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• SEP Mobidic DAC

  Data access committee for U1236 SEP datasets

  Dac EGAC50000000216

• DAC ICARUS LUNG 01

  Data access comittee for ICARUS LUNG 01

  Dac EGAC50000000459

• Validation of a targeted sequencing panel for multiple myeloma

  Study EGAS00001006164

• Data access committee for MS cervical lymph node scRNAseq dataset

  Dac EGAC50000000524

• Data access committee (DAC) for EPI-clone manuscript

  Dac EGAC00001003526

• Yale Policy for head and neck cancer and HPV clinical trials

  Dac EGAC00001003519

• DAC LIT AG Poeck

  DAC for LIT with associated group

  Dac EGAC50000000793

• DAC for Vitiligo studies from Immunology-Dermatology unit (CHU Bordeaux)

  Dac EGAC50000000773

• SickKids_Cancer Molecular Diagnostics

  Cancer Molecular Diagnostics at Hospital for Sick Children

  Dac EGAC50000000375

• LITS

  Difference in gene expression values between case and control, log2 values. Blood transcriptome from women participating in the Norwegian Women and Cancer study (NOWAC) Post-genome Cohort taken up to eight years before brest cancer diagnosis. Illumina HumanWG-6 version 3 or Illumina HumanHT-12 expression bead chip, combined on identical nucleotide universal identifiers.

  Dataset EGAD00010001400

• Immuno-nephrology Data Access Committee Amsterdam UMC

  In this experiment we investigated kidney immunology in two autoimmune kidney diseases (ANCA-associated glomerulonephritis and Lupus Nephritis). Single cell transcriptome analysis of CD45+ immune cells from freshly retrieved kidney biopsies of 5 AGN patiënts, 1 disease-control with lupus nephritis (class II), and 1 "healthy" nephrectomy control was performed using 10X Genomics technology.

  Dac EGAC50000000024

• EBNA2 ChIP-Re-ChIP in primary B-cells infected with EBV virus

  EBNA2 ChIP-Re-ChIP in primary bulk B cells 4 days post EBV-infection with B95-8. DNA binding elements of the viral master regulator EBNA2, EBNA2-CBF transcription factor complex or EBNA2-EBF1 transcription factor complex were analyzed to identify virally targeted genes.

  Dataset EGAD50000000301

• DCLRE1B/Apollo germline mutations associated with renal cell carcinoma impair telomere protection.

  We identified 2 germline mutations in the DCLRE1B gene encoding the Apollo protein by Whole Exome Sequencing (WES) in two families with inherited clear-cell Renal Cell Carcinoma. The raw data submitted here corresponds to WES performed on Genomic Platform at Gustave Roussy Institute.

  Dataset EGAD50000000311

• Inherited defects of piRNA biogenesis cause transposon de-repression, impaired spermatogenesis, and human male infertility

  Effect of biallelic variants in genes of the piRNA pathway on biogenesis of pachytene piRNAs. RNA isolated from snap frozen testicular tissue

  Study EGAS50000000397

• Tumor Profiler Project - AML scRNA data

  The dataset contains single-cell RNA seq data from 23 patients with Acute Myeloid Leukemia (AML). Samples were collected from bone marrow or blood. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format.

  Dataset EGAD50000000823

• Pregnancy-associated melanoma

  The aim of this project is to assess differences in intratumoral immune composition in pregnant melanoma patients versus non pregnant melanoma controls. Samples (N=25) were obtained from a local patient database. From archived FFPE we isolated RNA and performed NGS and bio-informatica data-analysis.

  Dataset EGAD50000000706

• RNAseq of samples from CLL patients treated with ibrutinib in vivo

  The dataset contains RNA sequencing data from 22 paired samples of 11 patients before and during ibrutinib therapy (median time on therapy 2 weeks; range 1-12 weeks). The sequencing was performed in two batches.

