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• NIH RECOVER-Pediatric: Understanding the Long-Term Impact of COVID on Children and Families

  The NIH Researching COVID to Enhance Recovery (RECOVER) initiative comprises a set of three combined retrospective and prospective, longitudinal and observational meta-cohort studies with nested case-control studies designed to define and characterize the epidemiology, natural history, clinical spectrum, and underlying mechanisms of post-acute effects of SARS-CoV-2 infection (PASC or Post-COVID syndrome) in a diverse study population representative of the general COVID-19 population in the US. Enrolled patients, with and without known SARS-CoV-2 infection, will be observed for clinical signs and symptoms of PASC and will be assessed for risk and resiliency factors and potential mediating factors associated with the severity and progression of PASC. The objective of the RECOVER initiative is to enhance knowledge of recovery from SARS-CoV-2 infections in order to support development of novel diagnostic and therapeutic interventions. Overarching scientific objectives are as follows:Characterize the incidence and prevalence of sequelae of SARS-CoV-2 infection.Characterize the spectrum of clinical symptoms, subclinical organ dysfunction, natural history, and distinct phenotypes identified as sequelae of SARS-CoV-2 infection. Define the biological mechanisms underlying pathogenesis of the sequelae of SARS-CoV-2 infection. The RECOVER observational studies comprise three cohorts across the lifespan (adult, pediatric, and tissue pathology (autopsy)). The data collection and data analysis plans for each cohort have been harmonized to use common data elements where feasible. Brief descriptions of each cohort are provided in the following paragraphs: 1) NIH RECOVER: A Multi-site Observational Study of Post-Acute Sequelae of SARS-CoV-2 Infection in Adults (see phs003463)The RECOVER adult cohort study is a combined retrospective and prospective, longitudinal, observational meta-cohort of individuals who will enter the cohort with and without SARS-CoV-2 infection and at varying stages before and after infection. Individuals with and without SARS-CoV-2 infection, and with or without PASC symptoms, will be followed to identify risk factors and occurrence of PASC. This study will be conducted in the United States and subjects will be recruited through inpatient, outpatient, and community-based settings. Study data including age, demographics, social determinants of health, medical history, vaccination history, details of acute SARS-CoV-2 infection, overall health and physical function, and PASC symptom screen will be reported by subjects or collected from the electronic health record using a case report form at specified intervals. Biologic specimens will be collected at specified intervals, with some tests performed in local clinical laboratories and others performed by centralized research centers or banked in the Biospecimen Repository. Advanced clinical examinations and radiologic examinations will be performed at local study sites with cross-site standardization. 2) A Multi-Center Observational Study: The RECOVER Post Acute Sequelae of SARS-CoV-2 (PASC) Pediatric Cohort Study (this study)The RECOVER pediatric study is a combined retrospective and prospective, longitudinal, observational meta-cohort of individuals ages newborn-25 years who will enter the cohort with and without SARS-CoV-2 infection at varying stages before and after infection. Individuals with and without SARS-CoV-2 infection and with or without PASC symptoms will be followed to identify risk factors and occurrence of PASC. This study recruit participants inpatient, outpatient, and community-based settings in the United States. Study data including age, demographics, social determinants of health, medical history, vaccination history, details of acute SARS-CoV-2 infection, overall health and physical function, and PASC symptoms will be reported by participants or collected from the electronic health record using a case report form at specified intervals. Biologic specimens will be collected at specified intervals, with some tests performed in local clinical laboratories and others performed by centralized research centers or banked in the Biospecimen Repository. Advanced clinical and radiologic examinations will be performed at local study sites with cross-site standardization. 3) NIH RECOVER: A Multi-site Pathology Study of Post-Acute Sequelae of SARS-CoV-2 Infection The RECOVER tissue pathology study is a cross-sectional study designed to define and characterize the epidemiology, natural history, clinical spectrum, and underlying mechanisms of post-acute effects of SARS-CoV-2 infection in a diverse population representative of the general COVID-19 population in the US. The autopsy study will characterize the pathology of PASC in (i) non-hospitalized patients who die 30 days or later from symptom onset of COVID-19, and (ii) hospitalized patients who die 30 days or later after discharge from a hospitalization for COVID-19. The study will include decedents who had previously fully recovered from SARS-CoV-2 infection (i.e., >30 days from onset in non-hospitalized, or >30 days from discharge in hospitalized patients), and decedents who meet clinical criteria of PASC as defined by the recent World Health Organization publication (see Section 5.4 below). The autopsy study will also explore the pathology of acute SARS-CoV-2 infection in a smaller subset of patients who died 15-30 days from symptom onset. This protocol defines the common set of clinical data elements, autopsy procedures for tissue collection, core measures, pathology protocols, shared pathology tissues, data elements, and methodology. Each investigator site is expected to perform autopsies on the decedents to address the pathophysiology of the potential long-term effects of SARS-CoV-2 infection on human health. The Consortium analysis plan aims to address research questions by incorporating: 1) tissue obtained from autopsies performed at each Phase II participant's site; and 2) tissue available from other pathology investigators/autopsy sites within the Consortium.

