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• Tumor Profiler Project - OV bulk transcriptomics data additional samples

  The dataset contains bulk transcriptomics data from 4 samples from 3 different patients with ovarian cancer. 3 samples were collected from the tumor, 1 sample from ascites. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format. These samples are from patients not classified as as having high-grade serous adenocarcinoma.

  Dataset EGAD50000001411

• MissionBio single cell DNA and protein seq for 2 samples

  This dataset contains MissionBio Targeted single-cell DNA and Protein sequencing data from a primary sample and a patient-derived xenograft (PDX) model, which is used to investigate the clonal evolution in the FOXF1/FENDRR ALL subtype. All the 2 samples are in bam file type.

  Dataset EGAD50000001793

• RNAseq from 6 organotypic co-cultures (OC cells bulk/OCSC with or without TME)

  The dataset contains samples of 6 organotypic co-cultures, assembled with patient-derived material from ovarian cancer (OC) patients. Tumor cells, both as bulk and as cancer stem cells-enriched (OCSC) populations, are cultured or not with in vitro peritoneal TME (for details see Battistini C et al, Tumor microenvironment-induced FOXM1 regulates ovarian cancer stemness, CDDis 2024). Dataset is composed by fastq file (paired end) type from bulk RNA-Seq.

  Dataset EGAD50000000523

• Transcriptomic analysis of metastatic colorectal cancer

  Metastatic colorectal cancer (mCRC) is the main cause of CRC mortality, with limited treatment options. Although immunotherapy has benefited some cancer patients, mCRC typically lacks the molecular features that respond to this treatment. However, recent studies indicate that the immune microenvironment of mCRC may be modified to enhance the effect of immune checkpoint inhibitors. This dataset was used to explore the metastatic immune microenvironment by comparing immune cell populations in colorectal liver (CLM), lung (mLu) and peritoneal (PM) metastases.

  Dataset EGAD50000000926

• Loss of RREB1 in pancreatic beta cells reduces cellular insulin content and affects endocrine cell gene expression

  Genome-wide studies have uncovered multiple independent signals at the RREB1 locus associated with altered type 2 diabetes risk and related glycaemic traits. However, little is known about the function of the zinc finger transcription factor Ras-responsive element binding protein 1 (RREB1) in glucose homeostasis or how changes in its expression and/or function influence diabetes risk.

  Dataset EGAD50000000515

• Arcagen – thoracic malignancies

  Arcagen is an EORTC/SPECTA pan-European project that aims to recruit 1000 rare cancer patients from different tumour domains of EURACAN. This study collected samples from advanced or metastatic rare cancer from patients older than 12, and analysed them using Foundation Medicine next-generation sequencing (NGS) panels (FoundationOne CDx for FFPE samples or FoundationOne Liquid CDx for blood samples). Here we are submitting the dataset that contain NGS files from rare thoracic malignancies (n=102)

  Dataset EGAD50000000168

• Dataset for Fragle Software Development and Evaluation

  Fragle is a deep learning based two stage model that quantifies ctDNA from blood plasma derived cfDNA bam files. Fragle was developed using some previously published datasets and some newly generated data. Fragle was evaluated using some validation cohorts and some unseen cohorts. Some of these cohorts are newly created consisting of total 365 low pass (2-3X) whole genome sequencing bam files mapped to hg19/GRCh37. This dataset contains these newly generated bam files.

  Dataset EGAD50000000167

• Next generation sequencing on cardiac samples in Hungarian patients of dilated cardiomyopathy

  Heterozygous (HET) truncating mutations in the TTN gene (TTNtv) encoding the giant titin protein are the most common genetic cause of dilated cardiomyopathy (DCM). We investigated 127 clinically identified DCM human cardiac samples with targeted sequencing using the TruSight Cardio panel on an Illumina MiSeq system with a special focus on TTNtvs. This dataset belongs to the publication of Kellermayer, D et al. Truncated titin is integrated into the human dilated cardiomyopathic sarcomere

  Dataset EGAD50000000066

• Expression array

  The whole study comprises of two patient cohorts. Screening cohort: 40 patients of Germany; validation cohort: 40 patients from Asia. Further, bile duct and CCA cell lines have been analyzed.
This dataset contains expression array data for 32 patients of the screening cohort with 8 of them having paired normal tissue plus an additional relapse tumor/normal pair of one of those 8 patients and a patient only with normal tissue. Data was generated on a HumanHT-12 v4 Bead Array (Illumina) and is stored in IDAT file format.

  Dataset EGAD00010002596

• GBM-Space: Spatial Transcriptomic Profiling of Glioblastoma (10x Genomics - Visium)

  Cancer cells display heterogeneous and dynamic states in glioblastoma, but how these malignant states arise and whether they follow a tractable cellular trajectory across tumours is poorly understood. Here, we generate a deep single cell and spatial multi-region atlas of 12 isocitrate dehydrogenase wild-type (IDH-wt) primary glioblastomas that integrates transcriptomic, epigenomic and genomic analysis to comprehensively characterise their tumour heterogeneity. The datasets in this study include sequencing data from Visium spatial transcriptomic (10x Genomics) profiling of these tumours.

  Dataset EGAD00001015527

• COVID-19 Challenge Project Single Cell Profiling

  Single-cell profiling of sero-negative and sero-positive humans that were inoculated with SARS-CoV-2. The cellular response during SARS-CoV-2 is profiled using single-cell transcriptomics, CITE-seq and single cell immune profiling, by sampling PBMCs and nasal swabs before and at multiple time points during SARS-CoV-2 infection. This one-of-a-kind cellular map will give unique temporal resolution of how nasal and immune cells respond to SARS-CoV-2 exposure and infection.

  Dataset EGAD00001012227

• Fusion gene analysis using multiplex single primer extension-based RNA-sequencing

  The whole study comprises of two patient cohorts. Screening cohort: 40 patients of Germany; validation cohort: 40 patients from Asia. Further, bile duct and CCA cell lines have been analyzed. This dataset contains fusion gene analysis using multiplex single primer extension-based RNA-sequencing for a subset of 25 patients of the screening cohort. Data was generated on Illumina NexSeq 550 device in paired-end mode and is stored in compressed FASTQ file format.

  Dataset EGAD00001011326

• Extended screen by deep amplicon sequencing

  The whole study comprises of two patient cohorts. Screening cohort: 40 patients of Germany; validation cohort: 40 patients from Asia. Further, bile duct and CCA cell lines have been analyzed. This dataset contains targeted DNA sequencing data of 40 tumor/normal pairs from the validation cohort plus 10 tumor/normal pairs of patients from the screening cohort for technical validation. Data was generated on Illumina HiSeq 2000 device in paired-end mode and is stored in BAM file format.

  Dataset EGAD00001011323

• Mtb infected and uninfected neutrophils after 1 and 6 hrs

  Fastq.gz files for mRNA sequenced from Mtb infected and uninfected neutrophils after 1 and 6 hrs. Samples were sequenced in 2 batched as indicated per experiment. Batch 1 was SE unstranded, 100bp on an Illumina HiSeq4000 sequencer and batch 2 unstranded, 150bp paired-end on an Illumina NovaSeq6000 sequencer. Phenotypic data for the samples is also included.

  Dataset EGAD00001010893

• WGS data from LCNEC patient derived tumor organoids (PDTOs) and matched parental tumors - SA

  The dataset includes cram files from WGS of 2 LCNEC tumors and matched PDTOs. For all tumors, cram files from WGS of matched normal tissue derived organoids from the corresponding patients is included. Analysis VCF files are also included in the dataset. The sequencing was done with a NovaSeq 6000 instrument.

  Dataset EGAD00001009990

• XP patients NGS data collection from Gustave Roussy.

  This dataset is composed of NGS data from 33 XP patients studied by WGS.

