3909 results for "*geneti*"

in 29.03 milliseconds.

• Genome Sequencing and Variant Calling of HCM Patients with MYH7 Variants

  To investigate potential genetic causes of cardiomyopathy we recruited 48 patients harboring rare MYH7 variants identified from panel-based testing and with a clinical manifestation of cardiomyopathy. Genome sequencing was performed to identify other potential causative variants and genetic modifiers of the cardiomyopathy phenotype, which varied among patients.

  Study phs004024

• Identifying the Genetic Basis of Variably Protease-Sensitive Prionopathy (VPSPr)

  Design: Sequencing of cases onlyMolecular technologies: Exome sequencing and custom targeted sequencing of PRNPAims: Identify modestly penetrant, high odds ratio variants conferring risk of variably protease-sensitive prionopathy (VPSPr)Population: n=67 autopsy-confirmed VPSPr cases, United States, 1997-2021Principal findings: Association to PRNP M129V replicated, no other causal variants identifiedData available: Raw sequencing data and metadata

  Study phs004012

• Epigenetic Control of Topoisomerase 1 by MacroH2A1.1

  DNA transactions introduce torsional constraints that pose an inherent risk to genome integrity. While topoisomerase 1 (TOP1) activity is essential for removing DNA supercoiling, aberrant stabilization of TOP1:DNA cleavage complexes (TOP1ccs) can result in cytotoxic single-stranded DNA lesions (SSLs). What protects the genome from aberrant TOP1 activity remains unknown. Using a combination of CUT&RUN and TOP1 Covalent Adduct Detection (CAD) Seq in MDA-MB-231 breast cancer cells (American Type Culture Collection, ATCC), we identified chromatin context as an essential means to ensure TOP1cc resolution at TOP1 hot spots. Through its ability to bind poly(ADP-ribose) (PAR), a protein modification required for TOP1cc repair, the histone variant macroH2A1.1 establishes a TOP1-permissive chromatin environment, while the alternatively spliced macroH2A1.2 isoform is unable to bind PAR or protect from TOP1ccs. MacroH2A1 isoform-specific analyses were based on reconstitution of macroH2A1.1 knockout cells with wild-type or PAR binding-deficient FLAG-tagged macroH2A1.1 in human breast cancer cells. Mechanistically, we find that macroH2A1.1 facilitates the recruitment of the TOP1cc repair factor XRCC1 in response to both endogenous and drug-induced topological stress. Impaired macroH2A1.1 splicing, a frequent cancer feature, was predictive of increased sensitivity to TOP1 poisons in a pharmaco-genomic screen in breast cancer cells, and macroH2A1.1 inactivation mirrored this effect in breast and ovarian cancer cells. Consistent with this, low macroH2A1.1 expression correlated with improved survival in cancer patients treated with TOP1 inhibitors (TOP1i). We propose that macroH2A1 alternative splicing serves as an epigenetic modulator of TOP1-associated genome maintenance and a potential cancer vulnerability.

  Study phs003729

• Epigenetic profiling of primary human thymocyte subsets

  Dynamic changes of the DNA methylation (DNAmeth) landscape drive differentiation of mature T lymphocytes. However, the role of DNAmeth-mediated regulation in thymocyte development remains unclear. Thus, we generated genome-wide DNAmeth and transcriptomic profiles of eight defined, ex vivo isolated primary human thymocyte subsets, to assess the epigenetic remodling taking place during human thymic T cell development. The generated data may also serve as a reference for the analysis of T cell-based inborn errors of immunity or for quality control purposes of in vitro generated T cell populations.

