ABSTRACT
There is mounting evidence of the value of clinical genome sequencing (cGS) in individuals with suspected rare genetic disease (RGD), but cGS performance and impact on clinical care in a diverse population drawn from both high-income countries (HICs) and low- and middle-income countries (LMICs) has not been investigated. The iHope program, a philanthropic cGS initiative, established a network of 24 clinical sites in eight countries through which it provided cGS to individuals with signs or symptoms of an RGD and constrained access to molecular testing. A total of 1,004 individuals (median age, 6.5 years; 53.5% male) with diverse ancestral backgrounds (51.8% non-majority European) were assessed from June 2016 to September 2021. The diagnostic yield of cGS was 41.4% (416/1,004), with individuals from LMIC sites 1.7 times more likely to receive a positive test result compared to HIC sites (LMIC 56.5% [195/345] vs. HIC 33.5% [221/659], OR 2.6, 95% CI 1.9-3.4, p < 0.0001). A change in diagnostic evaluation occurred in 76.9% (514/668) of individuals. Change of management, inclusive of specialty referrals, imaging and testing, therapeutic interventions, and palliative care, was reported in 41.4% (285/694) of individuals, which increased to 69.2% (480/694) when genetic counseling and avoidance of additional testing were also included. Individuals from LMIC sites were as likely as their HIC counterparts to experience a change in diagnostic evaluation (OR 6.1, 95% CI 1.1-∞, p = 0.05) and change of management (OR 0.9, 95% CI 0.5-1.3, p = 0.49). Increased access to genomic testing may support diagnostic equity and the reduction of global health care disparities.
Subject(s)
Genetic Testing , Rare Diseases , Whole Genome Sequencing , Humans , Male , Rare Diseases/genetics , Rare Diseases/diagnosis , Female , Child , Genetic Testing/methods , Child, Preschool , Adolescent , Adult , Infant , Genetic Diseases, Inborn/genetics , Genetic Diseases, Inborn/diagnosisABSTRACT
There is an increasing demand for supporting the adoption of rapid whole-genome sequencing (rWGS) by demonstrating its real-world value. We aimed to assess the cost-effectiveness of rWGS in critically ill pediatric patients with diseases of unknown cause. Data were collected prospectively of patients admitted to the Nicklaus Children's Hospital's intensive care units from March 2018 to September 2020, with rWGS (N = 65). Comparative data were collected in a matched retrospective cohort with standard diagnostic genetic testing. We determined total costs, diagnostic yield (DY), and incremental cost-effectiveness ratio (ICER) adjusted for selection bias and right censoring. Sensitivity analyses explored the robustness of ICER through bootstrapping. rWGS resulted in a diagnosis in 39.8% while standard testing in 13.5% (p = 0.026). rWGS resulted in a mean saving per person of $100,440 (SE = 26,497, p < 0.001) and a total of $6.53 M for 65 patients. rWGS in critically ill pediatric patients is cost-effective, cost-saving, shortens diagnostic odyssey, and triples the DY of traditional approaches.
Subject(s)
Critical Illness , Child , Cost-Benefit Analysis , Humans , Prospective Studies , Retrospective Studies , United States , Whole Genome Sequencing/methodsABSTRACT
Kaposi's sarcoma (KS), is an AIDS-associated neoplasm caused by the KS herpesvirus (KSHV/ HHV-8). KSHV-induced sarcomagenesis is the consequence of oncogenic viral gene expression as well as host genetic and epigenetic alterations. Although KSHV is found in all KS-lesions, the percentage of KSHV-infected (LANA+) spindle-cells of the lesion is variable, suggesting the existence of KS-spindle cells that have lost KSHV and proliferate autonomously or via paracrine mechanisms. A mouse model of KSHVBac36-driven tumorigenesis allowed us to induce KSHV-episome loss before and after tumor development. Although infected cells that lose the KSHV-episome prior to tumor formation lose their tumorigenicity, explanted tumor cells that lost the KSHV-episome remained tumorigenic. This pointed to the existence of virally-induced irreversible oncogenic alterations occurring during KSHV tumorigenesis supporting the possibility of hit and run viral-sarcomagenesis. RNA-sequencing and CpG-methylation analysis were performed on KSHV-positive and KSHV-negative tumors that developed following KSHV-episome loss from explanted tumor cells. When KSHV-positive cells form KSHV-driven tumors, along with viral-gene upregulation there is a tendency for hypo-methylation in genes from oncogenic and differentiation pathways. In contrast, KSHV-negative tumors formed after KSHV-episome loss, show a tendency towards gene hyper-methylation when compared to KSHV-positive tumors. Regarding occurrence of host-mutations, we found the same set of innate-immunity related mutations undetected in KSHV-infected cells but present in all KSHV-positive tumors occurring en exactly the same position, indicating that pre-existing host mutations that provide an in vivo growth advantage are clonally-selected and contribute to KSHV-tumorigenesis. In addition, KSHV-negative tumors display de novo mutations related to cell proliferation that, together with the PDGFRAD842V and other proposed mechanism, could be responsible for driving tumorigenesis in the absence of KSHV-episomes. KSHV-induced irreversible genetic and epigenetic oncogenic alterations support the possibility of "hit and run" KSHV-sarcomagenesis and point to the existence of selectable KSHV-induced host mutations that may impact AIDS-KS treatment.