  Dataset EGAD50000000879

• Tumor Profiler Project - MEL scRNA data

  The dataset contains 10x Chromium single-cell transcriptomics data from 65 samples from 62 different patients with melanoma. Samples were collected from the tumor. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format.

  Dataset EGAD50000000853

• BipEx_Landen_SWEBIC

  BipEx: Bipolar Exome Sequencing Broad & Karolinska Institutet. EGAS00001005860. "This research project was a collaboration between the Karolinska Institute and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of X SWEBIC Bipolar case samples from collaborators in Sweden. Genomic DNA from each samples was sequenced to a mean depth of 20x"

  Dac EGAC50000000142

• Whole Exome Sequences from Eivissan and Menorcan Individuals

  We analyzed Exome sequences of present day Eivissan and Menorcan individuals in order to expand on the knowledge about their demographic history and its functional consequences.

  Study EGAS50000000428

• BipEx_Pedersen_Karolinska

  "BipEx: Bipolar Exome Sequencing Broad & Karolinska Institutet. EGAS00001005856. ""This research project was a collaboration between the Karolinska Institute BioBank and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 4,765 control samples from collaborators in Sweden. Genomic DNA from each samples was sequenced to a mean depth of 20x."" "

  Dac EGAC50000000141

• scRaCH-seq fastq files

  We base called the raw data of nanopore sequencing using the Guppy software (v3.1.5) with “dna_r9.4.1_450bps_sup_prom.cfg” configuration. The passed reads (Qscore > 9) are deposited in this EGA study.

  Study EGAS50000000165

• Genome editing strategies to generate working models in Polycystic Kidney Disease

  Bulk RNA-seq of genome-edited HEK293T cell lines engineered to model specific PKD1 variants. These clones were created with the purpose of enabling the exploration of genotype-phenotype correlations in Polycystic Kidney Disease (PKD)

  Dataset EGAD50000001694

• DNA sequencing of sgRNAs enriched from the CRISPR-Cas9 screened HCC organoids

  There are 12 samples. The project aims to find enriched or depleted sgRNAs to identify functional genes in HCC progression and lenvatinib resistance

  Study EGAS50000001130

• WGS analysis of a glioma initiating cell line

  We here obtained whole-genome sequencing data to analyze transcription factor binding sequences and somatic mutations found in our RNA-seq analysis of glioma initiating cells.

  Study JGAS000096

• Elucidation of molecular mechanism of NAFLD-HCC

  We analysed the somatic mutation profile of 69 genes with recurrent genetic alterations reported in HCC using surgically-resected tumor tissues of non-viral HCC patients.

  Study JGAS000523

• Target sequencing of refractory adult Ph-negative B-ALL 1 patient

  We performed target sequensing of the bone marrow samples to gain a better understanding of refractoriness in a case of adult Ph-negative B-ALL

  Study JGAS000483

• UK_exomechip

  This dataset includes data from UK Multiple Sclerosis (MS) cases that were recruited through the University of Cambridge and included in the IMSGC exomechip experiment. Data from UK controls and additional UK cases that were recruited through other UK centres is available by direct application to those respective centres, as described in the original paper

  Dataset EGAD00010002019

• UK_immunochip

  This dataset includes data from UK Multiple Sclerosis (MS) cases that were recruited through the University of Cambridge and included in the IMSGC immunochip experiment. Data from UK controls and additional UK cases that were recruited through other UK centres is available by direct application to those respective centres, as described in the original paper.

  Dataset EGAD00010002049

• Angiosarcoma_follow_up_study

  A bespoke targeted pulldown experiment will be performed on patients with Angiosarcoma. the resulting products will be sequenced to determine the prevalence of previously found mutations in these patients.

  Study EGAS00001000405

• Chromatin_Profiling_in_Twins

  50 lymphoblastoid cell lines of adult female Twins which are part of the MuTHER study, processed with the FAIRE assay in order to generate maps of open chromatin.

