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• CBD-KEY-CITESEQ-LINKER: Linker file for CITEseq sequencing data

  Linker file for COMBAT CITEseq sequencing data. Links COMBAT sample IDs with sequencing pools and their associated raw sequence data. Sequence data can be found in the following datasets: ADT data: EGAD00001007962 GEX data: EGAD00001008007 VDJ (B-cell): EGAD00001007964 VDJ (T-cell): EGAD00001007965

  Dataset EGAD00001008008

• Sequencing data for oesophageal / related samples - Kazachenka et al (RNA)

  Data supporting: "The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes" RNAseq for 279 samples

  Dataset EGAD00001011076

• Sequencing data for oesophageal and related samples - Abbas et al (RNA)

  Data supporting: "Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma" Abbas et al (RNA for 197 samples)

  Dataset EGAD00001011269

• Clinical and Genetic Evaluation of Individuals with Undiagnosed Disorders through the Undiagnosed Diseases Network (UDN)

  The National Human Genome Research Institute and the NIH Clinical Center established the intramural Undiagnosed Diseases Program (UDP) in 2008 to make progress in uncovering, understanding, and treating rare disorders. Based on the success of the UDP, the NIH Common Fund established the Undiagnosed Diseases Network (UDN) in FY 2013 (Phase I, 9/16/2015-8/31/2018) to achieve this type of cross-disciplinary approach to disease diagnosis in academic medical centers around the United States. The NIH Common Fund expanded the network in 2018 (Phase II, 9/1/2018-6/20/2023) to increase the availability of diagnostic services, foster opportunities for collaboration between laboratory and clinical investigators, provide resulting data and protocols to the broader community, and assess development of a sustainable national resource after Common Fund support ends. The UDN transitioned from Common Fund in 2023. The National Institute of Neurological Disorders and Stroke (NINDS) will oversee the Network in Phase III, which launched in July 2023, with help from 17 different NIH Institutes and Centers along with the NIH Office of the Director. With help from patients, family members, patient advocacy groups, a Data Management and Coordinating Center (DMCC), several Clinical Sites, and other stakeholders, the NIH envisions the UDN evolving into a larger, diverse, and self-sustained network that fosters scientific discovery and provides expert diagnostic services for undiagnosed patients across the nation. The overarching goals of the UDN in Phase III include: Continuing the proven success of the UDN in improving the clinical evaluation of difficult-to-diagnose patients using a collaborative team approach and investigating and validating promising new diagnostic technologies. Facilitating research into the etiology of undiagnosed diseases by collecting and sharing standardized, high-quality clinical and laboratory data including genotyping, phenotyping, and documentation of environmental exposures. Promoting a broader integrated and collaborative community across multiple Clinical Sites and among laboratory and clinical investigators prepared to investigate the genetic, pathophysiologic, cell biologic, and molecular mechanisms underpinning these difficult-to-diagnose conditions.

  Study phs001232

• DNA and RNA sequencing data from Ovarian Carcinosarcoma patients from the Glasgow Cohort.

  In this study, we analysed DNA and RNA sequencing data from Ovarian Carcinosarcoma patients, from isolated carcinoma and sarcoma components and investigated DNA variants as well as gene expression. Genomic analyses from this data and further investigation from preclinical models of ovarian carcinosarcoma support the conversion theory for disease development and indicate that microtubule inhibitors could be used to suppress EMT and stimulate anti-tumour immunity.

  Study EGAS00001006605

• UCSF Sebaceous Carcinoma DAC for review of sequence data release from manuscript in Nature Communications, based in the UCSF Departments of Dermatology and Pathology

  Dac EGAC00001000850

• A tumor focused approach to resolving the etiology of DNA mismatch repair deficient tumors classified as suspected Lynch syndrome

  Routine screening of tumors for DNA mismatch repair (MMR) deficiency (dMMR) in colorectal (CRC), endometrial (EC) and sebaceous skin (SST) tumors leads to a significant proportion of unresolved cases classified as suspected Lynch syndrome (SLS). A tumor-focused testing approach reclassified 86.9% of SLS into Lynch syndrome, sporadic dMMR or MMR-proficient cases. These findings support the incorporation of tumor sequencing and alternate MLH1 methylation assays into clinical diagnostics to reduce the number of SLS patients and provide more appropriate surveillance and screening recommendations.

  Study EGAS50000000021

• Long-read whole genome sequencing as a tool for variant detection in inherited retinal dystrophies

  Advances in whole-genome sequencing (WGS) have significantly enhanced our ability to detect genomic variants underlying inherited diseases. In this study, we performed long-read WGS on 24 patients with inherited retinal dystrophies (IRDs) to validate the utility of nanopore sequencing in detecting genomic variations. We confirmed the presence of all previously detected variants and demonstrated that this approach allows for precise refinement of structural variants (SVs). Furthermore, we could perform genotype phasing by sequencing only the probands, confirming variants were inherited in trans. Moreover, nanopore sequencing enabled the detection of complex variants, such as transposon insertions and structural rearrangements. This comprehensive assessment illustrates the power of long-read sequencing in capturing diverse forms of genomic variation and in improving diagnostic accuracy in IRDs.

  Dataset EGAD50000001238

• RNA Editing Exome

  Exome sequencing data for tumor and matched normal samples of the EGAS00001000495 project.

  Dataset EGAD00001000626

• Global Anaplastic Thyroid Cancer Initiative

  Raw whole genome sequence data(fastq) for the GATCI project

  Dataset EGAD00001003236

• Oesophageal adenocarcinoma RNAseq from LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19)

  This dataset contains bulk transcriptomes from the inoperable cohorts of the LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19). Transcriptomes were prepared from pre-treatment oesophageal tumour biopsies using a ribodepletion approach in order to assess both previously reported (e.g. PD-L1 expression) and novel predictive expression-based biomarkers for immunochemotherapy treatment in this setting. On-treatment and post-treatment biopsies were generated as well to characterize response to therapy, and samples were also prepared from paired normal GI tissues for a subset of patients. scRNA-seq based deconvolution was also applied to bulk transcriptomes in this study to estimate the cell composition of tumour biopsies and assess the link between the presence of specific cell types with immunochemotherapy outcomes.

  Dataset EGAD00001009399

• non-malignant plasma cfRNA

  Dataset contains mRNA capture sequencing data from plasma of 125 different human donors: 88 patients with a non-malignant disease and 37 cancer-free controls. Samples were sequenced on a NovaSeq X and sequencing data is provided in FASTQ format.