Subject(s)
Cell Transformation, Viral , DNA Methylation , Gene Expression Regulation, Neoplastic , Gene Expression Regulation, Viral , Herpesvirus 8, Human , Neoplasms, Experimental , Plasmids , Sarcoma, Kaposi , Animals , Cell Line , Herpesvirus 8, Human/genetics , Herpesvirus 8, Human/metabolism , High-Throughput Nucleotide Sequencing , Mice , Neoplasms, Experimental/genetics , Neoplasms, Experimental/metabolism , Neoplasms, Experimental/pathology , Neoplasms, Experimental/virology , Plasmids/genetics , Plasmids/metabolism , Sarcoma, Kaposi/genetics , Sarcoma, Kaposi/metabolism , Sarcoma, Kaposi/pathology , Sarcoma, Kaposi/virologyABSTRACT
PURPOSE: This study aimed to estimate the cost-effectiveness of exome sequencing (ES) and genome sequencing (GS) for children. METHODS: We modeled costs, diagnoses, and quality-adjusted life years (QALYs) for diagnostic strategies for critically ill infants (aged <1 year) and children (aged <18 years) with suspected genetic conditions: (1) standard of care (SOC) testing, (2) ES, (3) GS, (4) SOC followed by ES, (5) SOC followed by GS, (6) ES followed by GS, and (7) SOC followed by ES followed by GS. We calculated the 10-year incremental cost per additional diagnosis, and lifetime incremental cost per QALY gained, from a health care perspective. RESULTS: First-line GS costs $15,048 per diagnosis vs SOC for infants and $27,349 per diagnosis for children. If GS is unavailable, ES represents the next most efficient option compared with SOC ($15,543 per diagnosis for infants and $28,822 per diagnosis for children). Other strategies provided the same or fewer diagnoses at a higher incremental cost per diagnosis. Lifetime results depend on the patient's assumed long-term prognosis after diagnosis. For infants, GS ranged from cost-saving (vs all alternatives) to $18,877 per QALY (vs SOC). For children, GS (vs SOC) ranged from $119,705 to $490,047 per QALY. CONCLUSION: First-line GS may be the most cost-effective strategy for diagnosing infants with suspected genetic conditions. For all children, GS may be cost-effective under certain assumptions. ES is nearly as efficient as GS and hence is a viable option when GS is unavailable.
Subject(s)
Exome , Child , Chromosome Mapping , Cost-Benefit Analysis , Exome/genetics , Humans , Infant , Quality-Adjusted Life Years , Exome Sequencing/methodsABSTRACT
The objective of this study was to determine whether treatment with human fibrinogen concentrate decreases the need for component blood therapy and blood loss in neonate and infant patients undergoing cardiopulmonary bypass. Pediatric patients (N = 30) undergoing elective cardiac surgery were randomized to receive human fibrinogen concentrate or placebo following cardiopulmonary bypass termination. The primary endpoint was the amount of cryoprecipitate administered. Secondary endpoints included estimated blood loss during the 24 h post-surgery; perioperative blood product transfusion; effects of fibrinogen infusion on global hemostasis, measured by laboratory testing and rotational thromboelastometry; and adverse events. No clinically significant differences were identified in baseline characteristics between groups. A significantly lower volume of cryoprecipitate was administered to the treatment group during the perioperative period [median (interquartile range) 0.0 (0.0-0.0) cc/kg vs 12.0 (8.2-14.3) cc/kg; P < 0.0001] versus placebo. No difference was observed between treatment groups in blood loss, laboratory coagulation tests, use of other blood components, or incidence of adverse events. FIBTEM amplitude of maximum clot firmness values was significantly higher among patients treated with human fibrinogen concentrate versus placebo (P ≤ 0.0001). No significant differences were observed in post-drug HEPTEM, INTEM, and EXTEM results. Human fibrinogen concentrate (70 mg/kg) administered after the termination of cardiopulmonary bypass reduced the need for transfusion with cryoprecipitate in a neonate and infant patient population.ClinicalTrials.gov identifier: NCT02822599.