  Study EGAS00001000097

• Feasibility_of_targeted_capture_sequencing_in_routinely_collected_FFPE_cancer_specimens

  Testing the feasibility of genome-scale sequencing in routinely collected formalin-fixed paraffin-embedded (FFPE) cancer specimens versus matched fresh-frozen samples using targeted pulldown capture prior to Illumina sequencing.

  Study EGAS00001000297

• EBV_AID_project

  Whole genome sequencing of EBV-transformed B cells in order to determine whether EBV induction of activation-induced cytidine deaminase (AID) produces genome-wide mutations and/or chromosomal rearrangements.

  Study EGAS00001000955

• The landscape of LAM disease

  Tumor biopsies from LAM disease were retrospectively analyzed by multiple techniques to characterize the alterations in patients ,to elucidate the landscape of genetic/genomic alterations.

  Study EGAS00001003534

• Feasibility_of_targeted_capture_sequencing_in_FFPE_cancer_specimens_2

  Testing the feasibility of genome-scale sequencing in routinely collected formalin-fixed paraffin-embedded (FFPE) cancer specimens versus matched fresh-frozen samples using targeted pulldown capture prior to Illumina sequencing.

  Study EGAS00001000402

• FFPE_CPA_Accreditation_Study

  FFPE CPA accreditation of genome-scale sequencing in routinely collected formalin-fixed paraffin-embedded (FFPE) cancer specimens versus matched fresh-frozen samples using targeted pulldown capture prior to Illumina sequencing.

  Study EGAS00001000466

• Angiosarcoma_follow_up_2_validation_study

  A bespoke targeted pulldown experiment will be performed on patients with Angiosarcoma. the resulting products will be sequenced to determine the prevalence of previously found mutations in these patients.

  Study EGAS00001000518

• Deconvolution of bulk RNA-Seq using single cell RNA-Seq

  In this study single cell RNA-Seq data was used to train a deconvolution algorithm. The algorithm was validated on paired bulk RNA-Seq profiles.

  Study EGAS00001006723

• FFPE_CPA_Accreditation_Study__Part_2

  FFPE CPA accreditation of genome-scale sequencing in routinely collected formalin-fixed paraffin-embedded (FFPE) cancer specimens versus matched fresh-frozen samples using targeted pulldown capture prior to Illumina sequencing.

  Study EGAS00001000692

• LINE_luminal_breast_cancer_Neoadjuvant_Chemotherapy_Study

  A targeted gene screen of 365 known cancer genes in luminal breast cancer samples pre-chemotherapy and at resection post-chemotherapy to evalaute clonal expansion of chemotherapy cancer cells.

  Study EGAS00001001223

• Whole exome sequencing study of cholesteatoma patients from affected families

  This study used whole exome sequencing on 21 patients with cholesteatoma from 10 families in order to identify variants that may attribute to cholesteatoma aetiology.

  Study EGAS00001006147

• Neuroblastoma Evolution

  Here, we quantify the somatic evolution of neuroblastomas by deep (80x) whole-genome sequencing, molecular clock analysis and population-genetic modeling in a comprehensive cohort (Hipo_K09R) covering all subtypes.

  Study EGAS00001006533

• MPNST_Data

  WES from 51 cases initially diagnosed as Malignant Nerve Sheath Tumours (MPNST) and RNA sequencing data from 10 MPNST cases. Find more information in article: Lyskjær et al, 2020, J Pathol, "H3K27me3 expression and methylation status in histological variants of malignant peripheral nerve sheath tumours".

  Dataset EGAD00001006253

• Chromatin accessibility in human monocytes differentiation

  This dataset consists of ATAC-seq data from human monocytes, monocyte-derived dendritic cells or monocyte-derived macrophages as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, it includes 39 samples.

