referenced and analysed to compile a reference list of monogenic disorders associated with ID. Multiple literature searches were used to quantify the health and social costs for the care of people with ID. Health and social expenditures and the current cost of whole-exome sequencing and whole-genome sequencing were quantified in relation to the more common causes of ID and their impact on lifespan.

RESULTS

On average, individuals with ID incur annual costs in terms of health costs, disability support, lost income and other social costs of US$172 000, accumulating to many millions of dollars over a lifetime.

CONCLUSION

The diagnosis of monogenic disorders through genomic testing provides the opportunity to improve the diagnosis and management, and to reduce the costs of ID through informed reproductive decisions, reductions in unproductive diagnostic tests and increasingly targeted therapies.

Healthcare trajectory of children with rare bone disease attending pediatric emergency departments

Background

Children with rare bone diseases (RBDs), whether medically complex or not, raise multiple issues in emergency situations. The healthcare burden of children with RBD in emergency structures remains unknown. The objective of this study was to describe the place of the pediatric emergency department (PED) in the healthcare of children with RBD.

Methods

We performed a retrospective single-center cohort study at a French university hospital. We included all children under the age of 18 years with RBD who visited the PED in 2017. By cross-checking data from the hospital clinical data warehouse, we were able to trace the healthcare trajectories of the patients. The main outcome of interest was the incidence (IR) of a second healthcare visit (HCV) within 30 days of the index visit to the PED. The secondary outcomes were the IR of planned and unplanned second HCVs and the proportion of patients classified as having chronic medically complex (CMC) disease at the PED visit.

Results

The 141 visits to the PED were followed by 84 s HCVs, giving an IR of 0.60 [95% CI: 0.48–0.74]. These second HCVs were planned in 60 cases (IR = 0.43 [95% CI: 0.33–0.55]) and unplanned in 24 (IR = 0.17 [95% CI: 0.11–0.25]). Patients with CMC diseases accounted for 59 index visits (42%) and 43 s HCVs (51%). Multivariate analysis including CMC status as an independent variable, with adjustment for age, yielded an incidence rate ratio (IRR) of second HCVs of 1.51 [95% CI: 0.98–2.32]. The IRR of planned second HCVs was 1.20 [95% CI: 0.76–1.90] and that of unplanned second HCVs was 2.81 [95% CI: 1.20–6.58].

Conclusion

An index PED visit is often associated with further HCVs in patients with RBD. The IRR of unplanned second HCVs was high, highlighting the major burden of HCVs for patients with chronic and severe disease.

Prospective, phenotype-driven selection of critically ill neonates for rapid exome sequencing is associated with high diagnostic yield

PURPOSE

To investigate the impact of rapid-turnaround exome sequencing in critically ill neonates using phenotype-based subject selection criteria.

METHODS

Intensive care unit babies aged <6 months with hypotonia, seizures, a complex metabolic phenotype, and/or multiple congenital malformations were prospectively enrolled for rapid (<7 day) trio-based exome sequencing. Genomic variants relevant to the presenting phenotype were returned to the medical team.

RESULTS

A genetic diagnosis was attained in 29 of 50 (58%) sequenced cases. Twenty-seven (54%) patients received a molecular diagnosis involving known disease genes; two additional cases (4%) were solved with pathogenic variants found in novel disease genes. In 24 of the solved cases, diagnosis had impact on patient management and/or family members. Management changes included shift to palliative care, medication changes, involvement of additional specialties, and the consideration of new experimental therapies.

CONCLUSION

Phenotype-based patient selection is effective at identifying critically ill neonates with a high likelihood of receiving a molecular diagnosis via rapid-turnaround exome sequencing, leading to faster and more accurate diagnoses, reducing unnecessary testing and procedures, and informing medical care.

Animal models of gene-alcohol interactions

Most birth defects arise from complex interactions between multiple genetic and environmental factors. However, our current understanding of how these interactions and their contributions affect birth defects remains incomplete. Human studies are limited in their ability to identify the fundamental causes of birth defects due to ethical and practical limitations. Animal models provide a great number of resources not available to human studies and they have been critical in advancing our understanding of birth defects and the complex interactions that underlie them. In this review, we discuss the use of animal models in the context of gene-environment interactions that underlie birth defects. We focus on alcohol which is the most common environmental factor associated with birth defects. Prenatal alcohol exposure leads to a wide range of cognitive impairments and structural deficits broadly termed fetal alcohol spectrum disorders (FASD). We discuss the broad impact of prenatal alcohol exposure on the developing embryo and elaborate on the current state of gene-alcohol interactions. Additionally, we discuss how animal models have informed our understanding of the genetics of FASD. Ultimately, these topics will provide insight into the use of animal models in understanding gene-environment interactions and their subsequent impact on birth defects.