Subject(s)
Cardiopulmonary Bypass , Fibrinogen , Blood Loss, Surgical/prevention & control , Cardiopulmonary Bypass/adverse effects , Cardiopulmonary Bypass/methods , Child , Fibrinogen/therapeutic use , Humans , Infant , Infant, Newborn , Pilot Projects , Prospective Studies , Thrombelastography/methodsABSTRACT
PURPOSE: To describe fundamental movement skill (FMS) practice patterns in the elementary physical education (PE) curriculum. METHODS: A cross-sectional survey was sent to PE teachers of grades 1 through 6. Sixty-eight responses were included for analysis. RESULTS: Only 38.2% of teachers taught all 12 FMS components. Compared with PE teachers for grades 4 to 6, a significantly higher proportion of PE teachers for grades 1 to 3 taught all 12 FMS and used direct instruction methods. For children falling behind, only 8.8% reported referring to an exercise program and no PE teacher sought a health care referral. A video abstract can be found in Supplemental Digital Content 1 (available at: http://links.lww.com/PPT/A342).
Subject(s)
Literacy , Physical Education and Training , Child , Cross-Sectional Studies , Exercise , Humans , Schools , Surveys and QuestionnairesABSTRACT
The advent of digital, electronic, and molecular technologies has allowed the study of complete genomes. Integrating this information into drug development has opened the door for pharmacogenomic (PGx) interventions in direct patient care. PGx allows clinicians to better identify drug of choice and optimize dosing regimens based on an individual's genetic characteristics. Integrating PGx into pediatric care is a priority for the Sanford Children's Genomic Medicine Consortium, a partnership of ten children's hospitals across the US committed to the innovation and advancement of genomics in pediatric care. In this white paper, we review the current state of PGx research and its clinical utility in pediatrics, a largely understudied population, and make recommendations for advancing cutting-edge practice in pediatrics.
Subject(s)
Genomics/trends , Pediatrics/trends , Pharmacogenetics/trends , Precision Medicine/trends , Child , HumansABSTRACT
Kaposi's sarcoma (KS) is an AIDS-defining cancer caused by the KS-associated herpesvirus (KSHV). Unanswered questions regarding KS are its cellular ontology and the conditions conducive to viral oncogenesis. We identify PDGFRA(+)/SCA-1(+) bone marrow-derived mesenchymal stem cells (Pα(+)S MSCs) as KS spindle-cell progenitors and found that pro-angiogenic environmental conditions typical of KS are critical for KSHV sarcomagenesis. This is because growth in KS-like conditions generates a de-repressed KSHV epigenome allowing oncogenic KSHV gene expression in infected Pα(+)S MSCs. Furthermore, these growth conditions allow KSHV-infected Pα(+)S MSCs to overcome KSHV-driven oncogene-induced senescence and cell cycle arrest via a PDGFRA-signaling mechanism; thus identifying PDGFRA not only as a phenotypic determinant for KS-progenitors but also as a critical enabler for viral oncogenesis.