  Dataset EGAD50000001806

• DupiAERD

  Dataset contains bulk RNA sequencing reads from 44 NERD patients under dupilumab therapy before and after aspirin provocation at baseline and after 24 weeks of treatment. Dataset is a multiplexed .bam file containing all sequencing reads with tagged identifiers.

  Dataset EGAD50000000565

• Genetics of Microcephalic Osteodysplatics Primordial Dwarfism

  This project aims to find causal variants in 50 patients diagnosed with Microcephalic Osteodysplastic Primordial Dwarfism (MOPD), of presumed recessive inheritance performing whole exome sequencing to ~50x mean depth.This is a collaboration with Prof A. Jackson, MRC Human Genetics Unit, Edinburgh

  Dataset EGAD00001000342

• Human placenta microRNA sequencing dataset

  Human placenta samples from 52: 5 first trimester , 7 second trimester, and 40 term placenta. Data is uploaded as BAM files.

  Dataset EGAD00001007766

• RNA-seq of BCR-ABL1 lymphoblastic leukemia

  This dataset is derived from whole-transcriptome sequencing (RNA-seq) of RNA from 57 BCR-ABL1 lymphoblastic leukemias (53 diagnostic, 4 relapse).

  Dataset EGAD00001010307

• Establishment of xenogfafts and cultured cell lines from clinical samples

  The purpose of the present study was to clarify the presence or absence of alterations in the molecular properties of patient-derived xenografts (PDXs) with up to eight passages in endometrial carcinomas. Alterations in the proportion of immunohistochemically positive/negative cells for PAX8, estrogen receptor, PAX2, and PTEN were observed in established PDXs of endometrioid carcinomas and carcinosarcomas, whereas proportions of cells with AE1/AE3, TP53, ARID1A PMS2, and MSH6 were maintained. Variants of cancer-associated genes in PDX compared to those in the parental tumors were examined in two cases, a frameshift deletion in BRCA1 was observed in the parental tumor tissue, and additional genomic alterations were found in the PDXs of this case. Genomic and phenotypic alterations in endometrial carcinoma PDXs relative to the parental tumors were observed and were partly associated with endometrial cancer-specific characteristics in cellular differentiation and gene mutations.

  Study JGAS000585

• Whole-genome sequencing across 449 samples spanning 47 ethnolinguistic groups provides insights into genetic diversity in Nigeria

  African populations have been drastically underrepresented in genomics research and failure to capture the genetic diversity across the numerous ethnolinguistic groups (ELGs) found in the continent has hindered the equity of precision medicine initiatives globally. Here, we describe the whole-genome sequencing of 449 Nigerian individuals across 47 unique self-reported ELGs. Population structure analysis reveals genetic differentiation amongst our ELGs, consistent with previous findings. From the 36 million SNPs and indels discovered in our dataset, we provide a high-level catalog of both novel and medically-relevant variation present across the ELGs. These results emphasize the value of this resource for genomics research, with added granularity by representing multiple ELGs from Nigeria. Our results also underscore the potential of using these cohorts with larger sample sizes to improve our understanding of human ancestry and health in Africa.

  Study EGAS00001007036

• Diverse mutational landscapes in human lymphocytes

  A lymphocyte suffers many threats to its genome, including programmed mutation during differentiation, antigen-driven proliferation and residency in diverse microenvironments. After developing protocols for single-cell lymphocyte expansions, we sequenced whole genomes from 717 normal naive and memory B and T lymphocytes and hematopoietic stem cells. All lymphocyte subsets carried more point mutations and structural variants than haematopoietic stem cells – the extra mutations were mostly acquired during differentiation, with burdens higher in memory than naive lymphocytes, although T cells also had a higher rate of mutation accumulation throughout life. Off-target effects of immunological diversification accounted for most of the additional differentiation-associated mutations in lymphocytes. Memory B cells acquired, on average, 18 off-target mutations genome-wide for every one on-target IGV mutation during the germinal centre reaction. Structural variation was 16-fold higher in lymphocytes than stem cells, with ~15% of deletions being attributable to off-target RAG activity. Mutational processes associated with ultraviolet light exposure and other sporadic mutational processes generated hundreds to thousands of mutations in some memory lymphocytes. The mutation burden and signatures of normal B lymphocytes were broadly comparable to those seen in many B-cell cancers, suggesting that malignant transformation of lymphocytes arises from the same mutational processes active across normal ontogeny. The mutational landscape of normal lymphocytes chronicles the off-target effects of programmed genome engineering during immunological diversification and the consequences of differentiation, proliferation and residency in diverse microenvironments.

  Dataset EGAD00001008107

• High-coverage whole exome sequence in non-TRU-type lung adenocarcinomas

  In order to elucidate the key genetic events in non-TRU-type lung cancer, we selected 43 non-TRU-type lung adenocarcinomas and performed a whole exome sequence and RNA-seq analysis using a next-generation sequencer. The results of the analysis identified mutations in TP53, KRAS and NKX2-1 as the top three significantly mutated genes, while the EGFR mutation was rare in this cohort. Eight NKX2-1 mutations (5 frameshift, 2 nonsense, and one missense) were identified, with one case harboring two distinct NKX2-1 mutations (missense and frameshift). All NKX2-1 mutants were transcriptionally inactive in reporter assays. Histologically, invasive mucinous adenocarcinomas accounted for most of the NKX2-1 mutations (5 cases), while 1 enteric and 1 acinar adenocarcinoma harbored the NKX2-1 mutation.

  Study JGAS000105

• Chromosome Y Philogeny in Sardinia

  Genetic variation within the male specific portion of the Y chromosome (MSY) can clarify the origins of contemporary populations, but previous studies were hampered by partial genetic information. Population sequencing of 1,204 Sardinian males identified 11,763 MSY single nucleotide polymorphisms (SNPs), of which 6,751 have not previously been observed. We constructed a MSY phylogenetic tree containing all main haplogroups found in Europe along with many Sardinian-specific lineage clusters within each haplogroup. The tree was calibrated with archaeological data from the initial expansion of the Sardinian population ~7,700 years ago. The ages of nodes highlight different genetic strata in Sardinia and reveal presumptive timing of coalescence with other human populations. We calculate a putative age for coalescence of ~180-200,000 years ago, consistent with previous mitochondrial DNA (mtDNA) based estimates.

