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• Single cell multi-omic data of glioblastoma evolution under therapy

  We report a single-cell multi-omics atlas of GBM longitudinal specimens that represents decades of biobanking. We identify novel cell-intrinsic and cell-extrinsic targets for therapy development which we validate in situ and in low-passage patient-derived cell lines. We identify novel genetic correlates of the mesenchymal cellular phenotype. These studies integrate disparate findings in the literature around hypermutation status and immunogenicity as well as the source of the mesenchymal shift at recurrence.

  Study EGAS00001004909

• Nasal epithelial cells of PCD and non-PCD patients grown at air-liquid interface for RNAseq analysis

  Nasal epithelial cells of PCD and non-PCD patients grown at air-liquid interface for RNAseq analysis. A total of 10 non-PCD patients (ALI day 14), 9 non-PCD patients (ALI day 21), 8 non-PCD patients (ALI day 28), 4 PCD patients (ALI day 14, day 21 and day 28), and 23 PCD patients (ALI day 21). Non-PCD patients and the 4 PCD patients on the three ALI days were sequenced at a depth of 100M reads, the remaining 23 PCD patients were sequenced at a depth of 70M. Overall sequencing design was rRNA depletion and 150bp paired-end.

  Dataset EGAD00001009498

• Batch1_Genotypes_Raw

  Genotypes generated for Puno cohort Batch 1. Case (PRE) and control (PUN) families were recruited in hospital, and additional unrelated controls were recruited in university (UNA). Raw genotypes no QC.

  Dataset EGAD00010002126

• PromethION (and Illumina) WGS and MinION transcriptome for a patient with diffuse large B-cell lymphoma.

  Dataset EGAD00001006204

• Rio Dataset

  Homologous recombination DNA repair deficiency and PARP inhibition activity in primary triple negative breast cancer. RNA-Seq data for paired baseline and end of treatment samples

  Dataset EGAD00001006120

• Raw sequencing data for PicoCNV and MutLX2 development papers

  Bulk tumour, germline and DigiPico WGS BAM files from patients 11611, 11615, 11619

  Dataset EGAD00001010302

• NHLBI TOPMed - NHGRI CCDG: Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

  This study contains whole genome sequence data. A case-control sample of individuals from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), a multicenter prospective cohort study of 16,415 persons of Cuban, Dominican, Mexican, Puerto Rican, Central American, and South American background (phs000810), was selected for whole genome sequencing, including participants with a history of physician-diagnosed asthma and asthma-free participants.

  Study phs001395

• A single-cell transcriptional gradient in human cutaneous memory T cells restricts Th17/Tc17 identity

  We identified a gradated transcriptional program of coordinately regulated inflammation-suppressive genes in psoriatic resident memory T cells. This dataset includes bulk RNA-seq for CRISPR-based deactivation of two core components of this inflammation-suppressive program, ZFP36L2 and ZFP36, in human PBMCs. It also includes scRNA-seq of cutaneous immune cells from psoriasis patients before and during therapeutic IL-23 blockade.

  Study EGAS00001006716

• Follicular lymphoma shallow whole genome sequencing and targeted sequencing of lymphoma panel

  Stage I and stage III/IV Follicular lymphoma samples, shallow whole genome sequencing for copy number analysis and targeted capture sequencing for mutation and translocation analysis.

  Dataset EGAD00001008385

• MicroRNA Biomarkers for Prediction of Preeclampsia

  Maternal serum was collected between 17-28 weeks gestation. Samples were obtained from the high-risk Placental Study at the University of California, San Diego (n=48) and from the average-risk Proteomic Assessment of Preterm Risk (PAPR) Study at Sera Prognostics (n=164). RNA was extracted from 500 microliter of maternal serum using the miRNeasy Micro kit (Qiagen). NEBNext Small RNAseq Library Preparation Kit was used for library construction.