Subject(s)
Mesenchymal Stem Cells/virology , Neovascularization, Pathologic/virology , Receptor, Platelet-Derived Growth Factor alpha/metabolism , Sarcoma, Kaposi/virology , Animals , Carcinogenesis/metabolism , Gene Expression/physiology , Herpesvirus 8, Human/genetics , Mesenchymal Stem Cells/cytology , Mice , Signal Transduction/physiologyABSTRACT
OBJECTIVE: The present study retrospectively ascertained whether liposomal bupivacaine (LB) injected subcutaneously after median sternotomy incisions in pediatric cardiac surgery patients is as efficacious as the ON-Q PainBuster pump (ON-Q) (Avonas Medical, Alpharetta, GA). DESIGN: Retrospective cohort comparison. SETTING: Pediatric hospital. PARTICIPANTS: Cardiac surgery patients who were treated with LB for elective cardiac surgery. INTERVENTIONS: Patients received 4 mg/kg of LB admixed with 0.25% bupivacaine and 0.9% normal saline. These patients were compared with an age- and procedure-matched control group of similar size treated with the ON-Q pump (continuous infusion 0.25% bupivacaine via subcutaneous catheter). Total analgesics used and route, other analgesics or sedatives, and pain scores (first 24 hours and cumulative) were tracked for 96 hours after surgery. MEASUREMENTS AND MAIN RESULTS: A total of 222 patients were equally divided between the two groups. Overall, the median (interquartile range) age was 6.5 (3.8-12.7) years. Unadjusted analysis suggested that patients in the LB group were administered a significantly higher dose of intravenous acetaminophen (77.4 v 60.0 mg/kg; p < 0.05). Extubation in the operating room was significantly higher in the LB patients (p < 0.05). Narcotic (morphine) administration was significantly higher in the ON-Q group (100.0% v 95.5%; p < 0.05). Although the median pain score within the first 24 hours was higher in LB patients (27.0 v 17.0; p < 0.05), there was a significantly greater difference observed in the Numeric Rating Scale area under the curve for the ON-Q group. CONCLUSIONS: LB is at least as effective as the ON-Q is for providing analgesia after median sternotomy incision in children.
Subject(s)
Cardiac Surgical Procedures , Sternotomy , Anesthetics, Local , Bupivacaine , Cardiac Surgical Procedures/adverse effects , Child , Humans , Pain, Postoperative/diagnosis , Pain, Postoperative/drug therapy , Pain, Postoperative/prevention & control , Retrospective Studies , Sternotomy/adverse effectsABSTRACT
INTRODUCTION: A major goal of the current personalized medicine era is to utilize pharmacogenetics (PGx) in order to influence how medications and therapies are prescribed by providers. However, disparities for prescribing medications between adults and children exist. Research has shown that children are not just small adults and there are different challenges for pediatric providers in regards to ordering and interpreting PGx tests. The goal of this study was to obtain an initial understanding of current pharmacogenetic testing by pediatric providers, as well as determine perceived barriers. METHODS: We distributed an online survey to pediatric providers at six different institutions across the U.S. RESULTS: Of the 252 respondents who completed the survey, 24 percent reported previously ordering PGx tests, however, over 90 percent of respondents reported they would feel more comfortable ordering and interpreting results with the assistance of a pharmacist, geneticist, genetic counselor or PGx expert. Additionally, participants identified specific barriers towards the utilization of PGx testing, as well as suggested solutions to overcome these barriers, including increasing provider education regarding testing, collaboration through a multidisciplinary team approach and established PGx programs. CONCLUSION: As the pharmacogenetic field continues to demonstrate clinical utility in the pediatric population, it will be important to continuously identify and address barriers that exist for providers to allow for more successful implementation of PGx in the pediatric setting, as well as enhance patient care.
Subject(s)
Pharmacogenetics , Physicians , Adult , Child , Humans , Pharmacists , Pharmacogenomic Testing , Precision MedicineABSTRACT
BACKGROUND: The Humpty Dumpty Falls Prevention Program was developed to address an unmet need to identify pediatric patients at risk of a fall event. PURPOSE: The aim of this study was to evaluate the performance of the Humpty Dumpty Fall Scale-Inpatient (HDFS) across a diverse, international pediatric population. In addition, the characteristics of patients who experienced a fall were analyzed. METHODS: A retrospective, cross-sectional design was used to assess fall risk across 16 hospitals and 2238 pediatric patients. Multiple and simple logistic regressions were performed to evaluate association of individual scale items and total score with falls during hospitalization. Reliability, sensitivity, and specificity of the HDFS were also assessed. RESULTS: Several of the HDFS items were significantly associated with the risk of falls in the pediatric population, but specificity of the tool is a concern to consider for future tool enhancement. CONCLUSIONS: Characteristics for further refinement of the HDFS were identified.
