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• POT1_splice_site_mutant_analysis

  We are interested in the contribution mutations in the Shelterin complex protein POT1 may have to the development of melanoma. We have identified a patient who carries a splice site mutation in POT1 and as part of our analysis of this gene we aim to sequence the transcriptome of this patient to see how this mutation influences splicing. RNA has been obtained from lymphocytes collected from the patient.

  Study EGAS00001000571

• The_Little_Princess_Knowledge_Bank_RNAseq

  The purpose of the knowledge bank is to serve as a community resource and to address the following specific questions about Wilms tumour: (1) Do genetic, epigenetic, or transcriptional features predict outcome and thus lend themselves to treatment stratification? (2) What are the genetic drivers of Wilms tumour, considering the entire histological spectrum of Wilms tumour including the most common subtypes classified as intermediate risk?

  Study EGAS00001005244

• Familial_Thrombocytosis_germline_exome_sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 3 relatives from a family with multiple affected familial thrombocytosis (FT) patients. Germline DNA from 2-4 patients affected with FT will be used to prepare libraries and sequenced in one lane of HiSeq sequencing, mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Study EGAS00001000088

• Mixed_Leukemia_Rearrangement_Screen

  Genomic libraries will be generated from total genomic DNA derived from Mixed Leukemia and MPD samples and subjected to total of eight lanes of 37 bp, paired end sequencing on the illumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000180

• Whole_Genome_sequencing_of_individuals_from_Carlantino__Italy

  This study includes whole-genome sequencing data (at 4x depth) of 100 individuals from an Italian genetic isolate population (Carlantino, abbreviated CARL) of the Italian Network of Genetic Isolates (INGI). The INGI-CARL_SEQ project aims to combine available extensive genetic and phenotypic data to the latest high-throughput genome sequencing technology and ad hoc statistical analysis to identify new rare genetic variants underlying complex traits.

  Study EGAS00001000460

• Developing somatic copy number and mutation calling tools for a bespoke sequencing platform

  We previously developed a linked-read sequencing platform (DigiPico) for analysing whole cancer genomes from picogram quantities of tumour DNA. The aim of this study was to develop and evaluate the specialised computational approaches required to obtain clinically useful results from the raw data. To this end, we performed matched DigiPico, bulk tumour and germline WGS on samples from four patients.

  Study EGAS00001007195

• HipSci genotyping microarray for embryonic stem cell control lines

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we use commercially available embryonic stem cell lines as control samples against which to compare HipSci's iPS cell lines. We performed genotyping analysis using the Infinium HumanExome BeadChip.

  Study EGAS00001001730

• ET_Exome

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 50 Essential Thrombocythemia Myeloproliferative Disease samples and matched normal DNA from the same patients. Samples will be multiplexed in one lane of Illumina HiSeq. Sequencing to a coverage of at least 30x will be performed and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Study EGAS00001000102

• Glioma_cell_lines_rearrangement_screen

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from commomon epithelial cancer samples and subjected to total of eight lanes of 37 bp, paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000202

• HipSci Methylation analysis for embryonic stem cell control lines

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we use commercially available embryonic stem cell lines as control samples against which to compare HipSci's iPS cell lines. We performed Methylation analysis using the Infinium HumanMethylation450 BeadChip.

  Study EGAS00001001728

• Non_Tumour_Renal_Cell_Line_Sequencing

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from commomon epithelial cancer samples and subjected to total of eight lanes of 37 bp, paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000205

• Analysis of transcriptomic profiles from affected and recovered muscle biopsies from children with reversible infantile respiratory chain deficiency.

  All patients carry mitochondrial mutation m.14674T>C but not must also carry mutations in related genes such as TRMU and EARS2. Analysis compares muslce biopsies of affected patients to controls, a patient after recovery to themselves during the the disease phase, and compared patients with additional EARS2 mutations to patients without pathogenic EARS2 mutations.

  Study EGAS00001004647

• INSIGHT: VHL Case Report

  The overall goal of this study is to uncover contributors to inherited cancer through analysis of individuals and families with, or at risk of, a hereditary cancer syndrome. In addition, we hope to elucidate novel mechanisms of tumourigenesis in hereditary cancer patients. This specific report highlights a rare case of VHL mosaicism and shows the value of tissue testing in VHL variant negative cases.

