The case for early use of rapid whole-genome sequencing in management of critically ill infants: late diagnosis of Coffin-Siris syndrome in an infant with left congenital diaphragmatic hernia, congenital heart disease, and recurrent infections.

Congenital diaphragmatic hernia (CDH) results from incomplete formation of the diaphragm leading to herniation of abdominal organs into the thoracic cavity. CDH is associated with pulmonary hypoplasia, congenital heart disease, and pulmonary hypertension. Genetically, it is associated with aneuploidies, chromosomal copy-number variants, and single gene mutations. CDH is the most expensive noncardiac congenital defect. Management frequently requires implementation of extracorporeal membrane oxygenation (ECMO), which increases management expenditures 2.4-3.5-fold. The cost of management of CDH has been estimated to exceed $250 million per year. Despite in-hospital survival of 80%-90%, current management is imperfect, as a great proportion of surviving children have long-term functional deficits. We report the case of a premature infant prenatally diagnosed with CDH and congenital heart disease, who had a protracted and complicated course in the intensive care unit with multiple surgical interventions, including postcardiac surgery ECMO, gastrostomy tube placement with Nissen fundoplication, tracheostomy for respiratory failure, recurrent infections, and developmental delay. Rapid whole-genome sequencing (rWGS) identified a de novo, likely pathogenic, c.3096_ 3100delCAAAG (p.Lys1033Argfs*32) variant in ARID1B, providing a diagnosis of Coffin-Siris syndrome. Her parents elected palliative care and she died later that day

Biallelic mutations in valyl-tRNA synthetase gene VARS are associated with a progressive neurodevelopmental epileptic encephalopathy.

Aminoacyl-tRNA synthetases (ARSs) function to transfer amino acids to cognate tRNA molecules, which are required for protein translation. To date, biallelic mutations in 31 ARS genes are known to cause recessive, early-onset severe multi-organ diseases. VARS encodes the only known valine cytoplasmic-localized aminoacyl-tRNA synthetase. Here, we report seven patients from five unrelated families with five different biallelic missense variants in VARS. Subjects present with a range of global developmental delay, epileptic encephalopathy and primary or progressive microcephaly. Longitudinal assessment demonstrates progressive cortical atrophy and white matter volume loss. Variants map to the VARS tRNA binding domain and adjacent to the anticodon domain, and disrupt highly conserved residues. Patient primary cells show intact VARS protein but reduced enzymatic activity, suggesting partial loss of function. The implication of VARS in pediatric neurodegeneration broadens the spectrum of human diseases due to mutations in tRNA synthetase genes

Assessment of Antibody Titers after SARS-CoV-2 Vaccination in Bangladesh: A Single Centre Observational Study

The SARS-CoV-2 virus, which emerged in Wuhan, China in 2019, led to the COVID-19 pandemic, posing a global healthcare challenge. The primary pathology involves viral replication in the early disease stages. COVID-19 vaccines play a crucial role in reducing susceptibility to future infections. Evaluating antibody levels and longevity post-vaccination is essential to assess vaccine effectiveness. This study aims to quantify antibody levels among hospital employees to analyze the immune response to vaccination.Methods: A single-center study was conducted to measure antibody levels among hospital employees. Data were collected from medical records, including the number of days post-vaccination (first and second doses), age, and antibody titers. Antibody titers were analyzed using a commercial Anti-SARS-CoV-2 kit. The study also examined antibody responses in individuals who had spontaneous SARS-CoV-2 infections post-vaccination. Results: There was a positive correlation between age and antibody titer. In COVID-19-positive individuals, a positive correlation was found between antibody titer and the duration between the first and second vaccine doses. In COVID-negative individuals, a negative correlation was observed. Male antibody titers had a skewness of 3.2, while female titers had a skewness of 2.6. Individuals who did not receive both vaccine doses had mean antibody titre 880.74 Au/ml and to those who received both doses 5530.11 Au/ml. Conclusions: COVID-19-positive individuals showed a stronger immune response post-vaccination. Despite waning immunity over time, vaccination led to significantly higher antibody titers in adults, reinforcing the importance of full-dose COVID-19 vaccination

Postmortem whole-genome sequencing on a dried blood spot identifies a novel homozygous SUOX variant causing isolated sulfite oxidase deficiency.

