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• Whole genome sequencing data of paediatric ETV6::RUNX1 acute lymphoblastic leukemia

  ETV6::RUNX1 (E::R) subgroup is the second most frequent form of B cell acute lymphoblastic leukemia (B-ALL) in childhood. This subgroup of ALL generally presents with low-risk features and responds well to chemotherapy with ensuing favorable prognosis. Some patients, however, have a slow response to induction treatment and carry increased risk for relapse.

  Study EGAS50000001599

• ICARUS-BREAST01-RNAseq

  Efficacy, safety and biomarker analysis of ICARUS-BREAST01: a phase 2 Study of Patritumab Deruxtecan in patients with HR+/HER2- advanced breast cancer. RNA-squencing is available for 44 samples comprising 22 samples collected at entry into the trial and 22 samples collected during treatment (cycle 1 day 3, cycle 1 day 19, or cycle 2 day 3) from 22 patients.

  Study EGAS50000000543

• RNA sequencing data of pediatric ETV6::RUNX1 acute lymphoblastic leukemia

  ETV6::RUNX1 (E::R) subgroup is the second most frequent form of B cell acute lymphoblastic leukemia (B-ALL) in childhood. This subgroup of ALL generally presents with low-risk features and responds well to chemotherapy with ensuing favorable prognosis. Some patients, however, have a slow response to induction treatment and carry increased risk for relapse.

  Study EGAS50000001801

• Whole Exome Sequencing of High grade T1 non-muscle invasive bladder cancer

  High-grade T1 (HGT1) bladder cancer (BC) is the highest risk subtype of non-muscle-invasive BC with unpredictable outcome and poorly understood risk factors. Here we performed whole exome sequencing across 61 HGT1 samples to identify genomic predictors of good outcome, recurrence or progression. This study includes somatic mutation calls and clinical data for 61 HGT1 tumors.

  Study EGAS00001004603

• Cell and Circuit-Specific Exploration of HIV Neurogenomics in Context of Opiate and Cocaine Misuse

  Utilizing frozen postmortem brain tissue from the Manhattan HIV Brain Bank, we performed cell-type-specific, genome-wide sequencing of three different types: 1) single-nucleus RNA-sequencing (snRNA-seq), 2) in situ Hi-C, and 3) HIV integration site sequencing (IS-seq). We assayed tissue from three different donor types: 1) HIV-uninfected control (HIV-), HIV-infected (HIV+), and HIV-infected with HIV encephalitis (HIVE), who served as a positive control for active CNS viral infection. The diagnosis of HIVE was made by a board-certified neuropathologist on routine histopathology, based on the presence of a microglial nodule encephalitis with characteristic multinucleated syncytial cells and staining for HIV p24 antigen. Other HIV-infected individuals (the HIV+ group) did not have this histologic evidence of active HIV brain replication, and were variable with regard to cART status and virologic control prior to death. Donor characteristics, including ante-mortem plasma HIV loads, CD4 counts, and cART status, were documented. Quality controls were used for each assay: For snRNA-seq we applied filters to remove low quality nuclei from analysis and performed experiments in which mouse tissue was mixed with human tissue to determine a reliable HIV read count threshold. For Hi-C, we used paired HIV- and HIVE samples and processed all samples in parallel, at the same time. Correlation analysis was used to ensure biological replicates were aligned. For IS-seq, each time the assay was run, a positive and negative control were included. This allowed us to ensure a lack of contamination in IS-seq libraries and that, when a particular sample failed to yield library, this was due to low levels of HIV rather than a failure of the assay. Altogether, we built an integrative dataset from 79 sequencing files, including snRNA-seq, and cell type specific Hi-C, IS-seq, and ChIP-seq datasets. Human autopsy brain samples were collected by the Manhattan HIV Brain Bank (MHBB, U24MH100931), using protocols under the supervision of the Icahn School of Medicine at Mount Sinai (ISMMS) Institutional Review Board. Written informed consent was obtained either from decedents or their primary next of kin. Major Findings: Reorganization of open/repressive (A/B) compartment structures in HIVE microglia encompassing 6.4% of the genome was linked to transcriptional activation of interferon (IFN) signaling and cell migratory pathways and was partially recapitulated by IFN-gamma stimulation of cultured microglia. In contrast, decreased expression and repressive compartmentalization of genes regulating neuronal health and signaling was seen in both HIVE and HIV+ microglia. IS-seq recovered 1,221 integration sites in the brain that displayed distinct genomic patterns as compared to peripheral lymphocyte integration and were enriched for chromosomal domains newly mobilized into a permissive chromatin environment in HIVE microglia. Viral transcription occurred in a subset of highly activated microglia comprising 0.003% of all nuclei in HIVE brain. Our findings point to a disruption of microglia-neuronal interactions in the HIV infected brain and an interrelation of retroviral integration and expression with interferon-associated remodeling of the microglial 3D genome during progression to HIVE. Search terms: HIV, postmortem brain, microglia, substance abuse, viral integration, chromosomal conformation capture, Hi-C, chromatin, single nuclei RNA-seq, Irf8, NeuN, HIV encephalitis, neuron-microglia interaction, cytokine

