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• Joint Addiction, Aging, and Mental Health Data Access Committee General Research Use Datasets (GSR Restricted) Collection

  This collection contains the Joint Addiction, Aging, and Mental Health Data Access Committee's authorized individual-level genomic datasets currently in dbGaP that are approved for General Research Use (GRU) and have no further limitations beyond those outlined in the model Data Use Certification Agreement. The public posting of Genomic Summary Results are not allowed. Access to this study collection will include additional authorized individual-level GRU datasets that become available. Renewal of this study collection is required annually. To request access to this study collection, select phs003421 in the dbGaP Authorized Access System.

  Study phs003421

• Single cell transcriptomics of human kidney organoid endothelium reveals vessel growth processes and arterial maturation upon transplantation

  Human induced pluripotent stem cell-derived kidney organoids have potential for disease modeling and regenerative medicine purposes. However, they lack a functional vasculature in in vitro culture. Here, we transplanted kidney organoids at day 7+12 of differentiation in the coelomic cavity of chicken embryos. We then compared human endothelial cells from transplanted organoids to their respective untransplanted controls at d7+13 and d7+20 using scRNAseq. We demonstrate metabolic and phenotypic effect of transplantation with increased endothelial cell proliferation and differentiation to a fetal-like renal arterial/afferent arteriolar phenotype.

  Study EGAS50000001068

• Lethal malformation syndrome

  Identification of the genetic basis of rare monogenic diseases can provide insights into disease mechanisms, biological pathways and potential therapeutic targets. Exome sequencing has proven to be a powerful, efficient strategy for the identification of the genes underlying rare Mendelian disorders. The genetic defect behind the lethal malformation syndrome under study is known in some cases and has proven useful in revealing the primary underlying defect. We have six typical unrelated families with no known mutation. The aim of this study is to identify the locus associated with this lethal malformation syndrome in these families using exome sequencing.

  Study EGAS00001000061

• Pathogenic Neurofibromatosis type 1 (NF1) RNA splicing resolved by targeted RNAseq

  Neurofibromatosis type 1 (NF1) is caused by loss-of-function variants in the NF1 gene. Approximately 10% of these variants affect RNA splicing and are either missed by conventional DNA diagnostics or are misinterpreted by in silico splicing predictions. Therefore, a targeted RNAseq-based approach was designed to detect pathogenic RNA splicing and associated pathogenic DNA variants. an in-house developed tool (QURNAS) was used to calculate the enrichment score (ERS) for each splicing event. RNA enrichment of NF1 and SPRED1 was done using SPET (NUGEN - NF1 only) and using SureSelect (Agilent - NF1 and SPRED1).

  Study EGAS00001005530

• Whole Exome Sequencing Study of TGFΒ Pathway Genes in HCV Liver Fibrosis

  Despite the astonishing progress in treating chronic hepatitis C virus (HCV) infection with direct-acting antiviral agents, liver fibrosis remains a major health concern in HCV infected patients, in particular due to the treatment cost and insufficient HCV screening in many countries. Only a fraction of patients with chronic HCV infection develop liver fibrosis. While there is evidence that host genetic factors are involved in the development of liver fibrosis, the common variants identified so far, in particular by genome-wide association studies, were found to have limited effects. Here, we conducted an exome association study in 88 highly selected HCV-infected patients with and without fibrosis. A strategy focusing on TGF-β pathway genes revealed an enrichment in rare variants of the endoglin gene (ENG) in fibrosis patients. Replication studies in additional cohorts (617 patients) identified one specific ENG variant, Thr5Met, with an overall odds ratio for fibrosis development in carriers of 3.04 (1.39-6.69). Our results suggest that endoglin, a key player in TGF-β signaling, is involved in HCV-related liver fibrogenesis.

  Study phs001902

• ICGC PedBrain: Deep-sequencing of childhood brain tumors.

  Brain tumors constitute the childhood tumors with the highest mortality rates and survival is often associated with severe long-term sequelae due to intensive multimodal treatment regimens. Thus, the PedBrainTumor network aims at the identification of robust biomarkers for clinical management and novel molecular targets for therapeutic interventions. Using massively parallel whole-genome sequencing, and transcriptome and methylome sequencing for subsets of cases, we aim to decipher the molecular causes of medulloblastoma as well as low-grade astrocytoma, and to identify markers to stratify patients for specialized treatment. As the PedBrain network is affiliated with clinical trials in medulloblastoma and pilocytic astrocytoma, validation cohorts for the translation of key findings into clinical settings are readily available.

