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• Youth Drug Abuse, ADHD and Related Disorders

  There are two major aims with this study. 1. To describe the developmental trajectory of (a) a community-based sample of youth with a childhood diagnosis of ADHD that has been prospectively followed from childhood into adulthood (approximately a 17-year span), and (b) a clinical sample of youth that received drug abuse treatment during adolescence (variable time span). 2. To examine the association of phenotypes of drug involvement severity and risk alleles that prior research has suggested to be associated with drug abuse and externalizing disorders. The sample (N=607) consists of three groups based on youth status: Treatment, High Risk, and Control. These groups are defined as follows: Treatment - attended treatment or a brief intervention for a substance use disorder during adolescence (n=402); High Risk - elevated scores on standardized measures of disruptive behaviors during childhood based on teacher and parent reports (n=142); Control - normative scores during childhood on standardized measures of disruptive behaviors based on teacher and parent reports, and absent of any DSM-based behavioral/mental disorder when assessed during childhood based on parent report (n=66). Among the 610 participants who provided DNA, 607 are usable samples.

  Study phs001734

• Single cell atlas of large B-cell lymphoma

  Large B-cell lymphomas (LBCL) are clinically and biologically heterogeneous lymphoid malignancies, shaped by complex tumor and microenvironments that play a critical role in disease progression. There has been no direct and comprehensive single-cell characterization of tumor microenvironment in LBCL that simultaneously captures lymphoid, myeloid, and stromal populations across a sufficiently large cohort to reveal reproducible and biologically meaningful patterns. Here, we performed single-nucleus multiome profiling, coupled with bulk DNA and RNA sequencing, on 232 tumor and control biopsies to comprehensively map cell subpopulations of LBCL. Through this integrative approach, we identified Lymphoma Microenvironment Archetype Profiles (LymphoMAPs)—distinct, reproducible patterns defined by the co-occurrence of functionally specialized cell subsets. We further characterized the cell-cell communication pathways that shape these transcriptional phenotypes within archetypes. Importantly, we discovered associations between specific LymphoMAPs and clinical and molecular features of LBCL, including response to CD19 CAR T-cell therapy. Our study provides a valuable resource of lymphoid, myeloid, and non-hematopoietic cell states in LBCL and offers a framework for understanding how the abundance and functional state of cells within the tumor microenvironment may drive inter-patient variability in therapeutic outcome.

  Study EGAS50000001022

• H3Africa - Deciphering Developmental Disorders in Africa

  Developmental disorders are typically rare conditions, causing an impairment in physical, learning, language, or behavioural areas. Genetic heterogeneity and highly variable clinical manifestations make diagnosing developmental disorders particularly challenging. Developmental disorders are increasing in prevalence in low- and middle-income countries, partly due to effective prevention and treatment of infectious diseases leading to a decrease in childhood mortality. New sequencing technologies are used effectively in the diagnosis of rare diseases and results can impact clinical practice significantly. Despite this international trend, very little implementation of these new approaches has taken place in low-resource settings, especially in Africa. The Deciphering Developmental Disorders in Africa (DDD-Africa) study aims to take advantage of an unbiased genotype-driven approach to improve healthcare services for patients. The study aims to recruit and perform detailed clinical phenotyping and exome sequencing (ES) on 500 African patients with a developmental disorder in whom a genetic diagnosis has not been confirmed. Where available, parents are also included in sequencing efforts. The project has two active research sites in Johannesburg (South Africa) and Kinshasa (Democratic Republic of Congo) representing diversity in geography, clinical, socio-economic, genetic and environmental factors.

  Study EGAS00001008319

• Genomics-based personalized oncology in cancer of unknown primary (CUP, project H021)