  Dataset EGAD00001009693

• RNAseq of primary mesothelioma cell lines

  Mesothelioma is an aggressive cancer associated with previous exposure to asbestos and dismal prognosis. Since a pemetrexed/cisplatin combination was introduced for treatment of mesothelioma, no new first- or second-line therapies have been discovered. Thus, to better understand what drives mesothelioma carcinogenesis and to identify potential targets for therapy, in this project we aim at performing RNAseq analysis of a panel of mesothelioma cells lines.

  Dataset EGAD00001009642

• ATAC-seq of metastatic prostate tumors

  This dataset includes Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data, in FASTQ format, from 70 metastatic castration-resistant prostate cancer tumor samples from the SU2C/PCF West Coast Dream Team (WCDT) project. The sequencing data is paired-end, 150 bp sequencing data from an Illumina NovaSeq 6000 machine. ATAC-seq libraries were prepared following the protocol described in Buenrostro et al. Nature Methods. 2013 (PMID: 24097267) and Corces et al. Nature Methods. 2017 (PMID: 28846090).

  Dataset EGAD00001009654

• RNAseq Iron-Treated iPSC-derived Microglia

  Iron accumulation in microglia has been observed in Alzheimer’s disease and other neurodegenerative disorders and is thought to contribute to disease progression through various mechanisms including neuroinflammation. To study the interaction between iron accumulation and inflammation, we treated human induced pluripotent stem cell-derived microglia (iPSC-MG) with an increasing concentration of iron, in combination with inflammatory stimuli such as interferon gamma and amyloid β, and performed RNA sequencing.

  Dataset EGAD00001008660

• ScRNA-seq of 6 human FL

  Follicular lymphoma (FL) is an indolent cancer of mature B-cells but carries increased risk of transformation to a more aggressive histology over time. We present here comprehensive profiling both tumor and immune compartments in 6 diagnostic FL biopsies by single-cell RNA sequencing. This confirmed results from 155 FL tumors characterized by mass cytometry (CyTOF) which revealed two distinct evolutionary trajectories with disparate risk of transformation and alternate biologies.

  Dataset EGAD00001007691

• RNA-seq from time-course experiment treating cells for 72h

  RNA sequencing from MSTO-211H cell line cultures treated for 72h with vehicle solution, palbociclib 250nM, or abemaciclib 250nM (N = 3, each). RNA-seq prepared using TruSeq Stranded mRNA libraries and sequenced with Illumina HiSeq 4000. Data is in raw fastq format, paired end. Some samples have been split in two lanes, with a final count of 24 fastq files.

  Dataset EGAD00001007737

• H3Africa AWI-Gen Phase 1 Pilot Microbiome Phenotype

  This is human phenotype data for participants in a gut microbiome study. This data was collected at the same time as the stool samples used for the microbiome component. Participants were also part of the AWI-Gen Phase 1 main study. https://www.ebi.ac.uk/ena/data/view/PRJEB40733

  Dataset EGAD00001006581

• Bottleneck Sequencing Of Human Tissue (Wgs) (2020-10-20)

  Bottleneck sequencing of human tissue including neurons, cord blood, sperm. 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 2020-10-20.

  Dataset EGAD00001006459

• Raw RNA-seq data for clinical efficacy and biomarker analysis of neoadjuvant atezolizumab in operable urothelial carcinoma in the ABACUS trial

  ABACUS is a single arm phase 2 study that investigated 2 cycles of atezolizumab (1200mg Q3) prior to cystectomy in 95 patients with muscle invasive transitional cell cancer (T2-4N0M0). Pathological complete response (pCR) occurring in ≥20% of patients was the primary endpoint. Biomarker analysis on sequential tissue was a co-primary endpoint. This dataset includes the raw RNA-seq data.

  Dataset EGAD00001006205

• Processed RNA-seq data for clinical efficacy and biomarker analysis of neoadjuvant atezolizumab in operable urothelial carcinoma in the ABACUS trial

  ABACUS is a single arm phase 2 study that investigated 2 cycles of atezolizumab (1200mg Q3) prior to cystectomy in 95 patients with muscle invasive transitional cell cancer (T2-4N0M0). Pathological complete response (pCR) occurring in ≥20% of patients was the primary endpoint. Biomarker analysis on sequential tissue was a co-primary endpoint. This dataset includes the TPM and raw counts tables.

  Dataset EGAD00001006199

• Novel manifestations of immune dysregulation and granule defects in gray platelet syndrome

  Gray Platelet Syndrome (GPS) is a rare recessive bleeding disorder resulting from biallelic variants in NBEAL2. As part of a comprehensive evaluation of the phenotype and genotype in 47 patients with GPS, four different blood cell-types (platelets, neutrophils, monocytes, and CD4-lymphocytes) were evaluated using bulk RNA-seq in five patients and five controls. These data are deposited in this archive in FASTQ format.

  Dataset EGAD00001005950

• Investigating the impact of MBD4 on the mutability of the germline (2020-01-15)

  We will be testing the hypothesis that MBD4 PTV germline carriers also show an increased number of C toT germline mutations in their offspring. 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 2020-01-15.

  Dataset EGAD00001005788

• Phylogenetic development of childhood tumours

  The aim of this study is to reconstruct the phylogenetic development of childhood tumours

  Dataset EGAD00001005770

• Clonality of circulating tumor cells in breast cancer brain metastases patients

  The incidence of brain metastases in breast cancer (BCBM) patients is increasing. These patients have a very poor prognosis and therefore identification of blood-based biomarkers, such as circulating tumor cells (CTCs) and understanding the genomic heterogeneity could help to personalize treatment options. In this study, DNA from individual CTCs as well as corresponding primary tumors and brain metastases were analyzed by next generation sequencing (NGS) in order to evaluate copy number aberrations and single nucleotide variations (SNVs).

  Dataset EGAD00001005020

• Melanoma post mortem analysis

  Despite multiple large-scale sequencing studies offering substantial insight into the genomic landscape of cutaneous melanoma, the molecular events surrounding disease progression and the resulting molecular heterogeneity between metastases have not been fully elucidated. We have been applying whole genome and transcriptome sequencing across metastases collected during post mortem. Herein we show the findings for the first such patient. This is a targeted pulldown validation in support of the whole-genome sequencing analysis of the metastatic tumours and targeted pulldown of the primary tumour.

  Dataset EGAD00001005073

• IBD Whole Genome Sequencing (2019-04-01)

  We will sequence at 15X coverage the genomes of 1536 IBD patients. These samples are currently onsite at Sanger and made available for sequencing via our collaboration with the UK IBD Genetics consortium. 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 2019-04-01.

  Dataset EGAD00001004880

• Oceanian and American population sequencing and phasing (2019-04-11)

  Whole-genome sequencing of human individuals from Polynesian and Native American populations, as well as 10x Genomics Chromium data from Polynesian, Native American and Aboriginal Australian populations, allowing for experimental phasing of haplotypes. 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 please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2019-04-11.

  Dataset EGAD00001004951

• Non-invasive prenatal diagnosis by genome-wide haplotyping of cell-free plasma DNA

  This dataset contains a total of 10 families and 51 samples presented in 'Non-invasive prenatal diagnosis by genome-wide haplotyping of cell-free plasma DNA' study, in which 9 of them are cfDNA samples and the rest of samples are gDNA samples. All the samples are targeted sequencing data with a custom 45Mb capture library . Raw pair-end fastq files for each sample is available.

  Dataset EGAD00001004989

• TTV018 RORC IBD-associated genotype effects on RORgT expression and function in ex vivo T cells (2019-02-15)

  RNA sequencing of peripheral immune cells from patients +/- an IBD risk variant. Peripheral immune cells +/- in vitro test compound treatment. 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 2019-02-15.