Rapid whole-genome sequencing (rWGS) has shown that genetic diseases are a common cause of infant mortality in neonatal intensive care units. Dried blood spots collected for newborn screening allow investigation of causes of infant mortality that were not diagnosed during life. Here, we present a neonate who developed seizures and encephalopathy on the third day of life that was refractory to antiepileptic medications. The patient died on day of life 16 after progressive respiratory failure and sepsis. The parents had lost two prior children after similar presentations, neither of whom had a definitive diagnosis. Postmortem rWGS of a dried blood spot identified a pathogenic homozygous frameshift variant in the SUOX gene associated with isolated sulfite oxidase deficiency (c.1390_1391del, p.Leu464GlyfsTer10). This case highlights that early, accurate molecular diagnosis has the potential to influence prenatal counseling and guide management in rare, genetic disorders and has added importance in cases of a strong family history and risk factors such as consanguinity

UPLC-ESI/MSn metabolic profiling of Cedrela odorata L. and Toona ciliata M. Roem and in vitro investigation of their anti-diabetic activity supported with molecular docking studies

IntroductionThe genus Cedrela is one of the phytochemically rich genera of the family Meliaceae. In this study, two Cedrela species, namely, Cedrela odorata and Toona ciliata M. Roem (formerly Cedrela toona), were selected for in-depth phytochemical profiling with the aid of UPLC-ESI/MSn analysis followed by evaluation of their anti-diabetic potential through assessment of in vitro α-amylase and α-glucosidase inhibitory effects, alongside the molecular docking studies on these target enzymes.Materials and methodsUPLC-ESI/MSn technique was applied to tentatively identify the extracts. The anti-diabetic properties were assessed using BioVision α-amylase and α-glucosidase inhibitor screening kits. Further, the molecular docking studies utilized PyRx® and Discovery Studio software.Results and discussionThe UPLC-ESI/MSn analysis led to the identification and quantification of 55 metabolites with their fragmentation patterns for the first time for these two species. Flavonoids represented the main identified class, followed by phenylpropanoids, terpenes, tannins, and others. The two species showed potent enzyme inhibition, where C. odorata and C. toona significantly inhibited α-amylase (IC50 = 4.83 ± 0.01 and 3.50 ± 0.03 μg/mL) compared to pioglitazone (IC50 = 2.17 ± 0.23 μg/mL), while their α-glycosidase inhibitory properties were also potent with (IC50 = 7.17 ± 0.01 and 6.50 ± 0.69 μg/mL), respectively, compared to acarbose (IC50 = 4.83 ± 1.02 μg/mL). The enzyme inhibitory activities were further confirmed by in silico molecular docking of the main identified components with the respective binding sockets in both α-amylase and α-glycosidase enzymes.ConclusionThese promising results could pave the way for a novel discovery of natural phytoconstituents with potent anti-diabetic activity

Rapid Whole Genome Sequencing Has Clinical Utility in Children in the PICU.

OBJECTIVES:Genetic disorders are a leading contributor to mortality in the neonatal ICU and PICU in the United States. Although individually rare, there are over 6,200 single-gene diseases, which may preclude a genetic diagnosis prior to ICU admission. Rapid whole genome sequencing is an emerging method of diagnosing genetic conditions in time to affect ICU management of neonates; however, its clinical utility has yet to be adequately demonstrated in critically ill children. This study evaluates next-generation sequencing in pediatric critical care. DESIGN:Retrospective cohort study. SETTING:Single-center PICU in a tertiary children's hospital. PATIENTS:Children 4 months to 18 years admitted to the PICU who were nominated between July 2016 and May 2018. INTERVENTIONS:Rapid whole genome sequencing with targeted phenotype-driven analysis was performed on patients and their parents, when parental samples were available. MEASUREMENTS AND MAIN RESULTS:A molecular diagnosis was made by rapid whole genome sequencing in 17 of 38 children (45%). In four of the 17 patients (24%), the genetic diagnoses led to a change in management while in the PICU, including genome-informed changes in pharmacotherapy and transition to palliative care. Nine of the 17 diagnosed children (53%) had no dysmorphic features or developmental delay. Eighty-two percent of diagnoses affected the clinical management of the patient and/or family after PICU discharge, including avoidance of biopsy, administration of factor replacement, and surveillance for disorder-related sequelae. CONCLUSIONS:This study demonstrates a retrospective evaluation for undiagnosed genetic disease in the PICU and clinical utility of rapid whole genome sequencing in a portion of critically ill children. Further studies are needed to identify PICU patients who will benefit from rapid whole genome sequencing early in PICU admission when the underlying etiology is unclear

Project Baby Bear: Rapid precision care incorporating rWGS in 5 California children’s hospitals demonstrates improved clinical outcomes and reduced costs of care