  Dataset EGAD00001007953

• BLUEPRINT: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cells (WGS)

  BLUEPRINT: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cells (WGS)

  Dataset EGAD00001002663

• sn-RNAseq profiling of the impact of a cytokine storm model in human cardiac organoids

  sn-RNAseq profiling of the impact of a cytokine storm model in human cardiac organoids

  Dataset EGAD00001007533

• Shallow WGS of neuroblastoma cell lines with large-scale chromosomal deletions induced through CRISPR-Cas9

  Shallow WGS of neuroblastoma cell lines with large-scale deletions induced through CRISPR-Cas9 and matching controls. Deletion of 11q was induced in the cell line SKNSH and loss of 6q was induced in the cell line NMB.

  Dataset EGAD00001007758

• Colorctal cancer WES/WGS analysis in Dr. Liu’s group in Sun Yat-sen University Cancer Center.

  The samples include paired tumor and normal tissues from 106 patients . High-coverage WES sequencing or whole genome sequencing of DNA samples were performed on the Illumina HiSeq 2000 system

  Dataset EGAD00001003551

• RNA sequencing data to study therapeutic targeting of ependymoma

  This dataset conatains RNA sequencing data from 24 patients. Up to two lanes per tumour sample have been seqeunced on a Illumina HiSeq2000 instrument in paired-end mode resulting in 58 Fastq files.

  Dataset EGAD00001003966

• Multiple Malignancy Familial Comparison

  Patient (who has had multiple malignancies) has previously been found to harbour a pathogenic p53 variant which is probably mosaic. This finding is based on exome sequencing performed elsewhere. In this study we will resequence the locus in question to ascertain whether the variant is indeed mosaic.

  Dataset EGAD00001001062

• 200PG : WGS Aligned Sequence (fastq)

  200PG : WGS Aligned Sequence (fastq) : Aligned WG sequence data (bam) in this dataset are from the 124 CPCGene Tumour/Normal Pairs used in the 200PG Study. https://www.ncbi.nlm.nih.gov/pubmed/28068672

  Dataset EGAD00001003139

• Lung Multi-site Targeted Sequence Capture

  DNA extracted from multiple biopsies taken from different areas of primary lung tumours will be subjected to targeted re-sequencing and analysed in order to assess intra-tumour heterogeneity with respect to mutations in a selection of cancer related genes.

  Dataset EGAD00001001017

• There are 22 pairs of LAML cases in this project which belongs to LAML-CN. The library is constructed by the Illumina protocol.

  There are 22 pairs of LAML cases in this project which belongs to LAML-CN.The library is constructed by the Illumina protocol.

  Dataset EGAD00001003317

• Maternal plasma data in FetalQuantSD accurate quantification of fetal DNA fraction by shallow-depth sequencing of maternal plasma DNA

  This dataset consist on 70 maternal plasma samples (bam files) used in the FetalQuantSD. The maternal plasma DNA samples were sequenced using the HiSeq 2000 platform (Illumina) with a 50-cycle paired-end mode.

  Dataset EGAD00001004324

• There are 66 pairs of LAML cases(complete genomics) in this project which belongs to LAML-CN.The library is constructed by the Completes Genomics protocol.

  There are 66 pairs of LAML cases(complete genomics) in this project which belongs to LAML-CN..The library is constructed by the Completes Genomics protocol.

  Dataset EGAD00001003310

• Somatic mutations in epithelial cells from endometriosis and normal uterine endometrium

  Somatic mutations in epithelial cells from endometriosis and normal uterine endometrium, with a total of 24 samples. Target enrichment was conducted by Agilent SureSelect Human All Exon V5 + IncRNA kit. Sequencing was conducted by Illumina HiSeq 2500 platform. Somatic mutation call was performed by Strelka.

  Dataset EGAD00001004186

• scMultiome

  This dataset gather scMultiomic data including RNA-seq and ATAC-seq in MM.1S in control and dex condition at 1h and 4h

  Dataset EGAD00001011140

• BLUEPRINT DNA methylation profiles of monocytes, T cells and B cells in type 1 diabetes-discordant monozygotic twins (Bisulfite-Seq data).