  Study phs003080

• IDENTIFICATION AND TARGETED MANAGEMENT OF A PATIENT WITH A NEURODEGENERATIVE DISORDER CAUSED BY BIALLELIC MUTATIONS IN SLC5A6

  We describe a sibling pair displaying an early infantile-onset, progressive neurodegenerative phenotype, with symptoms of developmental delay and epileptic encephalopathy developing from 12 to 14 months of age. Using whole exome sequencing, compound heterozygous variants were identified in SLC5A6, which encodes the sodium-dependent multivitamin transporter (SMVT) protein. SMVT is an important transporter of the B-group vitamins biotin, pantothenate and lipoate. The protein is ubiquitously expressed and has major roles in vitamin uptake in the digestive system, as well as transport of these vitamins across the blood-brain barrier. Pathogenicity of the identified variants was demonstrated by impaired biotin uptake of mutant SMVT. Identification of this vitamin transporter as the genetic basis of this disorder guided targeted therapeutic intervention, resulting clinically in improvement of the patient’s neurocognitive and neuromotor function. This is the second report of biallelic mutations in SLC5A6 leading to a neurodegenerative disorder due to impaired biotin, pantothenate and lipoate uptake. The genetic and phenotypic overlap of these cases confirms mutations in SLC5A6 as the genetic cause of this disease phenotype. Recognition of the genetic disorder caused by SLC5A6 mutations is essential for early diagnosis and to facilitate timely intervention by triple vitamin (biotin, pantothenate and lipoate) replacement therapy.

  Study EGAS00001003861

• Identification of drug resistance genes in melanoma by Exome Sequencing

  The cell lines in this study are a combination of internally sequenced (cosmic) and externally sequenced cell lines known to be “double-wild-type” (lacking BRAF and NRAS somatic mutations). These sequences were realigned in this data set for consistency.

  Dataset EGAD00001003260

• PD-associated regulatory variants in human dopaminergic neurons reveals modulators of SCARB2 and BAG3 expression

  SNPs have been associated with the risk of Parkinson’s disease but not in regulatory regions. While those potentially disrupt TFBS altering gene expression and contributing to cis-regulatory variation. To study changes in A and B compartment interactions and in topologically associated domains (TADs), we sequenced: - 3D chromatin contact using LowC, 6 samples. 3 replicates for each condition: smNPC (controls) cells and differentiated neurons after 30 days. Resulting paired-end are provided as BAM files. In order to confirm the predicted impact of the PD-associated allele of rs144814361 on BAG3 promoter, we proceeded with genome editing of the TH-REP1 cell line by using prime editing to insert the “T” allele at the position chr10:119651405 in the BAG3 promoter. - Chromatin accessibility using ATAC-seq, 9 samples of derived cell line TH-REP1. 3 replicates for each condition: 1) iPSC Wild Type 2) SNP-BAG3 variant in iPSC 3) SNP-BAG3 variant in smNPC. BAG3 variant: heterozygous for the SNP variant: rs144814361 (chr10 119651405) Resulting sequencing are provided as paired-end FASTQ files.

  Dataset EGAD50000002258

• Epi4K: Gene Discovery in 4,000 Epilepsy Genomes

  The Epi4K project began in 2011 as an international, multi-center study that seeks to identify and characterize the genetic bases of complex epilepsies. The Center without Walls Epi4K project includes three cores and four scientific projects, as well as a steering committee comprised of the primary study investigators and representatives from the National Institute of Neurological Disorders and Stroke (NINDS). The three cores include: (1) The Administrative Core which handles the overall coordination of Epi4K activities; (2) The Sequencing, Biostatistics and Bioinformatics Core which is responsible for generating the next-generation sequence data, inferring the genetic variation in each of the study participants, and performing the primary analyses to identify epilepsy genes; and (3) The Phenotyping and Clinical Informatics Core which verifies and archives all the phenotypic data from each study participant. The proposed number of patients to be sequenced and analyzed in the scientific projects is a minimum of 4,000; thus the Center was named "Epi4K: Gene Discovery in 4,000 Genomes". Project 1 addresses the genetics of rare and severe childhood epilepsies, including epileptic encephalopathies (infantile spasms and Lennox-Gastaut syndrome), and malformations of cortical development (periventricular nodular heterotopia and polymicrogyria). Exome and genome sequence data generated from DNA collected from patients will be screened for mutations (single nucleotide substitutions, small insertion-deletions, and copy number variations) that cause or contribute to the diseases. Project 2 is focused on genetic discovery in multiplex families. This study will use next-generation sequencing to identify genomic variation that influences risk for common subtypes of epilepsy including idiopathic generalized epilepsy and nonlesional focal epilepsy. Project 3 seeks to identify genetic determinants of prognosis in patients with a range of epilepsy disorders. This study will study established epilepsy cohorts with well-characterized data on seizure outcome to look for relationships between genetic variation and pharmacological control of seizures. Project 4 will use next-generation sequencing data (exome and genome) to screen for epilepsy-associated copy number variation across all Epi4K projects using novel computational algorithms.