Targeted gene panel sequencing for the rapid diagnosis of acutely ill infants

Background

Exome/genome sequencing (ES/GS) have been recently used in neonatal and pediatric/cardiac intensive care units (NICU and PICU/CICU) to diagnose and care for acutely ill infants, but the effectiveness of targeted gene panels for these purposes remains unknown.

Methods

RapSeq, a newly developed panel targeting 4,503 disease‐causing genes, was employed on selected patients in our NICU/PICU/CICU. Twenty trios were sequenced from October 2015 to March 2017. We assessed diagnostic yield, turnaround times, and clinical consequences.

Results

A diagnosis was made in 10/20 neonates (50%); eight had de novo variants (ASXL1, CHD, FBN1, KMT2D, FANCB, FLNA, PAX3), one was a compound heterozygote for CHAT, and one had a maternally inherited GNAS variant. Preliminary reports were generated by 9.6 days (mean); final reports after Sanger sequencing at 16.3 days (mean). In all positive infants, the diagnosis changed management. In a case with congenital myasthenia, diagnosis and treatment occurred at 17 days versus 7 months in a historical control.

Conclusions

This study shows that a gene panel that includes the majority of known disease‐causing genes can rapidly identify a diagnosis in a large number of tested infants. Due to simpler deployment and interpretation and lower costs, this approach might represent an alternative to ES/GS in the NICU/PICU/CICU.

The disproportionate cost of operation and congenital anomalies in infancy

BACKGROUND

Congenital anomalies are the leading cause of infant death and pediatric hospitalization, but existing estimates of the associated costs of health care are either cross-sectional surveys or economic projections. We sought to determine the percent of total hospital health care expenditures attributable to major anomalies requiring surgery within the first year of life.

METHODS

Utilizing comprehensive California statewide data from 2008 to 2012, cohorts of infants undergoing major surgery, with birth defects and with surgical anomalies, were constructed alongside a referent group of newborns with no anomalies or operations. Cost-to-charge and physician fee ratios were used to estimate hospital and professional costs, respectively. For each cohort, costs were broken down according to admission, birth episode, and first year of life, with additional stratifications by birth weight, gestational age, and organ system.

RESULTS

In total, 68,126 of 2,205,070 infants (3.1%) underwent major surgery (n = 32,614) or had a diagnosis of a severe congenital anomaly (n = 57,793). These accounted for $7.7 billion of the $18.9 billion (40.7%) of the total health care costs/expenditures of the first-year-of-life hospitalizations, $7.0 billion (48.6%) of the costs for infants with comparatively long birth episodes, and $5.2 billion (54.7%) of the total neonatal intensive care unit admission costs. Infants with surgical anomalies (n = 21,264) totaled $4.1 billion (21.7%) at $80,872 per infant. Cardiovascular and gastrointestinal diseases accounted for most admission costs secondary to major surgery or congenital anomalies.

CONCLUSION

In a population-based cohort of infant births compared with other critically ill neonates, surgical congenital anomalies are disproportionately costly within the United States health care system. The care of these infants, half of whom are covered by Medi-Cal or Medicaid, stands as a particular focus in an age of reform of health care payments.

The burden of rare diseases

The subject of rare disease numbers is rife with misconceptions, not just in websites and other layman's literature, but also in the medical literature. Various websites mention numbers that are not validated by any solid data, while in turn the medical literature cites the aforementioned websites as sources, thus perpetuating a number of myths about rare diseases and their burden. We review the existing literature on rare disease numbers, in an attempt to demystify the subject. Specifically, we summarize data pertaining to: (a) known number and cumulative prevalence of rare diseases; (b) rare disease-associated mortality; (c) rare disease-associated morbidity, including numbers on health care services related to rare diseases; and (d) orphan drug numbers.

Estimating the burden and economic impact of pediatric genetic disease

PURPOSE

To identify the economic impact of pediatric patients with clinical indications of genetic disease (GD) on the US health-care system.

METHODS

Using the 2012 Kids' Inpatient Database, we identified pediatric inpatient discharges with International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) codes linked to genetic disease, including well-established genetic disorders, neurological diseases, birth defects, and other physiological or functional abnormalities with a genetic basis. Cohort characteristics and health-care utilization measures were analyzed. Discharges with a GD-associated primary diagnosis were used to estimate the minimum burden; discharges with GD-associated primary or secondary codes established the maximum burden.

