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• Clinical Trial of COVID-19 Convalescent Plasma in Outpatients (C3PO)

  The Clinical Trial of COVID-19 Convalescent Plasma in Outpatients (C3PO) is a multicenter, randomized, single blind, two-arm, placebo controlled Phase III trial with blinded outcome assessments to establish the safety and efficacy of single dose of convalescent plasma for preventing the progression from mild to severe COVID-19 illness.

  Study phs002752

• UCSF Adult Glioma Study

  The UCSF Adult Glioma Study is a case-control study conducted at the University of California, San Francisco. The goals of the study were to discover inherited (genetic), developmental, immunologic and other risk factors for glioma and to determine molecular level tumor markers that would be helpful in classifying glioma into more homogeneous groups.

  Study phs001497

• Autopsy-Confirmed Parkinson Disease GWAS Consortium (APDGC)

  The APDGC was formed to conduct a genome-wide association study in individuals with neuropathologically confirmed Parkinson Disease (PD) and neuropathologically normal controls. The rationale for the study is that including only cases and controls with neuropathologically confirmed disease status will reduce diagnostic misclassification and increase power to detect novel genetic associations.

  Study phs000394

• Anti-tumor and Immune Stimulatory Activity of Iberdomide in Myeloma, Including Patients with Cereblon Dysregulation

  Study showing Iberdomide treatment leads to immune stimulation and shift to effector T cells in triple-class refractory patients and directly after IMiD therapy. This is the first clinical evidence that Iberdomide can overcome Cereblon defects associated with IMiD resistance in late-line myeloma patients.

  Study EGAS50000000265

• Osteosarcoma WGS on multiple tissue samples from six patients

  Osteosarcoma is a primary bone tumor that exhibits a complex genome characterized by gross chromosomal abnormalities. Osteosarcoma patients often develop metastatic disease, resulting in limited therapeutic options and poor survival rates. To gain knowledge on the mechanisms underlying osteosarcoma heterogeneity and metastatic process, it is important to obtain a detailed profile of the genomic alterations that accompany osteosarcoma progression. Therefore, in this study we performed WGS on multiple tissue samples from six patients with osteosarcoma, including the treatment naïve biopsy of the primary tumor, resection of the primary tumor after neoadjuvant chemotherapy, local recurrence and distant metastases.

  Dataset EGAD50000000475

• Multiple paralogues and recombination mechanisms contribute to the high incidence of 22q11.2 Deletion Syndrome

  The 22q11.2 deletion syndrome (22q11.2DS) is the most common microdeletion disorder. Why the incidence of 22q11.2DS is much greater than that of other genomic disorders remains unknown. Short read sequencing cannot resolve the complex segmental duplications (SDs) to provide direct confirmation of the hypothesis that the rearrangements are caused by non-allelic homologous recombination between the low copy repeats on chromosome 22 (LCR22s). To enable haplotype-specific assembly and rearrangement mapping in LCR22 clusters, we used whole genome (ultra-)long read sequencing of 9 duos (patients and parent of origin).

  Dataset EGAD50000000855

• Single individual whole genome sequencing of Jakun, Indigenous Peoples of the Peninsular Malaysia

  This study disected the genetic structure of a Jakun individual, a sub-tribe of Indigenous Proto-Malay from Peninsular Malaysia. They are postulated to have settled in Peninsular Malaysia approximately 4-6 KYA, during the last agricultural expansion. However, their genetic structure is still not well understood.

  Study EGAS50000000740

• De novo detection of somatic variants

  The Tumor Profiler Study is an observational trial combining a prospective diagnostic approach to assess the relevance of in-depth tumor profiling to support clinical decision-making with an exploratory approach to improve the biological understanding of the disease. This dataset contains scDNA-seq data for 3 ovarian cancer samples from the Tumor Profiler Study used to validate LongSom. LongSom is a computational workflow leveraging high-quality long-read scRNA-seq data to call de novo somatic single-nucleotide variants (SNVs), including in mitochondria (mtSNVs), copy-number alterations (CNAs), and gene fusions, to reconstruct tumor clonal heterogeneity.

  Dataset EGAD50000001292

• 10X snRNA-seq data from human FCDII postoperative brain tissues with mTOR pathway mutations

  Focal cortical dysplasia type II (FCDII) is linked to mTOR pathway mutations and drug-resistant epilepsy. Using 10X snRNA-seq on postoperative FCDII brain tissues, we characterized transcriptional alterations across cell types, revealing mTOR-related dysregulation. These findings provide insights into FCDII pathology and potential therapeutic target

  Study EGAS50000000964

• 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

• Development of actionable molecular targets and/or biomarkers for prognostication and patient stratification in gynecological cancer based on whole-exome sequencing and epigenomic analysis

  We collected 92 endometrial hyperplasia lesions (48 non-atypical from 30 cases and 44 atypical from 24 cases) and matched normal tissues/whole blood. The purpose of this study is to develop actionable molecular targets and/or biomarkers for prognostication and patient stratification.

  Study JGAS000642

• Whole genome sequence: cardiomyopathy, 1 HCM patient

  In this study, we analyzed the genomic information by whole genome sequencing using peripheral blood samples from patients with various cardiovascular diseases including severe heart failure to identify genetic variants related to the pathology of cardiovascular diseases. The purpose is to elucidate the underlying mechanism and develop new therapeutic interventions for cardiovascular disease.

  Study JGAS000704

• Whole genome sequence: cardiomyopathy, 1 ARVC patient

  In this study, we analyzed the genomic information by whole genome sequencing using peripheral blood samples from patients with various cardiovascular diseases including severe heart failure to identify genetic variants related to the pathology of cardiovascular diseases. The purpose is to elucidate the underlying mechanism and develop new therapeutic interventions for cardiovascular disease.

  Study JGAS000705

• A distinct monocyte cellular state links systemic immune dysregulation to pulmonary impairment in long COVID

  This is an independent cohort of Long COVID patients recruited from a rehabilitation centre. These patients had Long COVID from 8 months to more than 2 years since their acute COVID-19 disease. PBMC from these patients were collected and single cell transcriptomics dataset was generated.

  Study EGAS50000001216

• Identification of genetic mutations characteristic for recurrence and metastasis of lymphoma.

  We collected the cancerous tissues of the primary and recurrence tumors from the same patient with recurrent B cell lymphoma, and the purpose of this study is to find the characteristics of recurrent B cell lymphoma by carrying out a "molecular profiling", mainly the exome sequence analysis of these tissues.

  Study JGAS000087

• Intractable Cancer Therapy Development through a New Target Identification by Molecular Profiling

  We collected the cancerous tissues of the primary and recurrence tumors from the same patient with recurrent / metastatic breast cancer, and the purpose of this study is to find the characteristics of recurrent / metastatic breast cancers by carrying out a "molecular profiling", mainly the exome sequence analysis of these tissues.

  Study JGAS000075

• Biobank Japan WGS data of myocardial infarction and dementia

  The Biobank Japan (BBJ) Project started and has collected around 200,000 individuals with disease cases consisting of 51 diseases. The purpose of the BBJ is to realize personalized medicine. With the use of about 2200 samples in the BBJ, whole-genome sequnecing was conducted at RIKEN, Center for Integrative Medical Sciences.

  Study JGAS000381

• Transcriptome analysis of Williams syndrome

  Williams syndrome (WS) is a neurodevelopmental disorder caused by microdeletion on chromosome 7q11.23, and has attracted much attention for its distinctive features, such as hypersociability. However, it remains unclear which genes are involved in the complex phenotypes of their condition. Here, we performed transcriptome analysis of peripheral blood to identify genes associated with WS.

  Study JGAS000132

• Comprehensive genetic analysis of pediatric germ cell tumors

  Germ cell tumors (GCTs) are relatively rare tumors in children. Previous studies showed that adult testicular GCTs had some genomic alterations, but genetic basis of pediatric GCTs is still to be elucidated. We applied DNA methylation array analysis, whole-transcriptome sequencing, targeted capture sequencing, and SNP array analysis to fifty-one GCT samples.

  Study JGAS000204

• Identification of genetic mutations characteristic for recurrence and metastasis of gastric cancer.

  We collected the cancerous tissues of the primary and recurrence tumors from the same patient with recurrent / metastatic gastric cancer, and the purpose of this study is to find the characteristics of recurrent / metastatic gastric cancers by carrying out a "molecular profiling", mainly the exome sequence analysis of these tissues.

  Study JGAS000086

• Single-cell multi-omics and mtDNA genotyping of human peripheral blood cells

  This dataset comprises two mtscATAC-seq libraries (customized 10X ATAC-seq) generated from donor M80 and donor H05, and one DOGMA-seq library (customized 10X multiome) generated from donor H05, all derived from primary human peripheral blood mononuclear cells. Patient M80 is an 80-year-old male with mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS), while donor H05 is a healthy 5-year-old pediatric donor. The raw FASTQ files have been provided.