  Study EGAS00001005895

• Somatic_mutation_in_skin_epidermis__SMS_

  We aim to assess the range and depth of mutations in genes linked with cancer in skin epidermis surrounding lesions which are undergoing surgical removal. Patient history will be collected to provide a detailed outline of tumour type (including histology), skin type, and sunlight exposure. We will perform ultra-deep targeted sequencing using genes implicated in cancer to try and understand the background of mutations surrounding these lesions

  Study EGAS00001002165

• IVF Whole genome prediction

  Preimplantation Genetic Testing (PGT) of in vitro fertilized (IVF) embryos has been proposed as a method to reduce transmission of common disease, although comprehensive genetic assessment remains unavailable. Here we use a combination of molecular and statistical techniques to reliably and accurately infer inherited genome sequence in 110 embryos. We combine polygenic risk scores (PRS) and rare variation to model susceptibility across 12 common conditions.

  Study EGAS00001005619

• Cylindromas_sun_protected_and_exposed

  The project aims to look at mutational signatures in a rare inherited skin tumour syndrome called CYLD cutaneous syndrome. These patients develop multiple skin tumours that are seen at sun exposed and sun protected sites. We plan to carry out WGS on carefully curated tumours from such patients. We then plan to analyse this data for mutational signatures, comparing this between sun exposed and sun protected sites.

  Study EGAS00001002521

• Genetic Testing to Understand and Address Renal Disease Disparities

  People of African ancestry (Blacks) have increased risk of kidney failure due to numerous socioeconomic, environmental, and clinical factors. Two variants in the APOL1 gene (GeneID: 8542) are now thought to account for much of the racial disparity associated with hypertensive kidney failure in Blacks. One in 7 AAs carry this risk allele, but it is nearly absent in other populations; the variants protect against infection with African trypanosomiasis which is endemic to Africa. However, this knowledge has not been translated into clinical care to help improve patient outcomes and address disparities. It is unknown whether patient or clinician knowledge of genetic risk impacts patient care (i.e., renal surveillance, BP medication use/intensification) or outcomes such as BP control and CKD. GUARDD is a randomized trial to evaluate the effects and challenges of incorporating genetic risk information into primary care. Hypertensive, nondiabetic, adults with self-reported African ancestry, without kidney dysfunction, are recruited from diverse clinical settings and randomized to undergo APOL1 genetic testing at baseline (intervention) or at one year (waitlist control). Prior to enrolling their patients, providers are educated about genomics and APOL1. Guided by a genetic counselor, trained staff return APOL1 results to patients and provide low-literacy educational materials. Real-time clinical decision support tools alert clinicians of their patients' APOL1 results and associated risk status at the point of care. Our academic - community clinical partnership designed a study to generate information about the impact of genetic risk information on our primary outcome - patient care (renal surveillance by clinicians, of serum creatinine and/or urine albumin tests. with a sub-aim of reduction of systolic blood pressure). Secondary outcomes include impact on primary outcomes at 12 months, psycho-behavioral differences of patients between groups and over time, clinician knowledge, attitudes and beliefs at baseline and 12 months, and differences in outcomes between those tested and not tested. GUARDD will help establish the effective implementation of APOL1 risk informed management of hypertensive patients at high risk of CKD, and will provide a robust framework for future endeavors to implement genomic medicine in diverse clinical practices. It will also add to the important dialog about factors that contribute to and may help eliminate racial disparities in kidney disease.

  Study phs001620

• NHLBI GO-ESP Family Studies: Idiopathic Bronchiectasis of unknown etiology that is not related to cystic fibrosis or classic primary ciliary dyskinesia or immune deficiency or any other known causes

  The NHLBI "Grand Opportunity" Exome Sequencing Project (GO-ESP), a signature project of the NHLBI Recovery Act investment, was designed to identify genetic variants in coding regions (exons) of the human genome (the "exome") that are associated with heart, lung and blood diseases. These and related diseases that are of high impact to public health and individuals from diverse racial and ethnic groups will be studied. These data may help researchers understand the causes of disease, contributing to better ways to prevent, diagnose, and treat diseases, as well as determine whether to tailor prevention and treatments to specific populations. This could lead to more effective treatments and reduce the likelihood of side effects. GO-ESP is comprised of five collaborative components: 3 cohort consortia - HeartGO, LungGO, and WHISP - and 2 sequencing centers - BroadGO and SeattleGO. The major goal of this project is to apply next generation resequencing technology to identify disease-causing variants that cause bronchiectasis of unknown etiology (e.g. non cystic fibrosis (CF), classic primary ciliary dyskinesia (PCD), immune deficiency, or any other known cause of bronchiectasis), i.e., "idiopathic bronchiectasis." As part of our ongoing efforts to define the genetic cause of rare lung diseases, we have also studied families in whom diagnosis of PCD or other known etiologies could not be confirmed. We have systematically collected and stored the DNA and phenotypic data on each of the families in our cohort. The phenotypic data includes age, gender, ethnicity information, clinical data pertaining to the airways disease, including neonatal respiratory distress, otitis media, sinusitis and bronchiectasis, ciliary ultrastructure analysis, and microbial colonization (status of nontuberculosis mycobacterium). During the course of our study, we have acquired 98 unrelated patients in whom bronchiectasis seemed to be of unknown causes. We will be using 11 unrelated patients, 5 unrelated affected sib-pairs, and 3 affected sibs from a family from this cohort, based on 1) development of bronchiectasis in the absence of smoking, 2) a good family pedigree with available DNA, and 3) a family history of bronchiectasis and/or occurrence of airways disease in a sibling. Classic CF, PCD and immune deficiency were ruled out, based on the tests described above. Alpha-1 antiprotease deficiency work up was negative and none of the patients were tobacco users or smokers.