  Study phs000653

• LEF1 knockdown effects on human T cell transcriptome and chromatin accessibility profiles.

  LEF1 (Lymphoid Enhancer-Binding Factor 1) is a key transcription factor in T cell development and function, and its dysregulation has been implicated in various immune-related disorders. This study aimed to comprehensively characterize the transcriptional and epigenetic changes induced by LEF1 knockdown in human T cells. CD3+ T cells isolated from three healthy donors were transfected with either LEF1-specific siRNA or control siRNA, followed by activation with CD3/CD28 Dynabeads and culture in IL-2-containing media. Cells were harvested at 24, 48 and 72 hours post-transfection for multi-omics analysis including bulk RNA-seq, bulk ATAC-seq, single-cell CITE-seq (For CITE-seq, 48 and 72 hours only). This dataset provides insights into LEF1-dependent gene regulatory networks and chromatin accessibility patterns in activated human T cells, contributing to our understanding of T cell biology and potential therapeutic targets. This dataset is part of a comprehensive study investigating functional roles of risk polymorphisms in autoimmune diseases, particularly focusing on the rs58107865 variant at the LEF1 locus.

  Study JGAS000818

• ALLELE Consortium Glioblastoma Project

  Glioblastoma patient samples were sequenced for this project. The purposes of this project are: (1) to establish an umbrella protocol as a mechanism for identifying patients (in the USA and international sites) who agree to the collection, storage, and broad usage of their specimens and ongoing collection, and review of their medical information for the purposes of minimal-risk research and use of such data in clinical trials on which the patient may enroll; (2) to develop operations that facilitate investigator access to the data and/or tissue to conduct research, while minimizing risks to participants and promoting responsible conduct; and (3) to provide the infrastructure for the sharing of de-identified, coded samples, clinical data, and genomic data between participating investigators and institutions. Eligible patients include patients with known or suspected nervous system tumors or other neurologic diseases. Whole exome sequencing from the stated project will be released under this submission.

  Study phs003000

• Multi-Omic Profiling of Glioma Patient Tumors and Patient-Derived Model Systems

  We have created a resource of transcriptomic (RNAseq), genomic (whole-exome seq), and lipidomic (untargeted shotgun) profiling data from over 175 molecularly diverse glioma tumors and derivative models in orthotopic mouse xenografts and gliomasphere cultures from over 110 unique patient tumor lines. Provided in this dataset are matched bulk RNA and whole-exome paired-end sequencing data from resected gliomas and derived model systems performed on Illumina HiSeq and NovaSeq sequencing instruments. This comprehensive dataset powers multiple studies aiming to derive molecular signatures of intertumoral heterogeneity and perturbation responses in glioma. Through integrative multi-omic analyses in Minami, et al., 2023, PMID: 37236196, we identified that CDKN2A deletion remodels the GBM lipidome and consequently primes CDKN2A-deleted tumors for ferroptosis. Lipidomics data related to this study are publicly available here. In another study, we used a combination of molecular profiling and functional profiling of apoptotic potential to stratify patients into groups with differential vulnerability to the current standard-of-care in gliomas, and in combination with drugs targeting intrinsic apoptosis, largely informed but not limited to TP53 mutation status.