  To perform a comprehensive genomic characterization of 70 patients suffering from cancer of unknown primary (CUP) we used whole-exome, whole-genome, transcriptome and methylome analysis. We detected a substantial mutational heterogeneity with genes most commonly affected by SNVs, indels and fusions being TP53, TTN, MUC16, ABCA13, COL6A3, KRAS, LRP1B, XIRP2 and CSMD3. The most common fusion involved FGFR2, the most common focal deletion affected CDKN2A. A molecular tumor board recommended genomics-based therapies in 56/70 (80%) patients which were applied in 20/56 (35.7%) cases. Entity predictions based on transcriptome and methylome data could be made in up to 62/70 (88.6%) cases but were conclusive in only 16/48 (33.3%) cases. Germline analysis revealed 6 (likely) pathogenic mutations in 5 patients. Recommended therapies translated into a mean PFS2/1 ratio of 3.61 (median=2.25) with a median PFS1 of 89 days (n=17) compared to a median PFS2 of 182.5 days (n=20). Our data emphasize the clinical benefit of comprehensive genetic approaches in diagnostic and therapeutic management and underline the need for innovative, mechanism-based clinical trials in this heterogeneous group of diseases.

  Study EGAS00001004786

• Guardians of the genome: protecting DNA from endogenous sources of damage

  Mutational signatures are imprints of cell-intrinsic and extrinsic pathophysiological processes that have occurred through tumorigenesis. Experimental efforts to explore signature etiologies have produced a compendium of signatures of exogenous mutagens previously. Here, we unearth major sources of endogenous DNA damage and the genes that are critical to mitigating this innate stream of DNA damage under normal, physiological circumstances. We performed whole genome sequencing of 173 subclones of CRISPR-Cas9 knockouts of 43 genes in a human induced pluripotent stem cell system, in the absence of any added DNA damage. We reveal substitution and indel signatures that arise from those genes which are essential guardians of the genome. By detailed dissection and comparisons to cancer-derived signatures, we demonstrate interminable sources of constitutive DNA damage, and some mechanistic knowledge into how guardian genes preserve the genome. Based on these experimental insights, we develop and benchmark a tool for clinical classification of tumor samples.

  Dataset EGAD00001006055

• RNA-Seq dataset of Targeting the dark proteome to expand the lineage-retained antigen landscape in neuroblastoma

  This dataset contains bulk RNA-sequencing data generated to enable custom transcriptome assembly and to provide expression context for matched ribosome profiling in the discovery of lineage-retained neuroblastoma tumor antigens. RNA was sequenced from 183 neuroblastoma samples comprising cell lines, patient-derived tumor organoids, and primary patient tumors spanning the adrenergic (ADRN) and mesenchymal (MES) lineage states, with 101 samples prepared as rRNA-depleted (total RNA) libraries and 82 samples prepared as poly(A)-selected libraries. Libraries were sequenced paired-end (2x150 bp) on the Illumina NovaSeq 6000 platform. Raw data are provided as paired-end fastq.gz files.

  Dataset EGAD00001016124

• Environmental Arsenic and Diabetes Mellitus (Chihuahua Cohort)

  The Chihuahua Cohort was established as part of a larger NIEHS-funded project that used laboratory models (tissue culture and mice) and human subjects to examine the association between exposure to arsenic and diabetes, including identification of mechanisms underlying this association. All procedures involving human subjects were approved by institutional review boards at the University of North Carolina at Chapel Hill and Cinvestav-IPN (Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico). All participants provided signed informed consent. A total of 1,160 adults (≥ 18 years old) with a minimum 5-year uninterrupted residency in the Chihuahua study area were recruited between 2008 and 2012. Samples of drinking water were obtained from the participants' households. Data on residency, occupation, drinking-water sources and use, smoking, alcohol consumption, and medical history were recorded by a study questionnaire. Spot urine and fasting venous blood were collected during medical examination that included an oral glucose tolerance test (OGTT) with blood drawn 2 hr after a 75-g glucose dose. Plasma from both fasting and 2-hr blood samples was collected. Body mass index (BMI) of each participant was calculated from body weight and height. BMI cutoffs of ≥ 25.0, ≥ 30, and < 18.5 kg/m2 were used to define overweight, obese, and underweight individuals, respectively. Participants' waist circumference was also measured. Blood pressure was assessed using a manual sphygmomanometer. Three measurements were taken at intervals of at least 1 min, with a 5-min rest before obtaining the first reading; the mean of the last two measurements was used. The concentrations of arsenic in drinking water and arsenic species in urine were measured by hydride generation-atomic absorption spectrometry. The limit of detection for As in water as well as for As species in urine was 0.01 µg As/L. Creatinine concentration in urine was determined using an established colorimetric assay. DNA was isolated from blood for genotyping analysis.The following measures were taken: glucose concentration in fasting blood (FBG) and in blood collected 2 hours into OGTT (2HBG); concentrations of triglycerides, HDL and total cholesterol (TC) in fasting plasma; and LDL was calculated using the Friedewald equation. Diabetes was classified by FPG ≥ 126 mg/dL, 2HPG ≥ 200 mg/dL, or self-reported diabetes diagnosis or medication use (WHO/International Diabetes Federation 2006). Prediabetes was defined as the absence of diabetes with FPG ≥ 110 mg/ dL or 2HPG ≥ 140 mg/dL. Elevated fasting levels of each lipid were defined as plasma TG ≥ 150 mg/dL, TC ≥ 200 mg/dL, and LDL ≥ 130 mg/dL. Fasting HDL < 40 mg/dL in men and < 50 mg/dL in women were designated as low. Hypertension was defined by systolic blood pressure (SBP) > 140 mm Hg, diastolic blood pressure (DBP) > 90 mmHg, or self-reported use of anti-hypertensive medication. Genotyping analysis, which will be available in version 2 of this study, was carried out in a subset of ~600 subjects with focus on enzymes involved in the metabolism of arsenic, including AS3MT, GSTs.All data collected during the medical exams or generated by the above-described chemical and biochemical analysis of water, urine and blood/plasma, as well as results of the genotyping analysis are included in dbGaP. Data generated by metabolomics and epigenetic analyses in small subsets of the Chihuahua cohort are not included, but are available in published articles.