  Study phs000518

• A Phenotypic and Genomics Approach in a Multi-Ethnic Cohort to Subtype Systemic Lupus Erythematosus

  Systemic lupus erythematosus (SLE) is a complex autoimmune disease that affects multiple organ systems and varies in severity across different populations. To examine the clinical heterogeneity of SLE, we sought to identify different lupus subtypes within our multi-ethnic cohort using a clustering approach. Additionally, with genome-wide methylation and genotype data generated for our cohort, we applied integrative methods to investigate genetic and epigenetic risk factors. This integrative and computational approach revealed molecular differences associated with phenotypic clusters.

  Study phs001850

• Application of targeted long-read methylation sequencing to dissected lung cancer tissues

  To investigate DNA methylation patterns within the tumor microenvironment, multiple regions were dissected from fresh-frozen sections of two lung adenocarcinoma specimens using the Millisect system. These regions were annotated based on spatial transcriptome data. DNA samples extracted from these regions were subjected to targeted long-read methylation sequencing using t-nanoEM. To establish a control dataset, short-read whole-genome sequencing (WGS) was performed on the tumor and normal parts, and long-read WGS was performed on the tumor part.

  Study JGAS000757

• The genetic analysis of circulating tumor DNA in blood of the digestive cancer patients to investigate the prognostic factors of metastasis and reccurence.

  A Darwinian evolutionary shift occurred early in the neutral evolution of advanced colorectal carcinoma (CRC) and copy number aberrations (CNA) were essential in the transition from adenoma to carcinoma. Subsequent to the primary evolution, we now focus on the evolutionary principle of the genome to foster postoperative recurrence of CRC. SO, We compared CNA, single nucleotide variance (SNV), RNA sequences between 8 primary and 11 metastatic sites from 10 CRCR cases.

  Study JGAS000221

• WES sequencing of metastatic colorectal cancer patient-derived xenografts with known response to irinotecan.

  Chemotherapy is the standard-of-care treatment for metastatic colorectal cancer (mCRC) and benefits some patients, but what distinguishes responders from non-responders is unclear. In this study, we expand a pre-existing collection (https://doi.org/10.1158/2159-8290.CD-24-0556) of molecularly annotated patient-derived xenografts to uncover functional predictors of response to 5-FU and irinotecan combination therapy (FOLFIRI) in mCRC. We complemented previous mutational profiles with whole exome sequencing for 46 xenografts with known response to irinotecan.

  Study EGAS50000001484

• Bulk RNA sequencing of metastatic colorectal cancer patient-derived xenografts with known response to irinotecan

  Chemotherapy is the standard-of-care treatment for metastatic colorectal cancer (mCRC) and benefits some patients, but what distinguishes responders from non-responders is unclear. In this study, we expand a pre-existing collection (https://doi.org/10.1158/2159-8290.CD-24-0556) of molecularly annotated patient-derived xenografts to uncover functional predictors of response to 5-FU and irinotecan combination therapy (FOLFIRI) in mCRC. We complemented previous expression profiles with bulk RNAseq for 38 xenografts with known response to irinotecan.

  Study EGAS50000001485

• Spatial Profiling of Patient-Matched HER2 Positive Gastric Cancer Reveals Resistance Mechanisms to Trastuzumab and Trastuzumab Deruxtecan Sequencing

  HER2-positive gastric cancer (HER2+ GC) exhibits significant intra-tumoral heterogeneity and frequent development of resistance to HER2-targeted therapies. This study aimed to characterize the spatial tumor microenvironment (TME) and identify mechanisms of resistance to HER2 blockade including trastuzumab and trastuzumab deruxtecan (T-DXd) in HER2+ GC, with the goal of informing novel therapeutic strategies. We performed spatial transcriptomics on pre- and post-treatment samples from patients with HER2+ metastatic GC who received trastuzumab-based therapy.