  Study EGAS50000001106

• DHODH is a synthetic-lethal vulnerability in BCOR-deficient acute myeloid leukemia

  Acute Myeloid Leukemia (AML) remains challenging to treat, especially in cases with mutations in the BCL-6 co- repressor (BCOR), which are associated with poor prognosis and chemo-resistance. In this study, we reveal a synthetic lethal interaction between BCOR and dihydroorotate dehydrogenase (DHODH). We demonstrate that BCOR-deficient cells have a heightened sensitivity to DHODH inhibitors such as brequinar and leflunomide, that are already in clinical use. We confirm that DHODH inhibition selectively induces cell death in BCOR-mutant cells in multiple cellular models, in malignant and non-malignant cells, through chemical and genetic manipulation. Interestingly, we find that the dependency on DHODH does not stem from its role in de novo pyrimidine biosynthesis disruption. Rather, DHODH’s role in the electron transport chain, essential for mitigating reactive oxygen species, may be the physiological vulnerability that pushes BCOR-mutant cells toward cell death when DHODH is inhibited. DHODH inhibitors could be repurposed as targeted therapies for BCOR-mutant tumors, offering a promising strategy for precision medicine in AML and other cancers.

  Study EGAS50000001060

• Batches 1-3 prostatectomy analysis

  Whole Genome Sequencing Illumina HiSeq data from 95 men with prostate cancer. Samples were taken from primary tissue obtained at prostatectomy (target sequencing depth 50X) with matched blood control (target sequencing depth 30X). This data is from batches 1 to 3 and is the bulk of the data used in Wedge et al, Nature Genetics 2018 (PMID: 29662167). As of September 2020, some of the studies using these data include: Wedge et al, Nature Genetics 2018 (PMID: 29662167) Pan-Cancer Analysis of Whole Genomes, Nature 2020 (PMID: 32025007)

  Dataset EGAD00001001116

• Emirati Genome Project subset of 43,608 WGS samples for population-scale variant discovery and allele frequency mapping.

  Here, we present a comprehensive genomic characterization of a cohort of 43,608 Emirati genomes sequenced as part of the Emirati Genome Program (EGP). This study identified more than 421 million single nucleotide variants and indels and more than 600 million copy number- and structural variants. Small variants had 756 million molecular effects annotated. Of the identified variants, 69.04% were observed with more than one allele. Of 7.7 million polymorphic variants having an allele frequency (AF) of more than 5% in EGP, 1,348 have a predicted deleterious effect on a protein. Characterization of global variation reveals that EGP represents a genetic continuum encompassing the range of African, Asian, and European populations. It is best described by two Arabian, an Eurasian, and an African component, with the predominant Arabian component linked to mitochondrial haplogroups J and T, which are commonly attributed to the Middle East. Various aneuploidies of sex chromosomes were detected in 93 individuals overall and of chromosome 21 in 41 individuals. The median inbreeding coefficient and cumulative runs of homozygosity (ROHs) lengths were increased due to extensive consanguinity, being largest in the groups with Arabian main ancestry components and higher than reported for Qatar. Families were identified based on genetic relatedness and classified into 264 families with unrelated parents and 247 families with third- and fourth-degree consanguineous parents. Representative consanguineous pedigrees of families in EGP were outlined. Cumulative ROHs were affected by the main ancestry component and significantly increased in offspring of consanguineous parents, with a pronounced difference between 3rd and 4th-degree relatedness. Investigation of cumulative AFs of variants causing Mendelian diseases highlighted genes related to alpha- and beta-thalassemia (HBB, HBA2). It showed a high burden of variants causing severe recessive diseases, metabolic and retinal disorders, and hearing loss. In summary, EGP represents a landmark effort in characterizing the genetic diversity of the Emirati population, leveraging the largest Middle Eastern cohort reported to date.

  Study EGAS50000001071

• Omic Studies in Children's Respiratory and Environmental Workgroup (CREW) Cohorts

  Children's Respiratory Research Workgroup (CREW) is an NIH-funded project consisting of multiple individual U.S. cohorts and three scientific centers working together to identify phenotypes and causes of childhood asthma. CREW will include data from a large number of children and their families, with broad diversity in terms of ethnicity, family characteristics, neighborhoods and geographic locations. One of the primary goals of CREW is to put together sets of data and samples of participating cohorts to identify phenotypes of childhood asthma (i.e. specific subtypes of asthma that can be distinguished by clinical features such as natural history, triggers, exacerbation frequency, concurrent allergies, lung function, sex, etc). Omics studies will include genotyping, methylation, and RNA sequencing. By integrating the DNA genotyping with the expression, immunologic and clinical data, we will identify eQTL, inflammation QTL, and lung function QTL, as well as QTL associated with other biomarkers. Analyses will identify genetic, epigenetic, transcriptional and protein/metabolite profiles that are associated with specific exposures or phenotypes. As we obtain mechanistic insights about personal and early life risk factors, we will connect asthma phenotypes with underlying causes and pathogenic mechanisms to define endotypes of childhood asthma.