RESULTS

Of 5.85 million weighted discharges, 2.6-14% included GD-associated ICD-9-CM codes. For these discharges, mean total costs were $16,000-77,000 higher (P < 0.0001) in neonates and $12,000-17,000 higher (P < 0.0001) in pediatric patients compared with background, corresponding to significantly higher total charges and lengths of stay. Aggregate total charges for suspected GD accounted for $14 to $57 billion (11-46%) of the "national bill" for pediatric patients in 2012.

CONCLUSION

Pediatric inpatients with diagnostic codes linked to genetic disease have a significant and disproportionate impact on resources and costs in the US health-care system.

Views from the clinic: Healthcare provider perspectives on whole genome sequencing in paediatrics

Whole genome sequencing (WGS) is a transformative technology which promises improved diagnostic rates compared to conventional genetic testing strategies and tailored approaches to patient care. Due to the practical and ethical complexities associated with using WGS, particularly in the paediatric context, input from a broad spectrum of healthcare providers can guide implementation strategies. We recruited healthcare providers from the largest paediatric academic health science centre in Canada and conducted semi-structured qualitative interviews, exploring experiences with and perceptions of the opportunities and challenges associated with WGS. Interview transcripts were coded and analyzed thematically. Interviews were completed with 14 genetics professionals (geneticists and genetic counsellors) and 15 non-genetics professionals (physician sub-specialists and nurses). Genetics professionals ordered genetic tests more often and reported greater confidence on pre- and post-test genetic counselling compared to non-genetics professionals. Most healthcare providers endorsed WGS when a more specific test was either not available or not likely to yield a diagnosis. While genetics professionals raised concerns regarding the time demands associated with reviewing WGS variants, non-genetics professionals reflected concerns about knowledge and training. Providers' position on reporting secondary variants to parents drew upon but was not limited to the concept of best interests. Taken together, understanding practical and principled matters of WGS from healthcare providers' perspectives can guide ongoing efforts to implement WGS in paediatrics.

Population-based surveillance of congenital heart defects among adolescents and adults: surveillance methodology

BACKGROUND

Improved treatment of congenital heart defects (CHDs) has increased survival of persons with CHDs; however, no U.S. population-based systems exist to assess prevalence, healthcare utilization, or longer-term outcomes among adolescents and adults with CHDs.

METHODS

Novel approaches identified individuals aged 11-64 years who received healthcare with ICD-9-CM codes for CHDs at three sites: Emory University in Atlanta, Georgia (EU), Massachusetts Department of Public Health (MA), New York State Department of Health (NY) between January 1, 2008 (2009 for MA) and December 31, 2010. Case-finding sources included outpatient clinics; Medicaid and other claims data; and hospital inpatient, outpatient, and emergency visit data. Supplemental information came from state vital records (EU, MA), and birth defects registries (EU, NY). Demographics and diagnostic and procedural codes were linked, de-duplicated, and shared in a de-identified dataset. Cases were categorized into one of five mutually exclusive CHD severity groups; non-cardiac comorbidity codes were grouped into broad categories.

RESULTS

73,112 individuals with CHD codes in healthcare encounters were identified. Primary data source type varied: clinics (EU, NY for adolescents), claims (MA), hospital (NY for adults). There was a high rate of missing data for some variables and data varied in format and quality. Some diagnostic codes had poor specificity for CHD ascertainment.

CONCLUSIONS

To our knowledge, this is the first population-based, multi-site CHD surveillance among adolescents and adults in the U.S. Identification of people living with CHDs through healthcare encounters using multiple data sources was feasible, though data quality varied and linkage/de-duplication was labor-intensive.

Impact of next generation sequencing on our understanding of CAKUT

Congenital abnormalities of the kidney and urinary tract (CAKUT) form the leading cause of pediatric end-stage renal disease. Knowledge on the molecular mechanisms that underlie CAKUT leads to the improvement of DNA diagnostics and counseling regarding prognosis and recurrence risk estimation for CAKUT patients and their relatives. Implementation of next generation sequencing in research and diagnostic settings has led to the identification of the molecular basis of many developmental diseases. In this review, we summarize the efforts on next generation sequencing in CAKUT research and we discuss how next generation sequencing added to our understanding of CAKUT genetics. Although next generation sequencing has certainly proven to be a game changer in the field of disease gene identification and novel CAKUT-causing gene variants have been identified, most CAKUT cases still remain unsolved. Occurring with genetic and phenotypic heterogeneity along with incomplete penetrance, the identification of CAKUT etiology poses many challenges. We see great potential for combined -omics approaches that include next generation sequencing in the identification of CAKUT-specific biomarkers, which is necessary to optimize the care for CAKUT patients.

Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases

Genetic diseases are leading causes of childhood mortality. Whole-genome sequencing (WGS) and whole-exome sequencing (WES) are relatively new methods for diagnosing genetic diseases, whereas chromosomal microarray (CMA) is well established. Here we compared the diagnostic utility (rate of causative, pathogenic, or likely pathogenic genotypes in known disease genes) and clinical utility (proportion in whom medical or surgical management was changed by diagnosis) of WGS, WES, and CMA in children with suspected genetic diseases by systematic review of the literature (January 2011–August 2017) and meta-analysis, following MOOSE/PRISMA guidelines. In 37 studies, comprising 20,068 children, diagnostic utility of WGS (0.41, 95% CI 0.34–0.48, I² = 44%) and WES (0.36, 95% CI 0.33–0.40, I² = 83%) were qualitatively greater than CMA (0.10, 95% CI 0.08–0.12, I² = 81%). Among studies published in 2017, the diagnostic utility of WGS was significantly greater than CMA (P < 0.0001, I² = 13% and I² = 40%, respectively). Among studies featuring within-cohort comparisons, the diagnostic utility of WES was significantly greater than CMA (P < 0.001, I² = 36%). The diagnostic utility of WGS and WES were not significantly different. In studies featuring within-cohort comparisons of WGS/WES, the likelihood of diagnosis was significantly greater for trios than singletons (odds ratio 2.04, 95% CI 1.62–2.56, I² = 12%; P < 0.0001). Diagnostic utility of WGS/WES with hospital-based interpretation (0.42, 95% CI 0.38–0.45, I² = 48%) was qualitatively higher than that of reference laboratories (0.29, 95% CI 0.27–0.31, I² = 49%); this difference was significant among studies published in 2017 (P < .0001, I² = 22% and I² = 26%, respectively). The clinical utility of WGS (0.27, 95% CI 0.17–0.40, I² = 54%) and WES (0.17, 95% CI 0.12–0.24, I² = 76%) were higher than CMA (0.06, 95% CI 0.05–0.07, I² = 42%); this difference was significant for WGS vs CMA (P < 0.0001). In conclusion, in children with suspected genetic diseases, the diagnostic and clinical utility of WGS/WES were greater than CMA. Subgroups with higher WGS/WES diagnostic utility were trios and those receiving hospital-based interpretation. WGS/WES should be considered a first-line genomic test for children with suspected genetic diseases.

Children with suspected genetic disease are more likely to receive a diagnosis when gene sequencing technologies are employed. At present, a microarray test for short pieces of missing or extra chromosomes (chromosomal microarray, CMA) is the recommended test for diagnosing genetic disease in children. The recent use of whole-genome sequencing (WGS) and whole-exome sequencing (WES) for diagnosing genetic disease prompted Stephen Kingsmore at Rady Children’s Institute for Genomic Medicine in San Diego, California, USA, and colleagues to examine the effectiveness of these methods compared with CMA. Analyses of studies comprising over 20,000 children showed that using WGS and WES increased the likelihood of diagnosis and led to a change in inpatient management to prevent or ameliorate adverse health outcomes. The authors advocate the use of WGS or WES as a first-line genomic test for genetic disease in children.

Flow Cytometry to Evaluate Potential Developmental Toxicants in the Embryonic Stem Cell

Embryonic stem cells (ESC) are widely used due to their unlimited capacity of differentiation into different cell lineages, which makes ESC a viable choice as a toxicology test model. Toxicological analysis using embryonic stem cells (ESC) has become an important tool in toxicology procedures. Regarding toxicological analysis methods, flow cytometry (FC) is one technique designed to detect and evaluate cells in suspension, for example, ESC suspension, thus making possible to study different biological, physical, and/or chemical characteristics of cells. Thus, FC can be very useful for cell toxicology and tumorigenic analyses.

Introducing medical genetics services in Ethiopia using the MiGene Family History App

PURPOSE

Almost all low-income countries and many middle-income countries lack the capacity to deliver medical genetics services. We developed the MiGene Family History App (MFHA), which assists doctors with family history collection and population-level epidemiologic analysis. The MFHA was studied at St. Paul's Hospital in Addis Ababa, Ethiopia.