  Study EGAS50000000636

• scRNAseq of human primary nasal epithelium differentiated at air-liquid interface exposed to SARS-CoV2

  The nasal epithelium is a plausible entry point for SARS-CoV-2, a site of pathogenesis and transmission, and may initiate the host response to SARS-CoV-2. Antiviral interferon responses are critical to outcome of SARS-CoV-2. Yet little is known about the interaction between SARS-CoV-2 and innate immunity in this tissue. Here we applied single-cell RNA sequencing and proteomics to a primary cell model of human primary nasal epithelium differentiated at air-liquid interface.

  Study EGAS00001005633

• Endothelium-derived stromal cells contribute to bone marrow niche formation

  Comprehensive transcriptional characterization of bone marrow stromal cells by RNA sequencing was performed to determine the molecular properties/signatures of endothelium during niche formation.Here, we identify a rare subset of cells in the human fetal BM that co-express endothelial and stromal markers, including low-affinity nerve growth factor receptor (LNGFR/CD271). They display transcriptional reprogramming consistent with endothelial-to-mesenchymal transition (EndoMT), reflected in their potential to generate stromal cells with in vivo BM niche forming capacity.

  Study EGAS00001004946

• Genetic profiling of mucosal melanoma

  Primary mucosal melanomas (MMs) arise from melanocytes located in mucosal membranes lining the respiratory, gastrointestinal and urogenital tracts. MMs frequently present late and have a poor prognosis; the 5-year survival rate is only 14%. MM makes up only ~1.4% of all melanomas and it is this rarity that makes knowledge of the genetic changes that contribute to its pathogenesis limited to a small number of exome/genome studies and other targeted studies. Thus to investigate the somatic alterations and mutation spectra in MM genomes, we have extracted genomic DNA from formalin-fixed, paraffin-embedded (FFPE) human MMs, and subjected them to whole exome sequencing. Given the propensity of MM to metastasize, we will also be sequencing metastatic MM lesions; primary and metastatic lesions from the same individual represent an excellent opportunity to identify potential drivers of metastasis in MM. Finally we will sequence 'normal' DNA from the same individual, where possible, to exclude germline variations.

  Dataset EGAD00001003237

• CSER: Genomic Sequencing to Aid Diagnosis in Pediatric and Prenatal Practice: Examining Clinical Utility, Ethical Implications, Payer Coverage, and Data Integration in a Diverse Population

  Congenital abnormalities and developmental disorders affect 3-5% of live born infants and children. Despite advances in both pre- and post-natal treatment, the utility of genetic testing in diagnosing the etiology underlying such conditions in order to guide management has been frustratingly limited. Traditional genetic testing with specific gene tests, or even gene panels, is diagnostic in only a small percentage of cases. Recent technological advances in next generation sequencing (NGS) have led to the ability to sequence and interpret the entire exome relatively quickly, allowing a diagnosis in 25-30% or more of cases of developmental disorders when other genetic tests have not yielded a result. Although whole exome sequencing (WES) holds great promise for improved diagnosis leading to better clinical outcomes, challenges remain in determining how best to apply and utilize sequence data. Fulfilling the promise of WES also requires investigation of ELSI (ethical, legal, social) concerns, given skepticism in some communities that research will benefit them; economic considerations that ultimately determine access to and equitable use of WES; and a need to share clinical genetic results with families and across health care systems to enable better prognostication and management of rare conditions in community settings. We propose a Program in Prenatal and Pediatric Genomic Sequencing (P3EGS) at UCSF to examine the diagnostic and clinical utility of WES. P3EGS will recruit and study affected individuals and their parents, including pregnancies in which the fetus has a confirmed structural anomaly and children with previously undiagnosed developmental disorders that are likely of genetic etiology. Following consent and collection of standardized phenotypic data, the families will undergo WES as part of clinical care. To achieve diversity, patient ascertainment and recruitment will occur at four UCSF sites that serve a broad range of underrepresented minorities (target of 75%) and span the full socio-economic spectrum, including the underserved. Our specific aims will: 1) examine the clinical utility of WES, including assessment of a variety of health-related and reproductive outcomes, in undiagnosed individuals; 2) address ethical, social and economic issues in the delivery of genomic sequencing results to ancestrally and economically diverse populations through (2.1) a mixed methods, longitudinal empirical study of clinical interactions and experiences, (2.2) an economic analysis of insurance coverage, price and reimbursement of multigene tests, and (2.3) creation of an Ethics Advisory Board to respond to emerging issues and establishment of authentic stakeholder engagement; and 3) pilot a user-friendly web-based patient/provider application integrating genomic and clinical data as a shared evidence base to support result communication, interpretation and clinical decision making; the application will be based on the “Bioscreen” model created and successfully implemented at UCSF.