  Study phs003461

• Molecular and Clinical Analyses of PHF6 Mutant Myeloid Neoplasia Provide Clues as to Their Pathogenesis and Therapeutic Targeting

  PHF6 mutations (PHF6MT) are identified in various myeloid neoplasms (MN). However, little is known about the precise function and consequences of PHF6 in MN. Our comprehensive genomic analyses yielded three main findings. Firstly, we revealed a different pattern of genes correlating with PHF6MT in male and female cases. When analyzing male and female cases separately, in only male cases, RUNX1 and U2AF1 were co-mutated with PHF6. In contrast, female cases revealed co-occurrence of ASXL1 mutations and X-chromosome deletions with PHF6MT. Next, proteomics analysis revealed a direct interaction between PHF6 and the pioneer transcription factor RUNX1. Both proteins co-localize in active enhancer regions that define the context of lineage differentiation. Finally, we demonstrated a negative prognostic role of PHF6MT, especially in association with RUNX1. The negative effects on survival were additive as PHF6MT cases with RUNX1 mutations had worse outcomes when compared to cases carrying single mutation or wild-type.

  Study phs003303

• Delineation of the heterogeneous molecular landscape of HRS cells and their biological contributions to forming comprehensive TME ecosystems.

  The tissue architecture of classic Hodgkin Lymphoma (CHL) is unique among cancers and characterized by rare malignant Hodgkin and Reed-Sternberg cells that are co-evolving in a complex ecosystem of immune cells in the tumor microenvironment. The lack of a comprehensive systems-level interrogation has hindered the description of disease heterogeneity and clinically relevant molecular subtypes. Here, we employed an integrative, multimodal approach to characterize CHL tumors using malignant cell sequencing, spatial transcriptomics and imaging mass cytometry. We identified four molecular subtypes (CST, CN913, STB, and CN2P) each characterized by distinct clinical features, mutational patterns, malignant cell gene expression profiles, and spatial architecture of immune cell populations. Functional modeling of CSF2RB mutations, a characteristic feature of CST, revealed dysregulated oncogenic signaling and changes in tumor microenvironment crosstalk. These findings highlight the significance of multi-dimensional profiling in elucidating patterns of molecular alterations that drive immune ecosystems and underlie therapeutically exploitable vulnerabilities.

  Study EGAS00001008064

• Immune Profiles Study

  This study assesses glioma patient blood methylation longitudinally beginning pre-surgery through other clinically important timepoints. Progression and survival are studied in relation to methylation derived immunologic profiles and other characteristics. For this study, patients scheduled for surgery at University of California San Francisco (UCSF) for a possible newly diagnosed glioma (grades 2-4) or recurrent grade 2/3 glioma were consented and enrolled. Patients had blood collected pre-surgery and, if the pathology results confirm a glioma, every few weeks or months during their treatment (up to 30 total timepoints). Blood immunomethylomic profiles were measured at these timepoints to assess associations with glioma patient outcomes, clinical measures, other known prognostic markers, and imaging characteristics.