  Study phs002016

• Machine Learning Guided Signal Enrichment for Plasma Tumor-burden Monitoring Dataset

  Includes 4 Datasets: 1. 35 Control Plasma WGS samples sequenced on NovaSeq V1.0 Chemistry at the New York Genome Center. Denoted by CTRL-2XX naming scheme. 2. Plasma WGS from 17 patients with Small Cell Lung Cancer. Samples extracted at either Pretreatment or Postoperative at weeks 2 or 3. Denoted by SCLC-XX naming scheme. 3. Plasma WGS from a synthetic mixing study of a high-burden melanoma plasma sample with plasma bag, at estimated tumor concentrations of 10e-3, 10e-4, 10e-5, and 10e-6 for 2 replicates. Denoted by SM-repX naming scheme. 4. Assorted Plasma, Tumor, and Normal WGS from patients with NSCLC expressing high-burden for use in model training. Denoted by NSCLC-2XX naming scheme.

  Dataset EGAD00001011352

• 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

• ATACseq - Notch Signaling Maintains a Progenitor-Like Subclass of Hepatocellular Carcinoma

  To assess how Notch inhibition impacts chromatin accessibility and how chromatin changes relate to HNF4A and CEBPA activities, we performed Assay-for-Transposase-Accessible-Chromatin (ATAC) sequencing of LIV78 tumors, 72 hours after treatment with NOTCH2 blocking or control antibodies. Our TF activity and chromatin analyses thus lead to a model in which Notch inhibition leads to increased expression of CEBPA, thus enabling CEBPA to partner with HNF4A to jointly drive transcriptional programs and the underlying chromatin rearrangements that promote differentiation of progenitor-like tumor cells to a mature hepatocyte fate incompatible with tumor growth and maintenance.

  Study EGAS50000000516

• Processed Chromium Single Cell GEX, CSP and VDJ data from intestinal plasma cells of celiac disease patients

  The dataset contains processed sequencing data from Chromium Single Cell 5’ gene expression, human B cell VDJ and feature barcode (CSP) sequencing from transglutaminase 2-specific and other small intestinal and bone marrow plasma cells isolated from four celiac disease patients. The raw sequencing data has been processed with Cell Ranger v.6.0.2 with the multi and aggr functions using the pre-built Cell Ranger references GRCh38 version 2020-A for gene expression and GRCh38-alts-ensembl-5.0.0 for V(D)J analysis. The dataset consists of a gene expression and antibody capture expression matrix (cell barcodes and feature names in tsv.gz file, expression matrix in mtx.gz file) and VDJ sequences in AIRR format (csv file). A metadata file (csv file) details cells passing our custom quality control based on number of detected genes, UMIs, mitochondrial genes, immunoglobulin genes and a productively rearranged immunoglobulin heavy chain.

  Dataset EGAD50000002778

• Data Access Committee for data from EGAS00001002864: Genome analysis of oesophageal cancer and Barretts oesophagus

  Dac EGAC00001000863

• DAC for "Establishment and characterization of circulating tumor cells-derived organoids from metastatic breast cancer patients."

  Dac EGAC00001003514

• Oncogenic and immunological targets for matched therapy of pediatric blood cancer patients: Dutch iTHER study experience

  Study EGAS00001008218

• Molecular Classification of Lymph Node Metastases Subtypes Predict for Survival in Head and Neck Cancer

  Study EGAS00001003233

• The genomic diversity of Taiwanese Austronesian groups: implications for the ‘Into and Out of Taiwan’ models

  Study EGAS00001006911

• CLUC complete genomics dataset

  Complete genomics data for VCaP and PC346c.