  Study phs003286

• HBCC Postmortem Psychiatric Molecular Studies

  This postmortem study examines molecular, genetic and epigenetic signatures in the brains of hundreds of subjects with or without mental disorders conducted by the DIRP NIMH Human Brain Collection Core (HBCC). The brain tissues are obtained under protocols approved by the CNS IRB (NCT00001260), with the permission of the next-of-kin (NOK) through the Offices of the Chief Medical Examiners (MEOs) in the District of Columbia, Northern Virginia and Central Virginia. Additional samples were obtained from the University of Maryland Brain and Tissue Bank (contracts NO1-HD-4-3368 and NO1-HD-4-3383) (http://www.medschool.umaryland.edu/btbank/ and the Stanley Medical Research Institute: http://www.stanleyresearch.org/brain-research/). Clinical characterization, neuropathological screening, toxicological analyses, and dissections of various brain regions were performed as previously described (Lipska et al. 2006; PMID: 16997002). All patients met DSM-IV criteria for a lifetime Axis I diagnosis of psychiatric disorders including schizophrenia or schizoaffective disorder, bipolar disorder and major depression. Controls had no history of psychiatric diagnoses or addictions. SNP array: Array-based genotyping was performed on most samples published in this collection. The number of SNPs assayed via Illumina chips varied between 650,000 and 5 Million. Cerebellar tissue was generally used for genotyping studies. # Diagnosis SNP Array 1 Anxiety Disorder 1 2 Autism Spectrum Disorder 13 3 Bipolar Disorder 114 4 Control 387 5 Eating Disorder (ED) 2 6 Major Depressive Disorder (MDD) 186 7 Obsessive Compulsive Disorder (OCD) 5 8 Post-Traumatic Stress Disorder (PTSD) 0 9 Schizophrenia 220 10 Other 7 11 Tic Disorder 3 12 Undetermined 1 13 Williams Syndrome 2 Table: Numbers of samples in each diagnostic category. DNA extraction: 45-80 mg of cerebellar tissue was pulverized for DNA extractions. The QIAamp DNA mini Kit (Qiagen) method was employed for tissue DNA extraction. The tissue was initially lysed using Tissue Lyser (Qiagen) and extractions were accomplished according to manufacturer's protocol. The DNA was captured in 500uL elution buffer. The concentrations were measured using Thermo Scientific's NanoDrop 1000/NanoDrop ONE. The mean yield was 128.85 uG (+/- 79.48), the mean ratio of 260/280 was 1.87 (+/- 0.105), and the mean ratio of 260/230 was 2.48 (+/-1.75). Genotyping methods: Three types of Illumina Beadarray chips were used: HumanHap650Y, Human1M-Duo, and HumanOmni5M-Quad (San Diego, California). The genotyping was done according to the manufacturer's protocol (Illumina Proprietary, Catalog # WG-901-5003, Part # 15025910 Rev.A, June 2011). Approximately, 400ng DNA was used and each DNA sample was QC tested for 260/280 ratio by nanodrop and DNA band intactness on 2% agarose gel. Briefly, the samples were whole-genome amplified, fragmented, precipitated and resuspended in appropriate hybridization buffer. Denatured samples were hybridized on prepared Bead Array Chips. After hybridization, the Bead Chip oligonucleotides were extended by a single fluorescent labeled base, which was detected by fluorescence imaging with an Illumina Bead Array Reader, iScan. Normalized bead intensity data obtained for each sample were loaded into the Illumina Genome Studio (Illumina, v.2.0.3) with cluster position files provided by Illumina, and fluorescence intensities were converted into SNP genotypes. Microarray: We generated RNA expression data using array technology for psychiatric subjects compared to non-psychiatric subjects as controls. We used tissues from three different brain regions i.e. hippocampus, dorsolateral prefrontal cortex (DLPFC), and dura mater for a large cohort of individuals (total number 552 subjects for hippocampus, 800 for DLPFC and 146 for dura). Total RNA was extracted from ~100 mg of tissue using the RNeasy kit (Qiagen) according to the manufacturer's protocol. RNA quality and quantity were examined using the Bioanalyzer (Agilent, Inc) and NanoDrop (Thermo Scientific, Inc), respectively. Samples with RNA integrity number (RIN) # Diagnosis DLPFC Hippo Dura 1 Anxiety Disorder 1 0 0 2 Autism Spectrum Disorder 14 6 0 3 Bipolar Disorder 90 49 0 4 Control 336 270 75 5 Eating Disorder (ED) 2 1 0 6 Major Depressive Disorder (MDD) 144 87 0 7 Obsessive Compulsive Disorder (OCD) 5 3 0 8 Post-Traumatic Stress Disorder (PTSD) 6 0 0 9 Schizophrenia 192 125 71 10 Other 5 6 0 11 Tic Disorder 3 3 0 12 Undetermined 1 1 0 13 Williams Syndrome 2 1 0 Table: Numbers of samples in each diagnostic category. RNA-Seq of Dorso-lateral prefrontal cortex: All brains were collected and the dorsolateral prefrontal cortical (DLPFC) samples dissected at the HBCC, DIRP, NIMH. Dorsolateral prefrontal cortex (DLPFC) specimens were dissected from right or left hemisphere of frozen coronal slabs. The study was funded by the DIRP, NIMH under contract (#HHSN 271201400099C) with Icahn School of Medicine at Mount Sinai,1106402 One Gustave L. Levy Place, Box 3500, New York NY 10029-6574. RNA extraction, library preparation and sequencing were performed under contract at Icahn School of Medicine. The Common Mind Consortium (CMC) provided project management support. RNA isolation: Total RNA from 468 HBCC samples was isolated from approximately 100 mg homogenized tissue from each sample by TRIzol/chloroform extraction and purification with the Qiagen RNeasy kit (Cat#74106) according to manufacturer's protocol. Samples were processed in randomized batches of 12. The order of extraction for schizophrenia, bipolar, and MDD disorders and control samples was assigned randomly with respect to diagnosis and all other sample characteristics. The mean total RNA yield was 24.2 ug (+/- 9.0). The RNA Integrity Number (RIN) was determined by 4200 Agilent TapeStation System. Samples with RIN DLPFC RNA-Seq quantified expression data are provided for 364 samples. Data were generated, QC'd, processed and quantified as follows: RNA library preparation and sequencing: All samples submitted to the New York Genome Center for RNAseq were prepared for sequencing in randomized batches of 94. The sequencing libraries were prepared using the KAPA Stranded RNAseq Kit with RiboErase (KAPA Biosystems). rRNA was depleted from 1ug of RNA using the KAPA RiboErase protocol that is integrated into the KAPA Stranded RNAseq Kit. The insert size and DNA concentration of the sequencing library was determined on Fragment Analyzer Automated CE System (Advanced Analytical) and Quant-iT PicoGreen (ThermoFisher) respectively. Schizophrenia Bipolar Control 89 65 210 Table: Numbers of samples in each diagnostic category. RNA-Seq of subgenual anterior cingulate cortex (sgACC): All the 200 post-mortem brain samples (61 controls; 39 bipolar disorder; 46 schizophrenia; 54 major depressive disorder) were collected by the HBCC, DIRP, NIMH. RNA Extraction and Quality Assessment: Tissue from sgACC was pulverized and stored at -80°C. Total RNA was extracted from 50-80 mg of the tissue using QIAGEN RNeasy Lipid Tissue Mini Kit (QIAGEN, Cat. # 74804) with DNase treatment (QIAGEN, Cat. # 79254). The RNA Integrity Number (RIN) for each sample was assessed with high-resolution capillary electrophoresis on the Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, California). The concentration of RNA and their 260/280 ratio (2.1+/- 0.032 SD) were determined with NanoDrop (Thermo Scientific). RNA sequencing: Stranded RNA-Seq libraries were constructed after rRNA depletion using Ribo-Zero GOLD (Illumina). RNA sequencing was performed at National Institute of Health Intramural Sequencing Center (NISC). Schizophrenia Bipolar Control MDD 46 39 61 54 Table: Numbers of samples in each diagnostic category. Whole Genome Sequencing: All brains were collected and dissected at the HBCC, DIRP, NIMH. This study generates whole genome sequencing data using sequencing of DNA in the dorsolateral prefrontal cortex (DLPFC), anterior cingulate cortex (ACC) or cerebellum of 443 individuals with schizophrenia, bipolar disorder and major depressive disorder and non-psychiatric controls. The study was funded by the DIRP, NIMH under contract (#HHSN 271201400099C) with Icahn School of Medicine at Mount Sinai,1106402 One Gustave L. Levy Place, Box 3500, New York NY 10029-6574. DNA extraction, library preparation and sequencing were performed under contract at Icahn School of Medicine. The Common Mind Consortium (CMC) provided project management support. All specimens were dissected from right or left hemisphere of frozen coronal slabs. DNA Library Preparation and Sequencing: All samples submitted to the New York Genome Center for WGS were prepared for sequencing in randomized batches of 95. The sequencing libraries were prepared using the Illumina PCR-free DNA sample preparation Kit. The insert size and DNA concentration of the sequencing library was determined on Fragment Analyzer Automated CE System (Advanced Analytical) and Quant-iT PicoGreen (ThermoFisher) respectively. A quantitative PCR assay (KAPA), with primers specific to the adapter sequence, was used to determine the yield and efficiency of the adaptor ligation process. Performed on the Illumina HiSeqX with 30X coverage. Schizophrenia Bipolar Control 115 78 230 Table: Numbers of samples in each diagnostic category. ChIP-Seq: All brains were collected and the dorsolateral prefrontal cortical (DLPFC) samples dissected at the HBCC, DIRP, NIMH. This study generates epigenetic data using sequencing of DNA after chromatin immunoprecipitation (ChIP-Seq) for marks H3K4me3 and H3K27ac in the dorsolateral prefrontal cortex (DLPFC). Dorsolateral prefrontal cortex (DLPFC) specimens were dissected from right or left hemisphere of frozen coronal slabs. The study was funded by the DIRP, NIMH under contract (#HHSN 271201400099C) with Icahn School of Medicine at Mount Sinai,1106402 One Gustave L. Levy Place, Box 3500, New York NY 10029,6574. Chromatin precipitation, library preparation and sequencing were performed under contract at Icahn School of Medicine. The Common Mind Consortium (CMC) provided project management support. Chromatin immunoprecipitation (ChIP) assays for histone marks H3K4me3 and H3K27ac were carried out using Native ChIP. Micrococcal Nuclease (MNase) (Sigma, N3755) treatment was used to digest chromatin into mononucleosomes. The following antibodies were used for chromatin pull-down: anti-H3K4me3 (Cell Signaling, Cat# 9751BC, lot 7) and anti-H3K27ac (Active Motif, Cat# 39133, Lot # 31814008). Histone modification-enriched genomic DNA fragments were recovered using Protein A/G magnetic beads (Thermo Scientific, 88803-88938 or Millipore 16-663), and then washed, eluted, and treated with RNAse A and proteinase K. Final ChIP DNA products were isolated using phenol-chloroform extraction followed by ethanol precipitation. The efficiency of each ChIP assay was validated using Qubit concentration measurement and qPCR for positive (GRIN2B, DARPP32) and negative (HBB) control genomic regions. Only ChIP assays that passed quality control were further processed for library preparation and sequencing; this included ChIP DNA that was not detectable on Qubit but showed a good signal and expected enrichment patterns in qPCR. HISTONE_MARK H3K27ac H3K4me3 Input Bipolar 56 4 7 Control 158 11 24 Schizophrenia 79 11 12 Table: Numbers of individuals in each assay grouped by histone mark or input.Long-Read Whole-Genome Sequencing (WGS) Cohort Description: Brain specimens were obtained from the Human Brain Collection Core (HBCC), part of the NIH NeuroBioBank. Samples were collected under protocols approved by the NIH CNS Institutional Review Board (IRB) (NCT03092687), with informed consent from next-of-kin (NOK). Collection was coordinated through the Offices of the Chief Medical Examiners (MEOs) in Washington, D.C., Northern Virginia, and Central Virginia. Clinical metadata and documentation are publicly available via the NIMH Data Archive (NDA) (Collection #3151) https://nda.nih.gov/edit_collection.html?id=3151 Eligibility Criteria No clinical diagnosis of major neuropsychiatric or neurodegenerative diseaseNo diagnosis of cognitive impairment during life All individuals were confirmed to be neurologically normal at time of deathDemographics Initial cohort size: 155 individuals Ancestry: All individuals self-identified as African or African-admixed Mean age at death: 44.2 years (range: 18–85 years) Sex distribution: 36.4% femaleSample Processing: Frozen frontal cortex tissue was dissected and processed according to the public protocol: https://www.protocols.io/view/processing-human-frontal-cortex-brain-tissue-for-p-kxygxzmmov8j/v2. High-molecular-weight DNA was extracted and libraries were prepared using the Oxford Nanopore Technologies (ONT) LSK-114 kit. Sequencing was performed using ONT PromethION flow cells (R10.4.1 chemistry) Data Processing and Quality Control: Basecalling: Conducted using Guppy v6.38 Read Alignment: Reads were aligned to the GRCh38 reference genome using minimap2 Sample Identity Verification: Sample identity was validated by comparing ONT-derived SNP calls with matched short-read WGS genotypes to ensure concordance and prevent sample swaps Variant Calling and Phasing: Reads were base-called with Guppy v6.38. Reads were aligned to GRCh38 using minimap2. We verified sample identity by cross-checking ONT SNV calls with the existing short-read WGS genotypes, confirming no sample switches. The napu pipeline (https://github.com/nanoporegenomics/napu_wf) produced; haplotype-resolved assemblies, joint small-variant (SNV/indel) calls, and multi-caller structural-variant sets, all reported on GRCh38 and phased where possible. Raw signal data were basecalled to obtain 5-methyl-cytosine (5mC) status; methylation tags were added to the phased BAM files. Genome-wide methylation summaries are provided in BED format.Dataset Filtering and Exclusions: All 155 samples underwent sequencing and SNP-based ancestry inference 8 samples were excluded due to ancestry inconsistent with African or African-admixed background 1 sample was excluded due to insufficient sequencing quality Final Sample Set: 146 high-quality samples from individuals of African or African-admixed ancestry were retained for downstream analyses See PMID: 39764002 for further analysis detailsDiagnosis#SamplesControl155Table: Diagnostic Summary.Note: The data derived from HBCC resources were removed from dbGAP and are now available in the NIMH Data Archive (NDA). They include genotypes, short read whole genome sequencing (WGS), epigenetics (DNA methylation, ChIP-seq for histones), RNA expression (qPCR, microarray, RNA-seq, single nucleus RNA-seq) of various brain regions in cases with schizophrenia, bipolar disorder, major depression, substance use disorders and normative controls. Please access our NDA collection (https://nda.nih.gov/edit_collection.html?id=3151) for further detail.