  Dataset EGAD50000001489

• snRNA-seq schizophrenia control Prefrontal cortex

  In this study, we performed RNA sequencing of single nuclei from the prefrontal cortex of donors with and without schizophrenia using the 10x Genomics Chromium Single Cell protocol. The project rationale is to determine cell type specific transcriptomic changes between the two groups and linking them to the risk for schizophrenia.

  Study EGAS50000001703

• Hyperfibrinolysis

  As part of the Bloodomics collaboration we have several categories of pedigrees with diseases/syndromes relevant to cardiovascular diseases (CVD). One such pedigree, hyperfibrinolysis is associated with increased fibrinolytic activity, resulting in increased bleeding. Exome sequencing has been performed as part of a discovery program to ascertain potential causative variants of the clinical phenotype.

  Study EGAS00001000104

• sWGS on cfDNA and matching tumor DNA in pediatric cancer

  This dataset contains shallow whole genome sequencing data from paired cfDNA - tumor DNA samples of various pediatric cancer entities. Files are provided in fastq format. Samples were sequenced on an Ion Proton sequencer (Thermo Fisher Scientific) or a Hiseq3000 (Illumina). Data analysis is available at https://github.com/rmvpaeme/sWGS_pediatric_cancer.

  Study EGAS00001005198

• Screening_for_abnormal_CGI_methylation_in_primary_colorectal_tumours

  A common hallmark of neoplastic cells is abnormal acquisition of CpG island (CGI) methylation and the silencing of associated gene promoters. To determine the extent and distribution of CGI methylation in colorectal cancer, we solexa sequenced MBD affinity purified DNA prepared from five colorectal tumours and matched colon mucosa from the same individuals.

  Study EGAS00001000076

• IHEC DEEP Release August 2016

  Additional sequencing data for the German IHEC contribution (DEEP, http://deep.dkfz.de/, http://www.deutsches-epigenom-programm.de/). This is the additional data released in August 2016. Contains datatypes: - Whole Genome Bisulfite sequencing - ChipSeq (H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me3, H3K9me3, Input) - tRNA – not unmapped - mRNA - snRNA - Dnase Hypersensitive sites - RRBS - NOMe

  Study EGAS00001001937

• Hypothalamic transcriptome in Prader-Willi syndrome

  Transcriptional analysis of brain tissue from people with molecularly defined causes of obesity may highlight novel disease mechanisms and therapeutic targets. Prader-Willi syndrome (PWS) is a genetic obesity syndrome characterised by severe hyperphagia. We performed RNA sequencing of the hypothalamus from 4 individuals with PWS and 4 age-matched controls.

  Study EGAS00001002901

• Whole exome sequencing in familial Multiple Sclerosis

  The purpose of the study is to determine whether variants of genes are associated with greater risk of Multiple Sclerosis (MS). We used whole-exome sequencing in 138 individuals from 23 families including at least 2 members with MS. We compare patients with MS, patients with other autoimmune diseases (AID), and unaffected individuals.

  Study EGAS00001004204

• Targeted_Sequencing_of_Human_Myeloid_Malignancies

  This study involves targeted sequencing of samples from myeloid malignancies at different timepoints to assess clonal evolution of malignancya.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 EGAS00001001289

• Mutation_burden_in_sun_exposed_eyelid__MSSE_

  Eyelid skin from blepharoplasty surgery will be collected from patients of different ethnic origin (Chinese, Malay, Indian and Caucasion) exposed to tropical sunshine. 2mm2 biopsies will be collected and DNA sequenced using a specific bait capture set and at high depth. The aim is to try and see if different mutations expand in different ethnic populations.

  Study EGAS00001002512

• Bleeding

  As part of the Bloodomics collaboration we have several categories of pedigrees with diseases/syndromes relevant to cardiovascular diseases (CVD). One such group, is from individuals who exhibit severe bleeding with an unknown cause. Exome sequencing has been performed as part of a discovery program to ascertain potential causative variants of the clinical phenotype.

  Study EGAS00001000106

• The_life_history_of_colorectal_cancer_metastases_study_WGS_X10

  Whole genome sequencing of a series of metastasis collected from 2 patients at autopsy will be used to construct a life history of the cancer, including phylogenetic relationship between the different metastases an also whether there is evidence of convergence towards common biological processes that underpin the metastatic process but though different mutational events

  Study EGAS00001000864

• Whole-genome and transcriptome sequencing of tumor-stage mycosis fungoides

  Mycosis fungoides (MF) is the most common cutaneous T-cell lymphoma (CTCL), a group of malignancies derived from skin-homing malignant T cells. We subjected tumor biopsies from MF patients to whole-genome sequencing and RNA-sequencing to investigate genomic alterations and deregulated gene expression in the disease.

  Study EGAS00001002860

• Whole genome sequencing of Japanese HCCs

  To determine somatic mutation profiles and substitution signatures in Japanese HCC, we performed whole genome sequencing of 31 HCCs with various epidemiological backgrounds. Somatic mutations and rearrangements were determined as previously reported. The data will be deposited to the ICGC database and is used for further comparative and integrative analyses.

  Study EGAS00001000671

• Validation_of_AML_Mutational_Screening

  We recently worked-up a pulldown protocol for studying 21 genes recurrently mutated in AML (Study1770). Our manuscript is currently under revision and to address the reviewers' comments we need to validate some mutations by re-sequencing. In this add-on study we will be using PCR followed by MiSeq for this purpose.

  Study EGAS00001000430

• The genomic landscape of primary cutaneous anaplastic large cell lymphoma (pcALCL)

  Primary cutaneous anaplastic large cell lymphoma (pcALCL) is the second most common variant of cutaneous T-cell lymphoma. We subjected tumor biopsies from patients with pcALCL to whole-genome sequencing, whole-exome sequencing and RNA-sequencing to investigate genomic alterations and deregulated gene expression in the disease.

  Study EGAS00001004429

• Various_Platelet_Disorders

  As part of the Bloodomics collaboration we have several categories of pedigrees with diseases/syndromes relevant to cardiovascular diseases (CVD). One such group, is from individuals who have a platelet disorder with an unknown cause. Exome sequencing has been performed as part of a discovery program to ascertain potential causative variants of the clinical phenotype.

  Study EGAS00001000107

• Targeted_sequencing_of_candidate_genes_in_calcific_aortic_valve_stenosis

  The objective is to identify new disease genes involved in calcific aortic valve stenosis (CAVS) by screening newly identified candidate genes. The recruitment of patients with CAVS has been achieved by l’institut du thorax (Nantes, France). DNA from the selected patients has been analysed by targeted capture (Agilent SureSelect) and massively parallel sequencing (Illumina).

  Study EGAS00001000308

• A mutation in VPS15 (PIK3R4) causes a ciliopathy and affects IFT20 release from the cis-Golgi

  VPS15 is known as a VPS34-associated protein that functions in intracellular trafficking and autophagy. Here the authors identify a role for VPS15 in cilopathy and ciliary phenotypes, and show that it interacts with GM130 and functions in IFT20-dependent cis-Golgi to cilium trafficking.

  Study EGAS00001002075

• Single-cell RNA-seq data from metastatic ovarian cancer for quality control study

  Quality control is a crucial preliminary step in any single-cell RNAseq experiment, where hard thresholds are commonly used. In order to develop a methodology for a more precise cell filtering in the early steps of a scRNAseq data analysis, we collected tissue samples before chemotherapy from 4 patients.

  Study EGAS00001005066

• Exome sequencing of pseudomyxoma peritonei

  Pseudomyxoma peritonei (PMP) is a subtype of mucinous adenocarcinoma mainly restricted to the peritoneal cavity and most commonly originating from the appendix. In this study, we sequenced whole coding genome of nine PMP tumors and paired normal tissues in order to identify commonly mutated genes and signaling pathways affected in PMP.

  Study EGAS00001002418

• Studying the single cell characteristics of pancreatic cancer

  Pancreatic cancer is a dangerous malignancy in the pancreas. In this study we use single-cell RNA sequencing technique to help understand the transcriptome characteristics of pancreatic tumor cells. This study help understands the complex microenvironment of pancreatic tumors and will likely to benefit clinical research of pancreatic cancer treatments.

  Study EGAS00001003889

• Multi-omics of Richter syndrome

  Richter syndrome (RS) is the aggressive transformation of Chronic Lymphocytic Leukemia, mostly with Diffuse Large B-Cell Lymphoma histology. While histologically similar, RS and de novo DLBCLs present with different clinical courses. We characterized the RS epigenome by combining genome-wide DNA methylation with transcriptome-sequencing on a large RS cohort.

  Study EGAS00001005495

• Cerebrospinal fluid circulating tumour DNA allows the characterisation and monitoring of medulloblastoma

  The molecular characterisation of medulloblastoma, the most common paediatric brain tumour, is crucial for the correct management and treatment of this heterogenous disease. In this study we show that CSF ctDNA allows the molecular characterisation and monitoring of medulloblastoma. This can ultimately facilitate the clinical management of medulloblastoma patients.