  BLUEPRINT DNA methylation profiles of monocytes, T cells and B cells in type 1 diabetes-discordant monozygotic twins (Bisulfite-Seq data).

  Dataset EGAD00001002682

• Immunoglobulin sequences of self-reactive plasma cells in celiac disease

  Paired immunoglobulin heavy and light chain sequences were obtained from 803 single IgA plasma cells isolated from duodenal biopsies of five celiac disease patients. The cells were specific to discrete antigenic regions of the enzyme TG2, which is the main autoantigen in celiac disease.

  Dataset EGAD00001005029

• Data from Representation of genomic intratumor heterogeneity in multi-region non-small cell lung cancer patient-derived xenograft models

  Data from Representation of genomic intratumor heterogeneity in multi-region non-small cell lung cancer patient-derived xenograft models

  Dataset EGAD00001012228

• Born in Bradford (BiB)

  Dac EGAC00001003494

• Whole-exome sequencing of glioblastomas with long-term relapse interval

  Treatment options for GBM patients have not changed over the last 15 years, and the success of targeted therapy or immunotherapy has been disappointinglimited. Thus, the standard of care for GBM patients remains surgical resection followed by concomitant DNA alkylating agent therapy with temozolomide (TMZ) and radiation therapy (RT). However, the time to relapse is generally short (6.9 months on average) owing to the tumor’s ability to infiltrate normal parenchyma and its intrinsic resistance to radio-chemotherapy. Due to the lack of alternative treatment options, elucidating underlying resistance mechanism has come into major focus of research, with the hope for opening new ways of therapeutic intervention overcoming resistance. To explore therapy resistance driving events, we performed a study using a single-centric collective of matched pairs of therapy-naïve and post-therapeuticc tissue from GBM patients, selected based on a maximally long interval between resections of the initial and the recurrent tumors. This rare collective was analyzed by whole exome sequencing (WES), mRNA expression and miRNA expression profiling.

  Study EGAS00001006022

• Human liver NPCs single cell project

  Independent of their inflammatory phenotype, macrophages are key orchestrators of hepatic metabolism. Non-alcoholic fatty liver disease (NAFLD) often occurs in obese individuals and is among the most common causes of cirrhosis, the terminal chronic liver disease that may necessitate liver transplantation. While multiple populations of macrophages have been described in the human liver, their function and turnover in obese patients at high risk of developing NAFLD and cirrhosis is currently unknown. Herein we identified a specific human population of resident liver myeloid cells that protects against the metabolic impairment associated with obesity. By studying the turnover of liver myeloid cells in individuals undergoing liver transplantation using markers of donor-recipient mismatch, we made the novel discovery that liver myeloid cell turnover differs between humans and mice. Using single cell techniques and flow cytometry we determined that the proportion of the protective resident liver myeloid cells, denoted liver myeloid cells 2 (LM2), decreases during obesity. Functional validation approaches using human 2D and 3D cultures revealed that the presence of LM2 ameliorates the oxidative stress associated with obese conditions. Our study indicates that resident myeloid cells could be a therapeutic target to decrease the oxidative stress associated with NAFLD.

  Study EGAS00001007194

• Data Access Commitee for the project : Methylome profiling of human mesenchymal chondrosarcoma

  Dac EGAC00001003217

• Quantitative analysis of a novel DNA hypermethylation panel for lung cancer diagnosis

  Study EGAS00001007008

• Data Access Commitee for single-cell analysis of multiple myeloma and precursors

  Dac EGAC00001002920

• Data Access Committee for the Metastatic Breast Cancer Whole-exome sequencing study

  Dac EGAC00001000434

• DAC for patient-derived cell line samples

  Dac EGAC00001000594

• DAC for Direct Detection of Early-stage Cancers Using Circulating Tumor DNA

  Dac EGAC00001000701

• Data Access Committee for desmoplastic small round cell tumor (DSRCT) RNAseq data.