  Study phs004036

• Prevention and Early Treatment of Acute Lung Injury (PETAL) Crystalloid Liberal or Vasopressors Early Resuscitation in Sepsis (CLOVERS) (PETAL CLOVERS-BioLINCC)

  Data Access NOTE: Please refer to the "Authorized Access" section below for information about how access to the data from this accession differs from many other dbGaP accessions. Access to Biospecimens is through the NHLBI Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC). Biospecimens from PETAL CLOVERS include plasma, and whole blood. Please note that use of biospecimens in genetic research is subject to a tiered consent. Available Data: The data available for request now include Long Term Outcome data.Objectives: To compare the effects of a restrictive fluid strategy (with early use of vasopressors) to a liberal fluid strategy in participants with sepsis-induced hypotension.Background: Intravenous fluid resuscitation is a common therapy used in the initial treatment of participants with septic shock and sepsis-induced hypotension. The goal of initial fluid therapy is to increase depleted or functionally reduced intravascular volume that occurs in sepsis due to a vasodilated vascular network. However, intravenous fluid resuscitation can create dilutional coagulopathy, fluid overload, and pathogenic edema in the lungs and other organs. Vasopressor agents are also commonly used to treat hypoperfusion by inducing constriction of arterioles and venules and increasing cardiac contractility. Vasopressor therapy also comes with risks that include vasoconstriction resulting in tissue ischemia, increased cardiac workload, and arrhythmias. Clinicians have used these strategies, typically in combination, to provide supportive care for participants with sepsis-induced hypoperfusion. However, at the time of the CLOVERS study, there was limited data to guide specific use of these therapies, including fluid volumes, in the early care of participants with sepsis-induced hypotension. The CLOVERS study hypothesized that a restrictive fluid strategy used during the first 24-hours of resuscitation for sepsis-induced hypotension would lead to lower mortality before discharge home by day 90 than a liberal fluid strategy.Participants: A total of 1,563 participants, from 60 medical centers, of the planned 2,230 participants were enrolled, with 782 assigned to the restrictive fluid group and 781 to the liberal fluid group. Enrollment in the trial was ended after the second interim analysis due to a lack of significant difference observed between the two 24-hour strategies.Design: This study was a multi-center, prospective, phase 3 randomized non-blinded interventional trial of fluid treatment strategies in the first 24 hours for participants with sepsis-induced hypotension. Participants were randomly assigned in a 1:1 ratio to either a restrictive fluid strategy (with early vasopressor use) or a liberal fluid strategy. In each group, the assigned protocol was followed for a period of 24 hours. The restrictive fluid protocol prioritized vasopressors as the primary treatment for sepsis-induced hypotension, with 'rescue fluids' being permitted for prespecified indications that suggested severe intravascular volume depletion. The liberal fluid protocol consisted of a recommended initial 2000-ml intravenous infusion of isotonic crystalloid, followed by fluid boluses administered on the basis of clinical triggers (e.g., tachycardia) with 'rescue vasopressors' permitted for prespecified indications. A protocol amendment implemented in October, 2019, allowed for limiting the initial infusion to 1,000 ml if the participant's blood pressure and heart rate had stabilized and the clinical assessment was that the participant was unlikely to benefit from additional intravenous fluid administration. The clinical team could override the protocol-specified care instructions at any time if it was judged to be in the best interest of the participant.The primary outcome was death from any cause before discharge home by day 90. Secondary outcomes included 28-day measures of the number of days free from ventilator use, days free from renal-replacement therapy, days free from vasopressor use, days out of the ICU, and days out of the hospital. Conclusions: Among participants with sepsis-induced hypotension, the restrictive fluid strategy that was used in this trial did not result in significantly lower (or higher) mortality, or other measures of recovery such as length of hospital stay, before discharge home by day 90 than the liberal fluid strategy.