  Dataset EGAD00001002069

• Whole Genome Association Study of Systemic Lupus Erythematosus

  The goal of this collaborative study was to identify new genetic risk factors for Systemic Lupus Erythematosus (SLE). To do this we conducted a genome-wide scan by combining the resources and expertise from a number of SLE researchers to establish a large sample set comprising 1311 SLE cases and 3340 controls. The SLE case samples were genotyped from the following collections: 338 subjects from the Autoimmune Biomarkers Collaborative Network (ABCoN), an NIH/NIAMS funded repository, 141 subjects from the Multiple Autoimmune Disease Genetics Consortium (MADGC), 613 subjects from the University of California San Francisco (UCSF) Lupus Genetics, and 335 subjects from the University of Pittsburgh Medical Center (UPMC), plus 8 samples collected at The Feinstein Institute for Medical Research. A total of 3583 control samples were examined in the association analyses. As part of this project, 1861 control samples were selected and then genotyped from the New York Cancer Project (NYCP), based on self-described ethnicity, gender and age. In addition, genotype data from 1722 control samples (all self-described North Americans of European descent) were obtained from the publicly available iControlDB database (http://www.illumina.com/pages.ilmn?ID=231).

  Study phs000122

• Methotrexate Clearance GWAS in Acute Lymphoblastic Leukemia (ALL) Patients

  We estimated the plasma clearance of methotrexate from 1279 acute lymphoblastic leukemia (ALL) patients treated on the Children Oncology Group 9904 and 9905 trials (http://clinicaltrials.gov/show/NCT00005585 and http://clinicaltrials.gov/show/NCT00005596). Patients received either a 24-hour infusion of a 1 g/m2 dose or 4-hour infusion of a 2 g/m2 dose). Methotrexate clearance was lower in older children (p=7 x 10-7), females (p=2.7 x 10-4), and patients who received a delayed intensification phase (p=0.0022). In a genome-wide analysis, methotrexate clearance was associated with polymorphisms in the SLCO1B1 gene (p=2.1 x 10-11), which encodes for an organic anion transporter. This replicates findings using different schedules of high-dose methotrexate in ALL patients treated on St. Jude protocols. A combined meta-analysis yields a p-value of 5.7 x 10-19 for the association of methotrexate clearance with SLCO1B1 SNP rs4149056 (Trevino et al, PMID 19901119 and Ramsey et al, PMID 23233662). This data set includes the dependent variable of methotrexate clearance and all of the SNP data available from arrays.

  Study phs000637

• Whole-Exome Sequencing Study of Diabetic Nephropathy

  To identify rare variants of diabetic kidney disease (DKD), we conducted a whole-exome sequencing (WES) study. This study employed an extreme case–control design, which included a selection of the 593 most rapidly progressing DKD cases from the Chronic Renal Insufficiency Cohort (CRIC) Study (phs000524). In this two-stage WES study of DKD, participants with DKD from the CRIC were compared with control groups of participants without DKD from another cohort in the first stage. Suggestive signals identified in the first stage were confirmed in the second stage analysis among a diverse population with existing whole-genome sequencing (WGS) data. Generalized linear mixed models, which accounted for genetic relatedness and adjusted for age, sex and ancestry, were used to test associations between single variants and DKD. Gene-based aggregate rare variant analyses were conducted using an optimized sequence kernel association test implemented within our mixed model framework. As a result, we identified four novel gene loci, DIS3L2, KRT6B, ERAP2 and NPEPPS, that achieved exome-wide significance and may play an important role in the DKD disease course. This large WES study provides novel insights into DKD's molecular mechanisms.

  Study phs003429

• Finding structural variation and functional consequences from the primary leukemia cells (CLL) at the single-cell level

  In this study, we aimed to identify somatic structural variation of chronic lymphocytic leukemia (CLL) at the single-cell level and investigate its direct consequence on the nucleosome occupancy using scNOVA approach. For this purpose, we performed strand-specific single-cell sequencing of primary leukemia samples from 63-year-old female patient.

  Study EGAS00001004925

• SCLC study George et al. - WGS data set

  Whole genome sequencing was performed with DNA extracted from fresh-frozen tumor and normal material. Short insert DNA libraries were prepared with the TruSeq DNA PCRfree sample preparation kit (Illumina) for paired-end sequencing at a minimum read length of 2x100bp. Human DNA libraries were sequenced to an average coverage of minimum 30x for both tumor and matched normal. Murine DNA libraries of tumor and matched normal were both sequenced to a coverage of 25x.