  Study phs000979

• Allogeneic induced pluripotent stem (iPS) cell-derived cartilage transplantation for articular cartilage damage in knee joints: a phase I, first-in-human study

  Damaged articular cartilage seldom heals due to a limited capacity for self-repair, frequently leading to osteoarthritis. Regenerative interventions are expected to heal the damage. We have recently established a method to produce cartilage from induced pluripotent stem cells (iPSCs) in a clinically applicable process. The primary aim of this study was to evaluate the safety including tumorigenesis and the subsequence efficacy of allogeneic iPSC-derived cartilage transplantation into damaged areas of knee articular cartilage.

  Study EGAS50000001167

• T1DGC GWAS 1958 British Birth Cohort controls

  T1DGC genome-wide case-control association study for Type 1 Diabetes (T1D) using the 1958 British Birth Cohort as controls. The cases for this study are made available from the NCBI dbGAP.

  Study EGAS00000000038

• Transcriptomic profiles studies CAREs group - IDIBGI

  The purpose of this DAC document is to outline the principles and procedures governing access to the transcriptomic data generated from endothelial progenitor cells, or any biological origin from patients. Data Access Policy: 1) Access to this dataset is restricted and subject to approval by the DAC to ensure ethical and legal compliance. 2) The DAC reserves the right to evaluate all applications for access based on: 2.1) The scientific validity and merit of the proposed research. 2.2) The ethical considerations and adherence to data protection regulations, including GDPR. 2.3) The qualifications and affiliations of the applicants. 3) Applicants must submit a detailed research proposal, including objectives, methods, and anticipated outcomes. 4) Data usage is limited to the specified research project approved by the DAC. Any secondary use of the data requires additional approval. Confidentiality: All applicants must agree to maintain the confidentiality of the dataset. Personal identifiers have been pseudonymized to protect patient privacy. Application Process: 1) Researchers must complete the application form provided by the DAC. 2) Submit proof of ethical approval and relevant certifications for their research project. 3) Provide a signed agreement affirming adherence to the DAC's terms and conditions.