  Study phs004080

• Re-Evaluation of Systemic Early Neuromuscular Blockade

  This study of the ROSE trial data explored two distinct molecular subtypes of ARDS (Acute Respiratory Distress Syndrome) to better understand the disease's complexity and potential for personalized treatment. Previous studies had identified different inflammatory profiles in ARDS patients, with this research addressing three key questions: Can these molecular subtypes be consistently identified in a more severe group of ARDS patients? Do these subtypes respond differently to neuromuscular blockade treatment? What specific biological processes differentiate these inflammatory profiles? Advanced transcriptomic and protein analyses examined blood samples from ARDS patients. Analysis of these data revealed two main molecular phenotypes: Hypoinflammatory phenotype (60.4% of patients) Hyperinflammatory phenotype (39.6% of patients) Key findings demonstrated that the hyperinflammatory subtype was associated with:Significantly higher mortality rates relative to hypoinflammatory (61.6% vs. 30.3%)Significantly higher mortality rates relative to hypoinflammatory (61.6% vs. 30.3%)Distinct gene expression patterns related to immune responseUnique changes in genes associated with tissue remodeling and cellular processes Notably, the neuromuscular blockade treatment showed no difference in effects across these subtypes. Complex relationships emerged between gene expression and protein levels, with some genes closely matching their protein counterparts and others displaying more variable connections. The study concludes that these molecular phenotypes possess distinct clinical, protein, and genetic characteristics, suggesting potential for more precise, personalized approaches to ARDS treatment in the future.

  Study phs003929

• Oncogenome of Kaposi Sarcoma

  Kaposi Sarcoma (KS) is an aggressive cancer caused by the Kaposi Sarcoma Herpesvirus (KSHV/HHV-8). Individuals with immunodeficiencies, exemplified by HIV, have an elevated risk of developing KS. However, understanding of the genetic factors contributing to KS progression is still limited. To explore potential genetic alterations in KS that could offer biological or therapeutic insights, whole exome sequencing was performed on 78 KS tumors and matching normal skin samples from 59 adults with KS (46 with HIV-associated KS and 13 with HIV-negative KS) receiving treatment at the Uganda Cancer Institute in Kampala, Uganda. Results showed a very low mutational burden in all samples except one (median = 11 mutations), which is the smallest number of mutations found across all 33 cancer types in The Cancer Genome Atlas (TCGA). No recurrent mutations were identified. Mutational signatures included impaired DNA mismatch repair and smoking. There was no evidence suggesting that multiple tumors from the same patient originated from a single clone. The number of genome copy alterations per genome was higher in tumors from individuals without HIV and those with advanced-stage disease. This suggests that lesions that take longer to develop may accumulate more alterations, although the overall number of alterations remains low compared to other cancers. These findings suggest that KS pathogenesis differs from other cancers, with KSHV viral infection and the expression of viral oncogenes being the primary drivers of carcinogenesis, rather than clonal oncogenic transformation arising from genetic alterations of cancer-related cellular genes.