  Dac EGAC00001000851

• DAC for Oncogenic fate conversion by PRDM16s causes acute myeloid leukemia

  Dac EGAC00001001023

• EMBL genome biology research group for structural variation (Strand-seq application)

  Dac EGAC00001001091

• DAC for Integrated Genomic, Epigenetic, and Expression Analyses of Ovarian Cancer Cell Lines

  Dac EGAC00001001101

• Stanford Data Access Committee for Multi-Region WES of Metastatic Colorectal Cancer

  Dac EGAC00001001164

• Nicola Murray Centre for Ovarian Cancer Research Data Access Committee

  Dac EGAC00001001588

• Cancer Clinical Research Trust DAC for WES of HER2+ metastatic cancer samples

  Dac EGAC00001001632

• Data Access Commitee of the Princess Maxima Center for Pediatric Oncology

  Dac EGAC00001001948

• Data access committee for Gut microbiome of BA patients and normal controls

  Dac EGAC00001002146

• "DAC for RNAseq from regions of insitu and invasive human mammary ductal disease"

  Dac EGAC00001002538

• EGAD00010000831

  BLUEPRINT EpiMatch: harnessing epigenetics for haematopoietic stem cell transplantation

  Dataset EGAD00010000831

• irish_fineSTRUCTURE

  SNP data for 991 Irish individuals

  Dataset EGAD00010001479

• DNA Methylation data for EGAS00001002592

  Islet_HumanMethylation450K_ThurnerEtAl

  Dataset EGAD00010001695

• DAC for Tuebingen-Stuttgart cohort

  Dac EGAC00001000317

• Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Jackson Heart Study (JHS)

  Study phs002907

• A multi-center genome-wide association study for nasopharyngeal carcinoma

  Study EGAS00001006062

• DAC for Clonal driver neoantigen loss under EGFR TKI and immune selection pressures

  Dac EGAC00001003522

• Validation of cfDNA fragmentome analyses for early detection of liver cancer

  Study EGAS00001008111

• Whole Genome Comparisons of Breast Cancers and their Xenotransplants

  Early passage breast cancer xenografts have been proposed as alternatives to cell lines as model systems for studying the basic biology of tumors and for advancing therapy development. This study explores the relatedness of primary disease genomes to their matched xenotransplants. Using paired-end massively parallel sequencing 17 matched progenitor tumor, xenograft and normal trios were sequenced to at least 30-fold coverage with diploid coverage of at least 95% of the genome as determined by SNP array concordance. RNA sequence was generated from the xenograft tumors. The xenografts were derived from a spectrum of tumor samples from patients with both early and advanced breast cancer.

  Study phs000611

• Massachusetts General Hospital/Eisai National Institute of Mental Health (NIMH) Genetics Initiative Alzheimer's Disease GWAS - Affymetrix GeneChip Human Mapping 500K Array Set

  This study cohort was collected as part of the National Institute of Mental Health (NIMH) Alzheimer's disease Genetics Initiative Study. Recruitment of families, predominantly sibling, for the cohort was focused on local memory disorder clinics, nursing homes, and the surrounding community. Clinical evaluation was performed at the University of Alabama at Birmingham, Johns Hopkins University, and Massachusetts General Hospital/Harvard Medical School. Informed consent was obtained from all study participants, for participants with extensive cognitive impairment, a legal guardian or caregiver with power of attorney provided consent. To determine age of onset, a creditable informer was interviewed and medical records were evaluated.

