Whole genome sequencing reveals that genetic conditions are frequent in intensively ill children

Abstract Purpose: With growing evidence that rare single gene disorders present in the neonatal period, there is a need for rapid, systematic, and comprehensive genomic diagnoses in ICUs to assist acute and long‑term clinical decisions. This study aimed to identify genetic conditions in neonatal (NICU) and paediatric (PICU) intensive care populations. Methods: We performed trio whole genome sequence (WGS) analysis on a prospective cohort of families recruited in NICU and PICU at a single site in the UK. We developed a research pipeline in collaboration with the National Health Service to deliver validated pertinent pathogenic findings within 2–3 weeks of recruitment. Results: A total of 195 families had whole genome analysis performed (567 samples) and 21% received a molecular diagnosis for the underlying genetic condition in the child. The phenotypic description of the child was a poor pre‑ dictor of the gene identified in 90% of cases, arguing for gene agnostic testing in NICU/PICU. The diagnosis affected clinical management in more than 65% of cases (83% in neonates) including modification of treatments and care pathways and/or informing palliative care decisions. A 2–3 week turnaround was sufficient to impact most clinical decision‑making. Conclusions: The use of WGS in intensively ill children is acceptable and trio analysis facilitates diagnoses. A gene agnostic approach was effective in identifying an underlying genetic condition, with phenotypes and symptomatol‑ ogy being primarily used for data interpretation rather than gene selection. WGS analysis has the potential to be a first‑line diagnostic tool for a subset of intensively ill children. Keywords: Whole genome sequencing, Genetics, Genomics, Critically ill children, NICU, PICU<br/

Spinal muscular atrophy diagnosis and carrier screening from genome sequencing data

PurposeSpinal muscular atrophy (SMA), caused by loss of the SMN1 gene, is a leading cause of early childhood death. Due to the near identical sequences of SMN1 and SMN2, analysis of this region is challenging. Population-wide SMA screening to quantify the SMN1 copy number (CN) is recommended by the American College of Medical Genetics and Genomics.MethodsWe developed a method that accurately identifies the CN of SMN1 and SMN2 using genome sequencing (GS) data by analyzing read depth and eight informative reference genome differences between SMN1/2.ResultsWe characterized SMN1/2 in 12,747 genomes, identified 1568 samples with SMN1 gains or losses and 6615 samples with SMN2 gains or losses, and calculated a pan-ethnic carrier frequency of 2%, consistent with previous studies. Additionally, 99.8% of our SMN1 and 99.7% of SMN2 CN calls agreed with orthogonal methods, with a recall of 100% for SMA and 97.8% for carriers, and a precision of 100% for both SMA and carriers.ConclusionThis SMN copy-number caller can be used to identify both carrier and affected status of SMA, enabling SMA testing to be offered as a comprehensive test in neonatal care and an accurate carrier screening tool in GS sequencing projects

Autoinflammatory patients with Golgi-trapped CDC42 exhibit intracellular trafficking defects leading to STING hyperactivation and ER stress

Most autoinflammatory diseases are caused by mutations in innate immunity genes. Previously, four variants in the RHO GTPase CDC42 were discovered in patients affected by syndromes generally characterized by neonatal-onset of cytopenia and auto-inflammation, including hemophagocytic lymphohistiocytosis and rash in the most severe form (NOCARH syndrome). However, the mechanisms responsible for these phenotypes remain largely elusive. Here, we show that the recurrent p.R186C CDC42 variant, which is trapped in the Golgi apparatus, elicits a block in both anterograde and retrograde transports. Consequently, it favours STING accumulation in the Golgi in a COPI-dependent manner. This is also observed for the other Golgi-trapped p.*192 C*24 CDC42 variant, but not for the p.Y64C and p.C188Y variants that do not accumulate in the Golgi. We demonstrate that the two Golgi-trapped CDC42 variants are the only ones that exhibit overactivation of the STING pathway and the type I interferon response, and elicit endoplasmic reticulum stress. Consistent with these results, patients carrying Golgi-trapped CDC42 mutants present very high levels of circulating IFNα at the onset of their disease. In conclusion, we report further mechanistic insights on the impact of the Golgi-trapped CDC42 variants. This increase in STING activation provides a rationale for combination treatments for these severe cases.</p

Rare disease genomic testing in the UK and Ireland:Promoting timely and equitable access

Purpose and scope The aim of this position statement is to provide recommendations regarding the delivery of genomic testing to patients with rare disease in the UK and Ireland. The statement has been developed to facilitate timely and equitable access to genomic testing with reporting of results within commissioned turnaround times. Methods of statement development A 1-day workshop was convened by the UK Association for Clinical Genomic Science and attended by key stakeholders within the NHS Genomic Medicine Service, including clinical scientists, clinical geneticists and patient support group representatives. The aim was to identify best practice and innovations for streamlined, geographically consistent services delivering timely results. Attendees and senior responsible officers for genomic testing services in the UK nations and Ireland were invited to contribute. Results and conclusions We identified eight fundamental requirements and describe these together with key enablers in the form of specific recommendations. These relate to laboratory practice (proportionate variant analysis, bioinformatics pipelines, multidisciplinary team working model and test request monitoring), compliance with national guidance (variant classification, incidental findings, reporting and reanalysis), service development and improvement (multimodal testing and innovation through research, informed by patient experience), service demand, capacity management, workforce (recruitment, retention and development), and education and training for service users. This position statement was developed to provide best practice guidance for the specialist genomics workforce within the UK and Ireland but is relevant to any publicly funded healthcare system seeking to deliver timely rare disease genomic testing in the context of high demand and limited resources.</p

Bi-allelic Mutations in NDUFA6 Establish Its Role in Early-Onset Isolated Mitochondrial Complex I Deficiency.