Subject(s)
Accidental Falls/prevention & control , Inpatients/statistics & numerical data , Internationality , Risk Assessment , Surveys and Questionnaires , Adolescent , Adult , Child , Child, Preschool , Cross-Sectional Studies , Female , Hospitalization , Humans , Infant , Infant, Newborn , Male , Reproducibility of Results , Retrospective Studies , Young AdultABSTRACT
Autism spectrum disorders (ASDs) represent a group of childhood neurodevelopmental and neuropsychiatric disorders characterized by deficits in verbal communication, impairment of social interaction, and restricted and repetitive patterns of interests and behaviour. To identify common genetic risk factors underlying ASDs, here we present the results of genome-wide association studies on a cohort of 780 families (3,101 subjects) with affected children, and a second cohort of 1,204 affected subjects and 6,491 control subjects, all of whom were of European ancestry. Six single nucleotide polymorphisms between cadherin 10 (CDH10) and cadherin 9 (CDH9)-two genes encoding neuronal cell-adhesion molecules-revealed strong association signals, with the most significant SNP being rs4307059 (P = 3.4 x 10(-8), odds ratio = 1.19). These signals were replicated in two independent cohorts, with combined P values ranging from 7.4 x 10(-8) to 2.1 x 10(-10). Our results implicate neuronal cell-adhesion molecules in the pathogenesis of ASDs, and represent, to our knowledge, the first demonstration of genome-wide significant association of common variants with susceptibility to ASDs.
Subject(s)
Autistic Disorder/genetics , Chromosomes, Human, Pair 5/genetics , Genetic Predisposition to Disease/genetics , Genetic Variation/genetics , Brain/metabolism , Cadherins/genetics , Case-Control Studies , Cell Adhesion/genetics , Cell Adhesion Molecules, Neuronal/genetics , Cohort Studies , Genetic Markers/genetics , Genome-Wide Association Study , Genotype , Humans , Polymorphism, Single Nucleotide/genetics , Reproducibility of ResultsABSTRACT
Autism spectrum disorders (ASDs) are highly heritable, yet relatively few associated genetic loci have been replicated. Copy number variations (CNVs) have been implicated in autism; however, the majority of loci contribute to <1% of the disease population. Therefore, independent studies are important to refine associated CNV regions and discover novel susceptibility genes. In this study, a genome-wide SNP array was utilized for CNV detection by two distinct algorithms in a European ancestry case-control data set. We identify a significantly higher burden in the number and size of deletions, and disrupting more genes in ASD cases. Moreover, 18 deletions larger than 1 Mb were detected exclusively in cases, implicating novel regions at 2q22.1, 3p26.3, 4q12 and 14q23. Case-specific CNVs provided further evidence for pathways previously implicated in ASDs, revealing new candidate genes within the GABAergic signaling and neural development pathways. These include DBI, an allosteric binder of GABA receptors, GABARAPL1, the GABA receptor-associated protein, and SLC6A11, a postsynaptic GABA transporter. We also identified CNVs in COBL, deletions of which cause defects in neuronal cytoskeleton morphogenesis in model vertebrates, and DNER, a neuron-specific Notch ligand required for cerebellar development. Moreover, we found evidence of genetic overlap between ASDs and other neurodevelopmental and neuropsychiatric diseases. These genes include glutamate receptors (GRID1, GRIK2 and GRIK4), synaptic regulators (NRXN3, SLC6A8 and SYN3), transcription factor (ZNF804A) and RNA-binding protein FMR1. Taken together, these CNVs may be a few of the missing pieces of ASD heritability and lead to discovering novel etiological mechanisms.