  Study EGAS00001000532

• Facial Skin Biophysical Multi-Parameter and Microbiome-Based Korean Skin Cutoype (KSC) Determination

  In this study, we conducted an integrated analysis of skin measurements, clinical BSTI surveys, and the skin microbiome of 950 Korean subjects to examine the ideal skin microbiome-biophysical association. By utilizing four skin biophysical parameters, we identified four distinct Korean Skin Cutotypes (KSCs) and categorized the subjects into three aging groups based on their age distribution. We established strong connections between 15 core genera and the four KSC types within the three aging groups, revealing three prominent clusters of the facial skin microbiome. Together with skin microbiome variations, skin tone/elasticity distinguishes aging groups while oiliness/hydration distinguishes individual differences within aging groups. Our study provides prospective reality data for customized skin care based on the microbiome environment of each skin type.

  Study EGAS00001007334

• DNA Methylation-based diagnostic biomarkers for ESCC in Han Chinese population

  To validate the methylation status of the four candidate tumor suppressor genes (ADHFE1, EOMES, SALL1, TFPI2) in Han Chinese ESCC patients, we recruited 103 patients and obtained the paired tumors(entitled as T) and adjacent normal tissues (entitled as N) as well. Targeted bisulfite sequencing was conducted to detect the methylation profiles of these four genes in these 103 paired tissues. Furthermore, the raw sequence data (fastq files) was aligned using the BSseeker2 and this dataset included all of the bam file after alignment.

  Dataset EGAD00001004288

• ScRNA-seq of human kidney immune cells of patients with ANCA-associated glomerulonephritis, Lupus Nephritis against a healthy nephrectomy control

  ANCA-associated glomerulonephritis (AGN) associates with a high risk of end-stage kidneydisease. The role of kidney immune cells in local inflammation remains unclear. This study investigates kidney immune cell diversity and function. Kidney tissue from AGN patients (n=5) and a lupus nephritis (LN) patient (n=1) were aquired during a biopsy procedure for a clinical indication. Needle-core biopsies were obtained for histopathological examination, and an additional pass was performed to retrieve kidney tissue for scRNA-seq. Healthy kidney tissue (n=1) was obtained from a kidney that was surgically removed do tue due to a (non-invasive) papillary urothelial carcinoma. Immediately after collection, kidney tissue was processed into a single-cell suspension and sorted using a 4-color flow cytometry panel to isolate living, CD45+immune cells. To aid in the multi-omic characterization, surface markers and T and B cell repertoires were sequenced in 2 samples (1 AGN patient and the nephrectomy control). These samples were incubated with an oligo-antibody TotalSeq-C cocktail containing 130 unique cell surface antigens.

  Dataset EGAD50000000229

• Detection and characterization of lung cancer using cell-free DNA fragmentomes

  Lung cancer remains the leading cause of cancer death world-wide, largely due to its late diagnosis. Non-invasive approaches for assessment of cell-free DNA (cfDNA) provide an opportunity for detection and intervention that may have broader accessibility than current imaging approaches. Using a machine learning model for detecting tumor-derived cfDNA through genome-wide analyses of cfDNA fragmentation, we examined a prospective study of 365 individuals at risk for lung cancer (Lung Cancer Diagnostic Study, LUCAS), including 129 individuals ultimately diagnosed with lung cancer and 236 individuals determined to not have lung cancer. We externally validated the cancer detection model using an independent cohort of 385 non-cancer individuals and 46 predominantly early stage lung cancer patients. Combining fragmentation features with clinical risk factors and CEA levels followed by CT imaging detected 94% of patients with cancer across stages and subtypes, including 91% of stage I/II and 96% of stage III/IV, at 80% specificity. Genome-wide fragmentation profiles across ~13,000 ASCL1 transcription factor binding sites could be used to distinguish individuals with small cell lung cancer (SCLC) from those with non-small cell lung cancer (NSCLC) with high accuracy (AUC=0.98). Among individuals with lung cancer, a higher cfDNA fragmentation score was associated with tumor size and invasion, and represented an independent prognostic indicator of survival. These studies provide a facile approach for non-invasive detection of lung cancer and clinical management of this disease.

  Study EGAS00001005340

• EPIC arrays data for chemotherapy response project

  In this study, a total of 300 patients with MIBC receiving chemotherapy were included; 62 received NAC before cystectomy and 245 received first-line chemotherapy upon detection of locally-advanced (T4b) or metastatic disease. Treatment response, defined as pathological downstaging (< pTa,CIS,N0) after NAC or complete or partial response after first-line treatment (RECIST criteria). DNA methylation analysis was performed using DNA from 72 patients. We used 500 ng genomic DNA for bisulfite conversion followed by whole-genome amplification prior to hybridization to EPIC BeadChip (Illumina, San Diego, CA) overnight as described by the manufacturer and then scanned with the Illumina iSCAN system. Data provided here consist of 144 idat files.

  Study EGAS00001004515

• A Joint Linkage/Association Strategy to Interrogate AMD Genetic Susceptibility

  The cohort consists of a collection of large multigenerational families where minimally 4 members have advanced age related macular degeneration (AMD). Retinal photographs were used to determine AMD phenotype and genomic DNA extracted from whole blood was used for sequencing. Gender, age at phenotyping, smoking status, self-declared race and ethnicity, and pedigree relationships were collected. Analyses conducted were designed to elucidate the role of known AMD variants and polymorphisms in heritability within the familial cohort and to discover rare variants that may have large genetic effect on AMD in one or more families.

  Study phs001379

• SCI-MAP: Single Cell Microgel embedded iPS-cells to map molecular variability of cell differentiation using a systems biology approach.

  In the SCI-MAP project we will map cell states encountered across a previously established 49 day in vitro chondrogenic differentiation protocol. We do this to optimise the differentiation process for therapeutic and in vitro modelling ends. We collect epigenetic open chromatin and phenotypic transcriptome data to determine cell states and so performed single nucleus sequencing in two modalities: RNA- and ATAC-sequencing. Data was collected in a time series experiment at 7 points: Days 0, 3, 6, 8, 14, 21, and 49, starting with the first pilot data from day 21 (D21).

  Study EGAS50000001041

• Aberrant expression of SLAMF6 constitutes a targetable immune escape mechanism in acute myeloid leukemia

  In this study, we demonstrate that aberrant expression of SLAMF6 on acute myeloid leukemia (AML) cells serves as a novel immune escape mechanism that can be inhibited by antibodies against the SLAMF6 dimerization site. This constitutes a novel mechanism of checkpoint inhibition, which paves the way for immunotherapy in AML and other SLAMF6-expressing cancers. This study utilizes single cell sequencing data from the AML cell line HNT-34 co-cultured with normal T cells, with and without antibody targeting SLAMF6, as well as single cell data of 38 primary AML samples.