  Study phs003897

• Collagen XVII Promotes Pancreatic Cancer Through Regulation of PIK3R5

  Pancreatic ductal adenocarcinoma (PDAC) contains a desmoplastic stroma that promotes the aggressive biology of this disease. While the varied mechanisms by which fibrillar collagens contribute to PDAC have been defined, little is known about the contribution of transmembrane collagens. Among this class of collagens, Collagen XVII uniquely contains an extensive intracellular domain that connects intracellular cytoplasmic components with the extracellular matrix. Collagen XVII is best characterized as the defining component of the type I hemidesmosome, an anchoring complex that attaches epithelial cells to the underlying basement membrane. In this study, we characterize the expression of collagen XVII in PDAC and the mechanisms by which it contributes to PDAC biology. We demonstrate that crosstalk between PDAC cells and cancer associated fibroblasts drive collagen XVII expression in vitro and xenograft tumor models in vivo. Genetic depletion of collagen XVII in low-passage patient derived cell lines diminishes their metastatic potential and ability to form tumors in mice. Whole transcriptome sequencing of tumors formed by cells with diminished collagen XVII levels revealed dramatically lower levels of PIK3R5, a regulatory subunit of class IB phosphatidylinositol-3-kinase (PI3K) that interacts with G protein-coupled receptors. Consistent with this, collagen XVII-deficient tumors exhibited lower levels of phosphorylated AKT, a downstream effector of PI3K. The studies highlight the importance of collagen XVII signaling in PDAC and define a novel mechanism by which collagen XVII mediates activation of PI3K.

  Study phs003641

• NHLBI TOPMed: Lung Tissue Research Consortium (LTRC)

  Chronic obstructive pulmonary disease (COPD), a disease state characterized by airflow limitation that is not fully reversible, is the third leading cause of death in the U.S. COPD is a heterogeneous syndrome, with affected individuals demonstrating marked differences in lung structure (emphysema vs. airway disease); physiology (airflow obstruction); and other clinical features (e.g., exacerbations, co-morbid illnesses). Multiple genomic regions influencing COPD susceptibility have been identified by genome-wide association studies (GWAS), and rare coding variants can also influence risk for COPD. However, only a small percentage of the estimated heritability for COPD risk can be explained by known genetic loci. Like most complex diseases, COPD is influenced by multiple genetic determinants (each with modest individual effects). Emerging evidence supports the paradigm that complex disease genetic determinants are part of a network of interacting genes and proteins; perturbations of this network can increase disease risk. To identify this network, multiple Omics data will need to be analyzed with methods to account for nonlinear relationships and interactions between key genes and proteins. Our overall hypothesis is that integrated network analysis of genetic, transcriptomic, proteomic, and epigenetic data from biospecimens ranging from lung tissue to nasal epithelial cells to blood in highly phenotyped subjects will provide insights into COPD pathogenesis and heterogeneity. We will leverage the well-phenotyped, NHLBI-funded Lung Tissue Research Consortium (LTRC) to address these questions. We will perform multi-omics analysis in 1548 lung tissue and blood samples from the LTRC. With these multi-omics data, we will utilize a systems biology approach to understand relationships between multiple genetic determinants and multiple types of Omics data. We will begin by performing single Omics analyses in COPD vs. control lung, nasal, and blood samples. Next, we will integrate single Omics data with genetic variants identified by WGS to assist in fine mapping genetic determinants of COPD. We will then perform integrated network analysis of COPD with genetic and multiple Omics data using correlation-based, gene regulatory, and Bayesian networks. Subjects were recruited from Mayo Clinic, Universities of Colorado, Michigan, and Pittsburgh, and Temple University.

  Study phs001662

• 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

• Repeat expansions with small TTTCA insertions in MARCHF6 cause Familial Adult Myoclonus without Epilepsy

  Familial Adult Myoclonic Epilepsy (FAME) is a rare autosomal dominant disorder characterized by cortical tremulous myoclonus and generalized tonic clonic (GTCS) or myoclonic seizures. Intrafamilial variability regarding the prevalence of seizure has been reported. Despite apparent genetic heterogeneity, FAME is caused by the same TTTTA/TTTCA pentanucleotide repeat expansion in introns of seven different genes with no common function. Expansions containing only TTTTA repeats are benign, and only expansions including a TTTCA expansion insertion, which can be located 3' to the TTTTA expansion or in the middle of the TTTTA repeats, are pathogenic. We aimed to identify the underlying genetic cause of dominant cortical myoclonus without GTCS in two unrelated families. We used a combination of repeat-primed PCR, long-range PCR and nanopore sequencing to detect and characterize expansions at known FAME loci. We report a novel configuration of the FAME3 repeat expansion in MARCHF6 segregating with cortical myoclonus without epilepsy GTCS in both families. This expansion predominantly comprises elongated TTTTA repeats, ranging from 388 to 454 repeats, with the presence of only 5-11 TTTCA repeats at its 3' terminus (i.e., 5’-(TTTTA)~388-454(TTTCA)5-11-3’). This configuration exhibits greater stability upon meiotic transmission but somatic variability in TTTCA repeat number was detected at low level in blood. We observed an inverse correlation between the number of TTTCA repeats and the age at myoclonus onset. This study shows that as little as five TTTCA juxtaposed with expanded TTTTA expansions is sufficient to cause cortical myoclonus without GTCS. This finding has implications regarding possible pathophysiological mechanisms leading to FAME.

