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• HipSci_RNASEQ_Usher syndrome and congenital eye defects

  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 perform RNAseq on iPS lines from Usher syndrome and congenital eye defects.

  Study EGAS00001001997

• Keratinocyte_CRISPR_screens

  Immortalised HaCaT keratinocytes were transduced with Cas9 and the CRISPR-KO v1.1 genome-wide gRNA library. The gRNA library was prepared from genomic DNA isolated 14 days post library transduction. gRNA representation will be compared to the original CRISPR-KO v1.1 library to reveal genes essential for HaCaT survival and growth.

  Study EGAS00001002714

• Paediatric_CNS_tumour_autopsy_DNA_WES

  Paediatric gliomas likely have their origins in embryogenesis. This WES extension to the WGS study seeks to estimate the occurrence of driver mutations within the normal tissues of patients which have developed lethal brain tumours and compare the incidence between those that have a germline predisposition and those that don't.

  Study EGAS00001005642

• Integrated Exome-seq analysis of tumor thrombus

  We prospectively enrolled 83 patients with a renal mass and TT scheduled to undergo surgical resection. To accurately integrate genomic and transcriptomic findings and enable histological co-registration, simultaneous isolation of DNA and RNA was performed from individual samples characterized histologically through immediately flanking sections

  Study EGAS00001005511

• Integrated RNA-seq analysis of tumor thrombus

  We prospectively enrolled 83 patients with a renal mass and TT scheduled to undergo surgical resection. To accurately integrate genomic and transcriptomic findings and enable histological co-registration, simultaneous isolation of DNA and RNA was performed from individual samples characterized histologically through immediately flanking sections

  Study EGAS00001005512

• Single Cell MK and HSC sequencing

  In the current understanding of adult bone marrow hematopoiesis, megakaryocytes (MKs) originate from cells immuno-phenotypically indistinguishable from hematopoietic stem cells (HSCs), bypassing intermediate progenitors. Here, we use single cell RNA sequencing to characterize HSCs and MKs from human bone marrow, to investigate MK lineage commitment and maturation.

  Study EGAS00001004844

• Single cell RNA-seq from AD and PS patients

  We applied single cell immune profiling to gain a holistic view from immune cells infiltrating the skin to circulating immune cells, facilitating a better understanding of the two diseases in their entirety, and the identification of potential type-2 or type-3-disease-driving mechanisms.

  Study EGAS00001007055

• Cellular composition of spheres derived from lymph nodes of lung cancer patients

  To decipher the cell type composition within single spheres we performed RNA-Seq of 25 selected spheres of 4 different categories (including 8 signature-/balanced, 9 signature+/balanced, 1 signature-/aberrant, 7 signature+/aberrant). To track the individual cell types within single spheres we performed deconvolution analysis.

  Study EGAS00001007369

• RSV infection of primary bronchial epithelial cells in asthma

  Primary bronchial epithelial cells derived from healthy donors and asthma patients were differentiated in Air-Liquid-Interface condition and infected with the respiratory syncytial virus. Single-cell RNA sequencing analysis of these cultures was used to study the transcriptomic response of the cells to RSV.

  Study EGAS00001007450

• HCA_Immune_PBMC_Teichmann_LK_RNA_managed_acces

  The aim of this study is to characterise CD8 T cell populations that are specific to prevalent viruses in the healthy blood donors. We obtained PBMC samples from a commercial supplier that have been HLA-typed and pre-tested for reactivity against EBV, CMV, and influenza using ELISPOT and peptide pool stimulation.

  Study EGAS00001007936

• Assessment of genetic and epigenetic variation in human IPS cells

  In order to progress human induced pluripotent stem cells (hiPSCs) towards the clinic, several outstanding questions must be addressed. It is possible to reprogram different somatic cell types into hiPSCs but it is unlcear whether some cell types carry through fewer mutations through reprogramming (either due to mutations present in the primary cells, or mutations accumulated during reprogramming). Through in depth analysis of hiPSCs generated from different somatic cells, it will be possible to assess the variation in genetic stability of different cell types.