  Study EGAS50000001085

• TMD_AMKL_targeted_follow_up

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

  Study EGAS00001000569

• TMD_AMKL_targeted_follow_up_part_2

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

  Study EGAS00001000732

• Molecular profiling of EBV associated diffuse large B-cell lymphoma

  We describe distinct molecular mechanisms leading to recurrent activation of JAK-STAT signaling, perturbation of epigenetic regulators as well as other direct targetable alterations such as PD-L1 amplification and overexpression contributing to immune evasion of lymphoma cells. Using the LymphGen 2.0 classifier, we combine data of recurrent mutations, somatic copy number alterations, and structural variants in an integrative analysis . For the first time, we reveal that less than 20% of primary EBV+ DLBCLs can be attributed to established molecular clusters of DLBCL NOS emphasizing the unique molecular character of this disease.

  Study EGAS00001006400

• Whole blood RNA sequencing of individuals from Nepal

  This study utilized blood samples collected in Lalitpur, Nepal as part of the Strategic Typhoid Alliance across Africa and Asia (STRATAA) study. The dataset comprises whole blood RNAseq of 376 febrile individuals from Nepal. Blood was collected in PAXgene tubes and sent to Monash University (Melbourne, Australia) where RNA was extracted using the PAXgene Blood RNA kit before being sent to the Wellcome Sanger Institute (Hinxton, UK) for sequencing. Library prep used NEBNext Ultra II RNA custom kits on an Agilent Bravo WS automation platform with poly(A) pulldown. After PCR, plates were purified using Agencourt AMPure XP SPRI beads and libraries were quantified using Biotium Accuclear Ultra high sensitivity dsDNA Quantitative kits. Pooled libraries were normalised to 2.8 nM. Samples were globin depleted using KAPA RNA HyperPrep with RiboErase. Libraries were then subjected to 2x100bp paired-end sequencing on Illumina NovaSeq. Each library was sequenced to an average of 80 million reads. The STRATAA study was approved by the Nepal Health Research Council (NHRC, ref 283 306/2015) and OxTREC (Oxford Tropical Research Ethics Committee, ref 39-15). All participants provided informed consent for human genetic tests.

  Dataset EGAD00001011131

• Single-nuclei histone modification profiling of the adult human central nervous system unveils epigenetic memory of developmental programs

  Here, we profile the adult human CNS from distinct regions, sex and ages, for chromatin accessibility at the single-nuclei level. Tissue was collected from 20 different donors (10 male, 10 female) within the ages of 34 to 74 years old. Each donor donated fresh frozen white matter from the following three tissue regions: primary motor cortex (Brodmann area 4, BA4), arbor vitae cerebelli (CB) and fasciculi cuneatus and gracilis from and cervical spinal cord (CSC). Tissue was processed semi-randomly, ensuring that each batch of experiments had a representation of both sexes and all three tissue regions. Completed libraries were again randomly multiplexed during sequencing to minimize batch effects.

  Study EGAS50000000283

• Multiple Myeloma treated with anti-BCMA T-cell-redirecting therapy (1st Batch)

  Bone marrow samples were collected from patients treated with either anti-BCMA CART and/or anti-BCMA TCE. All samples were sorted using the StemCell EasySep Human CD138 positive selection kit II (StemCell, Cambridge, MA). The positive CD138+ were submitted for WGS, using peripheral blood mononuclear cells as normal matched. WGS was carried out by the Molecular Genomics Core Facility at Moffitt Cancer Center contingent on the availability of high-quality pre-treatment samples. Germline DNA was obtained from peripheral blood mononuclear cells, while tumor DNA was extracted from CD138-enriched bone marrow aspirate specimens using magnetic bead-based selection. Genomic DNA was isolated using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen). For library preparation, 100 ng of genomic DNA was fragmented using the Covaris ML230 focused ultrasonicator (Covaris, Inc.), followed by library construction with the TruSeq DNA Nano Library Prep Kit (Illumina) in accordance with manufacturer instructions. Library quality and fragment size distribution were assessed via Agilent TapeStation, and quantification was performed using the Kapa Library Quantification Kit (Roche). Sequencing was conducted on the Illumina NovaSeq 6000 system using S4-300 reagent kits with a 2×150 bp paired-end configuration. Tumor samples were sequenced to a median coverage of 60×, and matched germline controls to 30×. Reference Genome: GRCh38.

  Dataset EGAD50000002632

• Neoadjuvant chemotherapy alters the genomic landscape and immune microenvironment of breast cancers

  To characterize the effects of neoadjuvant chemotherapy (NAC) on the genome, transcriptome and tumor infiltrating leukocytes (TILs), we have conducted whole exome and whole transcriptome sequencing of a comprehensive, longitudinal breast cancer cohort consisting of 146 cases and 281 paired tumor samples. In total, 52 (38%) patients achieved pathologic complete response (pCR) while 85 patients (62%) had residual disease with standard chemotherapy regimen. Tumor biopsies were collected for each patient at three time points – pre-treatment, three weeks after the first cycle of anthracycline and cyclophosphamide (AC) and at the time of surgery after 3 more cycles of AC followed by 4 cycles of taxane or taxane plus Herceptin in case of HER2+ subtype.

  Study EGAS00001003354

• Human Brain Small Extracellular Vesicles Contain Selectively-Packaged, Full-Length mRNA

  sEVs were isolated from postmortem human brain tissue. RNA was extracted from the source brain tissue and the sEVs and prepared for RNA sequencing. cDNA was sequenced on the Illumina HiSeq using a 2x150 paired-end read configuration.

  Dataset EGAD50000000042

• Panel based plasma sequencing data for patients with NSCLC in TRACERx cohort

  Ultrasensitive circulating tumour DNA (ctDNA) detection can stratify clinical risk in early-stage non-small cell lung cancer (NSCLC). Here, we applied a whole-genome, tumour-informed approach to study ctDNA in more than 400 NSCLC of the TRACERx project. This study captures the plasma sequencing data from the project.

  Dataset EGAD50000002534

• Whole Exome Sequencing of 15 Human Embryonic Stem Cell Lines

  This dataset includes deep coverage (>60x) whole exomes of 15 human embryonic stem cell lines. Genomic DNA was purified and fragmented using the Illumina Nextera system for library preparation and sequenced using 150bp paired-end reads. Sequencing reads were aligned to the hg19 reference genome using the BWA MEM alignment program.