  Dataset EGAD00001004777

• Exome sequencing of advanced hepatocellular carcinoma

  The aim of our project is to decipher the genomic of advanced hepatocellular carcinoma using whole exome sequencing. To this purpose, we aim to compare genetic landscape of advanced hepatocellular carcinoma with early tumor in order to understand the mechanisms of tumor progression. This work will also help to identify new therapeutic targets potentially useful to treat patients at advanced stage. This dataset contain whole exome sequencing aligned reads for 41 tumor with matched normal samples

  Dataset EGAD00001004555

• snRNA-seq in white matter post-mortem tissue from MS and controls

  This Dataset is currently hosted by the European Nucleotide Archive. To access the data contained within the Dataset please follow the link below: https://www.ebi.ac.uk/ena/browser/view/PRJEB39323 Dataset consists of 20 snRNA-seq bam files from 10X v2. 5 samples from postmortem white matter tissue from non-neurological controls and15 samples from different MS lesions from the white matter tissue of 4 postmortem progressive MS patients.

  Dataset EGAD00001004544

• Targeted sequencing of cell-free DNA and white blood cells from 24 men with metastatic prostate cancer

  This dataset consists of aligned DNA sequencing data in BAM file format from cell-free DNA and white blood cells from 24 men with metastatic prostate cancer. One cell-free DNA sample and one white blood cell sample is available for each patient, resulting in 48 total BAM files in this dataset. The sequencing was performed using a hybrid capture-based targeted panel of 73 prostate cancer driver genes.

  Dataset EGAD00001004486

• Genetic screening of GPI-anchor protein synthesis (2018-08-13)

  This study will analyse the guide sequence which were used for making mutations in the Cas9-expressing cells. We used GeCKO v2 library which were released by Feng Zhang, 2014. 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 2018-08-13.

  Dataset EGAD00001004294

• Patient-derived neuroblastoma model system OHC-NB1

  The dataset is comprised of seven samples, one blood sample (germline control) of the patient, one neuroblastoma metastasis from the bone marrow and five derived cell models. The models include the primary culture, the first xenogenograft passage, a monolayer culture derived from the first xenograft passage and two samples of the fourth xenograft passage, cells and supernatant. For all these samples, whole-exome sequencing data have been generated. The BAM files contain the alignments against the human genome, assembly GRCh37, and also the unaligned reads.

  Dataset EGAD00001004138

• RNA-seq data from Follicular Lymphoma samples

  Dataset included RNA-seq data (Two Fastq files per sample as paired end sequencing was performed) from ribosomal-depleted total RNA in 28 Follicular Lymphoma (FL) criopreserved samples to analyze long non-coding RNA and coding transcript expression profiles. Sample metadata is referred to histological groups of FL tumors (FL1-3A versus FL3B/DLBCL) either in tumor purified cell samples (N=12) as in unpurified tumor samples including normal cells of the lymph node microenvironment (N=16).

  Dataset EGAD00001004109

• Gene Characterization in Carbohydrate metabolic alterations (neonatel diabetes & congenital hyperinsulinemic) in early childhood (2018-03-14)

  Whole Exome Sequencing of trios (proband + parents) or probands only with Neonatal Diabetes Mellitus (NDM) or Congenital Hyperinsulinism of Infancy (CHI) of unknown genetic origin. 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 2018-03-14.

  Dataset EGAD00001004040

• Pairs of whole genome sequencing repeated measurement sample pairs

  This dataset includes 186 whole genome sequencing samples which combine to create 93 pairs. Each pair is comprised of two sequencing experiments carried out on the same donor to the NIHR BioResource Rare Disease cohort. These samples have been used to validate the Telomerecat method (a method for estimating telomere length from whole genome sequencing).

  Dataset EGAD00001003809

• Genome Diversity in Africa Project - GemCode libraries (2017-07-05)

  High depth whole genome sequencing from GemCode (10x Genomics) DNA libraries containing long range linkage information for one Baganda trio and one Baganda child (parent already sequenced at high depth). 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 2017-07-05.

  Dataset EGAD00001003426

• Whole exome sequencing in patients with ALS and concomitant FTD lacking the C9orf72 repeat expansion

  Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are part of a clinical, pathological and genetic continuum. The purpose of the present study was to assess the mutation burden that is present in ALS and/or FTD known disease-causing genes in 54 patients (16 with available postmortem neuropathological diagnosis) with concurrent ALS and FTD (ALS/FTD) not-carrying the C9orf72 hexanucleotide repeat expansion, the most important genetic cause in both diseases.

  Dataset EGAD00001003409

• Barcelona kids with melanoma

  This set of samples is composed of eight young people (7-16 years old) that have developed melanoma with first-degree relatives that have also developed cancer, which suggests a genetic component to their disease. Here we want to sequence these samples in order to find the causative mutations. As these samples do not carry any of the high-penetrance mutations known to date, finding the genes(s) responsible will offer new insights into the genetic mechanisms underlying predisposition to melanoma.

  Dataset EGAD00001002198

• miRNA expression in response to LPS stimulus in macrophages

  Our lab is currently using macrophages as a model system for understanding how genetic variation modulates the response to external environmental stimulus. We want to extend this beyond regular polyadenylated RNA to small RNAs such as miRNAs. This project would cover the costs of a pilot to study miRNA response to LPS stimulus, and will be performed as part of a rotation project in the lab. We will require a small number of miRNA libraries and a single lane of MiSeq

  Dataset EGAD00001002196

• Whole genome sequencing of a Grem1 mutant human tumour

  The BMP antagonist Grem1 has been shown to be associated with a rare human polyposis syndrome (HMPS). We have shown that there is a 40KB duplication on chrom 15 found in some patients with HMPS. Traditional serrated adenomas (rare sporadic polyps) share some morphological features with HMPS polyps and it has long been hypothesised that they are the sporadic version of HMPS polyps. We have obtained of one of these lesions and in this project we aim to characterise this tumour.

  Dataset EGAD00001002182

• Study to investigate the prevalence of leukaemic mutations in whole blood DNA in a cohort of blood donors

  The aim of this study is to ascertain whether leukaemic mutations exist within the blood of people with otherwise normal haematopoeisis. To satisfy this aim we plan to look for 7 known leukaemic mutations in the whole blood DNA of a large cohort of blood donors who have normal haematopoesis. Genomic regions around mutational sites have been amplified using a 2 step PCR process which involves barcoding of individual patients

  Dataset EGAD00001001319

• Egypt Genome Project - high coverage whole genome sequencing

  All humans outside Africa are descendants of the same single exit, usually dated at 50-70 thousand years ago. However, the route taken out of Africa is still debated. The two main candidates are a northern route via Egypt and the Levant, or a southern route via Ethiopia and the Arabian Peninsula. We are generating genetic data to evaluate these two possibilities. In this study we propose to generate high-coverage sequencing data for 3 Egyptian samples.

  Dataset EGAD00001001380

• Egypt Genome Project - low coverage whole genome sequencing

  All humans outside Africa are descendants of the same single exit, usually dated at 50-70 thousand years ago. However, the route taken out of Africa is still debated. The two main candidates are a northern route via Egypt and the Levant, or a southern route via Ethiopia and the Arabian Peninsula. We are generating genetic data to evaluate these two possibilities. In this study we propose to generate low-coverage sequencing data for 100 Egyptian samples.

  Dataset EGAD00001001372

• RNA sequencing in blood samples of cluster headache patients

  Cluster headache is a relatively rare headache disorder, typically characterized by multiple daily, short-lasting attacks of excruciating, unilateral (peri-)orbital or temporal pain associated with autonomic symptoms and restlessness. To better understand the pathophysiology of cluster headache, we used RNA sequencing to identify differentially expressed genes and pathways in whole blood of patients with episodic (n = 19) or chronic (n = 20) cluster headache in comparison with headache-free controls (n = 20).