Subject(s)
Child Development Disorders, Pervasive/genetics , DNA Copy Number Variations , Adolescent , Algorithms , Case-Control Studies , Child , Child, Preschool , Female , Genetic Predisposition to Disease , Humans , Male , Polymorphism, Single Nucleotide , Receptors, GABA/genetics , Young AdultABSTRACT
BACKGROUND: Up to 20% of cancers worldwide are thought to be associated with microbial pathogens, including bacteria and viruses. The widely used methods of viral infection detection are usually limited to a few a priori suspected viruses in one cancer type. To our knowledge, there have not been many broad screening approaches to address this problem more comprehensively. METHODS: In this study, we performed a comprehensive screening for viruses in nine common cancers using a multistep computational approach. Tumor transcriptome and genome sequencing data were available from The Cancer Genome Atlas (TCGA). Nine hundred fifty eight primary tumors in nine common cancers with poor prognosis were screened against a non-redundant database of virus sequences. DNA sequences from normal matched tissue specimens were used as controls to test whether each virus is associated with tumors. RESULTS: We identified human papilloma virus type 18 (HPV-18) and four human herpes viruses (HHV) types 4, 5, 6B, and 8, also known as EBV, CMV, roseola virus, and KSHV, in colon, rectal, and stomach adenocarcinomas. In total, 59% of screened gastrointestinal adenocarcinomas (GIA) were positive for at least one virus: 26% for EBV, 21% for CMV, 7% for HHV-6B, and 20% for HPV-18. Over 20% of tumors were co-infected with multiple viruses. Two viruses (EBV and CMV) were statistically significantly associated with colorectal cancers when compared to the matched healthy tissues from the same individuals (p = 0.02 and 0.03, respectively). HPV-18 was not detected in DNA, and thus, no association testing was possible. Nevertheless, HPV-18 expression patterns suggest viral integration in the host genome, consistent with the potentially oncogenic nature of HPV-18 in colorectal adenocarcinomas. The estimated counts of viral copies were below one per cell for all identified viruses and approached the detection limit. CONCLUSIONS: Our comprehensive screening for viruses in multiple cancer types using next-generation sequencing data clearly demonstrates the presence of viral sequences in GIA. EBV, CMV, and HPV-18 are potentially causal for GIA, although their oncogenic role is yet to be established.
Subject(s)
DNA, Viral/isolation & purification , Gastrointestinal Neoplasms/diagnosis , Gastrointestinal Neoplasms/virology , High-Throughput Screening Assays , Coinfection/virology , Computational Biology , Cytomegalovirus/genetics , Cytomegalovirus/isolation & purification , DNA, Viral/genetics , Female , Herpesvirus 4, Human/genetics , Herpesvirus 4, Human/isolation & purification , Herpesvirus 8, Human/genetics , Herpesvirus 8, Human/isolation & purification , Human papillomavirus 18/genetics , Human papillomavirus 18/isolation & purification , Humans , Male , Sequence Analysis, DNA , Viral LoadABSTRACT
Objective: Multi-center implementation of rapid whole genome sequencing with assessment of the clinical utility of rapid whole genome sequencing (rWGS), including positive, negative and uncertain results, in admitted infants with a suspected genetic disease. Study design: rWGS tests were ordered at eight hospitals between November 2017 and April 2020. Investigators completed a survey of demographic data, Human Phenotype Ontology (HPO) terms, test results and impacts of results on clinical care. Results: A total of 188 patients, on general hospital floors and intensive care unit (ICU) settings, underwent rWGS testing. Racial and ethnic characteristics of the tested infants were broadly representative of births in the country at large. 35% of infants received a diagnostic result in a median of 6 days. The most common HPO terms for tested infants indicated an abnormality of the nervous system, followed by the cardiovascular system, the digestive system, the respiratory system and the head and neck. Providers indicated a major change in clinical management because of rWGS for 32% of infants tested overall and 70% of those with a diagnostic result. Also, 7% of infants with a negative rWGS result and 23% with a variant of unknown significance (VUS) had a major change in management due to testing. Conclusions: Our study demonstrates that the implementation of rWGS is feasible across diverse institutions, and provides additional evidence to support the clinical utility of rWGS in a demographically representative sample of admitted infants and includes assessment of the clinical impact of uncertain rWGS results in addition to both positive and negative results.