  Study EGAS50000000570

• KAT6A and KAT7 Histone Acetyltransferase Complexes Are Molecular Dependencies and Therapeutic Targets in NUP98-Rearranged Acute Myeloid Leukemia

  NUP98 fusion oncoproteins (FOs) are a hallmark of childhood acute myeloid leukemia (AML). NUP98 FOs drive leukemogenesis through phase-separated condensate formation and maintenance of an active chromatin landscape at stem cell-associated genes in cooperation with epigenetic regulators. Here we show that MYST family histone acetyltransferase (HAT) complex proteins including KAT6A/MOZ, KAT7/HBO1, and the common KAT6A/7 complex subunit BRPF1 associate with NUP98 FOs on chromatin and within condensates. MYST HATs are molecular dependencies in NUP98-rearranged (NUP98-r) leukemia, and genetic inactivation or pharmacologic inhibition of Kat6a and Kat7 impairs NUP98-r cell fitness. KAT6A/7 inhibition decreased global H3K23ac levels, displaced NUP98::HOXA9 from chromatin at the Meis1 locus, and led to myeloid cell differentiation. Additionally, KAT6A/7 inhibition decreased leukemic burden in multiple NUP98-r leukemia xenograft mouse models, synergized with Menin inhibitor treatment, and was efficacious in Menin inhibitor-resistant cells. In summary, we show that MYST family HATs are therapeutically actionable dependencies in NUP98-r AML.

  Study EGAS50000001075

• Direct genetic transformation bypasses tumor-associated DNA methylation alterations

  Tumors represent dynamically evolving populations of mutant cells, and many advances have been made in understanding the biology of their progression. However, key unresolved questions remain about the conditions that support their initial transformation, which cannot be easily captured in patient populations but are instead modeled using transgenic cellular or animal systems. Here, we used extensive patient atlas data to define common features of the tumor DNA methylation landscape as they compare to healthy human cells and used this benchmark to screen 21 engineered human and mouse models for their ability to reproduce these patterns. Notably, we find that genetically induced cellular transformation can trigger global changes in DNA methylation levels that are consistent with extensive proliferation but rarely recapitulate the widespread de novo methylation of Polycomb targets as found in clinical samples. Our results raise pertinent questions about the relationship between genetic and epigenetic aspects of tumorigenesis and provide an important molecular reference for evaluating existing as well as newer tumor models.

  Study EGAS50000000902

• Biallelic loss of function PAX4 variants are a Novel Cause of Transient Neonatal Diabetes

  The identification of genes in which loss of function (LoF) variants cause neonatal diabetes mellitus (NDM) can provide unique insights into the development and function of human pancreatic beta cells. We describe the identification of biallelic PAX4 LoF variants in 2 unrelated individuals with transient NDM: one due to a homozygous p.(Arg126*) PAX4 stop gain variant and a second due to a homozygous c.-352_104del 2.65kb deletion affecting the first 4 exons and promoter of the PAX4 Matched Annotation from NCBI and EMBL-EBI select transcript. We confirmed reduced transcript expression due to nonsense mediated decay for the e p.(Arg126*) variant in CRISPR-edited iPSC-derived pancreatic endoderm cells. Analysis of PAX4 binding through integration of CUT&RUN and RNA-sequencing in PAX4 depleted endocrine cells identified genes directly regulated by PAX4 involved in both pancreatic islet development and glucose-sensitive insulin secretion. The remitting and relapsing diabetes in both probands demonstrates that in contrast to mice PAX4 is not essential for the development of pancreatic beta-cells and supports differences in the requirements of functional beta-cell mass across the life-course.