  Dataset EGAD00001002726

• Epigenetic dysregulation in autism spectrum disorder

  Autism spectrum disorder (ASD) is a collection of neuro-developmental disorders characterized by deficits in social interaction and social communication, along with restricted and repetitive behaviour patterns. we globally interrogated the histone acetylomes of enhancers in a large cohort of ASD and control samples by analyzing tissue from three brain regions postmortem: prefrontal cortex (PFC), temporal cortex (TC) and cerebellum (CB). H3K27ac was selected as the representative acetylation mark and 288 ChIP-seq were performed on these postmortem samples.

  Dataset EGAD00001002725

• Somatic pseudogenes acquired during cancer development – RNAseq

  Insertion of processed pseudogenes is known to occur in the germline but has not previously been observed in somatic cells. Formation of pseudogenes could represent a new class of mutation in cancers and a new source of potential driver events.

  Dataset EGAD00001000639

• Study of 5'UTR Mutations in Prostate Cancer

  The 5' untranslated region (5' UTR) of mRNA controls the translation of specific transcripts through encoded cis-regulatory elements. Yet exceedingly little is known about the prevalence and function of 5' UTR mutations in cancer. We have uncovered many 5' UTR mutations in our analysis of localized and castration resistant prostate cancer patients, and hypothesize that systematic mutations in critical 5' UTR regulatory regions perturb gene expression to drive prostate cancer progression. To elucidate the functional 5' UTR regulatory landscape of prostate cancer, we have taken a multi-faceted approach including ribosome profiling, in vitro reporter assays and the development of a novel high throughput method to functionally access the impact of recurrent 5' UTR mutations on both transcription and translation.

  Study phs001825

• Predicting Chemotherapy-Induced Mucositis with Genetic and Clinical Factors

  We hypothesized that genetic variability in the enzymes/proteins involved in drug metabolism, inflammation, and immune function is a major underlying contributor to mucositis incidence and progression and that, based on this variability we can identify variants that influence risk, and develop a mucositis progression prediction model that improves on existing models by incorporating genetic variability along with clinical factors. Using genome wide association study (GWAS) combined with a pathway candidate gene approach and a modified case-control study method, we investigated the hypothesis in a sample of 1092 patients who received a myeloablative dose of melphalan (MEL) followed by autologous hematopoietic stem cell (ASCT) transplantation as treatment for multiple myeloma and for whom banked blood stem cell samples and clinical data were available.

  Study phs000545

• Cerebrospinal Fluid Analysis of HIV-1 Viral Burden in HIV-1 Infected Subjects: Response to Antiretroviral Therapy

  The purpose of this study is to provide a reference profile of small extracellular RNAs in body fluids. These samples were originally obtained in a study that had a different purpose. The purpose of the original study was to collect information on the changes in cerebrospinal fluid (CSF) related to HIV infection, including the viral burden (amount of virus) and the body responses of the infected individual, such as the number and types of lymphocytes in the CSF. In addition to looking at the number and types of lymphocytes in the CSF, this original study also examined the presence of markers of inflammation and other chemical changes, and the relationship of those changes to nervous system dysfunction in AIDS.

  Study phs001694

• SNP array analysis of spondylocostal dysostosis patient iPSCs and gene edited isogenic controls

  This study, "SNP Array Analysis of Gene Edited SDV Patient iPSCs" is part of a larger study where we applied our recently established experimental in vitro model system of the human segmentation clock, for the analysis of human segmentation defects of the vertebrae (SDV) including spondylocostal dysostosis (SCD). To this end we generated patient-derived iPSC lines, identified putative disease-causing mutations and corrected these mutations using CRISPR/Cas9-based genome editing technology. We identified in the patient-sample originally obtained from the NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research (#: GM13539) heterozygous compound mutations in MESP2. These mutations were corrected accordingly and the resulting clones were genotyped by SNP array analysis.

  Study phs001975

• A Phase I/II Trial of T Cell Receptor Gene Therapy Targeting HPV-16 E7 for HPV-Associated Cancers

  This is a phase I clinical trial testing the safety and efficacy of gene-engineered T cells expressing a T-cell receptor targeting an HLA-A*02:01-restricted epitope of HPV-16 E7 (E7 TCR T cells) in patients with metastatic HPV-16+ epithelial cancers. A total of 12 patients were treated. The maximum tested dose was tolerated. Side effects were most consistent with the expected toxicities of the lymphocyte-depleting conditioning regimen and high-dose aldesleukin. Six of the 12 patients demonstrated objective clinical responses. Translational studies of the infused T cell characteristics did not correlate strongly with clinical response. Genomic defects in the targeted peptide-HLA complex did demonstrate definitive mechanisms of resistance in some patients.

  Study phs002286

• Translational Research Investigating Underlying disparities in acute Myocardial infarction Patients' Health status (TRIUMPH)

  The Translational Research Investigating Underlying disparities in acute Myocardial infarction Patients' Health status (TRIUMPH) cohort is a cohort of 4340 patients prospectively enrolled after hospitalization for acute myocardial infarction (AMI) between June 1, 2005, and December 31, 2008 from 24 U.S. hospitals. Consenting patients had detailed chart abstractions of their medical history and processes of inpatient care, supplemented with a detailed baseline interview. Detailed genetic and metabolic data were obtained at hospital discharge in 2979 (69%) and 3013 patients (69%), respectively. Centralized follow-up interviews sought to quantify patients' post-discharge care and outcomes, with a focus on their health status (symptoms, function, and quality of life). Reprinted from [Article Citation], with permission from [Publisher].

  Study phs001518

• RNA Splicing Dysregulation in the Pathogenesis of Chronic Lymphocytic Leukemia

  RNA splicing dysregulation is a hallmark of cancers, promoting the onset and progression of disease. In chronic lymphocytic leukemia (CLL), spliceosome mutations leading to aberrant splicing occurs in approximately 20% of patients. However, the underlying mechanism for splicing defects in spliceosome unmutated CLL cases remains elusive. To discover posttranscriptional regulation of RNA splicing, we performed RNA sequencing using RNA derived from B cells from 6 healthy donors and 36 CLL patients, along with MAZTER sequencing from 9 CLL patients (8 matched with RNA sequencing cohort) and B cells from 5 healthy donors. We found that CLL cells have dysregulated m6A modification sites on transcripts from splicing factors, suggesting a critical role of m6A modification in RNA splicing dysregulation.

  Study phs003191

• Genomic Regions Associated with Susceptibility to Barrett's Esophagus and Esophageal Adenocarcinoma in African Americans: The Cross BETRNet Admixture Study

  Differences in rates of diseases between different populations with similar environments are presumed to be secondary to variability in population frequencies of disease causing alleles. Recently admixed populations such as African Americans (AAs) provide a natural opportunity to identify disease-causing variants by examining the ancestry of long chromosomal haplotypes. Admixture mapping approach can be successful in locating genes for diseases such as EAC whose rates varies markedly between the ancestral populations. This is a case only study with 54 African American cases and also on a subset of 28 cases with high genotyping quality. We seek to identify chromosome regions that have excess European ancestry and contrasting it to excess African ancestry.

  Study phs001454

• NIDDK IBD Genetics Consortium Repository Exome Chip

  The Illumina Infinium HumanExome+ BeadChip contains putative functional exonic variants selected from individual exome and whole-genome sequences from diverse populations. It includes nonsynonymous variants, splice variants and stop-altering variants. It also includes tags for previous GWAS-identified loci, ancestry informative markers, markers designed for identity by descent analyses, synonymous variants, fingerprint SNPs common to major genotyping platforms, mitochondrial SNPs, chromosome Y SNPs, and HLA tag SNPs. For more information as well as a detailed description of the variant calling and QC procedures, see Li et al. (2016). Li, D., et al. (2016) A pleiotropic missense variant in SLC39A8 is associated with Crohn's disease and human gut microbiome composition. Gastroenterology, 151, 1-9. PMID: 27492617.