METHODS

A needs assessment was used to assess Ethiopian physicians' experience with genetics services. The MFHA then collected patient data over a 6-month period.

RESULTS

The majority of doctors provide genetics services, with only 16% reporting their genetics knowledge is sufficient. A total of 1699 patients from the pediatric ward (n = 367), neonatal intensive care unit (NICU) (n = 477), and antenatal clinic (n = 855) were collected using the MFHA with a 4% incidence of a MFHA-screened condition present. The incidence was 11.7% in the pediatric ward, 3% in the NICU, and 0.5% in the antenatal clinic. Heart malformations (5.5% of patients) and trisomy 21 (4.4% of patients) were the most common conditions in the pediatric ward.

CONCLUSION

Medical genetics services are needed in Ethiopia. As other countries increase their genetics capacity, the MFHA can provide fundamental genetics services and collect necessary epidemiologic data.

Genomic approaches to the assessment of human spina bifida risk

Structural birth defects are a leading cause of mortality and morbidity in children world-wide, affecting as much as 6% of all live births. Among these conditions, neural tube defects (NTDs), including spina bifida and anencephaly, arise from a combination of complex gene and environment interactions that are as yet poorly understood within human populations. Rapid advances in massively parallel DNA sequencing and bioinformatics allow for analyses of the entire genome beyond the 2% of the genomic sequence covering protein coding regions. Efforts to collect and analyze these large datasets hold promise for illuminating gene network variations and eventually epigenetic events that increase individual risk for failure to close the neural tube. In this review, we discuss current challenges for DNA genome sequence analysis of NTD affected populations, and compare experience in the field with other complex genetic disorders for which large datasets are accumulating. The ultimate goal of this research is to find strategies for optimizing conditions that promote healthy birth outcomes for individual couples. Birth Defects Research 109:120-128, 2017. © 2016 Wiley Periodicals, Inc.

Genome-wide sequencing technologies: A primer for paediatricians

Genetic testing has been a routine part of paediatic medicine for decades. Over time, the number of genetic tests available for children presenting with features thought to be explained by an underlying genetic aetiology has expanded considerably. Genome-wide sequencing approaches (e.g., whole-exome sequencing, whole-genome sequencing) are now emerging as the most comprehensive approaches to genetic diagnosis that we have seen to date; multiple serial tests that were once required for a child under diagnostic investigation can now be accomplished in a single assay. Moreover, the performance of this single assay appears to be superior to the sum of its parts. Despite this promise, technical, ethical and access-related complexities require considerable attention prior to the implementation of these tools in mainstream paediatrics. To ready paediatricians for the eventual transition to genome-based diagnostics, herein we review both the elements and delivery considerations of this emerging technology.

Genetic disorders and mortality in infancy and early childhood: delayed diagnoses and missed opportunities

PURPOSE

Infants admitted to a level IV neonatal intensive care unit (NICU) who do not survive early childhood are a population that is probably enriched for rare genetic disease; we therefore characterized their genetic diagnostic evaluation.

METHODS

This is a retrospective analysis of infants admitted to our NICU between 1 January 2011 and 31 December 2015 who were deceased at the time of records review, with age at death less than 5 years.

RESULTS

A total of 2,670 infants were admitted; 170 later died. One hundred six of 170 (62%) had an evaluation for a genetic or metabolic disorder. Forty-seven of 170 (28%) had laboratory-confirmed genetic diagnoses, although 14/47 (30%) diagnoses were made postmortem. Infants evaluated for a genetic disorder spent more time in the NICU (median 13.5 vs. 5.0 days; p = 0.003), were older at death (median 92.0 vs. 17.5 days; p < 0.001), and had similarly high rates of redirection of care (86% vs. 79%; p = 0.28).

CONCLUSION

Genetic disorders were suspected in many infants but found in a minority. Approximately one-third of diagnosed infants died before a laboratory-confirmed genetic diagnosis was made. This highlights the need to improve genetic diagnostic evaluation in the NICU, particularly to support end-of-life decision making.