Genetic disorders are a leading contributor to mortality in neonatal and pediatric intensive care units (ICUs). Rapid whole-genome sequencing (rWGS)-based rapid precision medicine (RPM) is an intervention that has demonstrated improved clinical outcomes and reduced costs of care. However, the feasibility of broad clinical deployment has not been established. The objective of this study was to implement RPM based on rWGS and evaluate the clinical and economic impact of this implementation as a first line diagnostic test in the California Medicaid (Medi-Cal) program. Project Baby Bear was a payor funded, prospective, real-world quality improvement project in the regional ICUs of five tertiary care children's hospitals. Participation was limited to acutely ill Medi-Cal beneficiaries who were admitted November 2018 to May 2020, were <1 year old and within one week of hospitalization, or had just developed an abnormal response to therapy. The whole cohort received RPM. There were two prespecified primary outcomes-changes in medical care reported by physicians and changes in the cost of care. The majority of infants were from underserved populations. Of 184 infants enrolled, 74 (40%) received a diagnosis by rWGS that explained their admission in a median time of 3 days. In 58 (32%) affected individuals, rWGS led to changes in medical care. Testing and precision medicine cost $1.7 million and led to$2.2-2.9 million cost savings. rWGS-based RPM had clinical utility and reduced net health care expenditures for infants in regional ICUs. rWGS should be considered early in ICU admission when the underlying etiology is unclear

An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases

While many genetic diseases have effective treatments, they frequently progress rapidly to severe morbidity or mortality if those treatments are not implemented immediately. Since front-line physicians frequently lack familiarity with these diseases, timely molecular diagnosis may not improve outcomes. Herein we describe Genome-to-Treatment, an automated, virtual system for genetic disease diagnosis and acute management guidance. Diagnosis is achieved in 13.5 h by expedited whole genome sequencing, with superior analytic performance for structural and copy number variants. An expert panel adjudicated the indications, contraindications, efficacy, and evidence-of-efficacy of 9911 drug, device, dietary, and surgical interventions for 563 severe, childhood, genetic diseases. The 421 (75%) diseases and 1527 (15%) effective interventions retained are integrated with 13 genetic disease information resources and appended to diagnostic reports ( https://gtrx.radygenomiclab.com ). This system provided correct diagnoses in four retrospectively and two prospectively tested infants. The Genome-to-Treatment system facilitates optimal outcomes in children with rapidly progressive genetic diseases

Maternal Genome-Wide DNA Methylation Patterns and Congenital Heart Defects

The majority of congenital heart defects (CHDs) are thought to result from the interaction between multiple genetic, epigenetic, environmental, and lifestyle factors. Epigenetic mechanisms are attractive targets in the study of complex diseases because they may be altered by environmental factors and dietary interventions. We conducted a population based, case-control study of genome-wide maternal DNA methylation to determine if alterations in gene-specific methylation were associated with CHDs. Using the Illumina Infinium Human Methylation27 BeadChip, we assessed maternal gene-specific methylation in over 27,000 CpG sites from DNA isolated from peripheral blood lymphocytes. Our study sample included 180 mothers with non-syndromic CHD-affected pregnancies (cases) and 187 mothers with unaffected pregnancies (controls). Using a multi-factorial statistical model, we observed differential methylation between cases and controls at multiple CpG sites, although no CpG site reached the most stringent level of genome-wide statistical significance. The majority of differentially methylated CpG sites were hypermethylated in cases and located within CpG islands. Gene Set Enrichment Analysis (GSEA) revealed that the genes of interest were enriched in multiple biological processes involved in fetal development. Associations with canonical pathways previously shown to be involved in fetal organogenesis were also observed. We present preliminary evidence that alterations in maternal DNA methylation may be associated with CHDs. Our results suggest that further studies involving maternal epigenetic patterns and CHDs are warranted. Multiple candidate processes and pathways for future study have been identified

Stitching Solidarity: Belonging as a Muslim in the United States

This thesis presents collaborative and participatory craft-making as catalysts for dialogue regarding the surging Islamophobia after events such as the tragedy on September 11th and the 2016 presidential election. Inspired by the South Asian tradition of kanthas, I created a series of quilts out of my mother’s saris. The imagery embroidered and sewn onto the kanthas was informed by interviews with 11 Muslim participants who live in the United States. Each embroidered segment was based on an image that the participant suggested, which symbolically represented their strained sense of belonging based on their religious or cultural association with Islam. Five kanthas were sewn together to form a large tent; hanging, they created an enclosed space which could be entered. The audience was invited to enter the space and stitch or draw their own notions of how a “sense of belonging” could potentially be identified.The combined processes of cooperative making, textile craft, participatory installation, and involved dialogue in Stitching Solidarity attempt to demonstrate how this participatory art practice can record a history of lived experience, build and define community, and contribute to healing