  Study phs000483

• Spatiotemporal Transcriptome of the Human Brain

  Comprehensive knowledge about the spatiotemporal dynamics of the brain transcriptome is essential for a better understanding of neurodevelopment, sexual dimorphism, and evolution, as well as our increased susceptibility to certain brain disorders. We generated and analyzed genome-wide exon-level transcriptome data from 16 brain regions of 57 postmortem human brains, spanning from embryonic development to late adulthood and representing males and females of multiple ethnicities. We also performed genome-wide genotyping of 2.5 million SNPs and assessed genome normality for all donors. This study provides a comprehensive, publicly available dataset on the spatiotemporal human brain transcriptome and new insights into the transcriptional foundations of human neurodevelopment.

  Study phs000406

• Genomic analysis of head and neck squamous cell carcinoma upon acquired resistance to cetuximab

  Anti-epidermal growth factor receptor (EGFR) monoclonal antibodies (cetuximab) remain the only FDA-approved targeted therapy for patients with recurrent/metastatic head and neck squamous cell carcinoma (HNSCC). Unfortunately, most patients develop acquired resistance to cetuximab and there is currently no further therapeutic option for these patients (unmet clinical need), thereby highlighting the need to better understand resistance-causing mechanisms. Here, we carried out whole-exome sequencing on 2 cetuximab-sensitive and -resistant patient-derived xenograft models of HNSCC. Our data reveal several genetic alterations (mutations and copy number variations) associated with acquired resistance to anti-EGFR therapy.

  Study EGAS50000000800

• Population whole-genome bisulfite sequencing across two tissues highlights environment as principal source of human methylome variation

  The study includes whole-genome bisulfite sequencing (WGBS) on 34 adipose(7 MZ pairs, 6 DZ pairs and 8 singletons) and 27 blood (7 MZ pairs, 6 DZpairs and 1 singleton) DNA samples derived from a total of 43 female twinsbelonging to the MuTHER/TwinsUK cohort. We generated 11.5 billion 100bppaired-end reads covering 2.3 Tera-basepairs (Tbp) ofsequence using the Illumina HiSeq2000 or 2500 systems. Applying standardalignment methods and filters we obtain a mean genome coverage of 6.3-fold(range: 1.0- to 12.9-fold) for adipose and 8.7-fold (range: 0.7- to29.0-fold) for blood.

  Study EGAS00001001569

• August 2021 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  August 2021 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001008101

• A Phase I Study with a Personalized Neoantigen Cancer Vaccine in Melanoma

  Effective anti-tumor immunity in humans has been associated with presence of T cells targeting neoantigens that arise from non-silent tumor-specific mutations. Here we conducted whole-exome sequencing of tumor and normal cells from individual patients to identify mutations. We assessed the expression of mutated alleles by RNA-sequencing of tumor. We demonstrated the feasibility, safety and immunogenicity of a vaccine that targets up to 20 personal neoantigens predicted to be presented by the autologous patient tumor.Antigen-specific CD8+ T cells that can recognize and eliminate cancer cells play a crucial role in anti-tumor immune responses. Here we conducted single-cell sequencing of cells infiltrating melanoma specimens originating from 4 patients and determine the TCR clonality of the CD8+ tumor infiltrating cells. We investigated the relationship between T cell clonality and phenotypic cell states coupling single-cell transcriptome to single-cell TCR seq. The surface expression of a panel of protein was detected in parallel using CITE-Seq antibodies. Sorted tumor and peripheral blood specimens were processed in parallel.In order to discover cancer antigens derived from annotated and unannotated protein-coding regions of the genome, we carried out matched ribosome profiling (Ribo-seq), RNA-sequencing, and whole genome sequencing on one of the patients, as well as Ribo-seq on an additional patient. We used it to discover novel or unannotated open reading frames (nuORFs), their expression levels, as well as somatic mutations within them to predict potential neoantigens.