Rapid whole-genome sequencing decreases infant morbidity and cost of hospitalization

Genetic disorders are a leading cause of morbidity and mortality in infants. Rapid whole-genome sequencing (rWGS) can diagnose genetic disorders in time to change acute medical or surgical management (clinical utility) and improve outcomes in acutely ill infants. We report a retrospective cohort study of acutely ill inpatient infants in a regional children's hospital from July 2016-March 2017. Forty-two families received rWGS for etiologic diagnosis of genetic disorders. Probands also received standard genetic testing as clinically indicated. Primary end-points were rate of diagnosis, clinical utility, and healthcare utilization. The latter was modelled in six infants by comparing actual utilization with matched historical controls and/or counterfactual utilization had rWGS been performed at different time points. The diagnostic sensitivity of rWGS was 43% (eighteen of 42 infants) and 10% (four of 42 infants) for standard genetic tests (P = .0005). The rate of clinical utility of rWGS (31%, thirteen of 42 infants) was significantly greater than for standard genetic tests (2%, one of 42; P = .0015). Eleven (26%) infants with diagnostic rWGS avoided morbidity, one had a 43% reduction in likelihood of mortality, and one started palliative care. In six of the eleven infants, the changes in management reduced inpatient cost by $800,000-$2,000,000. These findings replicate a prior study of the clinical utility of rWGS in acutely ill inpatient infants, and demonstrate improved outcomes and net healthcare savings. rWGS merits consideration as a first tier test in this setting.

Paediatric genomics: diagnosing rare disease in children

The majority of rare diseases affect children, most of whom have an underlying genetic cause for their condition. However, making a molecular diagnosis with current technologies and knowledge is often still a challenge. Paediatric genomics is an immature but rapidly evolving field that tackles this issue by incorporating next-generation sequencing technologies, especially whole-exome sequencing and whole-genome sequencing, into research and clinical workflows. This complex multidisciplinary approach, coupled with the increasing availability of population genetic variation data, has already resulted in an increased discovery rate of causative genes and in improved diagnosis of rare paediatric disease. Importantly, for affected families, a better understanding of the genetic basis of rare disease translates to more accurate prognosis, management, surveillance and genetic advice; stimulates research into new therapies; and enables provision of better support.

Research in Rare Disease: From Genomics to Proteomics

Jessica Lacoste from the Donnelly Centre at the University of Toronto was awarded best poster at the annual Society of Biomolecular Imaging and Informatics meeting held in San Diego, September 2017. Her work focuses on characterizing the protein localization of variants involved in rare disease. The current works and future directions of research in rare disease are summarized in the following overview.

Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases

Genetic diseases are leading causes of childhood mortality. Whole-genome sequencing (WGS) and whole-exome sequencing (WES) are relatively new methods for diagnosing genetic diseases, whereas chromosomal microarray (CMA) is well established. Here we compared the diagnostic utility (rate of causative, pathogenic, or likely pathogenic genotypes in known disease genes) and clinical utility (proportion in whom medical or surgical management was changed by diagnosis) of WGS, WES, and CMA in children with suspected genetic diseases by systematic review of the literature (January 2011-August 2017) and meta-analysis, following MOOSE/PRISMA guidelines. In 37 studies, comprising 20,068 children, diagnostic utility of WGS (0.41, 95% CI 0.34-0.48, I² = 44%) and WES (0.36, 95% CI 0.33-0.40, I² = 83%) were qualitatively greater than CMA (0.10, 95% CI 0.08-0.12, I² = 81%). Among studies published in 2017, the diagnostic utility of WGS was significantly greater than CMA (P < 0.0001, I² = 13% and I² = 40%, respectively). Among studies featuring within-cohort comparisons, the diagnostic utility of WES was significantly greater than CMA (P < 0.001, I² = 36%). The diagnostic utility of WGS and WES were not significantly different. In studies featuring within-cohort comparisons of WGS/WES, the likelihood of diagnosis was significantly greater for trios than singletons (odds ratio 2.04, 95% CI 1.62-2.56, I² = 12%; P < 0.0001). Diagnostic utility of WGS/WES with hospital-based interpretation (0.42, 95% CI 0.38-0.45, I² = 48%) was qualitatively higher than that of reference laboratories (0.29, 95% CI 0.27-0.31, I² = 49%); this difference was significant among studies published in 2017 (P < .0001, I² = 22% and I² = 26%, respectively). The clinical utility of WGS (0.27, 95% CI 0.17-0.40, I² = 54%) and WES (0.17, 95% CI 0.12-0.24, I² = 76%) were higher than CMA (0.06, 95% CI 0.05-0.07, I² = 42%); this difference was significant for WGS vs CMA (P < 0.0001). In conclusion, in children with suspected genetic diseases, the diagnostic and clinical utility of WGS/WES were greater than CMA. Subgroups with higher WGS/WES diagnostic utility were trios and those receiving hospital-based interpretation. WGS/WES should be considered a first-line genomic test for children with suspected genetic diseases.