  Study phs001723

• Episodic Ataxia Syndrome: Longitudinal Study

  Individuals with episodic ataxia experience recurrent attacks of dizziness and incoordination; between attacks patients are typically normal. The majority of cases are likely caused by an inherited genetic mutation. However, in some patients we are unable to identify the mutation. So far, 2 genes have been identified which cause different types of episodic ataxia. Ultimately, when the actual mutation is identified the protein product of the gene can be studied and specific medications can be designed. During this study, we will clinically evaluate patients with EA and follow them over time to help us better characterize the disease. We will also obtain blood samples to test for the known genetic mutations. In the future, we plan to coordinate trials of medications for the treatment of these disorders.

  Study phs000521

• Inhibition of CDK4/6 Promotes CD8 T Cell Memory

  Inhibitors of Cyclin-Dependent Kinase 4 and 6 (CDK4/6) have been recently deployed for the treatment of advanced breast cancer. Despite their success, the mechanism of action of these drugs is unclear. In mice, treatment with a CDK4/6 inhibitor improve T cell memory responses and protect mice against tumor rechallenge. We aimed to identify the correlates of this finding in human subjects. In this study, blood was collected from 5 breast cancer patients before and during treatment with the CDK4/6 inhibitors abemaciclib or palbociclib. Blood was also collected from 2 breast cancer patients who did not receive a CDK4/6 inhibitor. Recently activated CD8 T cells (CD45RO+ CD45RA+) were sorted and subjected to single-cell RNA sequencing.

  Study phs002448

• Transcriptome and Epigenome of TIL Infusion for Cancer Immunotherapy

  Adoptive T cell therapy (ACT) using ex vivo–expanded autologous tumor-infiltrating lymphocytes (TILs) can mediate complete regression of certain human cancers. The impact of TIL phenotypes on clinical success of TIL-ACT is currently unclear. Samples were analyzed from TIL infusion products from metastatic melanoma human patients who responded to TIL-ACT (responders) and patients who did not (non-responders). Single cell transcriptome of TIL infusion products were analyzed for CD8 TIL phenotype and function. In patients with available neoantigen reactive TIL, single cell TCR clonotyping was performed to study anti-tumor TIL states between responders and non-responders. Epigenetic studies on TIL infusion products were performed using ATAC sequencing between paired CD39- C69- and CD39+ CD69+ CD8+ TILs.

  Study phs002436

• De Novo Characterization of Cell-Free DNA Fragmentation Hotspots in Plasma Whole-Genome Sequencing

  The raw sequencing data deposited here are low-coverage (~1X) whole-genome sequencing (WGS) of plasma cell-free DNA (cfDNA). The purpose is to validate the performance of early-stage cancer diagnosis in the Zhou et al. 2020 BioRxiv paper, mainly for two types of cancer: early-stage liver cancer and breast cancer. The cases and controls are matched with age, gender, smoking history, and alcohol usage. We developed a computational method to identify the cfDNA fragmentation hotspots from pooled low-coverage cfDNA WGS data. We found the cfDNA fragmentation hotspots are highly enriched in regulatory regions, such as open chromatin regions. The signals from these regions can help the diagnosis of early-stage cancers and their tissues-of-origin.

  Study phs003062

• Urothelial Cancer - Genomic Analysis to Improve Patient Outcomes and Research (UC-GENOME): a Bladder Cancer Advocacy Network (BCAN)-Led Collaborative Research Pilot Study - for Samples Collected at Johns Hopkins

  UC-GENOME is a real-world cohort of patients with metastatic urothelial carcinoma (UC). The study consisted of two co-equal aims: 1) to provide targeted DNA sequencing for clinical decision making at no cost to patients; and 2) to create a resource for collaborative translational science including a clinically annotated biobank. The submitted data represents the foundational analysis of 218 patients accrued at 7 academic medical centers. The analysis includes 176 patients with both targeted DNA sequencing and RNA sequencing. The genomic data was combined with clinical variables to model response to chemotherapy and immune checkpoint inhibitors (ICI).The larger dataset for this study can be found in dbGaP study phs003066.

  Study phs003094

• Screening Cases of Isolated Dystonia for Variants in CIZ1

  Recently, we have identified that variants in CIZ1 gene is associated with dystonia. To identify the prevalence of CIZ1 mutations in dystonia population, we use High resolution melting (HRM) to examine all the coding sequence in 3976 subjects with primary dystonia as well as 1819 subjects of normal controls. Indels in Q rich region of exon 2 in CIZ1 were identified in 21 subjects with dystonia but only 3 controls (P<0.05). Other single nucleotide change variants were also found in some of the patients which include a novel missense mutation (c.787A>G, p.R263G) found in a female patient with apparently familial dystonia. We confirmed that mutations in CIZ1 could be associated with dystonia but in rare cases.

  Study phs001455

• Genentech whole genome and transcriptome sequencing of four hepatocellular carcinoma patients

  Hepatitis B virus (HBV) infection is a major risk factor for hepatocellular carcinoma (HCC). In this study we sequenced the whole genome (~80X) and transcriptome of tumor and non-tumor samples from four HCC patients and identified over two hundred HBV integration sites. We found significant clonal expansion of HBV-integrated hepatocytes specifically in the tumor samples. We observed a diverse collection of genomic perturbations near viral integration sites, including gene disruption, viral promoter-driven human transcription, viral-human transcript fusion and DNA copy number alteration. We also sequenced one patient at ultra-high coverage (~240X) to build the most comprehensive HBV-integration landscape yet attempted. Our data suggest that the viral integration significantly expands carcinogenic opportunities in HBV-infected individuals.

  Study phs000384

• Exome Sequencing of Schizophrenia Cases and Controls in the South African Xhosa Population

  The goal of this international collaborative project is to identify genes responsible for Schizophrenia in the Xhosa population of South Africa. The vast majority of the genetic basis for Schizophrenia has yet to be explained. We hypothesize that genes and pathways important to Schizophrenia will harbor different, severe disease-causing mutations in different affected individuals. Given the genetic diversity of African populations, we expect to find genes for Schizophrenia that have not yet emerged from studies of other populations. This project will also foster the development of gene discovery research for neuropsychiatric disorders in Africa. Our approach will identify genes important for the disorder in populations worldwide. These genes will stimulate future efforts to develop more effective treatment and prevention strategies.

  Study phs000959

• Genomics of Brain Metastases

  Brain metastases are the most frequently occurring intracranial tumors in adults. Median survival after the diagnosis of a brain metastasis is in the order of a few months. Despite its large burden of disease and devastating clinical sequelae, we continue to have a limited understanding of the molecular mechanisms driving brain metastasis. We subjected 86 trios consisting of primary tumor, brain metastasis, and matched normal tissue to whole exome sequencing (WES). To analyze the data, we developed novel computational tools to perform an integrative analysis of somatic single nucleotide variants (SSNVs) and somatic copy-number alterations (SCNAs). This analysis allowed us to estimate the clonal architecture of the primary and metastatic samples of each patient, and to reconstruct a phylogenetic tree relating all of the subclones.

  Study phs000730

• Whole-Exome Sequencing and Targeted DNA Sequencing of Matched Ocular Melanocytosis and Uveal Melanoma

  Ocular melanocytosis is the most important predisposing condition for the eye cancer uveal melanoma (UM). Here we used whole-exome and deep targeted sequencing to identify for the first time a clonal Gq pathway mutation in ocular melanocytosis, which gave rise to UM. Additionally, we elucidated the order in which canonical genetic aberrations were acquired during tumor evolution. These findings provide a mechanistic explanation for the well-known clinical association of ocular melanocytosis with UM, and they provide new insights into UM tumor evolution. Reprinted from: Durante MA, Field MG, Sanchez MI, Covington KR, Decatur CL, Dubovy SR, Harbour JW. Genomic evolution of uveal melanoma arising in ocular melanocytosis, with permission from Cold Spring Harbor Molecular Case Studies.