  Study EGAS00001004651

• Genomic characterization of metastatic breast cancers

  While large efforts have been done to characterize early breast cancer, little is known about the genomic landscape of metastatic breast cancer. In the present study, we performed whole exome sequencing of 629 metastatic breast cancers, in order to identify new candidate targets and better stratify patients eligible for innovative therapies.

  Study EGAS00001003290

• CRISPR_single_cell_activation

  Single cell CRISPR activitaion analysis with 96 genes with the aim to build a quantative CRISPR activation model. 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 EGAS00001005528

• Melanoma_post_mortem_analysis

  This is a targeted pulldown validation in support of the existing whole-genome sequencing study of melanoma metastases (Canapps ID:1888). We are studying the genomic evolution of cutaneous melanoma metastases. In this pulldown analysis we are specifically sequencing the subclonal variants that we believe account for the variability between the metastases.

  Study EGAS00001003531

• Multi-region RNA sequencing of tumour regions and tumour-adjacent normal lung tissue

  TRACERx (TRAcking Cancer Evolution through therapy (Rx)) is a prospective cohort study designed to investigate intratumor heterogeneity (ITH) in relation to clinical outcome, and to determine the clonal nature of driver events and evolutionary processes in early stage non-small cell lung cancer (NSCLC).

  Study EGAS00001006517

• Correction of FFPE artefacts in WGS data

  The ability to precisely characterise mutational signatures from FFPE-derived DNA has tremendous translational potential. However, sequencing of DNA derived from FFPE material is known to be riddled with artefacts. To correct for this, we introduce FFPEsig, a computational algorithm to rectify the formalin-induced artefacts in the mutational profile.

  Study EGAS00001005331

• Identification of drug resistance genes in melanoma by small RNAs expression analysis

  We aim to sequence the small RNAs of 22 human melanoma cell lines in biological triplicate in order to define the microRNAs expression profile of each cell line. The data will be correlated to the mutation status and the sensitivity to a panel of drugs in order to identify genes whose deregulation is associated to drug resistance 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/

  Dataset EGAD00001003245

• HCA Female Reproductive Adult WSSS RNA

  HCA Endometrium_LM The endometrium regenerates monthly and its transformation is executed through dynamic changes in states and interactions of multiple cell types. Using transcriptomics methods we seek to profile changes of the endometrium across the menstrual cycle. Our map will have implications in women's health and cancer, by enabling the interpretation of GWAS analyses or the studying functional consequences of somatic mutations. 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/

  Dataset EGAD00001007909

• ATAC-seq in hiPSC-derived neurons after BDNF and KCl stimulations

  Brain-Derived Neurotrophic Factor (BDNF) is crucial for neuronal survival, differentiation, synaptic plasticity, memory formation, and neurocognitive health. Molecular mechanisms of BDNF promoting cellular survival and synaptic plasticity have been intensely studied, yet its role in genome regulation is obscure. Using human induced pluripotent stem cell (hiPSC)-derived neurons via lentiviral delivery of the neuronal transcription factor Ngn2, we performed a temporal profiling (1h, 6h and 10h) of chromatin accessibility upon BDNF treatment or depolarization (KCl) to identify BDNF-specific chromatin-to-gene expression programs.

  Dataset EGAD00001009100

• Identification of drug resistance genes in melanoma by mRNA gene expression

  We aim to sequence the mRNA transcriptome of 22 human melanoma cell lines in biological triplicate in order to define the gene expression profile of each cell line. The data will be correlated to the mutation status and the sensitivity to a panel of drugs in order to identify genes whose deregulation is associated to drug resistance 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/

  Dataset EGAD00001003244

• Hereditary Cancer Diagnostics with I2HCP gene panel

  Germline blood DNA sequencing data generated in routine diagnostics of hereditary cancer using the I2HCP gene panel (~135 genes). There are 130 samples sequenced in a MiSeq machine and 108 sequenced in a HiSeq machine. There is a partial overlap between those two sets, meaning that some samples were sequenced in both machines. There is a strong enrichment in samples with copy-number variants (CNV), both single- and multi-exon, since this dataset was compiled for a benchmarking effort of CNV calling tools for genetic diagnostics.

  Dataset EGAD00001006171

• Whole genome sequencing of Osteosarcoma clonal evolution

  Multiple large-scale genomic profiling efforts have been undertaken in osteosarcoma to define the genomic drivers of tumorigenesis, therapeutic response, and disease recurrence. The spatial and temporal intratumor heterogeneity could also play a role in promoting tumor growth and treatment resistance. Here, we conducted longitudinal whole-genome sequencing of 37 tumor samples from eight patients with osteosarcoma that relapsed or became refractory to initial therapy. We found that the chemoresistant population in recurrent osteosarcoma is subclonal at diagnosis, emerges at the time of primary resection due to selective pressure from neoadjuvant chemotherapy, and is characterized by unique oncogenic amplifications.

  Dataset EGAD00001011285

• Exome sequencing of a cohort of Rett syndromelike patients (2017-08-16)

  The aim of the project is the definition of the molecular defect in a cohort of Rett-like patients negative for mutations in known disease genes. To this aim, a number of unrelated trios (patients plus parents) will be analysed by exome sequencing. 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/ This dataset contains all the data available for this study on 2017-08-16.

  Dataset EGAD00001003564

• 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 unclear 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 EGAD00001000798

• Anaplastic Meningioma WGS-X10

  Anaplastic meningiomas are a rare, malignant variant of meningioma. At present there is no effective treatment for this cancer. The aim of the study is to identify somatic mutations in anaplastic meningiomas. We plan to sequence a set of 500 known cancer genes in 50 anaplastic meningioma and corresponding peripheral blood DNA samples. Bioinformatics will be used to analyse the results to assess the probability of these mutations being causal and so likely of critical importance for the tumour growth. Identification of these mutations will guide selection of appropriate compounds to effectively treat the disease.

  Dataset EGAD00001001267

• Mechanism and targeted therapy of Vemurafenib-Resistant Hairy-Cell Leukemia

  The discovery of the BRAF V600E mutation in almost all cases of hairy-cell leukemia has led to the widespread adoption of the BRAF inhibitor vemurafenib for treatment of chemotherapy-resistant cases. Impressive responses are reported; however, acquired resistance is common. Whilst diverse mechanisms of vemurafenib resistance have been elucidated in melanoma, the basis of resistance in HCL is unclear. Here we apply whole genome and deep targeted sequencing to investigate resistance mechanisms and potential therapeutic strategies in a patient with aquired resistance to vemurafenib.

  Dataset EGAD00001003923

• Mechanism and targeted therapy of Vemurafenib-Resistant Hairy-Cell Leukemia

  The discovery of the BRAF V600E mutation in almost all cases of hairy-cell leukemia has led to the widespread adoption of the BRAF inhibitor vemurafenib for treatment of chemotherapy-resistant cases. Impressive responses are reported; however, acquired resistance is common. Whilst diverse mechanisms of vemurafenib resistance have been elucidated in melanoma, the basis of resistance in HCL is unclear. Here we apply whole genome and deep targeted sequencing to investigate resistance mechanisms and potential therapeutic strategies in a patient with aquired resistance to vemurafenib.

  Dataset EGAD00001003924

• Exome sequencing of Congenital Heart Disease families Leuven

  This project aims to study at least 90 exomes from families with congenital heart disease. The samples have been selected in Leuven in collaboration with Koen Devriendt. Ethic approval has been sought for in Leuven, Belgium and a HDMMC agreement for submitting these samples is in place at the WTSI. The phenotype we wil primarily focus our analysis is severe Left Ventricular Outflow Tract Obstructions (LVOTO) and Atrioventricular Septal Defect (AVSD). The indexed Agilent whole exome pulldown libraries will be sequenced on 75bp PE HiSeq (Illumina).

  Dataset EGAD00001000796

• Transcriptomics of human olfactory mucosa

  The olfactory gene repertoire is largely species-specific, shaped by the nature and necessity of chemosensory information for survival in each species' niche. We are intrigued by this interspecific variation and started to investigate the olfactory transcriptome in primates for evidence of selection at the level of receptor gene choice. Having collected this data from two primates, we now wish to extend the analysis to humans. 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/

  Dataset EGAD00001003213

• Application of short-RNA-seq in post-mortem human hippocampi from the Calgary Brain Bank (CBB) to assess transcriptome-wide deregulation in processing of SINE Alu RNAs in Alzheimer’s disease

  Here, we investigate through short-RNA_seq in human hippocampi from the Calgary Brain Bank (CBB) whether Alu RNAs are processed in human brains, and whether their processing ratio is deregulated in brains of AD patients compared to healthy aging individuals.

  Study EGAS00001004973

• A rare CTSC mutation in Papillon-Lefèvre Syndrome

  Papillon-Lefèvre Syndrome (PLS) is an autosomal recessive monogenic disease caused by loss-of-function mutations in the CTSC gene. In this study we performed whole genome sequencing on two siblings, with the PLS-typical symptoms. After sequencing the CTSC gene was analyzed to confirm the PLS diagnosis genetically.