  Dac EGAC50000000607

• Dataset for "HPV integration induces gene fusions" (Illumina)

  Illumina whole-genome sequencing data for "HPV integration induces gene fusions" We performed short read whole-genome sequencing of five HPV+ head and neck cancer samples using Illumina. The reads are submitted in bam or fastq file format.

  Dataset EGAD50000001305

• Whole-genome sequencing data for inflammatory breast cancer patients

  This study reports the whole-genome sequencing data for 20 inflammatory breast cancer patients, each of whom has one normal blood sample and one breast tumor sample. Overall, there are 40 files included in this study, in the format of BAM.

  Dataset EGAD00001005749

• CHUM HNSCC biobank

  This Data Access Committee is responsible for reviewing and approving access requests to denominalized datasets generated by the CHUM HNSCC biobank, ensuring compliance with participant consent and ethical approvals.

  Dac EGAC50000001004

• Adipose Tissue Omics In Obesity

  This project used a multi-omics approach to study the adipose tissue transcriptome in humans with and without obesity. Our human cohort included males and females between the ages of 18-80 who underwent elective abdominal surgery at the University of Michigan and the Ann Arbor Veterans Affairs Healthcare System.Patients with advanced cancer or immuncompromised status were excluded. Visceral adipose tissue (VAT/omental) and subcutaneous adipose tissue (SAT/abdominal wall) were collected from subjects with obesity (BMI>=35) at the beginning of elective surgical procedures, placed on ice, and transported back to the laboratory for immediate processing. For adipose tissue stromal cells (ASC) isolation, adipose tissue was digested with Type II collagenase (2 mg/mL in PBS/2% BSA) at 37oC, 60min, centrifuged at 250 rcf, and the stromal-vascular cell pellet was retrieved, plated overnight, and the adherent cells passaged three times to enrich for ASC, which were then frozen in DMEM/F12, 15% fetal calf serum, and 10% DMSO in liquid nitrogen until use. Single nuclear sequencing was performed on preparations from intact adipose tissue. Bulk RNA sequencing and single cell sequencing were performed on ASC isolated from intact adipose tissue and cultured in 2D and 3D culture systems. We currently apply bulk, single cell, and single nuclear sequencing analyses to these tissues. One component of this project studies single nuclear sequencing in nuclei isolated from intact adipose tissues from human subjects with obesity, focusing on depot comparisons (VAT vs. SAT). This cohort also permits comparisons of adipose tissue transcriptomes between male and female subjects, controlling for age and BMI. Primary findings to date include identification of multiple ASC, adipocyte, and endothelial cell (EC) subpopulations, T-cell, and macrophage (MAC) populations that are in concordance with and expand upon other published datasets. Of two dominant ASC subpopulations, one (inflammatory-mesothelial, IM- ASC) is present in VAT, but absent in SAT, while the other (fibroadipogenic, FA-ASC) is present in both VAT and SAT. We identified multiple EC subtypes with features of lymphatic, venous, and arterial EC, and a PRDM16 expressing population with features of an EC progenitor. Immune cell populations match recent experimental validation of lipid-activated macrophage (LAM) phenotypes, TIM4 macrophages, and a prominent population of MRC1/CD206+ resident AT macrophages with expression signatures related to glucocorticoid activation. These data support depot-specific differences in ASC subpopulations and previously unrecognized EC heterogeneity within human AT, with the potential to shed light on functional differences in AT depot and disease state. Planned future studies include ATAC-Seq and other omics analyses. Another component of this project studies transcriptional responses of ASC in vitro to various stimuli, including different matrix environments. Current data includes bulk RNA Sequencing of human ASC from VAT and SAT differentiated into mature adipocytes in hydrogels of differing stiffness (3%, 5%, 10%) to define transcriptional responses to matrix environments of different stiffness. Primary findings to date include enrichment of adipogenesis and lipid and oxidative metabolic gene pathways in adipocytes in 5% relative to 3% hydrogels, while fibrotic gene pathways have been enriched in 3% hydrogels. These data demonstrate that intermediate density matrix promotes a more adipogenic, less fibrotic adipocyte phenotype geared towards increased lipid and aerobic metabolism. Planned future studies include expansion of intact tissues from our cohort studied with single nuclear sequencing, as well as further study of ASC responses in vitro to different biologic stimuli, including different matrix environments.