  Dataset EGAD00001001273

• Single cell sequencing of human normal luminal cells

  The dataset includes 12 paired FASTQ files (6 samples) with single cell transcriptome sequencing data of normal breast luminal cells from ducts and TDLUs derived from reduction mammoplasties from three patients. Chromium Single Cell 3’ Reagent Kit v2 or v3 (10x Genomics) were used for processing of cells, whereafter sequencing was performed using the Illumina® NextSeq500/550 High Output Kit v2. Cell Ranger was used for generating FASTQ files and files from different lanes were concatenated prior to uploading the data to EGA. "R1" files include the feature barcodes and UMIs, while "R2" files include the reads.

  Dataset EGAD00001008499

• 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

• Type I Interferon Exacerbates Mycobacterium Tuberculosis Induced Human Macrophage Death

  In this study, we tested whether type I interferons (IFN-I), namely IFN-alpha and IFN-beta, may promote Mycobacterium tuberculosis (Mtb) pathogenesis by exacerbating cell death of human monocyte-derived macrophages (MDM) infected with Mtb. We differentiated the MDM under two different published methods (see Document Method.pdf for Table 1 of Methods). To determine if MDM infected with Mtb upregulates IFN-I transcripts, signaling factors, or IFN-I stimulated genes (ISGs), the MDM were infected with Mtb or treated with an activator of stimulator of IFN genes (STING), diamidobenzimidazole (di-ABZI). STING activation acted as a positive control for IFN-I induction and ISG upregulation. Indeed, di-ABZI treated MDM differentiated under both methods upregulated ISGs 24 hpi. At 24 hour post treatment, MDM differentiated under one method, but not under another method, upregulated ISGs, such as ISG15, IFITM3, and CXCL10, upon Mtb infection. MDM differentiated under both methods upregulated ISGs upon di-ABZI treatment.

  Study phs003607

• Gastric_Mutational_Signatures__GMS_

  This study aims to characterise the mutation burdens and signatures of adult stem cells derived from different regions of the stomach in order to gain insight into the causes and preclinical evolution of the diverse cancer subtypes. Clonal populations of cells from different anatomical locations of the stomach will be derived through organoid culture and/or laser microdissection and interrogated by whole genome sequencing and/or targeted pulldown. A total of circa 300 samples from 20 – 30 donors (cancer and non-cancer patients undergoing total/partial gastrectomy) will be analysed for mutational burden and signatures and genomic findings correlated with topology, age, risk factors and different stages of pre-neoplastic or neoplastic progression.

  Study EGAS00001002939

• Gastric_Mutational_Signatures__GMS_

  This study aims to characterise the mutation burdens and signatures of adult stem cells derived from different regions of the stomach in order to gain insight into the causes and preclinical evolution of the diverse cancer subtypes. Clonal populations of cells from different anatomical locations of the stomach will be derived through organoid culture and/or laser microdissection and interrogated by whole genome sequencing and/or targeted pulldown. A total of circa 300 samples from 20 – 30 donors (cancer and non-cancer patients undergoing total/partial gastrectomy) will be analysed for mutational burden and signatures and genomic findings correlated with topology, age, risk factors and different stages of pre-neoplastic or neoplastic progression.

  Study EGAS00001002938

• Comparison of sequencing assays for sensitive detection of circulating tumour DNA in stage IA-IV breast cancer

  This study compared different assays for the detection of circulating tumour DNA (ctDNA) in serial plasma from stage IA-IV breast cancer patients, targeting structural variants (SVs), single nucleotide variants (SNVs) and/or somatic copy-number aberrations (SCNAs). SV-multiplex PCR, SNV-/SV-hybrid capture, and different depths of whole-genome sequencing (WGS) were used to evaluate ctDNA levels, demonstrating concordant results. SNV-hybrid capture targeting 1,347-7,491 mutations was the most sensitive assay, detecting 67% (36/54) of samples down to an allele fraction (AF) of 0.00024%. SV-multiplex PCR, targeting 21-47 mutations, detected 63% (34/54) of samples down to 0.00047% AF and has potential as a clinical assay.