  Study EGAS00001000215

• Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints (ECLIPSE)

  ECLIPSE was a longitudinal observational study of 2164 COPD subjects and a smaller number of smoking controls (337) and nonsmoking controls (245) followed regularly for three years, with three chest CT scans (at baseline, one year, and three years) (Vestbo, European Respiratory Journal 2008; 31: 869). Inclusion criteria included age 40-75, at least 10 pack-years of smoking, and spirometry in GOLD grades 2-4 (COPD cases) or normal spirometry with post-bronchodilator FEV1 >85% predicted and FEV1/FVC>0.7 (controls). Study visits were performed at enrollment, three months, and every six months thereafter with spirometry, questionnaires, and other clinical evaluations. The ECLIPSE CT scans have been analyzed with the VIDA software for emphysema and airway phenotypes. ECLIPSE has provided key insights into the clinical epidemiology of COPD, including COPD exacerbations (Hurst, NEJM 2010; 363: 1128) and lung function decline in COPD (Vestbo, NEJM 2011; 365: 1184). ECLIPSE has been used in a number of genetic studies of COPD susceptibility and protein biomarkers(Faner, Thorax 2014; 69: 666). Genome-wide gene expression microarray data are available in 147 induced sputum samples from COPD subjects and 248 peripheral blood samples from COPD and control subjects.

  Study phs001252

• Novel immunodeficiency caused by homozygous mutations of SLC19A1

  The male proband suffered from infancy oral lesions, recurrent fever, diarrhea, vomiting, atopic dermatitis, dark discoloration patches on his skin and lip fissures; he suffered from anemia (megaloblastic), thrombocytopenia, hypogammaglobulinemia and lymphopenia; his growth and development are delayed. Whole exome sequencing identified only one variant predicted to have high impact and to potentially explain the patient’s phenotype, a homozygous missense chr21:46950793:C:T (hg19) SLC19A1 NM_194255:c.1042G>A (p.G348R). Sanger sequencing and segregation analysis confirmed the presence of the homozygous SLC19A1 c.1042G>A (G348R) missense variant in the proband, with a heterozygous state in his family. The same homozygous SLC19A1 variant was identified in a distantly-related male patient with a similar phenotype presentation, while his healthy family members were heterozygous. SLC19A1 is a folate transporter, and thus folic acid supplementation was performed for the proband: platelet counts normalized rapidly and anemia improved; hair and skin discoloration, mouth lesions and chronic diarrhea improved. In contrast, neurological and developmental issues remained unchanged and treatment had only a partial effect on the immune system. This further confirmed the causal role of SLC19A1 for the proband's condition.

  Study EGAS50000000356

• Non-canonical NF-κB signaling skews B cells away from germinal center to low-affinity effector fate

  The non-canonical (NC) NF-κB pathway is a central regulator of B-cell development and survival, yet its role during B-cell mediated adaptive responses remains uncharted. Here, we uncover an unanticipated regulatory function for NC NF-κB in shaping humoral immunity. High-resolution mapping of NC NF-kB status in B cells from human lymphoid tissues revealed low activity in germinal center B-cells (GCB) than effector subsets, suggesting a selective attenuation. Consistently, mice model harboring B-cells with enforced NC NF-κB activation revealed near- complete loss of GCB and high-affinity antibodies, following vaccination. GCB loss was not driven by intrinsic defects in formation or expansion, but by an immune-niche dysregulation marked by regulatory T-cell expansion. Mechanistically, NC NF-κB activation promoted B-cell- derived IL-10, and blocking this axis normalize the niche and rescue GCB. Concurrently, NC NF- κB signaling boosted low-affinity antibody responses by transcriptionally priming follicular B- cells for plasmacytic differentiation. Together, these findings position NC NF-κB as a tunable rheostat linking B-cell signaling to immune-niche control and humoral immunity.

  Study EGAS50000001646

• Spatial multi-omic map of human myocardial infarction

  Myocardial infarction is a leading cause of mortality worldwide 1 . While advances have been made in acute treatment, an incomplete understanding of remodelling processes has limited the effectiveness of therapies to reduce late-stage mortality 2 . Here, we generate an integrative high- resolution map of human cardiac remodelling after myocardial infarction using single-cell gene expression, chromatin accessibility, and spatial transcriptomic profiling of multiple physiological zones at distinct time points in myocardium from myocardial infarction and control patients. Multimodal data integration allowed us to evaluate cardiac cell-type compositions at increased resolution, yielding insights into changes of the cardiac transcriptome and epigenome through the identification of distinct tissue structures of injury, repair and remodelling. We identified and validated disease-specific cardiac cell-states of major cell-types and analysed them in their spatial context, evaluating their dependency on other cell-types. Our data elucidates molecular principles of human myocardial tissue organisation, recapitulating a gradual cardiomyocyte and myeloid continuum following ischemic injury. In total, our study provides an integrative molecular map of human myocardial infarction and represents an essential reference for the field and paves the way for advanced mechanistic and therapeutic studies of cardiac disease.

  Study EGAS00001006330