Isolated complex I deficiency is a common biochemical phenotype observed in pediatric mitochondrial disease and often arises as a consequence of pathogenic variants affecting one of the ∼65 genes encoding the complex I structural subunits or assembly factors. Such genetic heterogeneity means that application of next-generation sequencing technologies to undiagnosed cohorts has been a catalyst for genetic diagnosis and gene-disease associations. We describe the clinical and molecular genetic investigations of four unrelated children who presented with neuroradiological findings and/or elevated lactate levels, highly suggestive of an underlying mitochondrial diagnosis. Next-generation sequencing identified bi-allelic variants in NDUFA6, encoding a 15 kDa LYR-motif-containing complex I subunit that forms part of the Q-module. Functional investigations using subjects' fibroblast cell lines demonstrated complex I assembly defects, which were characterized in detail by mass-spectrometry-based complexome profiling. This confirmed a marked reduction in incorporated NDUFA6 and a concomitant reduction in other Q-module subunits, including NDUFAB1, NDUFA7, and NDUFA12. Lentiviral transduction of subjects' fibroblasts showed normalization of complex I. These data also support supercomplex formation, whereby the ∼830 kDa complex I intermediate (consisting of the P- and Q-modules) is in complex with assembled complex III and IV holoenzymes despite lacking the N-module. Interestingly, RNA-sequencing data provided evidence that the consensus RefSeq accession number does not correspond to the predominant transcript in clinically relevant tissues, prompting revision of the NDUFA6 RefSeq transcript and highlighting not only the importance of thorough variant interpretation but also the assessment of appropriate transcripts for analysis

Cell–Matrix Adhesion: The Wech Connection

SummaryIntegrins link the extracellular matrix to the cytoskeleton via a complex of proteins: the integrin–cytoskeleton link. A recent study in Drosophila has uncovered a new component of the link, Wech, and shown that it is essential for integrin-mediated adhesion

Etude de la morphogénèse au cours du développement et de l'évolution (caractérisation fonctionnelle du gène ovol/shavenbaby chez la drosophile)

TOULOUSE3-BU Sciences (315552104) / SudocSudocFranceF

Atterrer les rieurs (jean-Jacques Rousseau entre la gaieté et la risée (1712-1778))

Contrairement aux idées reçues, Jean-Jacques Rousseau a aimé le rire et la gaieté: différents écrits, souvent allègres, depuis les œuvres autobiographiques jusqu à ses comédies, nous le prouvent. La Correspondance Complète le confirme: goût du comique, badinage, rire sentimental, bonhomie et même humour caractérisent le Citoyen de Genève que l on oppose traditionnellement à Voltaire pour son manque de légèreté. Bien plus, les notions de gaieté et le rire s intègrent à son système philosophique, et contribuent à enrichir sa conception de la société, de l éducation, de l enfance et même des femmes bien au-delà de la seule Lettre à d Alembert. Inversement, l écrivain s est méfié de manière innée du rire de dérision, et surtout du persiflage, dont il s est vu la victime dans les salons de Paris. De plus, à partir de 1750 et surtout de la réforme de 1756, le Citoyen, devenu le pourfendeur des rires sur le plan intellectuel et moral, devient lui-même, progressivement, la risée de Paris, de Genève et de Londres (de la part de personnalités aussi différentes que Palissot, Voltaire, Walpole, Grimm ou Diderot) au point d imaginer l existence du complot en 1766 à Wootton, et d y perdre un peu de sa raison - mais jamais vraiment de sa gaieté originelle.Contrary to generally accepted ideas, Jean-Jacques Rousseau liked the laughter and the cheerfulness: various writings (his novel Julie ou La Nouvelle Héloïse, his four comedies, his autobiographical works, and even pamphlets), often joyful, prove it. The Complete Correspondence confirms this idea: taste of comic, pleasantry, sentimental laughter, and even humor characterize the Citizen of Geneva who is traditionally opposed to Voltaire for his lack of lightness or wit. Moreover, the notions of cheerfulness and laughter fit his philosophical system, and enrich his conception of society, education, childhood and even women well beyond the Lettre à d Alembert sur les spectacles published in 1758. Conversely, and in a more conventional way, the writer used to distrust in an innate way, derision, and the persiflage he was the victim in the salons of Paris. Especially from 1750 and more specifically after the personal reformation in 1756, Rousseau was the slayer of laughter at an intellectual and moral level, and he became gradually the victim of the laughing stock of Paris, Geneva and London (from personalities as diverse as Palissot, Voltaire, Walpole, Diderot and Grimm) so much as to imagine the existence of the complot at Wootton in 1766.PARIS4-Bib. électronique (751059905) / SudocSudocFranceF