  Dataset EGAD00001003446

• Prostate Cancer Whole Genome Validations

  We propose to definitively characterise the somatic genetics of Prostate cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. This study will aim to validate the findings of the whole genome study by re-sequencing regions of interest using a bespoke pulldown bait. See ICGC website for more information: http://icgc.org/icgc/cgp/70/508/71331

  Dataset EGAD00001000621

• Achilles tendinopathy exome data

  Exemplar asymptomatic controls (n=10, 6 males) and exemplar cases with chronic Achilles tendinopathy (n=10, 6 males), representing divergent extremes of the phenotype spectrum were selected for WES. Individual samples were sequenced at paired ends on the Illumina HiSeq 2000/2500 platform at 30X coverage using the Agilent V5+UTR (71Mbp) capture kit.

  Dataset EGAD00001004362

• Analysis of circulating miRNAs for the identification of new prognostic and predictive markers in gastro-entero-pancreatic neuroendocrine tumour (GEP-NET)

  NGS profiling of the entire miRNOme conducted on the plasma of 24 samples obtained from well-differentiated, advanced, metastatic and inoperable G1, G2 and G3 GEP-NET patients. Sequencing was performed on NexSeq platform

  Dataset EGAD00001010840

• Single-Cell Genome Sequencing of Gastrointestinal Carcinomas

  We experimentally derived copy number profiles and transcriptome profiles of gastrointestinal cancers using single cell sequencing. Using a microfluidic droplet partitioning system, we isolated individual cells of a suspension from a primary solid tumor into droplets. These droplets tag the resultant genomic or transcriptomic material with an identifying barcode that enables bioinformatic single cell tracking. From this joint analysis, we determined the overall level of genomic instability for gastrointestinal cancers as well as transcriptomic consequences from these events.

  Study phs001711

• C9ORF72 Hexanucleotide Repeat Sequence Genotyping Project

  This study reports long-range and high-resolution repeat sizing of the C9orf72 repeat region for 2095 samples from the National Institute of Neurological Disorders and Stroke (NINDS) repository's ALS collection. Genomic DNA samples were analyzed with a PCR assay (AmplideX® PCR/CE C9orf72 Kit) and resolved on capillary electrophoresis. Expanded samples were also analyzed using a gene-specific assay and resolved by capillary electrophoresis (up to 145 GGGGCC hexanucleotide repeats) and AGE agarose gel electrophoresis (up to 950 hexanucleotide repeats, respectively).

  Study phs001718

• Transcriptomic and epigenetic characterization of ex vivo expanded T cells

  In this study, we investigated the transcriptomic and epigenetic landscape of primary human T cells stimulated ex vivo under various conditions. Naïve CD8+ T cells isolated from healthy donor PBMCs were subjected to ex vivo stimulation and used for bulk RNA-seq and ATAC-seq library preparation. These datasets were generated to characterize global changes in gene expression and chromatin accessibility associated with ex vivo T-cell stimulation. The data may support comparative analyses of molecular states arising under distinct culture conditions.

  Study EGAS50000001718

• Whole Exome Sequencing of Waldenström Macroglobulinemia (WM) Precursor Conditions

  In this study we aimed to comprehensively characterize the genomic landscape of WM precursor conditions and identify potential biomarkers of progression to symptomatic WM by means of Whole Exome Sequencing (WES) of CD19-selected samples from 139 patients, primarily with IgM-MGUS and asymptomatic WM. Overall, our study shows that genomic profiling of patients’ tumor at the time of aWM diagnosis might represent an improved strategy for identifying patients at high risk to progression who could benefit from earlier intervention.

  Study EGAS50000001249

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by shallow whole genome sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by downstream shallow whole genome sequencing (WGS) for copy number landscape profiling for 10 samples. Seven out of 10 samples (even some with low tumour content or of old age) produced good quality genomic data, detecting sCNA in all carcinoma population samples but not in the stromal populations.

  Dataset EGAD50000001895

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by shallow whole genome sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by downstream shallow whole genome sequencing (WGS) for copy number landscape profiling for 10 samples. Seven out of 10 samples (even some with low tumour content or of old age) produced good quality genomic data, detecting sCNA in all carcinoma population samples but not in the stromal populations.

  Dataset EGAD50000001894

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by shallow whole genome sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by downstream shallow whole genome sequencing (WGS) for copy number landscape profiling for 10 samples. Seven out of 10 samples (even some with low tumour content or of old age) produced good quality genomic data, detecting sCNA in all carcinoma population samples but not in the stromal populations.

  Dataset EGAD50000001893

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by shallow whole genome sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by downstream shallow whole genome sequencing (WGS) for copy number landscape profiling for 10 samples. Seven out of 10 samples (even some with low tumour content or of old age) produced good quality genomic data, detecting sCNA in all carcinoma population samples but not in the stromal populations.

  Dataset EGAD50000001892

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by shallow whole genome sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by downstream shallow whole genome sequencing (WGS) for copy number landscape profiling for 10 samples. Seven out of 10 samples (even some with low tumour content or of old age) produced good quality genomic data, detecting sCNA in all carcinoma population samples but not in the stromal populations.

  Dataset EGAD50000001891

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by shallow whole genome sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by downstream shallow whole genome sequencing (WGS) for copy number landscape profiling for 10 samples. Seven out of 10 samples (even some with low tumour content or of old age) produced good quality genomic data, detecting sCNA in all carcinoma population samples but not in the stromal populations.

  Dataset EGAD50000001889

• DAC Study assessing the efficacy and safety of durvalumab plus olaparib plus fulvestrant in selected metastatic or locally advanced ER-positive, HER2-negative breast cancer patients.

  DAC for Study assessing the efficacy and safety of durvalumab plus olaparib plus fulvestrant in selected metastatic or locally advanced ER-positive, HER2-negative breast cancer patients.

  Dac EGAC50000000694

• Germline Pan-cancer Lynch syndrome sequencing dataset from India

  The dataset consists of germline whole exome sequencing data generated on the Illumina NovaSeq X Plus platform for 48 patients with MSI-high/ MMRd gastro-intestinal and genito-urinary cancers, in order to detect Lynch syndrome.

  Dataset EGAD50000002088

• RRBS - MBD4-deficient AML

  Reduced Representation Bisulfite Sequencing for WEHI-AML-1 and WEHI-AML-2. RRBS libraries were made with the NuGEN Ovation RRBS Methyl-Seq System. Bisulfite conversion was performed with the Qiagen Epitect kit. Sequencing was performed on an Illumina HiSeq2500.

  Dataset EGAD00001003567

• Whole Genome (WG) sequencing data files for H_NO-JB001

  DNA was derived from the primary tumour, lung metastasis, and peri-aortic lymph node metastasis. DNA from the spleen was used as a normal control.WG sequencing produced ~30-fold (primary tumour, spleen normal)-50-fold (lung metastasis) coverage

  Dataset EGAD00001001253

• DESIGN-VUMC RNA-seq

  RNA-Seq data of 55 HPV-negative HNSCC specimens from patients treated at the VU medical Centre, Amsterdam, The Netherlands. HNSCC biopsy samples obtained prior to treatment (chemo-radiotherapy) were used for polyA mRNA sequencing.