  Study EGAS00001005040

• DAC Johns Hopkins University - AML scRNAseq study

  This is the Data Access Committee (DAC) from Johns Hopkins University for the study scRNAseq of acute myeloid leukemia

  Dac EGAC50000000242

• CNCD Recall by Genotypes

  This is a DAC to handle recall by genotype studies by the conducted by the Center for Non-Communicable Disease Karachi, Pakistan.

  Dac EGAC50000000937

• MPNST exome and genome

  This is the complete dataset (exome and genome) for the EGAS00001000974 study.

  Dataset EGAD00001001040

• 108 WGS of epileptic patients from the CENet cohort

  Dataset is described in doi: https://doi.org/10.1101/2022.12.13.22283363

  Dataset EGAD00001011301

• Natural History and Structural Functional Relationships in Fabry Renal Disease

  Fabry disease is a rare genetic disease with deficient activity of an enzyme, which leads to accumulation of inclusions in different organs including kidney, heart and vessels. The purpose of the study is to conduct a cross-sectional investigation of the natural history of Fabry renal disease and measure renal function and renal structure in male and female Fabry's patients. The study will utilize the resultant cross-sectional information to determine the renal structural parameters or composite of parameters that most closely relates to the onset and progression of clinical renal disease in Fabry patients. This is an observational, cross-sectional study of 60 individuals with Fabry disease. Those participating in the study will be evaluated during a one day visit and on a PRN basis. The primary study objectives are as follows: To study the natural history of Fabry renal disease and measure renal function and renal structure in male and female Fabry's patients. These patients would encompass the broad age range from childhood to adulthood and from normal renal function to moderate renal insufficiency [serum creatinine (SCr) ≤ 2.5mg/dl (chronic kidney disease or CKD3)]. To utilize the resultant cross-sectional information to determine the renal structural parameters or composite of parameters that most closely relates to the onset and progression of clinical renal disease in Fabry patients.

  Study phs001333

• BRAIN Cell EncyclOpeDia of Transcribed Elements (BRAINcode)

  BRAINCODE: How Does the Human Genome Function in Specific Brain Neurons? The human brain comprises about 86 billion neurons whose function is central to human biology. How does the human genome program high performing neurons and neural networks in response to experience? What subprograms does the genome express in physiologically and morphologically distinct brain cells? The goal of the BRAIN Cell encyclOpeDia of transcribed Elements Consortium (BRAINcode) is to provide a map of gene expression - both protein-coding and non-coding - in specific cell types, not in culture, but in situ in brains of people. Going beyond traditional mRNA sequencing, polyadenylated and non-polyadenylated transcripts were ultra deeply sequenced using ribo-depleted RNA from neurons laser-captured from human post-mortem brains. Three prototypical neuron types, dopamine neurons, pyramidal neurons, and Betz cells, were prioritized because of their key biologic roles and differential vulnerability to important neurodegenerative diseases such as Parkinson's or Alzheimer's disease. Genetic variation between individuals was examined for correlation with differences in transcribed sequences to identify regions of the genome that influence whether, how, and how much a transcript is expressed in specific cell types in human brains. Our results indicate a vast universe of annotated and novel non-coding RNAs expressed in brain cells and suggest a more diverse and much more complex transcriptional architecture than previously imagined.

  Study phs001556

• Drug screening of patient-derived organoids from colorectal peritoneal metastases

  Colorectal cancer (CRC) patients with peritoneal metastases (CRPM) have limited treatment options and the lowest CRC survival rates. We trialed the possibility of organoid directed precision treatment for CRPM patients. CRPM organoids (peritonoids) isolated from patients underwent next-generation sequencing and medium-throughput drug panel testing ex vivo to identify specific drug sensitivities for each patient. We measured the utility of such a service including: success of peritonoid generation, time to cultivate peritonoids, reproducibility of the medium-throughput drug testing, and documented changes to clinical therapy as a result of the testing. Peritonoids were successfully generated and validated from 68% (19/28) of patients undergoing standard care. Genomic and drug profiling was completed within 8 weeks and a formal report ranking drug sensitivities was provided to the medical oncology team upon failure of standard care treatment. This resulted in a treatment change for 2 patients, one of whom had a partial response despite previously progressing on multiple rounds of standard care chemotherapy. The barrier to implementing this technology in Australia is the need for drug access and funding for off-label indications. In conclusion, our approach is feasible, reproducible and can guide novel therapeutic choices in this poor prognosis cohort, where new treatment options are urgently needed. This platform is relevant to many solid organ malignancies.

  Study phs002023

• AIDS Linked to the Intravenous Experience (ALIVE) Cohort

  The AIDS Linked to the Intravenous Experience (ALIVE) Study is a long-standing community based research effort that includes past and current injection drug users (IDUs). ALIVE has been ongoing since 1988 and is one of the longest-running community-based cohorts of IDUs in existence. The primary objectives when the study started were to characterize the incidence and natural history of HIV among injection drug users (IDUs). At each study visit, participants undergo a series of questionnaires that elicit information about substance use (including drugs used and route of administration) and a blood draw. A subsample of 1200 subjects was selected for genotyping for the NIDA Smokescreen effort who report heroin injection and have existing peripheral blood samples (isolated buffy coat). In addition to injected heroin, ALIVE subjects are assessed on lifetime and previous six months use of marijuana (76.3%), crack (55.5%), snorted cocaine (48.3%), injected cocaine (89.9%), injected speedball (87.0%), and smoking heroin (9.0%). The sample is 33.4% female, ~85% African-American and assessed through a mean maximum age of 49.9 years old. Importantly, subjects are not assessed to meet DSM criteria, but all subjects report having injected drugs. We provide demographic data (age at assessment, sex, self-reported race) and drug use data (lifetime "use" ever endorsed) for each drug class/route described above for each subject

  Study phs001494

• INdiana GENomics: Implementing an Opportunity for the Under Served (INGENIOUS)

  The INGenious trial planed to enroll a total of 6,000 patients, with 2,000 patients assigned to a pharmacogenetic testing arm and 4,000 to a control arm who will be followed, but not tested. It is randomized between an intervention arm and one that receives no intervention in order that the genotyped group can be compared with one in which undisturbed, routine clinical care is carried out in patients taking the same drugs. Both arms will be followed for a year after being prescribed a targeted medication. Patients randomized into the intervention arm that are prescribed one or more of the 27 targeted index medication will receive pharmacogenomic testing using a custom micro-array measuring 43 Single nucleotide polymorphisms in 14 genes. The study is being conducted by the Indiana University School of Medicine and the Indiana University Institute of Personalized Medicine in collaboration with the Eskenazi and Indiana University Health Systems and will evaluate the economic and clinical outcomes associated with embedding a pharmacogenomics program in a system that serves as the primary health care safety-net in Indianapolis, Indiana. By successfully implementing a pharmacogenomics program and integrating it with the Electronic Health Record and Clinical Decision Support system, physicians will be able to optimize patient care by delivering tailored therapeutic decisions based on the patient's individual genetics.

  Study phs001701

• Center for Common Disease Genomics [CCDG] - Autoimmune: Inflammatory Bowel Disease (IBD) Exomes and Genomes

  The National Human Genome Research Institute (NHGRI) has funded a collaborative large-scale genome sequencing effort to comprehensively identify rare risk and protective variants contributing to multiple common disease phenotypes. Called the Centers for Common Disease Genomics (CCDG), this initiative will explore a range of diseases with the ultimate goal of: undertaking variant discovery for enough different examples of disease architectures and study designs to better understand the general principles of the genomic architecture underlying common, complex inherited diseases; understanding how best to design rare variant studies for common disease; developing resources, informatics tools, and innovative approaches and technologies for multiple disease research communities and the wider biomedical research community. The initial focus of the CCDGs will be in cardiovascular disease (early-onset coronary artery disease, atrial fibrillation, hemorrhagic stroke), neuropsychiatric disease (epilepsy, autism), and autoimmune/inflammatory disease (type 1 diabetes, inflammatory bowel disease). The Broad Institute is one of four selected CCDG project centers. The overarching aim of the Inflammatory Bowel Disease (IBD) program is to define the full allelic spectrum of protein-altering variation in genes associated to IBD, and assess their role in both Crohn's Disease (CD) and Ulcerative Colitis (UC) risk. The whole genome sequencing data generated here is comprised of samples from US-based diverse populations including African American, Puerto-Rican, Caribean and Cuban origins.