  Dataset EGAD00001000384

• Sequencing probands and families with severe insulin resistance syndromes

  This is an ongoing project and continuation to all the sequencing we have been doing over the last few years. We have some additional families and probands with syndromes of insulin resistance not previously sequenced within uk10k or other core funded projects. We would like to complete the sequencing in all of the good quality families and probands we have, this would require another ~50 samples to be WES sequenced. This cohort has already proven to be a rich source of interesting findings with papers in Science and Nature genetics.

  Dataset EGAD00001000694

• Anthropological dataset 1 for The admixture histories of Cabo Verde

  Datasets used in the article "The genetic and linguistic admixture histories of the islands of Cabo Verde" by Laurent R et al. eLife 2023 (DOI: https://doi.org/10.7554/eLife.79827 - URL: https://elifesciences.org/articles/79827) File name "eGAdeposit_233CaboVerde_SampleInfo_FINAL_01062022.txt" Column 1 corresponds to individual alphanumeric codes as in the "eGAdeposit_233CaboVerde_GenotypeFile_FINAL_01062022.vcf" genotype file Column 2 corresponds to individual's biological sex as per genetic inference Column 3 corresponds to individual's self-reported age in years Column 4 corresponds to individual's self-reported cumulated number of years spent in academic or professional education

  Dataset EGAD00001008976

• Genome-wide gene expression analysis following CRISPRi of transposable elements

  human induced pluripotent stem cells constitutely expressing the CRISPRi machinery were transduced with gRNAs targeting genomic regions of transposable elements (TEs), and differentiated to neural progenitor cells. The aim of the study was to annotate the function of these TEs in the context of early neurodevelopmental processes.

  Study EGAS00001008265

• SCANDARE MACARON project

  Among gynecological cancers, high-grade serous ovarian cancer has the highest prevalence and more than 75% of patients have advanced stage at diagnosis with a 5-year survival of 40%. When the initial complete surgical removal is not possible (60% of patients), an interval surgery can be considered after three to four cycles of neoadjuvant chemotherapy to reduce the tumor mass. However, in approximately 50% of cases the tumor has little or no response to neoadjuvant chemotherapy. Therefore, identification of potential drug targets, biomarkers and/or pathways whose modulation can help in the prevention, interception, or curing of the disease is essential to address the unmet need. Therefore, MACARON project aims to address these issues through the identification of shared neoantigens arising out of somatic alterations and aberrant transcriptional programs in ovarian cancer DNA/RNA datasets.

  Dac EGAC50000000104

• Interruption of BTK Inhibitor Improves Response to SARS-CoV-2 Booster Vaccination in Patients with Chronic Lymphocytic Leukemia

  This study investigates the effect of booster SARS-CoV-2 vaccination and Bruton tyrosine kinase inhibitor (BTKi) interruption on antibody response to vaccination. Patients with chronic lymphocytic leukemia (CLL) are immunocompromised, at increased risk of infection, and have historically poor response to immunization. BTKi therapy is a standard treatment for CLL in frontline and salvage settings and further suppresses antibody vaccine responses.

  Study phs003319

• Identification of rare variants associated with cardiovascular traits in Cilento isolates

  The aim of this project is to identify rare genetic variants of large effect implicated in complex diseases by focusing on the study of cardiovascular diseases and related quantitative traits in a well characterized isolated population in Cilento area, Italy. The reference panel has been selected carefully in order to maximize the imputation coverage and quality on the all population samples. The selected individuals should meet three criteria: selected individuals should be chip-genotyped and closely related to the maximum number of chip-genotyped individuals so as to maximize imputation coverage; relatedness between selected individuals should be minimal, so as to minimize redundancy in genetic information of the reference panel. We perform exome sequencing on samples from 250 individuals from the Campora and Gioi-Cardile populations.

  Dataset EGAD00001002195

• Oral Microbiome in Esophageal Adenocarcinoma

  The purpose of our study was to assess the influence of oral microbiota on the development of esophageal cancer. Our preliminary case-control studies reported a global alteration of foregut microbiome in esophageal adenocarcinoma with the strongest changes found in the oral microbiome. We hypothesise that commensal oral bacteria are capable of activating or degrading carcinogens in cigarette smoke and therefore may contribute to esophageal carcinogenesis. We conducted a prospective study nested in two large US cohorts, to determine whether oral microbiota are associated with subsequent esophageal adenocarcinoma.