  Study EGAS00001006040

• Whole-genome sequencing of high-grade serous ovarian cancer (HGSC) tumours and matched normals from long-term survivors.

  Whole-genome sequencing of high-grade serous ovarian cancer (HGSC) tumours and matched normals from long-term survivors performed as part of the Multidisciplinary Ovarian Cancer Outcomes Group (MOCOG) study. The dataset includes fastq files from 58 HGSC tumours (53 primary tumours and 5 recurrent tumours) and 53 matched normals from 53 long-term survivor patients. Sequence libraries were generated from tumour and matched normal genomic DNA using the KAPA HyperPrep PCR-free library preparation kit (Roche) according to manufacturer’s instructions. Sequencing was carried out by the Kinghorn Centre for Clinical Genomics Sequencing Laboratory (Sydney, Australia) on the HiSeq X Ten System (Illumina) to a minimum base coverage of 30-fold for normal DNA and 60-fold for tumour DNA samples.

  Dataset EGAD00001009398

• WGoxBS and SureSelect data of the POPS placenta samples

  We carried out whole-genome oxidative bisulfite sequencing (WGoxBS) in the placentas of two healthy female and two healthy male pregnancies generating an average genome depth of coverage of 25x. The sex-specific differential methylation pattern observed in this region was validated in additional 8 healthy placentas (including 2 from the WGoxBS) using SureSelect in-solution target capture. For WGoxBS, placental genomic DNA (4 µg) from 4 healthy pregnancies was processed to achieve 10 kb fragments with the g-Tube (Covaris), according to the manufacturer's instructions. To increase the number of uniquely sequenced reads, two independent libraries were generated for each individual. Multiplexed sequencing was carried out on the Illumina MiSeq, HiSeq 2000, and HiSeq 2500 instruments with 2x100, 2x50 and 2x125 cycles using MiSeq Reagent Kit v3, HiSeq SBS Kit v3 and HiSeq SBS Kit v4, respectively. For SureSelect in-solution capture, placental genomic DNA (3.5 µg) from 8 healthy pregnancies (including 2 from the WGoxBS) was fragmented by the Covaris S220 system according to the SureSelect Methyl-Seq target enrichment protocol (Agilent). All 8 libraries were pooled and sequenced on the Illumina HiSeq 2500 instrument with 2 × 125 cycles using HiSeq SBS Kit v4 and a single lane of the Illumina HiSeq 4000 instrument with 2 × 150 cycles using HiSeq 3000/4000 SBS Kit following Illumina's guidelines (Illumina Application Note: Epigenetics February 2016).

  Dataset EGAD00001003136

• Liquid biopsy-based minimal residual disease monitoring for early risk stratification and decision-making in advanced non-small cell lung cancer

  Circulating tumor DNA (ctDNA)-based minimal residual disease (MRD) monitoring shows promise for risk stratification and decision-making in cancer patients. However, factors like background noise from non-tumor DNA, clonal haematopoiesis, and non-shedding tumors may complicate manual interpretation and limit its clinical application. In this proof-of-concept study in advanced non-small cell lung cancer (NSCLC) patients treated with immune checkpoint inhibitors (ICIs), we developed an algorithm that automatically classifies serial cell-free DNA (cfDNA) samples, thereby enabling reliable and reproducible interpretation, and preventing time-consuming manual interpretation in approximately 75% of patients. Importantly, application of the algorithm allowed early risk stratification and decision-making, specifically identifying approximately 35% of patients with short-term clinical benefit and approximately 25% of patients who may potentially benefit from treatment escalation. Simultaneous serum tumor marker (STM) monitoring further improved risk stratification and decision-making in our study, enabling accurate identification of all patients with a clinical benefit of at least one year.

  Study EGAS50000001554

• March 2019 data update 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.