  Study phs001642

• NHLBI TOPMed: Best ADd-on Therapy Giving Effective Response (BADGER)

  BADGER is a 56-week randomized, double-blind, three-treatment, three-period cross-over trial that will evaluate the differential improvement in control that is achieved following three separate treatment interventions in children whose asthma is not acceptably controlled on a low dose of ICS (per NAEPP guidelines). All participants will enter an 8-week run-in period during which time they will receive a dose of 1x ICS (fluticasone 200 μg/day). During this 8-week time period, running 2-week averages to establish the lack of acceptable asthma control will be calculated. Thus, a child could qualify for randomization at any time during this 8-week run-in period. This approach should maximize both patient safety and successful enrollment. Children will continue to receive 1x ICS during the entire treatment phase. During each period of the treatment phase, they also will receive one add-on therapy in the form of LABA, LTRA or additional 1x ICS. The order of the add-on therapy assignment will be determined by randomization into one of six treatment sequences (order determined randomly). Each treatment period will be 16 weeks in length; the initial 4 weeks of each period will be considered to be the washout period for the previous treatment. The primary outcome measures will be frequency of asthma exacerbations, asthma control days, and FEV1.

  Study phs001728

• National Heart, Lung, and Blood Institute (NHLBI) Bench to Bassinet Program: The Pediatric Cardiac Genetics Consortium (PCGC) Study

  Multi-center, prospective observational cohort study of individuals with congenital heart defects (CHD). Phenotypic data and source DNA derived from 10,000 probands, parents, and families of interest are being collected to investigate relationships between genetic factors and phenotypic and clinical outcomes in patients with CHD. Phenotype data will be stored at dbGaP, while molecular and sequence data will be stored at BioData Catalyst. The PCGC Cohort is utilized in the following dbGaP substudies. Please click on the following substudies below or in the "Substudies" section of this top-level study page phs001194 PCGC Cohort. phs000571 PCGC: whole exome sequences, whole genome sequences, targeted sequences, MIP sequences, and SNP array data phs001843 PCGC-CMG Collaboration: whole genome sequences The Gabriella Miller Kids First Pediatric Research Program (Kids First) subset of the PCGC project (phs001194) is now accessible through a separate dbGaP study accession: phs001138. To access this dataset, please submit a Data Access Request (DAR) for phs001138. Approval of this DAR will be expedited for approved users of phs001194. To learn about other Kids First datasets visit https://kidsfirstdrc.org/.NHLBI's TOPMed program has provided additional Whole Genome Sequencing for PCGC participants - that data is accessible through a separate dbGaP sudy accession: phs001735. Access to this data set should be requested through a Data Access Request (DAR) for phs001735.

  Study phs001194

• Genomic characterization of retinoblastoma (targeted sequencing)

  Retinoblastoma is the most frequent intraocular malignancy in children, originating from a maturing cone precursor in the developing retina. Little is known on the molecular basis underlying the biological and clinical behavior of this cancer. Here, using multi-omics data, we demonstrate the existence of two retinoblastoma subtypes. Subtype 1, of earlier onset, includes most of the heritable forms. It harbors few genetic alterations other than the initiating RB1 inactivation and corresponds to differentiated tumors expressing mature cone markers. By contrast, subtype 2 tumors harbor frequent recurrent genetic alterations including MYCN-amplification. They express markers of less differentiated cone together with neuronal/ganglion cell markers with marked inter- and intra-tumor heterogeneity. The cone dedifferentiation in subtype 2 is associated with stemness features including low immune and interferon response, E2F and MYC/MYCN activation and a higher propensity for metastasis. The recognition of these two subtypes, one maintaining a cone-differentiated state, and the other, more aggressive, associated with cone dedifferentiation and expression of neuronal markers, opens up important biological and clinical perspectives for retinoblastomas. In this study, we performed targeted sequencing of the exonic regions of RB1, BCOR and ARID1A on 37 samples from the series of 102 retinoblastomas. Among them, 23 samples were not subjected to whole-exome sequencing, and 14 samples have the whole-exome sequencing data (deposited in EGAS00001005248).

  Study EGAS00001005550

• Aggressive genomic features in clinicallyindolent primary HHV8-negative effusion-based lymphoma

  Human herpesvirus 8-negative effusion-based lymphoma (HHV8-negative EBL) is a distinct lymphoma entity related to fluid overload states caused by underlying medical conditions. Due to a phenotypical resemblance with secondary effusion of diffuse large B-cell lymphoma (DLBCL), HHV8-negative EBL is easily misdiagnosed. However, in contrast to DLBCL, HHV8-negative EBL follows a mild clinical course, underpinning the importance to differentiate between the two entities. Only limited molecular data of HHV8-negative EBL has been reported and characteristic genomic patterns are lacking. We performed extensive genomic profiling on 8 HHV8-negative EBL cases. A mean number of 33.6 copy number gains and losses per case were found, with recurrent focal deletions of chromosome 3p14.2 and 6q21 in 6/8 cases, encompassing tumor supressor genes FHIT and PRDM1, respectively. We observed a high rate of mutations across genes frequently involved in DLBCL, including patterns of somatic hypermutation. The most abundant hotspot mutation was found in MYD88L265P (3/8 cases). In addition, 5/8 cases had one or more translocations, involving MYC, BCL2, BCL6, TP63, EXOC2 and KMT2D, with Ig and non-Ig partners. We conclude that HHV8-negative EBL is characterized by genomic features that are commonly found in more aggressive B-cell lymphomas, but despite this follow an indolent clinical course.

  Study EGAS00001002743

• Evolution of DNA repair defects during malignant progression of low-grade gliomas after temozolomide treatment.

  Temozolomide (TMZ) increases the overall survival of patients with glioblastoma (GBM), but its role in the clinical management of diffuse low-grade gliomas (LGG) is still being defined. DNA hypermethylation of the O 6 -methylguanine-DNA methyltransferase (MGMT) promoter is associated with an improved response to TMZ treatment, while inactivation of the DNA mismatch repair (MMR) pathway is associated with therapeutic resistance and TMZ-induced mutagenesis. We previously demonstrated that TMZ treatment of LGG induces driver mutations in the RB and AKT-mTOR pathways, which may drive malignant progression to secondary GBM. To better understand the mechanisms underlying TMZ-induced mutagenesis and malignant progression, we explored the evolution of MGMT methylation and genetic alterations affecting MMR genes in a cohort of 34 treatment-naïve LGGs and their recurrences. Recurrences with TMZ-associated hypermutation had increased MGMT methylation compared to their untreated initial tumors and higher overall MGMT methylation compared to TMZ-treated non-hypermutated recurrences. A TMZ-associated mutation in one or more MMR genes was observed in five out of six TMZ-treated hypermutated recurrences. In two cases, pre-existing heterozygous deletions encompassing MGMT, or an MMR gene, were followed by TMZ-associated mutations in one of the genes of interest. These results suggest that tumor cells with methylated MGMT may undergo positive selection during TMZ treatment in the context of MMR deficiency.

  Study EGAS00001001179

• Exome and RNA sequencing of relapsed TCF3-PBX1 t(1;19) acute lymphoblastic leukemia

  TCF3-PBX1 (E2A-PBX1) is a recurrent gene fusion in B-cell precursor lymphoblastic leukemia (BCP-ALL), which is caused by the translocation t(1;19)(q23;p13). TCF3-PBX1 BCP-ALL patients typically benefit from chemotherapy; however, many relapse and subsequently develop resistant disease with few effective treatment options. Mechanisms driving disease progression and therapy resistance have not been studied in TCF3-PBX1 BCP-ALL. Here, we aimed to identify novel treatment options for TCF3-PBX1 BCP-ALL by profiling leukemia cells from a relapsed patient, and determine molecular mechanisms underlying disease pathogenesis and progression. By drug sensitivity testing of leukemic blasts from the index patient, control samples and TCF3-PBX1 positive and negative BCP-ALL cell lines, we identified the phosphatidylinositide 3-kinase delta (p110δ) inhibitor idelalisib as an effective treatment for TCF3-PBX1 BCP-ALL. This was further supported by evidence showing TCF3-PBX1 directly regulates expression of PIK3CD, the gene encoding p110δ. Other somatic mutations to TP53 and MTOR, as well as aberrant expression of CXCR4, may influence additional drug sensitivities specific to the index patient and accompanied progression of the disease. Our results suggest that idelalisib is a promising treatment option for patients with TCF3-PBX1 BCP-ALL while other drugs could be useful depending on the genetic context of individual patients.

  Study EGAS00001001876

• A genomic approach towards an understanding of clonal evolution and disease progression in multiple myeloma

  Multiple Myeloma (MM) is a largely incurable haematological malignancy defined by the clonal proliferation of malignant plasma cells within the bone marrow. Clonal heterogeneity has recently been established as a feature in MM, however, the subclonal evolution associated with disease progression has not been described. We used whole exome sequencing to analyse 10 paired patient samples, providing new insights into the progression from Monoclonal Gammopathy of Undetermined Significance (MGUS) and Smouldering MM (SMM), to symptomatic MM. We confirm that clonal heterogeneity is a common feature at diagnosis and that the driving events involved in disease progression are more complex than previously reported. While we observe some previously identified known “drivers” of MM, we find that the driving events involved in progression are complex and not limited to the known SNVs or CNVs. The RAS/MAPK pathway was found to be the most frequently deregulated pathway, with recurrent mutations in KRAS and NRAS observed in patients at both MGUS/SMM and MM stages. We reveal that MM evolution is mainly characterised by the phenomenon of clonal stability, where the subclonal plasma cell populations identified at MM progression are already present in the asymptomatic MGUS/SMM stages. These subclonal populations could be amenable to therapeutic intervention to arrest transformation to MM.

