Implementation of Early Next-Generation Sequencing for Inborn Errors of Immunity:A Prospective Observational Cohort Study of Diagnostic Yield and Clinical Implications in Dutch Genome Diagnostic Centers

OBJECTIVE: Inborn errors of immunity (IEI) are a heterogeneous group of disorders, affecting different components of the immune system. Over 450 IEI related genes have been identified, with new genes continually being recognized. This makes the early application of next-generation sequencing (NGS) as a diagnostic method in the evaluation of IEI a promising development. We aimed to provide an overview of the diagnostic yield and time to diagnosis in a cohort of patients suspected of IEI and evaluated by an NGS based IEI panel early in the diagnostic trajectory in a multicenter setting in the Netherlands. STUDY DESIGN: We performed a prospective observational cohort study. We collected data of 165 patients with a clinical suspicion of IEI without prior NGS based panel evaluation that were referred for early NGS using a uniform IEI gene panel. The diagnostic yield was assessed in terms of definitive genetic diagnoses, inconclusive diagnoses and patients without abnormalities in the IEI gene panel. We also assessed time to diagnosis and clinical implications. RESULTS: For children, the median time from first consultation to diagnosis was 119 days versus 124 days for adult patients (U=2323; p=0.644). The median turn-around time (TAT) of genetic testing was 56 days in pediatric patients and 60 days in adult patients (U=1892; p=0.191). A definitive molecular diagnosis was made in 25/65 (24.6%) of pediatric patients and 9/100 (9%) of adults. Most diagnosed disorders were identified in the categories of immune dysregulation (n=10/25; 40%), antibody deficiencies (n=5/25; 20%), and phagocyte diseases (n=5/25; 20%). Inconclusive outcomes were found in 76/165 (46.1%) patients. Within the patient group with a genetic diagnosis, a change in disease management occurred in 76% of patients. CONCLUSION: In this cohort, the highest yields of NGS based evaluation for IEI early in the diagnostic trajectory were found in pediatric patients, and in the disease categories immune dysregulation and phagocyte diseases. In cases where a definitive diagnosis was made, this led to important disease management implications in a large majority of patients. More research is needed to establish a uniform diagnostic pathway for cases with inconclusive diagnoses, including variants of unknown significance

Upgrading of organic waste: production of the copolymer poly-3-hydroxybutyrate-co-valerate by Ralstonia eutrophus with organic waste as sole carbon source

Two types of fermented organic waste (trade and industry waste and fruit and vegetable waste) were successfully used as a sole carbon source to produce poly-3-hydroxybutyrate-co-valerate (PHBV) by Ralstonia eutrophus (formerly Alcaligenes eutrophus) via oxygen limitation. The production of PHBV could be optimized by optimizing the oxygen transfer through the fermentor. Thereby, a peak concentration of 1.1 g PHBV per liter cell suspension, 40 w% of cell dry weight, was obtained at an aeration rate of 0.24 mol O2/h·kg biomass. The yield of PHBV on the fatty acid concentration in the organic waste was 0.16 g polymer/g volatile organic matter. The process obtained, compares well with the commercial production process of PHBV based on glucose.

Genetic defects in PI3K delta affect B-cell differentiation and maturation leading to hypogammaglobulineamia and recurrent infections

Background: Mutations in PIK3CD and PIK3R1 cause activated PI3K-8 syndrome (APDS) by dysregulation of the PI3K-AKT pathway. Methods: We studied precursor and peripheral B-cell differentiation and apoptosis via flowcytometry. Furthermore, we performed AKT-phosphorylation assays and somatic hypermutations (SHM) and class switch recombination (CSR) analysis. Results: We identified 13 patients of whom 3 had new mutations in PIK3CD or PIK3R1. Patients had low total B cell numbers with increased frequencies of transitional B cells and plasmablasts, while the precursor B-cell compartment in bone marrow was relatively normal. Basal AKT phosphorylation was increased in lymphocytes from APDS patients and natural effector B cells where most affected. PI3K mutations resulted in altered SHM and CSR and increased apoptosis. Conclusions: The B-cell compartment in APDS patients is affected by the mutations in PI3K. There is reduced differentiation beyond the transitional stage, increased AKT phosphorylation and increased apoptosis. This B cell phenotype contributes to the clinical phenotype. (C) 2017 Published by Elsevier In