  March 2019 data update for cord blood CD34+CD38-, CMP, GMP, MEP, monocyte, erythroid precursor, B cell and primary AML total blasts reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium. This dataset contains data for samples: CEMT0158 CEMT0159 CEMT0160 CEMT0161 CEMT0162 CEMT0163 CEMT0164 CEMT0165 CEMT0166 CEMT0167 CEMT0168 CEMT0169 CEMT0170 CEMT0171 CEMT0172 CEMT0189

  Dataset EGAD00001004950

• Next-generation molecular analysis of surgical margins in oral squamous cell carcinoma for assessment of microscopic residual disease and personalized postoperative treatment decision

  Background : Patients operated for an early oral squamous cell carcinoma (OSCC) with clear margins have a 5-year local relapse rate of around 15%. Assessing the microscopic residual disease (MRD) remains a challenge. In a phase II prospective trial, we evaluated the tetranucleotide microsatellite instability markers in the surgical margins in T1-T2 OSCC resected with pathologically clear margins. Goal : Detect MRD in surgical margins and adapt the postoperative decision-making Details : Whole exome sequencing (WES) on early oral squamous cell carcinoma (OSCC) with clear margins, and on resection margins, 86 patients with a median follow-up of 58 months (range 30.4-83 months)

  Study EGAS50000000823

• MethylScan data of plasma samples

  10ng from each cfDNA sample was used as the input material. For gDNA samples, 1.5-2ug each was first sonicated by Covaris R230 system (Woburn, MA). Next, size-selection with 0.8x-1.5x two-step Ampure XP beads was performed to enrich the 150-200bp fragments. 200ng of the size-selected gDNA was used as input material. The pre-capture library construction was performed with NEB UltraII DNA library prep kit for Illumina (Ipswich, MA) and the adapter was the methylated EM-seq adapter. Before the first PCR amplification, the gDNA samples were subjected to bisulfite conversion by QIAGEN Epitect kit, and cfDNA samples were subjected to enzymatic conversion by NEBNext enzymatic methyl-seq kit if the hybrid capture panel designed for converted DNA was used downstream. Twist panel hybrid capture was performed with their standard protocol (Twist Bioscience, South San Francisco, CA). The concentration of the post-capture library after the second PCR amplification was measured by Qubit 1xdsDNA HS kit (ThermoFisher, Waltham, MA). Their quality was examined by TBE-UREA PAGE and Bioanalyzer before sequencing. Libraries were then sequenced with 150bp paired-end reads on Illumina machines by Genewiz, Inc. (South Plainfield, NJ, USA). This dataset contains MethylScan data of the plasma samples from 248 noncancer individuals and 27 cancer patients (17 liver and 10 GI-tract cancers).

  Dataset EGAD00001015815

• DAC for Greenland Studies of University of Copenhagen and University of Southern Denmark.

  Dac EGAC00001000736

• Access Committee for Separation, characterization, and identification of individuals from multi-person blood mixtures

  Dac EGAC00001002646

• eQTL-CHiC DAC

  The Data Access Committee for eQTL-CHiC and related data from Ray-Jones et al., 2024.

  Dac EGAC50000000445

• DAC for Transcriptomic and genomic profiling of fragile X syndrome unmethylated full mutation carriers

  Dac EGAC50000000416

• DAC_Circadian_Neuroendocrinology

  DAC for projects of the group Circadian Neuroendocrinology at the Department of Endocrinology and Metabolism at Amsterdam UMC.

  Dac EGAC50000000692

• Patient WGS for #198

  Whole genome sequencing of patient tumour and blood

  Dataset EGAD50000000217

• PDAC

  ctDNA and protein markers for earlier detection of pancreatic cancers

  Dataset EGAD00001004399

• DAC Longitudinal Multi-Omics Study Reveals Molecular Drivers and Tumor Microenvironment in Extramedullary Multiple Myeloma

  Data access requests for the raw data used in publication "Longitudinal Multi-Omics Study Reveals Molecular Drivers and Tumor Microenvironment in Extramedullary Multiple Myeloma"

  Dac EGAC50000000016

• uganda_autosomes

  Genotype data (in binary PLINK format) and imputed data (with merged 1000Gp3 and AGVP reference panel in GEMMA BIMBAM dosage format) for 1391 individuals from EMaBS in Entebbe, Uganda.