  Study EGAS00001002850

• Hyperhaploid Multiple Myeloma

  Hyperhaploid multiple myeloma is a rare numerical aberration group defined by a range of 24-34 chromosomes which is associated with a poor prognosis. Hyperhaploid samples were sequenced by either exome or targeted panel sequencing. Samples had a median of 13 monosomies (range 12-14), which in general were those not associated with trisomies in hyperdiploid samples. The chromosomes traditionally trisomic in hyperdiploid myeloma were disomic in hyperhaploid myeloma with retention of heterodisomy. We examined the hyperhaploid samples for frequently mutated genes and found that 9/9 (100%) hyperhaploid samples had a mutation in TP53, exceeding the overall rate of mutation in newly diagnosed patients (5.5%), indicating an oncogenic dependency in this group. All samples with TP53 mutation also had monosomy of chromosome 17, indicating bi-allelic inactivation of TP53. As such, this high risk group is part of Double-Hit myeloma. DNA was obtained from either CD138+ cells from the bone marrow of multiple myeloma patients (tumor) or from stem cell harvests from the same patient (control). 100 ng of DNA was fragmented, end-repaired, and adapters ligated using the HyperPlus kit (KAPA Biosystems). After PCR amplification the libraries were hybridized with probes against either the entire exome (MedExome, Nimblegen) or a targeted panel of 140 genes using SeqCap reagents (Nimblegen). Hybridized libraries underwent further amplification before being sequenced on a NextSeq500 (Illumina) using 75 bp paired end reads.

  Study EGAS00001003203

• EXOME-WIDE ASSOCIATION ANALYSIS OF CORONARY ARTERY DISEASE IN THE KINGDOM OF SAUDI ARABIA POPULATION

  Coronary Artery Disease (CAD) remains the leading cause of mortality worldwide. Mortality rates associated with CAD have shown an exceptional increase particularly in fast developing economies like the Kingdom of Saudi Arabia (KSA). Over the past twenty years, CAD has become the leading cause of death in KSA and has reached epidemic proportions. This rise is undoubtedly caused by fast urbanization that is associated with a life-style that promotes CAD. However, the question remains whether genetics play a significant role and whether genetic susceptibility is increased in KSA compared to the well-studied Western European populations. Therefore, we performed an Exome-wide association study (EWAS) in 832 patients and 1,076 controls of Saudi Arabian origin to test whether population specific, strong genetic risk factors for CAD exist, or whether the polygenic risk score for known genetic risk factors for CAD, lipids, and Type 2 Diabetes show evidence for an enriched genetic burden. Our results do not show significant associations for a single genetic locus. However, the heritability estimate for CAD for this population was high (h2 = 0.53, S.E. = 0.1, p = 4e-12) and we observed a significant association of the polygenic risk score for CAD that demonstrates that the population of KSA, at least in part, shares the genetic risk associated to CAD in Western populations.

  Study EGAS00001001645

• HELIUS cohort

  The gut microbiota composition is unique to every individual but is shaped by common factors including diet, lifestyle, medication use, early-life determinants, living environment or genetics. Most of these factors may be influenced by ethnicity. This study explored variations in fecal microbiota composition in 6048 individuals with different ethnic backgrounds living in the same geographical area (Amsterdam, the Netherlands). The HELIUS data are owned by the Amsterdam University Medical Centers, location AMC in Amsterdam, The Netherlands. To allow sharing of microbiome data collected in HELIUS with (inter)national researchers, 16s rRNA sequence analysis has been stored at the European genome-phenome archive (EGA; accession code EGAD00001004106). This requires that access needs to be granted, also because the HELIUS data are stored with relevant phenotypical variables. Access is granted to all researchers affiliated with an internationally recognized research institution who request to use the HELIUS data within the EGA context, after having signed the data transfer agreement. Any researcher can request the data by submitting a proposal to the HELIUS Executive Board as outlined at http://www.heliusstudy.nl/en/researchers/collaboration, by email: heliuscoordinator at amsterdamumc dot nl. The HELIUS Executive Board will check proposals if they do not conflict with ethical approvals and informed consent forms of the HELIUS study.

  Study EGAS00001002969

• MutWP1__CRUK_Grand_Challenge_Mutographs_of_Cancer__head___neck

  The Mutographs project aims to advance our understanding of the causes of cancer through studies of mutational signatures. Led by Mike Stratton, together with Paul Brennan, Ludmil Alexandrov, Allan Balmain, David Phillips and Peter Campbell, this large-scale international research endeavour was awarded a Cancer Research UK Grand Challenge. Different patterns of somatic mutation are generated by the different environmental, lifestyle and genetic factors that cause cancer, many of them are still unknown. Within Mutographs, the International Agency for Research on Cancer is coordinating the recruitment of 5000 individuals with cancer (colorectal, renal, pancreatic, oesophageal adenocarcinoma or oesophageal squamous cancers) across 5 continents to explore whether different mutational signatures explain marked variation in incidence. In brief, through an international network of collaborators around the world, biological materials are collected, along with demographic, histological, clinical and questionnaire data. Whole genome sequences of tumour-germline DNA pairs are generated at the Wellcome Trust Sanger Institute. Non-tumour DNA is also studied for some cancer types. Somatic mutational signatures are subsequently extracted by non-negative matrix factorisation methods and correlated with risk factors data. Through an enhanced understanding of cancer aetiology, Mutographs unprecedented effort is anticipated to outline modifiable risk factors, lead to new approaches to prevent cancer, and provide opportunities to empower early detection, refine high-risk groups and contribute to further therapeutic development.

  Study EGAS00001005450

• Transcriptomic analysis of Acute Myeloid Leukemia stem cells

  Acute Myeloid Leukemia (AML) is characterized by the accumulation of clonal myeloid blast cells unable to differentiate into mature leukocytes. Chemotherapy induces remission in the majority of patients, but relapse rates are high and lead to poor clinical outcomes. Since this is primarily caused by chemotherapy-resistant leukemic stem cells (LSCs), it is essential to eradicate LSCs to improve patient survival. LSCs have predominantly been studied at the transcript level, thus lacking information about post-transcriptionally regulated genes and associated networks. Here we extend our previous report on LSC proteomes to healthy age-matched hematopoietic stem and progenitor cells (HSPCs) and correlate the proteomes to the corresponding transcriptomes. By comparing LSCs to leukemic blasts and healthy HSPCs, we validate candidate LSC markers and highlight novel and potentially targetable proteins that are absent or only lowly expressed in HSPCs. In addition, our data provides strong evidence that LSCs harbor a characteristic energy metabolism, adhesion molecule composition, as well as RNA processing properties. Furthermore, correlating proteome and transcript data of the same individual samples highlights the strength of proteome analyses, which are particularly potent in detecting alterations in metabolic pathways. In summary, our study provides a comprehensive proteomic and transcriptomic characterization of functionally validated LSCs, blasts and healthy HSPCs, representing a valuable resource helping to design LSC-directed therapies.

  Study EGAS00001004402

• Targeted de-methylation of the FOXP3-TSDR

  CD4+ regulatory T cells (Tregs) are key mediators of immunological tolerance and promising effector cells for immuno-suppressive adoptive cellular therapy to fight autoimmunity and chronic inflammation. Their functional stability is critical for their clinical utility and has been correlated to the demethylated state of the TSDR/CNS2 enhancer element in the Treg lineage transcription factor FOXP3. However, proof for a causal contribution of the TSDR de-methylation to FOXP3 stability and Treg induction is so far lacking. We here established a powerful transient-transfection CRISPR-Cas9-based epigenetic-editing method for the selective de-methylation of the TSDR within the endogenous chromatin environment of a living cell. The induced de-methylated state was stable over weeks in clonal T cell proliferation cultures even after expression of the editing complex had ceased. Epigenetic editing of the TSDR resulted in FOXP3 expression, even in its physiological isoform distribution, proving a causal role for the de-methylated TSDR in FOXP3 regulation. However, successful FOXP3 induction was not associated with a switch towards a functional Treg phenotype, in contrast to what has been reported from FOXP3 overexpression approaches. Thus, TSDR de-methylation is required, but not sufficient for a stable Treg phenotype induction. Therefore, targeted demethylation of the TSDR may be a critical addition to published in vitro Treg induction protocols which so far lack FOXP3 stability.