  Study phs001835

• CAGE Profiling of ncRNAs in Hepatocellular Carcinoma Reveals a Strong Activation of Retroviral LTR Promoters in Virus-Induced Tumors

  The ncRNA transcriptome of human hepatocellular carcinoma (HCC) is largely unexplored. We used CAGE to characterize transcription start sites across different etiologies of human HCCs with emphasis on ncRNAs. Here we report that retroviral LTR promoters, expressed in healthy tissues such as testis and placenta but not liver, are widely activated in HCC. Despite HCC heterogeneity, a subset of LTR-derived ncRNAs were more than 10-fold up-regulated in the vast majority of samples. HCCs with a high LTR activity mostly had a viral etiology, were less differentiated and showed higher risk of recurrence. CAGE enabled us to build a promoter map for HCC, which uncovers a new layer of complexity in HCC genomics.

  Study phs000885

• Center for Common Disease Genomics (CCDG) - Cardiovascular: BioImage Cohort

  The genetic basis of cardiovascular disease in individuals of non-European ancestry remains largely unknown. Availability of ethnically diverse study populations is essential to fully investigate the underlying causes of disease. The BioImage Study enrolled adults aged 55-80 in a prospective observational study. Subjects had no prior history of cardiovascular disease, but were identified to be at intermediate to high risk for atherosclerotic cardiovascular events (PMID: 25790876). The recruiting target was a cohort with similar demographics to the US population in terms of race and ethnicity. Produced as part of the NHGRI Centers for Common Disease Genomics, this study contains whole genome sequence data and variant calls from 922 African American participants of the BioImage Study.

  Study phs002325

• VCRC Genetic Repository One Time DNA Protocol

  The purpose of this study is to identify genes that increase the risk of developing vasculitis, a group of severe diseases that feature inflammation of blood vessels. Better methods are needed to recruit patients with these rare diseases into cohorts of adequate size for high-quality genetics studies, and the existing infrastructure of the Vasculitis Clinical Research Consortium (VCRC) provides the means for such recruitment. Results of these studies will provide vasculitis researchers with insight into the causes of these diseases and generate new ideas for diagnostic tests and therapies, and will be of great interest to the larger communities of researchers investigating vasculitis and other autoimmune, inflammatory, and vascular diseases. This study will enhance the VCRC Data and Specimen Repository.

  Study phs001712

• Lifestyle, Infertility, Fertility, and Evaluation (LIFE) Study

  The purpose of this study is to provide a reference profile of small extracellular RNAs in body fluids. These samples were originally obtained in a study that had a different purpose. The purpose of the original study was to establish a data and biological specimen repository to advance future research into male reproductive health and urologic health. Semen from semen analyses, as part of standard of care at the Center for Reproductive Health, was collected and stored in a tissue bank for future research purposes. These samples and associated clinical data (including age, race, education level, medical history and diet, environmental exposures and laboratory values, fertility diagnosis and infertility treatments) will help researchers understand any urological disorders and male reproductive health issues.

  Study phs001692

• Low Density Genotyping from the Fragile Families and Child Wellbeing Study

  The Fragile Families and Child Wellbeing Study (FFCWS) is based on a stratified, multistage sample of 4898 children born in large U.S. cities (population over 200,000) between 1998 and 2000, where births to unmarried mothers were oversampled by a ratio of 3 to 1. This sampling strategy resulted in the inclusion of a large number of Black, Hispanic, and low-income families. The project “Low Density Genotyping from the Fragile Families & Child Wellbeing Study” uses saliva collected from a subset of FFCWS children at Year 9 and from teens at Year 15 to examine genetic variation using a genome-wide assay (Illumina PsychChip). In addition to the genotype data, a limited set of self reported and anthropomorphic measures are included.

  Study phs002417

• Multicenter International Cross-Sectional Evaluation of Pulmonary Alveolar Proteinosis (MICEPAP) Trial

  The purpose of this study is to (1) compare a technically improved assay with an existing assay used to measure serum anti-GM-CSF antibodies in stored serum samples previously obtained from patients diagnosed with either primary, secondary, congenital or idiopathic pulmonary alveolar proteinosis (PAP), other chronic diseases or disease-free, healthy individuals; (2) determine the prevalence and levels of anti-GM-CSF autoantibodies and (3) define the breadth of the autoimmune antibody responses in primary PAP patients from the United States, Japan, Australia, and Europe using previously collected serum samples; and (4) using a chart review approach, compare the clinical, radiologic and laboratory features of primary PAP patients to determine if differences exist among patients in these globally geographically distributed regions.

  Study phs001309

• Whole Exome Sequencing for Familial Intracranial Aneurysm (FIA I-II) Study

  The goal of this study is to identify the genes underlying the risk of intracranial aneurysm (IA). The FIA Study initially recruited families appropriate for linkage analysis. Therefore, the recruitment focus was not only on probands with a family history of IA but also required that biological samples be obtained for at least two affected family members. Family members underwent detailed interviews for medical, social and family history, and provided blood samples for DNA extraction. Over 400 multiplex IA families were recruited and enrolled. The whole exome sequencing project aims to identify novel and rare (in the general population) genetic variants that are enriched in seven extended multiplex families with a strong familial aggregation of intracranial aneurysms.

  Study phs000636

• Analysis of Recurrently Protected Genomic Regions in Urine Cell-Free DNA

  This study investigated fragmentation patterns in urine and plasma cell-free DNA and evaluated the relevance of such analysis for cancer diagnostics using urine samples. Specifically, we performed whole-genome sequencing at variable depths and evaluated genome-wide coverage in urine and plasma samples, relative to known genome annotation features. Tumor/germline exome sequencing data included was used to identify genome-wide copy number changes and their effect on cfDNA fragmentation in corresponding genomic regions in urine samples. Data included in this submission is whole-genome sequencing of urine and/or plasma cell-free DNA from healthy volunteers and/or cancer patients, and whole-exome sequencing of tumor DNA and germline DNA (peripheral blood cells) from cancer patients. 

  Study phs002273

• DAC for Early detection of ovarian cancer using cell-free DNA fragmentomes and protein biomarkers

  Ovarian cancer is a leading cause of death from gynecological malignancies worldwide. No effective screening methods exist resulting in tumor detection at advanced stages where treatment is less effective. In this study, we used whole-genome cell-free DNA (cfDNA) fragmentome and protein biomarker (CA-125 and HE4) analyses to evaluate 591 women, mostly post-menopausal, from the European Union or the United States with ovarian cancer, benign adnexal masses, or without ovarian lesions. Using a machine learning model that incorporated multi-analyte fragmentome data and protein measurements, we evaluated the detection of ovarian cancer in two clinical settings, detection of ovarian cancers among a healthy population, and classification of adnexal masses as benign or malignant. The combined approach detected ovarian cancer with specificity >99% and sensitivity of 72%, 69%, 87%, and 100% for stages I–IV, respectively (AUC=0.96, 95% CI: 0.94-0.99), including 90% of high grade serous ovarian cancers. At the same specificity, CA-125 alone detected 34%, 62%, 63%, and 100% of ovarian cancers for stages I–IV (p=0.001, two-sided test of equal proportions). Additionally, our approach differentiated benign masses from ovarian cancers with high accuracy (AUC of 0.88, 95% CI=0.83-0.92). These results were validated in an independent population. These findings show that integrated cfDNA fragmentome and protein analyses detect ovarian cancers with high performance, enabling a new accessible approach for noninvasive ovarian cancer screening and diagnostic evaluation.