  Study phs002324

• Prevention and Early Treatment of Acute Lung Injury (PETAL) Acetaminophen in Sepsis: Targeted Therapy to Enhance Recovery (ASTER) (PETAL ASTER-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 ASTER include plasma, urine and whole blood. Please note that use of biospecimens in genetic research is subject to a tiered consent. Objectives: To determine whether acetaminophen increases days alive and free of organ dysfunction in sepsis participants compared with placebo.Background: Acetaminophen (paracetamol) has many effects that can be beneficial in sepsis treatment, including analgesia, antipyresis, cyclooxygenase-2 inhibition, as well as a potent and specific hemoprotein reduction that can block hemoglobin-induced oxidation of lipids and other substrates. The majority of sepsis participants experience elevated circulating cell-free hemoglobin levels, which is associated with development of organ dysfunction including acute respiratory distress syndrome (ARDS) and death.Acetaminophen has been found in observational studies to be associated with improved survival in critically ill sepsis participants with elevated plasma cell-free hemoglobin, and small clinical trials have had positive sepsis participant outcomes such as reduced plasma biomarkers of lipid peroxidation and improved kidney function. However, a large, randomized trial of acetaminophen administration for treatment of fever in participants with suspected infection did not show a mortality benefit. The NHLBI PETAL Network initiated ASTER as a larger phase trial to examine the utility of plasma cell-free hemoglobin level as a biomarker for future sepsis trials and whether acetaminophen would increase the number of days alive and free of organ support for participants with sepsis and respiratory or circulatory organ dysfunction. Participants: A total of 447 participants were enrolled and randomized, 227 to the acetaminophen arm and 220 to the placebo arm. Data from 40 participants who were randomized to the Vitamin C arm, which was stopped early (see Design section below), is also included.Design: ASTER was a phase 2b multicenter, randomized, double-blind trial. The study originally had a 3-arm platform trial in which participants were randomized 1:1:1 to treatment with intravenous acetaminophen, vitamin C, or a common placebo. The vitamin C arm of the trial was stopped after enrolling 79 participants due to external clinical trial data for vitamin C.Participants randomized to the acetaminophen arm received acetaminophen at the dose of 1 g in 100 mL diluent (or 15 mg/kg if actual body weight was Conclusions: Intravenous acetaminophen was considered to be safe but did not significantly improve days alive and free of organ support in critically ill sepsis participants. There was no significant interaction between cell-free hemoglobin levels and acetaminophen.

  Study phs003900

• Acute Respiratory Distress Network (ARDSNet) Study 04 Assessment of Low Tidal Volume and Elevated End-Expiratory Volume to Obviate Lung Injury (ALVEOLI-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. BiospecimensAccess to Biospecimens is through the NHLBI Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC). Biospecimens from ARDSNet-ALVEOLI include Plasma and DNA. Please note that use of biospecimens in genetic research is subject to a tiered consent. Available Data Outcome data regarding organ failure free days are not available. Objectives The ARDS Network is a consortium of clinical centers and a coordinating center to design and test novel therapies for the treatment of Acute Lung Injury (ALI) and Acute Respiratory Distress Syndrome (ARDS). The ARDS Network 01/03 trials included an investigation of the efficacy and safety of Ketoconazole and Respiratory Management in the treatment of ALI and ARDS (KARMA). The Ketoconazole arm of the KARMA study was later stopped due to an inability to show efficacy. Participants continued to be randomized to the respiratory management arms of the study (ARMA), which compared two ventilator strategies: a tidal volume of 6 mL/kg versus 12 mL/kg. The LARMA phase of the study investigated the efficacy of Lisofylline and Respiratory Management. The objective of the ALVEOLI study was to compare clinical outcomes of participants with ALI and ARDS treated with a higher end-expiratory lung volume/lower FiO2 versus a lower end-expiratory lung volume/higher FiO2 ventilation strategy. The ALVEOLI study tested the hypothesis that mortality from ALI and ARDS would be reduced with a mechanical ventilation strategy designed to prevent lung injury from repeated collapse of bronchioles and alveoli at end-expiration. Background Most participants requiring mechanical ventilation for ALI and ARDS receive positive end-expiratory pressure (PEEP) of 5 to 12 cm of water. Higher PEEP levels may improve oxygenation and reduce ventilator-induced lung injury but may also cause circulatory depression and lung injury from overdistention. PEEP levels higher than traditional levels may reduce ventilator-induced lung injury by decreasing the proportion of nonaerated lung and higher PEEP levels may allow arterial-oxygenation goals to be met at a lower level of inspired oxygen (FiO2). Participants A total of 550 participants were randomized to receive mechanical ventilation with either lower or higher PEEP levels, which were set according to different tables of predetermined combinations of PEEP and fraction of inspired oxygen. Conclusions Participants with acute lung injury and ARDS who receive mechanical ventilation with a tidal-volume goal of 6 ml per kilogram of predicted body weight and an end-inspiratory plateau-pressure limit of 30 cm of water, clinical outcomes were statistically similar whether lower or higher PEEP levels are used. (Brower, et al., 1004; PMID: 15269312).