  Study phs001451

• Cancer-associated fibroblasts promote drug resistance in ALK-driven lung adenocarcinoma cells by upregulating lipid biosynthesis

  Targeted therapy interventions using tyrosine kinase inhibitors (TKIs) provide encouraging treatment responses in ALK-rearranged lung adenocarcinomas, yet resistances occur almost inevitably. Apart from tumor cell-intrinsic resistance mechanisms, accumulating evidence supports a role of cancer-associated fibroblasts (CAFs) in affecting the therapeutic vulnerability of lung cancer cells. Here, we aimed to investigate underlying molecular networks shaping the therapeutic susceptibility of ALK-driven lung adenocarcinoma cells via tumor microenvironmental cues using three-dimensional (3D) spheroid co-culture settings. We show that CAFs promote therapy resistance of lung tumor cells against ALK inhibition by reducing apoptotic cell death and increasing cell proliferation. Using single-cell RNA-sequencing analysis, we show that genes involved in lipogenesis constitute the major transcriptional difference between TKI-treated homo- and heterotypic lung tumor spheroids. CAF-conditioned medium and CAF-secreted factors HGF and NRG1 were both able to promote resistance of 3D-cultured ALK-rearranged lung tumor cells via AKT signaling, which was accompanied by enhanced de novo lipogenesis and supression of lipid peroxidation. Notably, simultaneous targeting of ALK and SREBP-1 was able to overcome the established CAF-driven lipid metabolic-supportive niche of TKI-resistant lung tumor spheroids. Our findings highlight a crucial role of CAFs in mediating ALK-TKI resistance via lipid metabolic reprogramming and suggest new ways to overcome resistance towards molecular directed drugs by targeting vulnerabilities downstream of oncogenic signaling.

  Study EGAS50000000135

• Initial whole genome sequencing of plasma cell neoplasms in First Responders exposed to the World Trade Center attack of September 11, 2001

  The World Trade Center (WTC) attack of September 11, 2001 created an unprecedented environmental exposure to known and suspected carcinogens. High incidence of multiple myeloma (MM) and precursor conditions has been reported among first responders to the WTC disaster. To expand on our prior screening studies, and to characterize the genomic impact of the exposure to known and potential carcinogens in the WTC debris, we were motivated to perform whole genome sequencing (WGS) of WTC first responders and recovery workers who developed a plasma cell disorder after the attack. PATIENTS AND METHODS: We performed WGS of 9 CD138-positive bone marrow mononuclear samples from patients who were diagnosed with plasma cell disorders after the WTC disaster. RESULTS: No significant differences were observed in comparing the post-WTC driver and mutational signatures landscape with 110 previously published WGS from 56 patients with MM and the CoMMpass WGS cohort (n=752). Leveraging constant activity of the single base substitution mutational signatures 1 and 5 over time, we estimated that tumor-initiating chromosomal gains were windowed to both pre- and post-WTC exposure. CONCLUSIONS: Although limitations in sample size preclude any definitive conclusions, our findings suggest that the observed increased incidence of plasma cell neoplasms in this population is due to complex and heterogeneous effects of the WTC exposure that may have initiated or contributed to progression of malignancy.

  Study EGAS00001004467

• Genomewide Association Study of Inflammatory Bowel Disease - Combined Controls

  WTCCC genome-wide case-control association study for Inflammatory Bowel Disease (IBD) using six disease collections together with the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000007

• BLUEPRINT release August 2014, Bisulfite-Seq for hematopoietic multipotent progenitor cell

  Bisulfite-Seq data for 1 hematopoietic multipotent progenitor cell sample(s). 8 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001000917

• Myelofibrosis Etiology and Transplant Outcomes

  The Myelofibrosis Etiology and Transplant Outcomes study is a collaboration between the National Cancer Institute and the Center for International Blood and Marrow Transplant Research (CIBMTR). The study aims to identify genomic factors affecting myelofibrosis pathogenesis and prognosis.

  Study phs002635

• Comprehensive genomic characterization of early stage bladder cancer - whole exome sequencing data

  For this project about non-muscle invasive bladder cancer (NMIBC), we analysed WES data from 438 patients. The dataset is composed of 876 BAM files: 438 tumor samples and 438 paired blood samples.

  Study EGAS50000000511