  Dac EGAC50000000332

• The Cancer Dependency Map (DepMap)

  The Cancer Dependency Map (DepMap) aims to accelerate precision cancer medicine by creating a comprehensive map of tumor vulnerabilities. The DepMap project genomically profiles a wide range of cancer models and characterizes them for their sensitivity to genetic and compound perturbations. The data is computationally analyzed to create a systematic overview of the genetic dependencies and compound sensitivities of cancer types and the predictive biomarkers that point to patient populations most likely to benefit from targeting of these vulnerabilities. The DepMap public portal has become a comprehensive resource to identify cancer vulnerabilities by providing datasets at scale, cutting-edge computational tools, and sophisticated visualization tools that together have accelerated the discovery of novel targets and biomarkers. Please visit Depmap.org to access the public portal.

  Study phs003444

• Genomics of Glomerular Disorders

  The purpose of the "Genomics of Glomerular Disorders" study is to identify genetic contributions to primary glomerulopathies. This repository includes a total of N = 4,238 patients with a kidney biopsy diagnosis of a primary glomerular disorder across the following categories: focal segmental glomerulosclerosis (FSGS, N = 583), Henoch-Schönlein purpura nephritis (HSPN, N = 403), IgA nephropathy (IgAN, N = 1,555), membranous nephropathy (MN, N = 1,003), and minimal change disease (MCD, N = 694). The dataset includes a total of 2,290 patients recruited into the Cure Glomerulonephropathy (CureGN) study and another 1,948 patients from the Columbia University CKD Biobank (i.e., non-CureGN patients). The sample sizes by phenotype are counted based on enrollment diagnoses. The repository includes 3,958 WGS samples and 2,129 RNA-seq samples.

  Study phs002480

• Health Effects of Arsenic Longitudinal Study

  The Health Effects of Arsenic Longitudinal Study (HEALS), a multidisciplinary and large prospective cohort study in Araihazar, Bangladesh, was established to evaluate the effects of full-dose range arsenic (As) exposure on various health outcomes. We applied array-based genotyping technologies to baseline DNA samples from a subset of the HEALS study and linked those genotypes to data on arsenic species measured in urine. We used these data to identify regions influencing arsenic metabolism (AS3MT and FTCD). We also applied array-based DNA methylation technologies to baseline DNA samples from a subset of individuals from HEALS. These data were linked to data on arsenic concentration (in both urine and drinking water) to identify regions of the genome where DNA methylation is impacted by arsenic exposure.

  Study phs003839

• Multi-omics profiling identifies two epithelioid sarcoma molecular subtypes with distinct signaling and immune characteristics

  Epithelioid sarcoma (EpS) is an aggressive sarcoma, characterized by the loss of SMARCB1 expression. EpS is traditionally classified as distal or proximal according to clinicopathological features, but its molecular characteristics remain largely unknown. To establish an EpS molecular classification and uncover determinants of inter- and intra-patient heterogeneity in EpS, we used multi-omics profiling and integrated the genomic, transcriptional and methylome landscapes with single-cell RNA sequencing on fresh samples as well as spatial transcriptomics. We identified two molecular subtypes of EpS: “distal-like” and “proximal-like”, which were distinct from the histological subtypes. Distal-like tumors include all morphological distal subtypes and a subset of proximal and hybrid EpS. They express a specific molecular single-cell derived epithelial-to-mesenchymal transition signature, which associates with improved patient survival and includes Desmoglein 2 (DSG2), which we identify as a potential routine immunohistochemical biomarker to improve diagnosis. Distal-like EpS also display increased peri-tumoral CD8+ T cell infiltrates and specific tumor-immune cell interactions. Conversely, proximal-like EpS harbor a higher inter-tumoral molecular heterogeneity with some cases resembling other SMARCB1-deficient tumors by DNA methylation profiling, and increased intra-tumoral pro-tumoral macrophage infiltrates. Our study introduces a novel molecular classification of EpS with prognostic value, associated diagnostic biomarkers and distinct tumor immune microenvironments, which extends beyond traditional clinicopathological classification. This paves the way for precision medicine-based therapeutic strategies for patients with EpS.

  Dac EGAC50000000552

• APOBEC Mutagenesis, Kataegis, Chromothripsis in EGFR-Mutant Osimertinib-Resistant Lung Adenocarcinomas

  Expanding on studies investigating apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like (APOBEC) mutagenesis in histological transformation of epidermal growth factor receptor (EGFR)-mutant lung cancers, it has been hypothesized that mutational signature analysis may help better understand acquired resistance to targeted therapies. Using mutational signature analysis in Receptor Tyrosine Kinase (RTK) driven lung adenocarcinomas, more specifically EGFR mutant lung cancer, APOBEC dominant mutational signatures were noted more frequently in subclonal post Tyrosine Kinase Inhibitor (TKI) treatment biospecimen samples and in the presence of large-scale genomic rearrangements. This is hypothesized to be due to the pressure of treatment with TKIs; a fact that should be further explored and can be potentially manipulated in order to overcome drug resistance.

  Study phs003812

• Establishment and genomic analysis of mixed phenotypic acute leukemia cell lines

  Among acute leukemias, mixed phenotype acute leukemias (MAPL; mixed phenotype acute leukemiae), which have both acute myeloid and acute lymphocytic leukemia traits, are generally considered resistant to chemotherapy, especially those with t(9;22) MPAL has a poorer prognosis than other forms of MPAL and is a challenge to overcome. MPAL accounts for less than 1% of all acute leukemias, and the rarity of this disease makes it difficult to conduct clinical studies to develop treatments for the disease. Therefore, we planned to establish cell lines based on acute leukemia cells (JMPAL-1) obtained from MPAL patients, and to analyze information such as gene mutations related to disease development based on these cell lines for therapeutic purposes.

  Study JGAS000721

• Investigation of a method for generating cells for regenerative medicine using comprehensive nucleic acid analysis of iPS cell-derived cardiomyocytes.

  Regenerative medicine for heart failure is expected to restore cardiac function by using human iPS cells (hiPSCs). In our laboratory, it was shown that transplantation of cardiomyocytes (CMs) derived from hiPSCs into a pig model of myocardial infarction improves the disease condition. However, the instability of differentiation efficiency and tumorigenicity after transplantation are still issues to be resolved. We attempt to identify and analyze the genes and DNA methylation associated with the induction of differentiation of hiPSCs into CMs with the aim of achieving stable induction of CMs differentiation. Furthermore, we aim to analyze genes involved in tumorigenesis in CMs, and to develop a predictive marker for tumorigenesis to ensure the safety of cells before transplantation.

  Study JGAS000665

• Development of Novel Chondrosarcoma Organoid Models for Drug Discovery

  Chondrosarcoma is a rare and aggressive malignant bone tumor characterized by resistance to conventional chemotherapy and radiotherapy. Its pathogenesis remains poorly understood, although recurrent mutations such as IDH1 have been implicated in tumor development. We treated patients with chondrosarcoma at the Osaka International Cancer Institute and established two organoid cultures from resected tumor specimens using a modified air-liquid interface method. After serial passaging, the organoids were successfully xenografted into NOD-scid IL2Rgnull (NSG) mice. The established organoids retained key histological features and genetic characteristics of the original tumors. These organoid models provide a novel and reliable platform for studying the biology of chondrosarcoma and may facilitate the development of effective therapeutic strategies for this treatment-resistant tumor.

  Study JGAS000834

• Research on the identification of cancer stem cells for peidatric and adult malignancies.

  In recent years, "cancer stem cells" have been reported to exist in many cancers. Many reports have shown that they are the main cause of cancer recurrence. The aim of this study is to test whether cancer stem cells can be identified using patient samples. We will perform omics analysis of rare pediatric cancers by integrating genomics, transcriptomics, proteomics and metabolomics, including somatic and germline mutations, to deepen our understanding of the biological characteristics of the target disease. Based on the knowledge gained and clinical information from patients, we will conduct preclinical pharmacological studies using mouse models and in vitro models to investigate the therapeutic effects of novel therapeutic agents and novel therapeutic strategies such as cellular therapies.