ABSTRACT
Objective: Long COVID, marked by persistent, recurring, or new symptoms post-COVID-19 infection, impacts children's well-being yet lacks a unified clinical definition. This study evaluates the performance of an empirically derived Long COVID case identification algorithm, or computable phenotype, with manual chart review in a pediatric sample. This approach aims to facilitate large-scale research efforts to understand this condition better. Methods: The algorithm, composed of diagnostic codes empirically associated with Long COVID, was applied to a cohort of pediatric patients with SARS-CoV-2 infection in the RECOVER PCORnet EHR database. The algorithm classified 31,781 patients with conclusive, probable, or possible Long COVID and 307,686 patients without evidence of Long COVID. A chart review was performed on a subset of patients (n=651) to determine the overlap between the two methods. Instances of discordance were reviewed to understand the reasons for differences. Results: The sample comprised 651 pediatric patients (339 females, M age = 10.10 years) across 16 hospital systems. Results showed moderate overlap between phenotype and chart review Long COVID identification (accuracy = 0.62, PPV = 0.49, NPV = 0.75); however, there were also numerous cases of disagreement. No notable differences were found when the analyses were stratified by age at infection or era of infection. Further examination of the discordant cases revealed that the most common cause of disagreement was the clinician reviewers' tendency to attribute Long COVID-like symptoms to prior medical conditions. The performance of the phenotype improved when prior medical conditions were considered (accuracy = 0.71, PPV = 0.65, NPV = 0.74). Conclusions: Although there was moderate overlap between the two methods, the discrepancies between the two sources are likely attributed to the lack of consensus on a Long COVID clinical definition. It is essential to consider the strengths and limitations of each method when developing Long COVID classification algorithms.
ABSTRACT
Nine out of 19 genes encoding GABAA receptor subunits have been linked to monogenic syndromes characterized by seizures and developmental disorders. Previously, we reported the de novo variant p.(Thr300Ile) in GABRA4 in a patient with epilepsy and neurodevelopmental abnormalities. However, no new cases have been reported since then. Through an international collaboration, we collected molecular and phenotype data of individuals carrying de novo variants in GABRA4. Patients and their parents were investigated either by exome or genome sequencing, followed by targeted Sanger sequencing in some cases. All variants within the transmembrane domain, including the previously reported p.(Thr300Ile) variant, were characterized in silico and analyzed by molecular dynamics (MD) simulation studies. We identified three novel de novo missense variants in GABRA4 (NM_000809.4): c.797 C > T, p.(Pro266Leu), c.899 C > A, p.(Thr300Asn), and c.634 G > A, p.(Val212Ile). The p.(Thr300Asn) variant impacts the same codon as the previously reported variant p.(Thr300Ile) and likely arose post-zygotically as evidenced by sequencing oral mucosal cells. Overlapping phenotypes among affected individuals included developmental delay (4/4), epileptiform EEG abnormalities (3/4), attention deficits (3/4), seizures (2/4), autistic features (2/4) and structural brain abnormalities (2/4). MD simulations of the three variants within the transmembrane domain of the receptor indicate that sub-microsecond scale dynamics differ between wild-type and mutated subunits. Taken together, our findings further corroborate an association between GABRA4 and a neurological phenotype including variable neurodevelopmental, behavioral and epileptic abnormalities.
Subject(s)
Developmental Disabilities , Epilepsy , Mutation, Missense , Phenotype , Receptors, GABA-A , Humans , Receptors, GABA-A/genetics , Male , Epilepsy/genetics , Epilepsy/pathology , Developmental Disabilities/genetics , Developmental Disabilities/pathology , Female , Child , Child, Preschool , AdolescentABSTRACT
Children with rare, relapsed or refractory cancers often face limited treatment options, and few predictive biomarkers are available that can enable personalized treatment recommendations. The implementation of functional precision medicine (FPM), which combines genomic profiling with drug sensitivity testing (DST) of patient-derived tumor cells, has potential to identify treatment options when standard-of-care is exhausted. The goal of this prospective observational study was to generate FPM data for pediatric patients with relapsed or refractory cancer. The primary objective was to determine the feasibility of returning FPM-based treatment recommendations in real time to the FPM tumor board (FPMTB) within a clinically actionable timeframe (<4 weeks). The secondary objective was to assess clinical outcomes from patients enrolled in the study. Twenty-five patients with relapsed or refractory solid and hematological cancers were enrolled; 21 patients underwent DST and 20 also completed genomic profiling. Median turnaround times for DST and genomics were within 10 days and 27 days, respectively. Treatment recommendations were made for 19 patients (76%), of whom 14 received therapeutic interventions. Six patients received subsequent FPM-guided treatments. Among these patients, five (83%) experienced a greater than 1.3-fold improvement in progression-free survival associated with their FPM-guided therapy relative to their previous therapy, and demonstrated a significant increase in progression-free survival and objective response rate compared to those of eight non-guided patients. The findings from our proof-of-principle study illustrate the potential for FPM to positively impact clinical care for pediatric and adolescent patients with relapsed or refractory cancers and warrant further validation in large prospective studies. ClinicalTrials.gov registration: NCT03860376 .