  Study phs003390

• Gut metagenome/FINRISK 2002 (Salosensaari et al. Nature Comms 2021)

  The main goal of the project is the study the associations between the gut metagenome and human health. The dataset contains data for n=7211 FINRISK 2002 participants who underwent fecal sampling. Demultiplexed shallow shotgun metagenomic sequences were quality filtered and adapter trimmed using Atropos (Didion et al., 2017), and human filtered using Bowtie2 (Langmead and Salzberg, 2012).

  Study EGAS00001005020

• Preeclampsia InterPregGen Consortium: Whole Genome Sequencing of 100 unrelated Uzbeks (DNA samples from the Institute of Immunology, Uzbek Academy of Sciences, Tashkent, Uzbekistan; Republic Specialized Scientific Practical Medical Centre of Obstetrics and Gynecology, Tashkent, Uzbekistan)

  Whole genome sequencing of 100 unrelated Uzbeks in order to impute genotypes into PE cases and controls from Uzbekistan and to provide genetic data and infrastructure for future genetic studies in Uzbekistan and Central Asia more generally and to fill a gap in worldwide information as Central Asia is not adequately represented in available genomic data. This dataset is one component of the InterPregGen FP7 project. DNA samples for this component were collected by InterPregGen Consortium collaborators in Tashkent, Uzbekistan at the Institute of Immunology, Uzbek Academy of Sciences and at the Republic Specialized Scientific Practical Medical Centre of Obstetrics and Gynecology.

  Dataset EGAD00001005466

• VA APOLLO Project - Research for Precision Oncology (RePOP)

  The Research for Precision Oncology Program (RePOP) is a research activity that establishes a cohort of Veterans diagnosed with cancer and who have had genomic analyses performed on their tumor tissue as part of standard of care. All data relevant to a patient's cancer and cancer care will be collected under RePOP, including patient demographics, co-morbidities, genomic analysis, treatments, medications, lab values, imaging studies, and outcomes. All RePOP participants will have signed/verbal informed consent and signed HIPAA authorization to have their data stored and shared from RePOP's Precision Oncology Program Data Repository (PODR). The Applied Proteogenomics OrganizationaL Learning and Outcomes (APOLLO) network is a collaboration between NCI, the Department of Defense (DoD), and the Department of Veterans Affairs (VA) to incorporate proteogenomics into patient care as a way of looking beyond the genome, to the activity and expression of the proteins that the genome encodes. The emerging field of proteogenomics aims to better predict how patients will respond to therapy by screening their tumors for both genetic abnormalities and protein information, an approach that has been made possible in recent years due to advances in proteomic technology.

  Study phs001374

• Single-Cell Multiomics of the Immune Microenvironment in T-Cell Acute Lymphoblastic Leukemia

  We present single-cell transcriptome and surface protein expression (CITE-seq) data from four healthy donors and fifteen pediatric T cell acute lymphoblastic leukemia (T-ALL) patients at diagnosis and at different treatment timepoints (days 1 – 6 and at time of remission). Mononuclear cells from peripheral blood (PB; longitudinal) or bone marrow (BM; diagnosis only) were isolated and CD45high immune cells and CD45dimCD7+ malignant cells were sorted and subsequently pooled to enrich for immune cells. For comparison,CD45high immune cells from four healthy donors were also sorted. Single-cell sequencing of the transcriptome and surface protein expression (204 antibodies) was performed using the 10x Genomics platform.Multiomics analyses resulted in the identification of a T-ALL subgroup characterized by a remodeled immune microenvironment at initial diagnosis. This immune landscape is dominated by the presence of non-malignant CD4-CD8-TCRab T cells that interact with CXCL16 expressing non-classical monocytes. Leukemia cell intrinsic transcriptional rewiring in these patients is associated with activation of Rap1 signaling.

  Study phs004269

• Examination of Engineered LINE-1 Integration Events in HeLa Cells

  Long Interspsesed Element-1 (LINE1 or L1) encodes two proteins (ORF1p and ORF2p) required for its mobilization (i.e. retrotransposition) in the human genome. Human ORF2p, a 150kDa protein, has endonuclease (EN) and reverse transcriptase (RT) activities. L1 EN is classified as apurinic/apyrimidin-like endonuclease (APE) and is responsible for initiating target-site primer reverse transcription (TPRT) during the L1 retrotransposition cycle. During canonical TPRT, the L1 EN activity makes a single-strand endonucleolytic nick at a double-strand DNA target sequence in genomic DNA. The endonucleolytic nick is typically made at an L1 EN degnerate consensus cleavage sequence (5'-TTTT/A-3') exposing a free 3' hydroxy group that can be used as a primer by the ORF2p L1 RT activity to reverse transcribe the associated L1 RNA. Here, we characterized over 21,000 de novo engineered L1 retrotransposition events in HeLa cells to determine if L1 exhibits overt integration preferences in the human genome. Bru-seq of HeLa cells to determine actively transcribed regions of the genome was also performed. This Bru-seq data was used to determine if engineered L1 integration events preferentially integrate into transcribed regions of the genome, and to determine which strand during transcription may present itself as preferential during L1 retrotransposition.

  Study phs001669