  Study JGAS000623

• Identification of potential blood biomarkers for early diagnosis of Alzheimer���s disease through immune landscape analysis

  Mild cognitive impairment (MCI) is a clinical precursor of Alzheimer���s disease (AD). Recent genetic studies have reported on associations between AD risk genes and immunity. Here, we obtained samples and data from 317 AD, 432 MCI, and 107 cognitively normal (CN) subjects and investigated immune-cell type composition and immune clonal diversity of T-cell receptor (TRA, TRB, TRG, and TRD) and B-cell receptor (IGH, IGK, and IGL) repertoires through bulk RNA sequencing. Our prognosis prediction model using the potential blood-based biomarkers for early AD diagnosis, which combined two immune repertoires (IGK and TRA), WDR37, and clinical information, successfully classified MCI patients into two groups, low and high, in terms of risk of MCI-to-AD conversion.

  Study JGAS000532

• C-MACH reduced-representation bisulfite sequencing (RRBS)

  Umbilical cord blood (CB) has been commonly used as an epigenetic surrogate of fetuses. Here, we propose umbilical cord tissue (UC) as an alternative surrogate for epigenetic studies on fetuses. To explore the feasibility to examine UC epigenome by deep sequencing, we determined CpG methylation profiles of human postnatal UC by reduced representation bisulfite sequencing. We compared DNA methylomes between UC and CB. To investigate the effect of folate during pregnancy on fetal DNA methylation, we compared fetal UC DNA methylation between low and high levels of maternal plasma folate. Our study suggests that UC is useful as an alternative surrogate for studying environmental effects on DNA methylation in human fetuses, compensating CB by providing additional information about epigenetic regulation of genes.

  Study JGAS000171

• Assessment of de novo copy number variations in Italian patients with schizophrenia.

  We investigated de novo CNVs in the whole genomic DNA of schizophrenia patients and their parents and, specifically, in putative enhancer motifs.Study participants were part of a wider multicenter study, involving an Italian cohort of schizophrenia patients recruited by members of INRP - Italian Network for Research on Psychoses.Whole genomic DNA obtained from 46 family trios of schizophrenia probands was analyzed using the Enhancer Chip, a customized array CGH developed using the Agilent SurePrint G3 8X60K format, which is able to investigate the whole genome with a 300Kb resolution, specific disease loci at a tenfold higher resolution, and that was highly enriched in probes in more than 1.250 enhancer elements selected from the Vista Enhancer Browser (PLoS One. 2012;7(12):e52264).

  Study EGAS00001002159

• Integrated genomic analysis identifies recurrent mutations and evolution patterns driving the initiation and progression of follicular lymphoma.

  follicular lymphoma (FL), the most common indolent non-Hodgkin’s lymphoma, remains incurable. A well-recognized complication of FL is its transformation to a diffuse large B-cell lymphoma (DLBCL)-morphology in a subset of patients, for which the clinical outcomes are poor. Recent genetic profiling and single case studies of donor-derived FL following stem cell transplantation had alluded to the putative existence of a ‘long lived’ tumor-initiating progenitor cell compartment from which successive disease events occurred. To chronicle the genetic changes associated with progression to transformation, we conducted whole-genome sequencing (WGS) of FL-tFL pairs and matched germline (GL) samples from six patients, a total of 20 genomes.

  Study EGAS00001000399

• The 3D evolution of glioma cell populations

  Study description: A detailed understanding of heterogeneity in solid tumors has been limited due to insufficient sampling and a lack of knowledge from where within the tumor the sample was taken from. We present here a novel resource - the 3D Glioma Atlas - in which we record the precise, three-dimensional (3D) coordinate for each of 8-20 spatially-distinct samples obtained from each patient tumor.By revealing how genetic alterations and tumor cell states are patterned in glioma in 3D space, our Atlas shows that genetic diversity is more regionally confined in indolent as compared to aggressive tumors, that recurrent tumors have a greater density of genetic diversity, and that more aggressive tumors have greater tumor-wide transcriptomic heterogeneity.

  Study EGAS00001003710

• Genomic and immune profiling of pre-invasive lung adenocarcinoma

  Adenocarcinoma in situ and minimally invasive adenocarcinoma are the pre-invasive forms of lung adenocarcinoma. The genomic and immune profiles of these lesions are poorly understood. Here we report exome and transcriptome sequencing of 98 lung adenocarcinoma precursor lesions and 99 invasive adenocarcinomas. We have identified EGFR, RBM10, BRAF, ERBB2, TP53, KRAS, MAP2K1 and MET as significantly mutated genes in the pre/minimally invasive group. Classes of genome alterations that increase in frequency during the progression to malignancy are revealed. These include mutations in TP53, arm-level copy number alterations, and HLA loss of heterozygosity. Immune infiltration is correlated with copy number alterations of chromosome arm 6p, suggesting a link between arm-level events and the tumor immune environment.

  Study EGAS00001004006

• WES samples of patients with anti-PD-1 resistant HNSCC from a non-randomized, open-label phase 1b clinical trial

  Immune checkpoint blockade (ICB) is an effective treatment for a subset of patients with head and neck squamous cell carcinoma (HNSCC); however, the majority remain refractory. In a nonrandomized, open-label Phase 1b clinical trial, participants with recurrent and/or metastatic (R/M) HNSCC who had progressed on ICB were treated with low-dose 5-azacytidine (5-aza) daily for either 5 or 10 days, in combination with durvalumab and tremelimumab. The primary objective was to determine the biologically effective dose of 5-aza. In this study, whole exome sequencing (WES) was performed on baseline samples from 12 participants, and genomic alterations were analyzed to access the genetic background of these participants.

  Study EGAS50000000729

• Integrative analysis of small cell lung cancer

  Small-cell lung cancer (SCLC) is an aggressive lung tumor subtype. We conducted integrated analysis of genome sequencing, transcriptome, and copy number analysis and found an extremely high mutation rate of 7.4±1 protein-changing mutations per million basepairs. Evidence for inactivation of TP53 and RB1 was found in all sequenced cases. Furthermore, we identified recurrent mutations in CREBBP, EP300, and MLL, observed mutations in PTEN, in SLIT2, and EPHA7, as well as focal amplifications of the FGFR1 locus. As a major feature of SCLC we found mutation in histone modifying genes, observed genome alterations that are therapeutically tractable, and provide a framework for identifying biologically relevant genes in the context of a high mutation rate. Peifer et al., 2012, Nature Genetics.

  Study EGAS00001000299

• Genome-wide mutation analysis of germinal-center B-cell derived lymphomas within the ICGC MMML-Seq Consortium

  Germinal-center B-cell derived lymphomas (GCB-lymphomas) are the most common B-cell lymphomas in children and adults, with Burkitt Lymphomas (BL) predominating in childhood and follicular lymphoma (FL) and diffuse large B-cell lymphomas (DLBCL) predominating in older age groups. The cell-of-origin in all these lymphomas is supposed to be a germinal center B-cell and transformation of FL in DLBCL or intermediate DLBCL/BL (intL) can occur. In the framework of the German ICGC MMML-Seq we are currently exploring sequencing data of GCB-lymphomas and paired normal controls as well as normal B-cell subsets separated by FACS. This includes whole genome, transcriptome, miRNAome and whole methylome datasets.

  Study EGAS00001000394

• DPY30_ChIP_seq

  H9 human embryonic stem cells (hESCs) were cultured in feeder-free chemically-defined conditions in medium containing 10ng/ml Activin A and 12ng/ml FGF2 (Vallier L. 2011, Methods in Molecular Biology, 690: 57–66). Chromatin immunoprecipitation was performed as described in Brown S. et al. 2011. Stem Cells 29: 1176–85 by using 5ug of anti-DPY30 antibody (Sigma, cat. number HPA043761). This protocol was performed in control hESCs (expressing a scrambled shRNA) and in hESCs stably expressing an shRNA against DPY30 (Sigma, clone n. TRCN0000131112).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 EGAS00001001132