  Study EGAS00001004867

• Intratumoural heterogeneity and immune modulation in lung adenocarcinoma of female smokers and never smokers

  Lung cancer is still the leading cause of cancer death worldwide despite declining smoking prevalence in industrialised countries. Although lung cancer is highly associated with smoking status, a significant proportion of lung cancer cases develop in patients who never smoked, with an observable bias towards female never smokers. A better understanding of lung cancer heterogeneity and immune system involvement during tumour evolution and progression in never smokers is therefore highly warranted. We employed single nucleus transcriptomics of surgical lung adenocarcinoma (LADC) and normal lung tissue samples from patients with or without smoking history. Immune cells as well as fibroblasts and endothelial cells respond to tobacco smoke exposure by inducing a highly inflammatory state in normal lung tissue. In the presence of LADC, we identified differentially expressed transcriptional programmes in macrophages and cancer-associated fibroblasts, providing insight into how the niche favours tumour progression. Within tumours, we distinguished eight subpopulations of neoplastic cells in female smokers and never smokers. Through pseudotemporal ordering, we inferred a trajectory towards two differentiated tumour cell states implicated in cancer progression and invasiveness. A proliferating cell population sustaining tumour growth exhibits differential immune modulating signatures in both patient groups. Our results resolve cellular heterogeneity and immune interactions in LADC, with a special emphasis on female never smokers and implications for the design of therapeutic approaches.

  Study EGAS00001006331

• Field Studies of Human Immunity to Amebiasis in Bangladesh (NIH Birth Cohort) and Exploration of the Biologic Basis for Underperformance of Oral Polio and Rotavirus Vaccines in Bangladesh (PROVIDE)

  NIH birth cohort study Amebiasis is a common cause of diarrhea and is associated with malnutrition in grade-school aged children in an urban slum of Dhaka, Bangladesh. Field Studies of Human Immunity to Amebiasis in Bangladesh was designed to determine the contribution of amebiasis to illness in the first 2 years of life when most deaths due to diarrhea occur, and understand the immunologic and genetic factors that protect children from amebiasis. The hypothesis underlying the study is that susceptibility to amebiasis is determined by host innate and acquired immune responses that vary between individuals in part due to: human genetic polymorphisms; environmental influences including malnutrition and concurrent geohelminth infection; and virulence differences among Entamoeba histolytica genotypes. Specific aims proposed in the design of the study were to: a) Measure the incidence of amebiasis and correlate it with human and parasite genetic polymorphisms, immune responses, and environmental factors such as geohelminth infection and malnutrition; b) Test the hypothesis that protective immunity is mediated both by innate immune responses initiated via TLR stimulation as well as by mucosal IgA against the Gal/GalNAc lectin and systemic IFN-γ; c) Test for the association of common genetic polymorphisms in host innate and acquired immune genes with incidence of amebiasis. 629 newborn babies were enrolled and followed regularly through bi-weekly surveillance for diarrheal episodes, anthropometry at 3-month interval until 60 months of age. The infants that were consented for GWAS analysis were genotyped in 3 separate batches at different times, on 3 different arrays. Quality control was performed on the 3 separate data sets and then jointly after merging. Genetic data available on 447 infants together with their phenotype data is made available in this submission PROVIDE (Performance of Rotavirus and Oral Polio Vaccines in Developing Countries) Study Oral polio and rotavirus vaccines are significantly less effective in children living in the developing world. Environmental enteropathy, which is associated with intestinal inflammation, decreased absorption and increased permeability, may contribute substantially to oral vaccine failure in developing country settings. The primary objective of the study was to determine the association of environmental enteropathy with the efficacy of oral polio and rotavirus vaccines in children in Bangladesh. Secondary and exploratory objectives were designed to address other possible causes of oral vaccine underperformance including malnutrition, interference with maternal or breastmilk antibodies, changes in gut microbiota, and genetic susceptibility. The PROVIDE study was structured as a 2x2 clinical trial with a prospective birth cohort enrollment of 700 infants and their mothers in the urban slum of Mirpur, Dhaka, Bangladesh. All children received the full series of Bangladesh's Expanded Program on Immunization vaccines, including oral polio vaccine (OPV) and followed for their first 2 years of life. Half the children were randomized to receive an inactivated polio vaccine (IPV) for their 4th dose at 39 weeks instead of the standard OPV dose. In the other trial, half the infants received the 2-dose rotavirus vaccine (Rotarix) with delayed dosing at 10 and 17 weeks of age. A detailed description of the study design and procedures can be obtained from PROVIDE methods publication: Kirkpatrick B.D., Colgate R.E., Mychaleckyj J.C., Haque R., Dorothy D.M., Carmolli M.P., et al. (2015) Am J Trop Med Hyg 92, 744-751 The Poliovirus trial and results are described in Mychaleckyj et al, Vaccine 2016 The Rotavirus trial and results are described in Colgate et al, Clin Infect Dis 2016 The PROVIDE infants were genotyped on a custom Affymetrix Axiom array (30K SNPs) at the University of Virginia Center for Public Health Genomics; and on a pre-production version of the Illumina MEGA v2 chip at the Wellcome Trust Sanger Institute, UK. The latter genotyping was performed under the auspices of the VaccGene Consortium. Analyses are ongoing to identify variants associated with the included phenotypes. A manuscript describing the genotyping methods and analysis is in preparation for the initial phenotypes. The Infection Malnutrition Bangladesh Cohort is utilized in the following dbGaP sub-studies. To view genotypes, other molecular data, and derived variables collected in these sub-studies, please click on the following sub-studies below or in the "Sub-studies" box located on the right hand side of this top-level study page phs001475 Infection Malnutrition Bangladesh Cohort. phs001476 Amebiasis Immunity phs001478 Polio Rotavirus Vaccines phs001665 Cryptosporidiosis Enteropathogens

  Study phs001475

• Lung Tissue Research Consortium (LTRC-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. Biospecimens: Access to Biospecimens is through the NHLBI Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC). Biospecimens from LTRC include DNA, Plasma, Serum, Tissue - FFPE Cassettes, Tissue – RNALater Frozen, and Tissue - Snap Frozen. Please note that use of biospecimens in genetic research is subject to a tiered consent. Objectives: The LTRC was a biobank resource established by the NHLBI to collect and distribute lung tissue, blood samples, clinical data, and radiographic studies from participants with chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF), other related idiopathic interstitial pneumonias (IIP) and interstitial pneumonias associated with connective tissue diseases who undergo medically-indicated lung resection. All tissue and blood specimens and clinical data were banked centrally and stored for distribution to external investigators who have approved study proposals to investigate the pathogenesis or management of lung diseases. The ultimate goal of this program was to enable research that illuminates the pathobiology of lung diseases and leads to novel interventional treatments for these conditions. Background: Chronic lung diseases are a main cause of death and disability in the United States. COPD affects over 14 million individuals in the United States and represents the third leading cause of mortality. Cigarette smoking is a major risk factor. However, only one of six individuals who smoke develops COPD. This could imply either an individual susceptibility or an additional immunologic or infectious injury to lung cells. Current treatments offer symptomatic relief, but do not prevent disease progression. Better understanding of disease pathogenesis, including the potential roles of lung parenchymal cell apoptosis, immunologic injury, and inflammation may lead to therapies that improve survival and quality of life. Interstitial pneumonias, including IPF and those associated with connective tissue disease, are less common than COPD, but for many of these diseases there are poor outcomes. For example, IPF has a 50% survival rate 2-3 years following diagnosis, and currently no treatment exists which prolongs survival. The prevalence of IPF is approximately 28 cases per 100,000. The underlying histology of IPF is usual interstitial pneumonia (UIP), which can also occur in connective tissue diseases. The incidences of other interstitial pneumonias such as non-specific interstitial pneumonia (NSIP) or acute interstitial pneumonia (AIP) are less frequent but also occur as an expression of interstitial lung disease in the connective tissue diseases. Moreover, there is significant crossover of these three interstitial pneumonias so that cases of IPF/UIP may also reveal fibrotic NSIP and be complicated by episodes of AIP. This implies common injuries but dissimilar histological responses. All of these processes are characterized by epithelial injury, uncontrolled fibroproliferation and the deposition of collagen, irrespective of the histology. It is clear that a better understanding of the genesis of the interstitial pneumonias is required before effective interventions can be developed. Participants: A total of 4,486 participants were enrolled, and lung tissue was obtained from 3,333 of these participants.Design: Written informed consent of each participant was required before any LTRC procedure was performed. Phenotypic data were then obtained that included recording of relevant medical information, a limited exposure history, radiological evaluation, and pulmonary physiological and lung function testing. Questionnaires were administered to determine the extent of symptoms, associated medical illnesses, smoking, environmental and occupational exposures, and quality of life. Laboratory testing included pulmonary function testing, a six-minute walk test, and chest x-ray CT. Blood specimens were collected both for defining the clinical phenotype of donors and to obtain serum, plasma, and DNA for later investigative purposes. At the time of surgery, lung tissues were collected and processed for long-term storage. The LTRC collected only the 'non-tumorous' portions of lung tissue from surgical procedures performed for primary or metastatic lung tumors and received those specimens only after the local pathologist had procured all tissue required for clinical care. Samples of appropriate size were cut and placed in formalin, RNAlater, glutaraldehyde, or liquid nitrogen within 30 minutes of excision (approximately 5% of cases exceeded this target time). Blood and tissue specimens were subsequently shipped to a central Tissue Repository for further processing and long-term storage. A Radiology Center provided quality control and quality assessment of CT data. A Data Coordinating Center managed study operations and maintained a repository of study data. Conclusions: LTRC established a biospecimen collection that is unique in its size, diseases included, standardization of methods, and extent of phenotypic data, serving as a valuable resource to facilitate research on the pathobiology of lung diseases.