  Study phs002998

• DAXX restoration suppresses alternative lengthening of telomeres in ATRX wild-type cells

  Many tumors maintain chromosome ends through a telomerase-independent, homologous recombination based mechanism called alternative lengthening of telomeres (ALT). While ALT occurs in only a subset of tumors, it is strongly associated with mutations in the genes encoding components of the histone H3.3 chaperone complex, ATRX and DAXX. To date the mechanistic role of ATRX and particularly DAXX mutations in potentiating ALT remains poorly understood. We identify an osteosarcoma cell line, G292, with a unique chromosomal translocation resulting in loss of DAXX function, while retaining functional ATRX. Using this distinctive resource, we demonstrate that introduction of wild type DAXX suppresses the ALT phenotype and restores localization of the ATRX/DAXX complex to PML bodies. This provides the first direct molecular evidence that ongoing DAXX deficiency is essential for maintenance of the ALT phenotype and highlights the potential for therapeutic targeting of this oncogenic pathway.

  Study phs001495

• Validation_of_a_Haloplex_platform_for_targeted_re_sequencing_of_the_exons_of_25_genes

  We recently used the Agilent SureSelect platform to re-sequence a set of genes known to bemutated in human AML. The results from 10 AML DNA samples were very satisfactory, butthe effort required was significant.Thus, we decided to re-sequence the same genes using the Haloplax system for targetenrichment in 48 AML samples. We planned to do this using MiSeq and have data from apilot of 3 samples. The data is promising but coverage appears pathcy so far.However, in order to get a better understanding of the data we will need deeper sequencing. Wewill need two lanes of HiSeq to get the same degree coverage as Sureselect.his data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001000285

• Exome Sequencing in Moebius Syndrome

  Möbius syndrome (MBS; MIM 157900) is a neurological disorder that is characterized by paralysis of the facial nerves and variable other congenital anomalies. The etiology of this syndrome has been an enigma since the initial description in 1880 by von Graaefe and in 1888 by Möbius, and it has been debated for decades whether MBS has a genetic or a non-genetic etiology. Here, we reveal various de novo mutations affecting two genes, PLXND1 and REV3L. The finding that de novo mutations can cause Möbius syndrome will have considerable impact on further research, as well as in diagnostics. PLXND1 and REV3L represent totally unrelated pathways involved in hindbrain development: neural migration and DNA translesion synthesis, essential for the replication of endogenously damaged DNA. However, analysis of Plxnd1 and Rev3l-mutant mice revealed that both genetic defects converge at the facial branchiomotor nucleus, affecting either motoneuron migration or proliferation.

  Study EGAS00001001250

• Human NXPE1 mediates variation in sialic acid O-acetylation in Colon Tissue

  Sialylation, and its modifications, have important consequences for development, differentiation and immune system regulation in nearly all human tissues. An accounting of all the genes responsible for modifying sialic acids is incomplete, with only one pathway for O-acetylation being well-defined in humans. Using whole genome sequencing of normal human colorectal tissue we identify a haplotype on chromosome 11 that is associated with differences in mild periodic acid Schiff staining (mPAS), a marker of acetylation of sialic acids. Of the genes in this region, only SNPs from NXPE1 correlate perfectly in a validation data set. NXPE1 protein expression by IHC also correlates with mPAS staining patterns in homozygous, as well as heterozygous colon crypts that have undergone spontaneous gain of the mPAS phenotype. Manipulation of NXPE1 expression with CRISPR-Cas9 causes changes to modified sialic acid levels in both 2D cell line and 3D normal colon organoid models. These findings suggest NXPE1 may cause O-acetylation of sialic acids in colorectal tissue, potentially defining NXPE as a new family of sialic acid-modifying genes.

  Study EGAS00001007704

• Fastq files used for searching for variants associated with endometriosis at 9p21 region

  We performed target re-sequencing for 1.29 Mb interval of chromosome 9 (chr9:21299764–22590271, hg19). NimbleGen SeqCap EZ choice system was used as a target enrichment method (Roche Diagnostics). A DNA probe set complementary to the target region was designed by NimbleDesign. The libraries were sequenced on the Illumina MiSeq platform with 2×150-bp paired-end module (Illumina). Fastq files for 48 Japanese patients with endometriosis are deposited.

  Dataset EGAD00001001942

• Base modification analysis using single molecule real-time sequencing

  Based on the kinetic characteristics of single-molecule real-time sequencing, we implement a method to directly detect DNA modifications such as 5mC. However, there are room to further improve the accuracy of whole-genome-wide DNA modifications. Therefore, this study aims to utilize deep learning methods for the comprehensive profiling of multiple DNA modifications, including 5mC, 5hmC, and 6mA, using SMRT-seq.

  Study EGAS50000000366