  Study phs003714

• Rapid Acceleration of Diagnostics - Digital Health Technologies (RADx-DHT): NIH Digital Health Solutions for COVID-19: Clear2Go - A Digital Identity Wallet for Health Status

  Clear2Go is a solution/app that provides digital, non-refutable cryptographic proof of testing or vaccination that can be used to evaluate risk of allowing individuals to return to normal work, travel, and public life activities. It is a mobile service that maps a person's vetted identity and biometrics to the phone and then cryptographically binds it with their COVID-19 test and vaccination records. The person can then prove their status by utilizing the credentials with a QRCode or NFC tap.DOI: https://rapids.ll.mit.edu/10.57895/b2d6-8060

  Study phs002628

• RNA-Seq of Whole Blood from Pediatric Sickle Cell Anemia (SCA) Patients

  The aim of this study is to define the immune cell transcriptome by next generation RNA sequencing in blood from individuals with SCA, in comparison to healthy African American controls. This study has a cross-sectional case-control design. We will compare the transcriptome profiles of blood mononuclear cells from healthy age-matched African American children without cardiovascular disease or risk factors (“Controls”) to those of children with SCA, age 5 -21 years, who are not receiving chronic red blood cell transfusions or hydroxyurea therapy to identify genes that are differentially expressed in SCA. 

  Study phs002687

• Stanford Center for Urologic Genomics: Genomic Analysis of Benign Prostatic Hyperplasia

  Benign prostatic hyperplasia (BPH) entails growth in the central regions of the prostate gland and is common among older men. BPH obstructs urinary outflow, resulting in voiding symptoms for which current treatments that target prostate physiology are only partially effective. A better understanding of BPH may suggest new treatment strategies that target its pathophysiology. The overall goal of the study is to apply next-generation sequencing-based approaches to investigate BPH, to discover new insight into BPH disease processes and new targets for precision therapy, and to determine whether the hyperplasia reflects underlying clonal expansions of prostatic cells.

  Study phs001698

• Wnt Activity Reveals Context-Dependent Genetic Effects on Gene Regulation in Neural Progenitors

  In this study we aimed to identify context-dependent regulatory functions of common genetic variation after stimulation of the canonical Wnt pathway. Fetal cortical tissue between 14 and 21 gestation weeks was subjected to RNA-Sequencing (242 samples) and ATAC-Sequencing (222 samples) to profile expression and chromatin accessibility, respectively. Considering donor genotypes, we were able to identify eQTLs, caQTLs, as well as response QTLs of both categories. The dataset provided here includes 242 RNA-sequencing files in bam format and 222 ATAC-sequencing files in bam format. We also provide 83 donor genotypes in VCF format (hg38).

  Study phs003642

• "BaTwa" populations from Zambia retain ancestry of past hunter-gatherer groups

  We genotyped and analyzed over two million genome-wide SNPs from two BaTwa populations (40 individuals by population), and from three comparative farming populations (10 to 21 individuals by population) in order to: (i) determine if the Zambian BaTwa carry any genetic material linking them to past hunter-gatherer-groups, and (ii) characterize the genetic affinities of past Zambian hunter-gatherer-groups. We found that both BaTwa populations harbor a hunter-gatherer- like genetic component, representing ∼19% (Bangweulu) and ∼31% (Kafue) of their genetic ancestry, while the rest of their ancestry is similar to western Africans.