  Study phs002139

• Human Epilepsy Genetics: Mosaic Mutations in Focal Epilepsy

  This study investigates the role of somatic mosaic mutations in human focal epilepsies, including focal cortical dysplasia (FCD) and mesial temporal lobe epilepsy (mTLE). It leverages genomic and single-cell transcriptomic data from surgically resected brain tissue to identify pathogenic variants and characterize their effects on specific cell types and molecular pathways. The study employs methods such as deep whole-exome and targeted sequencing, single-nucleus RNA sequencing (snRNA-seq), and integrated genotype-transcriptome profiling (e.g., GO-TEN) to define the cellular architecture and functional consequences of mosaic mutations. Data generated under this project aim to elucidate mechanisms of epileptogenesis and support discovery of potential therapeutic targets.

  Study phs004124

• Transcriptomic analysis of membranes from proliferative vitreoretinal diseases and isolated human retinal pigment epithelium

  This study investigates the transcriptomic profiles of proliferative vitreoretinal diseases (PVD) membranes, including proliferative vitreoretinopathy and epiretinal membranes collected from patients undergoing surgery, as well as human retinal pigment epithelial cells isolated from post-mortem donor eyes. Total RNA was extracted using AllPrep DNA/RNA Micro Kit (Qiagen) and cDNA libraries were prepared using the Ovation Solo RNA-seq Kit (Tecan). Multiplexed libraries were loaded onto a NovaSeq 6000 platform (Illumina), and sequences were generated using a 200-cycle kit. This study includes over 80 pathological and healthy samples to allow comparison of gene expression profiles and gain insights into the molecular mechanisms of PVD.

  Study EGAS50000001253

• Development of a fully human glioblastoma-in-brain-spheroid model for accelerated translational research

  In glioblastoma (GBM) the intricate interplay between tumor cells and the surrounding microenvironment plays a crucial role in tumor progression, invasion, and therapeutic resistance. So far, studying these interactions in a controlled and representative model system has been challenging. Here, we report the development of hGliCS, a human glioma-cortical spheroid model that allows the elucidation of the biology of GBM cells and their interactions with a human-specific brain-like microenvironment and neurons. GBM cells efficiently invade the cortical spheroids, forming a well-connected network of communicating cells. The heterogeneous cellular states of the GBM cells within this model closely resembled findings previously observed in glioblastoma patients and in mouse xenografts. We observed a transition from predominantly mesenchymal-like cells to heterotopic states with a high diversity. In contrast to the substantial changes observed in the tumor cell population, the impact of the GBM cells on the neurons was minimal. We further demonstrate the suitability of hGliCS to test compounds targeting tumor-specific neurobiological features.

  Study EGAS50000000757