  Dataset EGAD00001005716

• DESIGN-MAASTRO RNA-seq

  RNA-Seq data of 17 HPV-negative HNSCC specimens from patients treated at the MAASTRO clinic, Maastricht, The Netherlands. HNSCC biopsy samples obtained prior to treatment (chemo-radiotherapy) were used for polyA mRNA sequencing.

  Dataset EGAD00001005717

• sWGS of CRC patients

  Paired end (47/98) and single end (51/98) shallow whole genome sequencing (sWGS) data for the identification of somatic copy number alterations (SCNA) and the estimation of tumor fractions in plasma DNA of colorectal cancer (CRC) patients.

  Dataset EGAD00001006101

• PFA ependymoma study -RNA-seq data

  RNA-seq fastq files for the 16 samples used in Michealraj et al. Cell 2020. The samples include PFA and ST ependymoma tissues, normal pediatric brain as control and PFA ependymoma lines.

  Dataset EGAD00001006046

• sWGS of CTCL patients

  Paired end shallow whole genome sequencing (sWGS) data for the identification of somatic copy number alterations (SCNA) and the estimation of tumor fraction and ploidy sorted malignant CD3+/Vb+ T-cells and corresponding CD19+ non-malignant B-cells

  Dataset EGAD00001006901

• Whole exome sequencing

  reference whole exome sequence serving as a reference of individuals. Includes the fastq files of each individual (labelled S1-S5) and the called variants in vcf format merge for all individuals.

  Dataset EGAD00001008728

• The University of Hong Kong Gastric Cancer RHOA Study RNASeq Data

  RNAseq data generated from paired tumor frozen tissues in which the tumor organoids were established for cell-cell or cell-matrix adhesion dependency assay.

  Dataset EGAD00001008830

• IVF Retrospective Study

  This dataset contains BAM files for 9 samples from individuals involved in a retrospective IVF trial. The BAM files were derived from whole genome sequencing. The 9 individuals consist of three trios containing mother, father and child samples.

  Dataset EGAD00001008147

• Targeted sequencing of brain AVMs

  Targeted sequencing data to look for the involvement of genes in the RAS-MAPK pathway, angiogenesis and brain vascular disorders among others, in brain AVMs

  Dataset EGAD00001009695

• MASS_Pilot: Muscle and Ageing Science Study - Collaboration with Wellcome Sanger Institute to characterise skeletal muscle ageing using Human Cell Atlas approaches (2025-07-31)

  Transcriptomic analysis of skeletal muscle, to understand the mechanisms of muscle ageing. . This dataset contains all the data available for this study on 2025-07-31.

  Dataset EGAD00001015670

• Whole genome DNA sequencing for two long-lived humans.

  Two long-lived human samples were sequenced to a mean 20x coverage genome wide. Sequencing was done using the Illumina hi-seq platform, alignment to GRCh37/hg19 reference genome was done using the BWA alignment tool.

  Study EGAS00001000877

• Dataset_for_linked_WES_and_WGS_data_from_EGAS00001004813 which belong also to EGAS00001005537 for germline controls of rare cancers

  WES/WGS sequencing data of 37 germline runs, which were uploaded to umbrella studies. The sequencing was always paired. The WGS sequencing was on HiSeq X Ten using the Illumina TruSeq DNA Nano Kit. The WES Sequencing was on HiSeq4000 with Agilent Sureselect V5+UTR.

  Dataset EGAD00001010046

• DAC for the Study EGAS00001006374: Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies. snRNAseq of 79 (61 CM patients + 18 controls).

  Dac EGAC00001002804

• BREAKFAST trial DAC

  Data Access Committee for BREAKFAST trial datasets, IFOM-ETS The AIRC Institute of Molecular Oncology and INT Istituto nazionale Tumori Milano, Italy.

  Dac EGAC50000000401

• SpainUDP Data Access Committee

  Data access committee handling data access requests for RNAseq data related to the Spanish Undiagnosed Rare Diseases Program SpainUDP cohort.

  Dac EGAC50000000932

• WTCCC2 Pre-eclampsia

  Genotype data from the Affymetrix 6.0 platform for 4,375 Colombian pre-eclampsia cases and controls

  Dataset EGAD00010001647

• TSACP TruSeq Amplicon Panel dataset

  TSACP TruSeq Amplicon Panel dataset for the TraIT cell line use case

  Dataset EGAD00001002109

• GATCI whole genome sequencing fastqs

  Raw whole genome sequencing data (fastq) for the GATCI project

  Dataset EGAD00001005926

• The Genetic Landscape of BCL2 Break Negative Follicular Lymphoma

  Background: 15% of high and 50% of low stage FL lack the t(14;18). Nevertheless, most of these cases express BCL2 by so far unknown mechanisms. Principals/Methodology: To find molecular mechanisms, triggering FL-pathogenesis in t(14;18)-negative FL, the exonic SNV-profiles of 33 FL with and 16 FL without t(14;18) were assessed by whole exome-sequencing and external SNV-data integration. The SNV-profile of the whole exome-sequenced FL was correlated with copy number, LOH and gene-expression data. Finally, the N-glycosylation status was assessed (LympTrack assay) in a separate validation cohort. Results: SNVs in FL with and without t(14;18) affected different genes, but accumulated in similar pathways, e.g. apoptosis, epigenetic processes and cell cycle/proliferation. Mutations in genes associated with immune-response were more prominently and those associated with NFkB and N-glycosylation selectively enriched in t(14;18)-negative FL. ~50% of mutated genes showed BCL2-asociation at high confidence in FL with and without t(14;18). Moreover, among the genes mutated in t(14;18)-negative FL 555 (~1/3) were affected by copy number alterations and/or copy-neutral LOH, 125 were differently expressed between FL with and without t(14;18) (p<0.01) and 62 were differentially expressed and affected by copy number alterations and/or copy-neutral LOH. N-glycosylation was strongly reduced in t(14;18)-negative FL as compared to results reported for historical FL cohorts. Conclusion: These results suggest a stronger crosstalk with the microenvironment that may compensate for the lack of N-glycosylation and a diverse portfolio of SNVs that may contribute to the upregulation of BCL2 and FL pathogenesis in t(14;18)-negative FL.