  Study phs001527

• Breakpoint detection using long insert whole genome sequencing

  In this study, we hypothesize that shallow long insert whole genome sequencing (LI-WGS) increases our power for detecting breakpoints compared to shallow short insert WGS. We performed a priori analyses to demonstrate the benefits of LI-WGS, developed a long insert library preparation protocol based off Illumina's protocol, and compared LI-WGS against short insert WGS on test samples. We then used long insert WGS to identify translocations and copy number changes in tumor and germline samples collected from cancer patients with different malignancies.

  Study phs000646

• NHLBI TOPMed: Genetic Epidemiology Network of Salt Sensitivity (GenSalt)

  The GenSalt study aims to identify genes which interact with dietary sodium and potassium intake to influence blood pressure in Han Chinese participants from rural north China. Whole genome sequencing will be conducted among 1,860 participants of the Genetic Epidemiology Network of Salt Sensitivity (GenSalt) Study. We will work in collaboration with participating TOPMed studies to identify novel common, low-frequency and rare variants associated with an array of cardiometabolic phenotypes. In addition, we will explore the relation of low-frequency and rare variants with salt-sensitivity among GenSalt study participants.

  Study phs001217

• NHLBI's Collection of Datasets for General Research Use (Public Posting of Genomic Summary Results: Not Allowed)

  This collection contains all of NHLBI's authorized individual-level genomic datasets currently in dbGaP that are approved for General Research Use (GRU) and have no further limitations beyond those outlined in the model Data Use Certification Agreement. The public posting of Genomic Summary Results are not allowed. Access to this study collection will include additional authorized individual-level GRU datasets that become available. Renewal of this study collection is required annually. To request access to this study collection, select phs003132 in the dbGaP Authorized Access System.

  Study phs003131

• NHLBI's Collection of Datasets for Health / Medical / Biomedical Research Use (Public Posting of Genomic Summary Results: Allowed)

  This collection contains all of NHLBI's authorized individual-level genomic datasets currently in dbGaP that are approved for Health/Medical/Biomedical (HMB) Research Use and have no further limitations beyond those outlined in the model Data Use Certification Agreement. The public posting of Genomic Summary Results are allowed. Access to this study collection will include additional authorized individual-level HMB datasets that become available. Renewal of this study collection is required annually. To request access to this study collection, select phs003134 in the dbGaP Authorized Access System.

  Study phs003134

• Deep Sequencing of 3 Cancer Cell Lines on 2 Sequencing Platforms (Illumina HiSeqX and NovaSeq)

  To test the performance of a new sequencing platform, develop an updated somatic calling pipeline and establish a reference for future benchmarking experiments, we performed whole-genome sequencing of 3 common cancer cell lines (COLO-829, HCC-1143 and HCC-1187) along with their matched normal cell lines to great sequencing depths (up to 278X coverage) on both Illumina HiSeqX and NovaSeq sequencing instruments. This dataset can be used for benchmarking purposes by the genomic community and as a reference call set for scientists using these 3 cell lines.

  Study phs001839

• Genomic Analysis of Bevacizumab-induced Hypertension

  Bevacizumab use in the treatment of cancer can lead to the development of hypertension in some patients, and high-grade toxicity can limit therapy or lead to cardiovascular complications. The factors that contribute to interindividual variability in blood pressure rise during bevacizumab treatment are not well understood. In the present study, whole exomes and flanking regulatory regions of candidate genes associated with vasodilation and blood pressure were sequenced in bevacizumab-treated subjects with the objective of identifying genes harboring multiple variants associated with severe, early-onset bevacizumab-induced hypertension.

  Study phs001597

• Caregiving as a Natural Stressor in Studies of the Role of Genes That Affect Serotonin Function in Regulating Risk Factors for Coronary Heart Disease (CAREGIVER)

  The burden of caregiving for an ill relative has been shown to interact with existing comorbidities to increase risk of several health outcomes including metabolic syndrome and blood pressure reactivity. The CAREGIVER study was developed to compare cardiometabolic risk factors in caregivers and controls. These risk factors include physiologic measures, psychologic measures, neighborhood characteristics, and genetic and genomic factors. DNA and plasma were collected and used for examination of cardiometabolic and stress biomarkers, genotyping and methylation analysis.

  Study phs001747