  Study phs003913

• Identification of cis- and trans-regulatory variation modulating microRNA expression levels in human fibroblasts

  MicroRNAs (miRNAs) are regulatory noncoding RNAs that affect the production of a significant fraction of human mRNAs via post-transcriptional regulation. Interindividual variation of the miRNA expression levels is likely to influence the expression of miRNA target genes and may therefore contribute to phenotypic differences in humans, including susceptibility to common disorders. The extent to which miRNA levels are genetically controlled is largely unknown. In this report, we assayed the expression levels of miRNAs in primary fibroblasts from 180 European newborns of the GenCord project and performed association analysis to identify eQTLs (expression quantitative traits loci). We detected robust expression for 121 miRNAs out of 365 interrogated. We have identified significant cis- (10%) and trans- (11%) eQTLs. Furthermore, we detected one genomic locus (rs1522653) that influences the expression levels of five miRNAs, thus unraveling a novel mechanism for coregulation of miRNA expression

  Study EGAS00000000056

• SCANDARE MACARON

  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.

  Study EGAS50000000145

• Evolutionary Trajectories of Small Cell Lung Cancer under Therapy

  Small cell lung cancer (SCLC) is one of the deadliest human cancers with a five-years survival rate of less than 7%. The standard of care for extensive-stage SCLC consists of systemic treatment with platinum and etoposide, recently combined with PD-L1 immune checkpoint inhibitors (ICI). SCLC patients show high sensitivity to platinum-based chemotherapy, followed by rapid recurrence, which distinguishes SCLC from most human cancers. Unfortunately, second-line treatment with other chemotherapeutics or immunotherapy is only marginally effective, and patients ultimately succumb to their disease. We performed whole exome sequencing, whole genome sequencing and transcriptome sequencing of multiple tumor regions from 65 patients with SCLC. We determined tumor phylogenies at diagnosis and throughout chemotherapy and immunotherapy by multi-region sequencing of 160 tumors from 65 patients, to thus decipher the evolutionary processes underlying the remarkable sensitivity of small cell lung cancer (SCLC) to chemotherapy.

  Study EGAS50000000169

• UK Biobank whole cohort directly genotyped and imputed data (~500,000 participants)

  Genotype data is available for all 500,000 participants in the UK Biobank cohort. Genotyping has been performed using the Affymetrix UK BiLEVE Axiom array on an initial 50,000 participants and the remaining 450,000 participants have been genotyped using the Affymetrix UK Biobank Axiom® array. The two arrays are extremely similar (with over 95% common content).Quality control and imputation (to over 90 million SNPs, indels and large structural variants) has been performed by a collaborative group headed by the Wellcome Trust Centre for Human Genetics.The following data are available:* A clean set of QC’ed genotype calls* Confidence values that a genotype call is correct* Intensity data to generate cluster plots* Extensive QC information regarding SNPs and samples including SNP metrics, batch effects, population structure and relatedness* Imputed dataFor further information, please refer to the UK Biobank website

  Study EGAS00001002399

• ARST17B2-Q Germline and Somatic Genetic Landscape of Pediatric Rhabdomyosarcoma

  Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children. While these malignancies display aberrant myogenic differentiation, relatively little is known about genetic susceptibility to RMS, or how genetic variants influence subsequent somatic events and may be used in risk stratification strategies. A small percentage of cases are associated with mutations in TP53 (Li-Fraumeni syndrome), HRAS (Costello syndrome), and PTCH1 (nevoid basal cell carcinoma syndrome/Gorlin syndrome), suggesting the genetic origins of childhood RMS. In spite of this, little work has been done to characterize genetic susceptibility to this malignancy. We plan to leverage samples collected as part of D9902 to conduct one of the largest germline genomic studies of RMS. We anticipate that once genetic associations are identified, researchers can use the information to develop better strategies to detect, treat, and prevent childhood RMS.

  Study phs003192

• Genotyping NIGMS Chromosomal Aberration and Inherited Disorder Samples

  As part of an effort to correlate molecular copy number variation determinations with state of the art karyotype analyses, 716 samples derived from 697 individuals from the Chromosomal Aberrations and Inherited Disorders collections of the NIGMS Human Genetic Cell Repository were genotyped and analyzed for CNV determination by the Microarray Center at the Coriell Institute for Medical Research. Karyotyping is performed on all cell cultures in the Repository with reported chromosome abnormalities. The samples chosen for genotyping in this study are intended to represent a diverse set of copy number variants, but the selection was also weighted to over-sample commonly manifested types of aberrations. When available, the ISCN description of the sample based on G-banding and FISH analysis is included in the phenotypic data. Karyotypes for these cells can be viewed in the online Repository catalog (http://ccr.coriell.org/Sections/Collections/NIGMS/?SsId=8).

  Study phs000269

• Female Infertility: Primary Ovarian Insufficiency

  Premature ovarian failure, or primary ovarian insufficiency (POI) is a phenotype of diminished or absent ovarian function occurring in 1-2% of reproductive aged women. Most cases occur spontaneously. Evaluation of the gametes in women with POI is difficult and invasive. Practitioners must often rely on indirect biomarkers of ovarian function and oocyte health, making it difficult to identify patients who may benefit from therapies allowing them to achieve pregnancy utilizing their own oocytes. This study will generate exome sequences from POI patients in an effort to elucidate the causes of unexplained POI and to better understand the normal processes of ovarian aging. A better understanding of the genetics of ovarian function may lead to new non-invasive tools for managing women's reproductive health, and direct better use of existing biomarkers in diagnosis, screening and predicting clinical outcomes.

  Study phs001174

• Rapid Acceleration of Diagnostics - Digital Health Technologies (RADx-DHT): NIH Digital Health Solutions for COVID-19: IBM Covid19 Contact Tracing and Data Exchange Tools

  The goal of this project is to develop both contact tracing and secure data exchange tools. The contact tracing solution securely combines data from a variety of sources (including manual self-report data and mobile device surveys) to enable tracing of contacts with individuals that have tested positive for COVID-19 or have been exposed to COVID-19. The data exchange solution is a secure mechanism that empowers users to control the data they share in the course of their return to work, including the ability to provide a verifiable health status claim. These tools are being used by an employer to evaluate the risk of allowing individuals to return to normal activities, and also the ability to trace user contact with individuals diagnosed with or suspected of having contracted COVID-19. DOI: https://rapids.ll.mit.edu/10.57895/h0an-m559

  Study phs002516

• Genomic Factors Involved in Chromosome Rearrangements

  Approximately 15-20% of children referred for chromosomal microarray analysis (CMA) testing have a clinically relevant CNV that in many cases explains their phenotype. The goal of this study is to discover the genomic factors that mediate chromosome rearrangements and the phenotypic effects of chromosome rearrangements. We hypothesize that particular DNA sequences are susceptible to breakage and rearrangement. To this end, we fine-map chromosome breakage sites and analyze the DNA motifs that underlie double-strand breaks (DSBs). Our studies will also capture the genomic structure of breakpoint junctions, which will allow us to determine the mechanisms of DNA repair that shape different types of chromosome rearrangements. We also correlate chromosome rearrangements with clinical features to establish genotype-phenotype correlations. Defining critical regions of deletion or duplication is the first step to identifying candidate genes responsible for particular phenotypes.

  Study phs000845

• DAXX restoration suppresses alternative lengthening of telomeres in ATRX wild-type cells

  Many tumors maintain chromosome ends through a telomerase-independent, homologous recombination based mechanism called alternative lengthening of telomeres (ALT). While ALT occurs in only a subset of tumors, it is strongly associated with mutations in the genes encoding components of the histone H3.3 chaperone complex, ATRX and DAXX. To date the mechanistic role of ATRX and particularly DAXX mutations in potentiating ALT remains poorly understood. We identify an osteosarcoma cell line, G292, with a unique chromosomal translocation resulting in loss of DAXX function, while retaining functional ATRX. Using this distinctive resource, we demonstrate that introduction of wild type DAXX suppresses the ALT phenotype and restores localization of the ATRX/DAXX complex to PML bodies. This provides the first direct molecular evidence that ongoing DAXX deficiency is essential for maintenance of the ALT phenotype and highlights the potential for therapeutic targeting of this oncogenic pathway.

  Study phs001495