  Study EGAS50000000378

• Rapid Acceleration of Diagnostics - Underserved Populations (RADx-UP) Collection of General Research Use Datasets

  This individual-level collection of datasets contains all the RADx Underserved Populations (RADx-UP) studies in dbGaP for General Research Use (GRU) and have no further limitations beyond those outlined in the model RADx Data Use Certification Agreement. Access to this study collection will include additional authorized individual-level GRU datasets that become available. Renewal of this study collection is required annually. Access to studies in this collection is on the RADx® Data Hub. To request access to this study collection, select phs003832 in the dbGaP when submitting a data access request.

  Study phs003832

• Rapid Acceleration of Diagnostics - Tech Program (RADx-Tech) Collection of General Research Use Datasets

  This individual-level collection of datasets contains all the RADx® Tech Programs (RADx-Tech) studies in dbGaP for General Research Use (GRU) and have no further limitations beyond those outlined in the model RADx Data Use Certification Agreement. Access to this study collection will include additional authorized individual-level GRU datasets that become available. Renewal of this study collection is required annually. Access to studies in this collection is on the RADx® Data Hub. To request access to this study collection, select phs003831 in the dbGaP when submitting a data access request.

  Study phs003831

• Rapid Acceleration of Diagnostics - Radical (RADx-rad) Collection of General Research Use Datasets

  This individual-level collection of datasets contains all the RADx® Radical (RADx-rad) studies in dbGaP for General Research Use (GRU) and have no further limitations beyond those outlined in the model RADx Data Use Certification Agreement. Access to this study collection will include additional authorized individual-level GRU datasets that become available. Renewal of this study collection is required annually. Access to studies in this collection is on the RADx® Data Hub. To request access to this study collection, select phs003834 in the dbGaP when submitting a data access request.

  Study phs003834

• Reconstruction of the personal information from human genome reads in gut metagenome sequencing data

  Human DNA present in fecal samples can result in a small number of human reads in gut shotgun metagenomic sequencing data. However, it is currently unclear how much personal information can be reconstructed from such reads and this has not been quantitatively evaluated. Such a quantitative evaluation is necessary to clarify the ethical concerns related to data sharing and to enable the efficient use of human genetic information in stool samples, such as for research and forensics. Here, we used genomic approaches to reconstruct personal information from fecal metagenomes of 343 Japanese individuals with associated human genotype data.

  Study JGAS000600

• RNAseq of MCL cell lines

  This study profiles the transcriptomic response of the Mino-VEN-R and Jeko-BTK-R mantle cell lymphoma (MCL) cell lines to pirtobrutinib (PBN) treatment using bulk RNA sequencing. Mino-VEN-R models drug-tolerant persister (DTP) cells that arise during exposure to non-covalent BTK inhibitors. Building on our recent findings that DTP cells undergo metabolic and phenotypic state transitions governed by TCA cycle reprogramming, this dataset aims to capture gene expression changes associated with treatment-induced plasticity. The results contribute to a broader multi-omic framework exploring mechanisms of resistance and therapeutic vulnerability in MCL.

  Study EGAS50000001087

• Longitudinal analysis of treatment induced genomic alterations in gliomas

  Here, we report the longitudinal whole exome sequencing analysis of a patient with a primary GBM and two recurrences, demonstrating the heterogeneity caused by the therapy induced molecular changes and their implications for clinical decision-making. This analysis revealed the impact of temporal evolution for tumors under the pressure of treatment. We presented that while targeted treatments eliminated some sensitive clones, there were clones that were enriched leading to resistance. This study demonstrates the importance of longitudinal genomic profiling to adjust to the dynamic nature of therapy induced molecular changes to improve the outcomes of precision therapies.

  Study EGAS00001002168

• Pancreatic cancer organoids recapitulate disease and allow personalized drug screening

  We report derivation of 30 Patient-Derived Organoid lines (PDOs) from tumors arising in the pancreas and distal bile duct. PDOs recapitulate tumor histology and contain genetic alterations typical for pancreatic cancer. In vitro testing of a panel of 76 therapeutic agents revealed sensitivities currently not exploited in the clinic. The PRMT5 inhibitor EZP015556, shown to target MTAP negative tumors, was validated as such, but also appeared to constitute an effective therapy for a subset of MTAP+ tumors. Taken together, the work presented here provides a platform to identify novel therapeutics to target pancreatic tumor cells using PDOs.

  Study EGAS00001003369

• RNA sequencing data of 142 samples from 142 patients with HER2+ breast cancer treated with letrozole or tamoxifen (SOLTI PAMELA trial)

  PAMELA (NCT01973660) is a non-randomized, open-label, multicentric, prospective translational research study in stage I-IIIA HER2+ breast cancer designed to evaluate the ability of the PAM50 intrinsic subtypes to predict pCR in the breast (pCRB) following 18 weeks of neoadjuvant lapatinib and trastuzumab (+/- hormonal therapy if hormone receptor [HR] positive). Patients with HR+ disease received letrozole (if postmenopausal) or tamoxifen (if pre-menopausal). The primary objective was to compare the pCRB rates of the HER2-E versus the non-HER2-E subtypes in the intent-to-treat population.