  Study EGAS50000000857

• High-grade B-cell lymphoma, not otherwise specified: an LLMPP study

  Molecular characterization of high-grade B-cell lymphoma, not otherwise specified (HGBCL-NOS), is hindered by its rarity, evolving definition, and poor diagnostic reproducibility. To address this challenge, we analyzed 92 HGBCL-NOS tumors collected across Lymphoma/Leukemia Molecular Profiling Project sites. These tumors were profiled using whole-genome sequencing (WGS) or whole-exome sequencing (WES) to identify somatic mutations, WGS or low-pass WGS to detect copy number alterations, targeted capture sequencing to assess MYC and BCL2 structural variants, and RNA sequencing. The genetic features of HGBCL-NOS were compared to those of diffuse large B-cell lymphoma (DLBCL-NOS) and EBV-negative adult Burkitt lymphoma (BL). DLBCL-NOS tumors underwent targeted capture sequencing using a panel of 125 genes recurrently mutated in aggressive B-cell lymphomas. BL biopsies were drawn from the Burkitt Lymphoma Genome Sequencing Project and had available WGS (dbGaP Study Accession: phs000527.v18.p6).

  Study EGAS50000000932

• Germline WES of serrated polyposis syndrome

  The serrated polyposis syndrome (SPS) is a disease with a mainly unknown inherited genetic basis characterized by the presence of multiple and/or large serrated polyps in the colon and a higher associated risk for colorectal cancer (CRC). The objective of the present study was to identify new SPS/CRC germline predisposition genes by using whole-exome sequencing in two affected SPS patients from the same family.

  Study EGAS50000000765

• Admixture histories of São Tomé e Príncipe.

  In this study, we aim to reconstruct the complex genetic admixture histories of the population of São Tomé e Príncipe, an archipelago in the Gulf of Guinea that experienced successive waves of forced and deliberate migration from Africa since the 15th century, during and after the Trans-Atlantic Slave Trade.

  Study EGAS50000000920

• Enhancer profiling to identify identifies epigenetic markers of endocrine resistance in metastatic castration resistant prostate cancer patients

  Study EGAS00001006161

• Multi-omic analyses from a randomized phase II study of epigenetic priming followed by nivolumab in previously treated metastatic non-small cell lung cancer

  Emergence of resistance to immune checkpoint blockade (ICB) mandates the development of strategies for ICB sensitization. We aimed to understand the effects of epigenetic priming in re-shaping the tumor microenvironment, together with molecular drivers of therapeutic response of epigenetic therapy followed by ICB in non-small cell lung cancer (NSCLC; NCT01928576). This was done through a multi-omic approach encompassing both genomic and transcriptomic analyses. Findings suggest that epigenetic therapy may reshape the tumor microenvironment towards a more inflamed phenotype and prime responses to immunotherapy.

  Study EGAS50000000913

• Multi-omic dataset utilized in the analysis of a phase II study of epigenetic priming followed by nivolumab in lung cancer

  This dataset includes sequence files from whole exome sequencing and bulk RNA sequencing of tissue and blood biospecimens from a phase II clinical trial investigating epigenetic priming followed by immune checkpoint blockade in non-small cell lung cancer (NSCLC; NCT01928576). There are 78 whole exome sequencing files and 36 bulk RNA sequencing files included in this dataset.

  Dataset EGAD50000001336

• DAC for EGA study: Multi-omic analyses from a randomized phase II study of epigenetic priming followed by nivolumab in previously treated metastatic non-small cell lung cancer

  This is the Data Access Committee for the EGA study: Multi-omic analyses from a randomized phase II study of epigenetic priming followed by nivolumab in previously treated metastatic non-small cell lung cancer (temp ID 800).

  Dac EGAC50000000563