  Study EGAS00001002164

• Diet driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome

  This study profiled baseline gut (fecal) microbiota signatures and dietary patterns of 103 trial patients from Australia and the Netherlands treated with neoadjuvant ICIs for high risk resectable metastatic melanoma and performed an integrated analysis with data from 115 patients with melanoma treated with ICIs in the United States. We observed geographically distinct microbial signatures of response and immune-related adverse events. Overall, response rates were higher in Ruminococcaceae-dominated microbiomes than in Bacteroidaceae-dominated microbiomes. Poor response was associated with lower fiber and omega 3 fatty acid consumption and elevated levels of C-reactive protein in the peripheral circulation at baseline.

  Study EGAS00001006982

• Genome-wide Association Study and Meta-Analysis of Ewing Sarcoma

  We combined a set of 122 French Ewing sarcoma (EWS) cases from the Institut Curie, 19 EWS cases from the National Cancer Institute (NCI) Center for Cancer Research (CCR), and 29 EWS cases from the NCI Bone Disease and Injury Study. All EWS cases were confirmed by medical record review and the presence of a specific EWSR1-ETS translocation were noted when data was available. Each participant provided informed consent and each participating study was approved by the Institutional Review Boards of their study center. DNA was extracted using standard methods from blood, saliva (Oragene), or buccal cells. All de novo genotyping of EWS cases was performed at the NCI CGR on the Illumina OmniExpress-24 v1.1 array. Genotyping was performed according to manufacturer's guidelines using the Infinium HD Assay automated protocol.

  Study phs001549

• Screening for tryptophan conversion in human stool samples

  The goal of this study was to compare the tryptophan metabolism of different human fecal microbiota. To this end we enriched human stool samples in culture medium and measured growth and metabolite concentrations after 48h of culture. We quantified the consumption of tryptophan and the production of typical tryptophan derivaties.

  Study EGAS50000000548

• Identification of four new susceptibility loci for testicular germ cell tumour, including variants near GAB2, GSPT1 and ZFPM1

  Genome wide association studies (GWAS) have identified multiple risk loci for testicular germ cell tumour (TGCT), revealing a polygenic model of disease susceptibility strongly influenced by common variation. To identify further SNPs associated with TGCT we conducted a multistage GWAS with a combined dataset of >25,000 individuals (6,059 cases and 19,094 controls). We identified new risk loci for TGCT at 3q23 (rs11705932, TFDP2, P = 1.5 x 10-9), 11q14.1 (rs7107174, GAB2, P = 9.7 x 10-11), 16p13.13 (rs4561483, GSPT1, P = 1.6 x 10-8) and 16q24.2 (rs55637647, ZFPM1, P = 3.4 x 10-9). We additionally present detailed functional analysis of these loci, identifying a statistically significant relationship between rs4561483 risk genotype and increased GSPT1 expression in TGCT patient samples. These findings provide additional support for a polygenic model of TGCT risk and further insight into the biological basis of disease development.

  Study EGAS00001001302

• Multi-layered population structure in Island Southeast Asians

  The history of human settlement in Southeast Asia has been complex and involved several distinct dispersal events. Here we report the analyses of 1825 individuals from Southeast Asia including new genome-wide genotype data for 146 individuals from three Mainland Southeast Asian (Burmese, Malay and Vietnamese) and four Island Southeast Asian (Dusun, Filipino, Kankanaey and Murut) populations. While confirming the presence of previously recognized major ancestry components in the Southeast Asian population structure, we highlight the Kankanaey Igorots from the highlands of the Philippine Mountain Province as likely the closest living representatives of the source population that may have given rise to the Austronesianexpansion. This conclusion rests on independent evidence from various analyses of autosomal data and uniparental markers. Given the extensive presence of trade goods, cultural and linguistic evidence of Indian influence in Southeast Asia starting from 2.5kya we also detect traces of a South Asian signature in different populations in the region dating to the last couple of thousand years.

  Study EGAS00001001738

• Fecal Microbiota Transplantation for refractory immune checkpoint inhibitor-associated colitis

  We report the first case series of ICI associated colitis successfully treated with fecal microbiota transplantation (FMT), with reconstitution of the gut microbiome and a relative increase in the proportion of regulatory T cells (Tregs) within the colonic mucosa. These preliminary data provide evidence that modulation of the gut microbiome may abrogate ICI-associated colitis.

  Study EGAS00001003217

• RNA sequencing of peripheral blood samples from 17 Greenlanders

  The data contain whole deep RNA sequencing of leukocytes from 17 Greenlanders. RNA was purified from peripheral blood with the PAXGene Blood miRNA Kit (Qiagen). The RNA sequencing library was prepared following the instructions of the TruSeq RNA Sample Prep Kit v2 (Illumina). For mRNA isolation and fragmentation 200 ng of total RNA was purified by oligo-dT beads. The qualified libraries were amplified on cBot to generate the cluster on the flowcell (TruSeq PE Cluster Kit V3–cBot–HS, Illumina). The amplified flow cell was sequenced paired-end on the HiSeq 4000 System (TruSeq SBS KIT-HS V3, Illumina).

  Dataset EGAD00001003814

• Data Access Committee for the Nichols Group at LHSC

  Dac EGAC00001002164

• MELIS-UPF - Endocrine Regulatory Genomics Lab

  DAC for accessing human data produced by the Endocrine Regulatory Genomics Lab at MELIS-UPF (Barcelona, Spain).

  Dac EGAC50000000224

• ITER-FIISC Data Access Committee (Sepsis)

  DAC for Whole-exome variant calling of individuals from the study of sepsis and acute distress respiratory syndrome in Spain.

  Dac EGAC50000000641

• CLUSTER DAC

  The DAC for CLUSTER Consortium datasets relating to JIA and healthy controls RNAseq data and their associated clinical data.

  Dac EGAC50000000426

• Single cell sequencing in D425

  Single cell sequencing aligned BAM files for the D425 cell line

  Dataset EGAD50000002304

• Oncoscan CNV FFPE SNP-arrays (Affymetrix, Thermo Fisher Scientific) for the study "Molecular profiling of EBV associated diffuse large B-cell lymphoma"

  Dataset EGAD00010002363

• ITER-FIISC Data Access Committee (WES-CIRdb)

  DAC for the data deposit of "Expanding CIRdb, a comprehensive catalog of whole-exome sequencing data of Canary Islanders".