  Study EGAS00001006410

• TMD_AMKL_targeted_follow_up

  Genomic libraries will be generated from total genomic DNA derived from 200+ patients with childhood Transient Myeloproliferative Disorder (TMD) and or Acute Megakaryocytic Leukemia (AMKL) as well some matched constitutional samples (n < 50). Libraries will be enriched for a selected panel of genes using a bespoke pulldown protocol. 96 Samples will be individually barcoded and subjected to up to two lanes of Illumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the characterisation of known gene mutations in cancer as well as the validation of potentially novel variants identified by prior exome sequencing.

  Study EGAS00001000569

• The_Causes_of_Clonal_Blood_Cell_Disorders_Study___SCOR

  We will take a bone marrow aspirate and peripheral blood samples from a healthy patient aged around 60, and use flow cytometry to isolate 100 HSCs, 50 MEPs, and 50 GMPs. We will grow these up into colonies, then whole genome sequence each colony. Somatic mutations will act as a unique barcode for each clone. We will then design a panel for targeted resequencing of the mutations that we find. It will then be possible to look for these mutations in the peripheral blood over several years, to see the dynamics of how HSCs contribute to the peripheral blood in health.

  Study EGAS00001002132

• TMD_AMKL_targeted_follow_up_part_2

  Genomic libraries will be generated from total genomic DNA derived from 200+ patients with childhood Transient Myeloproliferative Disorder (TMD) and or Acute Megakaryocytic Leukemia (AMKL) as well some matched constitutional samples (n < 50). Libraries will be enriched for a selected panel of genes using a bespoke pulldown protocol. 96 Samples will be individually barcoded and subjected to up to two lanes of Illumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the characterisation of known gene mutations in cancer as well as the validation of potentially novel variants identified by prior exome sequencing.

  Study EGAS00001000732

• Role_of_Epigenetic_Memory_in_Human_Induced_Pluripotent_Stem_Cells_Pilot

  Fibroblasts have been shown to re-program into induced pluripotent stem (hiPS) cells, through over-expression of pluripotency genes. These hiPS cells show similar characteristics to embryonic stem cells including cell surface markers, epigenetic changes and ability to differentiate into the three germ layers. However it is unclear as to the extent of changes in gene expression through the re-programming process.. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001000742

• Transcriptome sequencing of intravenous leiomyomatosis and uterine myoma

  Up to now, there are two hypothesis about the pathogenesis of the relationship of intravenous leiomyomatosis and uterine myoma. One theory suggests that the IVL comes from the smooth muscle cell in the vessel wall.The other theory indicates that the IVL derives from the uterine myometrium. However, limited to the technology, few studies have been deeply explore the underlying relation. In this study, we employ the RNA sequencing to explore the molecule relationship between IVL and uterus myoma. In order to identify the molecule relationship between IVl and uterine myoma we conducted transcriptome sequencing and bioinformaitc analysis

  Study EGAS00001002504

• T-cell reconstitution after reduced dose ATLG induction in kidney transplant recipients

  Pre-sensitized kidney transplant recipients have a higher risk for rejection following kidney transplantation and therefore receive a lymphodepletional induction therapy with anti human T-lymphocyte globulin (ATLG). The time course of lymphocyte reconstitution with regards to overall and donor-reactive T-cell receptor (TCR) specificity remains elusive. In this study we aimed to describe the TCR repertoire in a reduced dose ATLG regimen making it possible to evaluate shifts in the shape of the immune repertoire and to detect the reappearance of donor-reactive T-cells following reduced lymphodepletional induction therapy.

  Study EGAS00001005941

• Human Developmental Biology Resource (HDBR) abnormal fetal samples

  The HDBR (www.hdbr.org) is a human embryonic and fetal tissue bank supplying registered researchers with access to these valuable research materials up to 22 weeks post-conception (PMC4640175). All of the samples collected are analysed for chromosomal abnormalities, and all samples with an abnormal phenotype are either analysed by SNP array, or exome sequenced. This dataset is generated from those abnormal samples that have been analysed by exome sequencing. To request access to this dataset, or if any researcher is interested in obtaining tissue from any of the samples HDBR collect, please email enquiries@hdbr.org.

  Study EGAS00001006300