  Dac EGAC50000000966

• SSBP1 sample

  The dataset includes exome sequencing results for a patient with SSBP1 mutations that cause a complex optic atrophy spectrum disorder

  Dataset EGAD00001005475

• Single Chromatin Fiber Profiling in the Human Brain

  We developed a human postmortem brain-applicable ‘Fiber-seq' protocol for genome-scale, PCR-free single molecule sequencing of on average 8-10kb long chromatin fibers, to map nucleosome positioning and nucleosome-depleted regions which include, for example, active promoters and enhancers. We generated two Fiber-seq reference sets, one from sorted non-neuronal NeuN- prefrontal cortex (PFC) nuclei from a 32 year old female donor, with total of 11,143,795 reads/fibers, and median of 30-fold genomic coverage. The other reference set was generated on sorted prefrontal NeuN+ neurons, from two 24 year old brain donors (1 female/1 male), with a combined total read/fiber count of 4,749,556 and median of 20-fold genomic coverage. Each of the peaks in the Fiber-seq libraries seq signal correlated with the ATAC peak levels in the neuronal and non-neuronal ATAC-seq libraries, respectively (promoters, clusters 1, 3; NeuN+, r = 0.574; NeuN-, r=0.683, PHowever, Fiber-seq detected 19,978 highly significant peaks which, while showing some non-significant/near-background ATAC-Seq alignments, lacked a corresponding site-specific enrichment in conventional short-read ATAC- and ChIP-seq datasets. However, 60% of these peaks were in repetitive DNA elements. Therefore, long read single chromatin fiber sequencing, which exceed the base pair length of conventional short-read libraries by two orders of magnitude, could capture many actively regulated repeat elements at the site of specific gene loci, that otherwise would remain unmappable by conventional ATAC-, and histone- ChiP-seq.

  Study phs003771

• Determinants of Venetoclax Resistance

  The study aimed to identify genetic determinants of resistance to Venetoclax, a recently approved BCL-2 inhibitor for patients with chronic lymphocytic leukemia (CLL). Whole exome sequencing of tumor samples from 6 CLL patients relapsing on Venetoclax revealed clonal evolution when comparing pre- and post-Venetoclax samples. Genetic screens for genes involved in sensitivity to Venetoclax and investigations of resistant cell lines (including OCI-Ly1) revealed MCL-1 and regulators of cellular energy metabolism (AMPK pathway) to drive resistance to Venetoclax. Further explorations of patient samples confirmed MCL-1 expression and AMPK activation to be increased at relapse on Venetoclax.

  Study phs001875

• human CMV-specific CD8+ T cells

  In this study we established a comprehensive workflow to collect multi-omics single-cell data using a commercially available micro-well based platform. This included whole transcriptome, cell surface markers (targeted sequencing-based cell surface proteomics), T cell specificities, adaptive immune receptor repertoire (AIRR) profiles and sample multiplexing. With this technique we identified novel paired T cell receptor sequences for three prominent human CMV epitopes. In addition, we review the ability of dCODE dextramers to detect antigenspecific T cells at low frequencies by estimating sensitivities and specificities when used as reagents for single-cell multi-omics.

  Study EGAS50000000633

• Unraveling metastatic progression of breast cancer

  To reconstruct the trajectories of BC progression, we performed exome sequencing (Illumina HiSeq2000, Truseq DNA sample preparation kit v2 and Exome Enrichment Kit v2; alignement done with BWA, substitutions and indels called with GATK and DINDEL respectively) coupled to validation by Sequenom and deep re-sequencing (ongoing), as well as copy number (CN) analyses (Oncoscan, Affymetrix) on DNA from matched primary (n=1-6/pt), axillary lymph node (ALN, n=1-6 for 4 pts), local recurrence (for 1 pt) and distant metastatic (n=1-5/pt) FFPE samples obtained from an autopsy series of 10 BC pts.

  Study EGAS00001000760

• NRG1 Fusions in KRAS Wild-type Pancreatic Cancer (H021)

  We used whole-genome and transcriptome sequencing to identify clinically actionable gene fusions in young adults with KRAS wild-type (KRASwt) pancreatic ductal adenocarcinoma (PDAC). These alterations included recurrent NRG1 rearrangements predicted to drive PDAC development through aberrant ERBB receptor-mediated signaling, and pharmacologic ERBB inhibition resulted in clinical improvement and remission of liver metastases in two patients with NRG1-rearranged tumors that had proved resistant to standard treatment. Our findings demonstrate that systematic screening of KRASwt tumors for oncogenic fusion genes will substantially improve the therapeutic prospects for a sizeable fraction of PDAC patients.

  Study EGAS00001002759

• Total NF1 sequence in the patients with neurofaibromatosis type1

  We analyzed whole NF1 gene region at DNA (including whole exon and intron sequences) and RNA (full length cDNA of leukocyte) level for 20 patients with neurofibromatosis type 1.

  Study JGAS000288

• Exome sequencing data, phenotypic information, and somatic mutation analysis results for 44 diagnosis-relapse DLBCL pairs

  This dataset contains exome sequencing data, phenotypic information, and somatic mutation analysis results for 44 diagnosis-relapse DLBCL pairs. Exon sequencing data were captured using the Agilent HaloPlex exon kit. bam files were obtained from illumina sequencing followed by BWA alignment.

  Dataset EGAD50000000049

• Common clonal origin of chronic myelomonocytic leukemia and B cell acute lymphoblastic leukemia in a patient with a germline CHEK2 variant

  Whole exome sequencing data obtained from sorted leukemic clones and a buccal swab as germline reference. The dataset contains raw sequencing data (paired-end reads) for 3 samples (2 leukemic, 1 buccal swab), for a total of 6 fastq files.

  Dataset EGAD00001007644

• scATAC sequence runs of 29 samples of RRMM (multiple myeloma) tumors

  scATAC sequencing was performed of 29 samples of RRMM tumors using 10xGenomics for the preparation and NovaSeq6000 for sequencing.

  Dataset EGAD00001009683

• CIDR Estrogen Receptor Negative Breast Cancer in African American Women: DNA Methylation, Reproductive Events, and Mammary Epithelial Cell Populations

  We conducted methylation profiling of breast tumor DNA from Formalin-Fixed Paraffin-Embedded (FFPE) samples for 1,550 cases from a cohort of Black women from the Black Women’s Health Study (BWHS), the Women’s Circle of Health Study (WCHS), and from the Pathways Study using the Illumina MethylationEPIC array. We will examine differentially methylated loci (DML) between ER+ and ER- tumors, and by age at onset of breast cancer. Combining these data with previously analyzed samples (n=385), we will consider associations between reproductive risk factors and top DML by age at diagnosis and ER status, examining the complex relationships between methylation, tumor and patient characteristics, and reproductive risk factors using structural equation modeling.

  Study phs002688