  Dataset EGAD00010002578

• Pineoblastoma Single-Nuclei RNA-seq Data Access Committee (St. Jude)

  Committee responsible for reviewing and approving external access requests to controlled-access pediatric brain tumor transcriptomic datasets from St. Jude Children's Research Hospital, ensuring alignment with patient consent and institutional ethics policies.

  Dac EGAC50000000839

• Exome sequencing of tumor samples

  We utilized exome sequencing for DNA obtained from saliva (germline DNA) and the four spatially separated tumor foci and 3 corresponding lymph node metastases

  Dataset EGAD00001000762

• Sequencing data for the manuscript "Multi-focal sampling of de novo metastatic prostate cancer reveals complex polyclonality and enables accurate clinical genotyping"

  This submission includes targeted and whole exome paired-end fastq files.

  Dataset EGAD00001009651

• 2_cortical-neurons_HD_vs_Ctrl_DMSO_Branaplam

  n=3 Ctrl and n=3 HD iPSC lines differentiated into cortical neurons were treated with DMSO or 10nM Branaplam for 72h and RNA-seq was performed.

  Dataset EGAD00001008808

• Whole Genome Sequencing of Two Family Trios with 22q.11.2 Deletion Syndrome

  Two subjects with 22q11.2 deletion syndromes (22q11DS) and their parents were recruited for a whole genome sequencing study to identify candidate genetic modifiers of the various phenotypes seen in 22q11DS. Both probands had a typical 3 megabase deletion on chromosome 22q11.2 but discordant phenotypes.

  Study phs000837

• Whole exome sequence analysis in sporadic amyotrophic lateral sclerosis

  To identify a susceptible gene for amyotrophic lateral sclerosis, exome sequence analysis was conducted in patients with amyotrophic lateral sclerosis and control subjects to perform whole genome association studies. In this data set, exome sequencing data of 11 patients with amyotrophic lateral sclerosis was included.

  Study JGAS000013

• Raw FASTQ files from TSO500 hybrid capture sequencing of prostate cancer tissue and plasma.

  This dataset contains raw genomic sequencing data in FASTQ format for a total of 49 libraries. It includes 22 samples derived from formalin-fixed paraffin-embedded (FFPE) tissue and 27 samples from plasma cell-free DNA (cfDNA). All samples were processed using the Illumina TruSight Oncology 500 (TSO500) hybrid capture panel to identify relevant genomic alterations. These files represent the primary, non-aligned data used for the comparative performance analysis described in the associated study.

  Dataset EGAD50000002463

• Exomes of High-risk Prostate cancer

  DNA extracted from tumoral tissue of 39 patients was used for exome sequencing. As a comparison, DNA extracted from blood was used as a non-tumoral control. DNA was captured using the EZ SeqCap v3 exome kit from Roche and sequenced using an Illumina HiSeq instrument.

  Study EGAS00001001015

• the Yemeni-Somali 5 million SNP array dataset

  The three new samples (two from Yemen and one from Somalia) that carry a maternal lineage affiliated with the Malagasy motif were assayed for genome-wide SNP genotypes using the Illumina Human Omni5 Bead Chip (Illumina), which surveys 4,284,426 single nucleotide markers regularly spaced across the genome.

  Study EGAS00001003425

• BLUEPRINT release August 2016, RNA-Seq for late basophilic and polychromatophilic erythroblast, on genome GRCh38

  RNA-Seq data for 1 late basophilic and polychromatophilic erythroblast sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002402

• Keratinocyte CRISPR screens (2019-08-14)

  Immortalised HaCaT keratinocytes were transduced with Cas9 and the CRISPR-KO v1.1 genome-wide gRNA library. The gRNA library was prepared from genomic DNA isolated 14 days post library transduction. gRNA representation will be compared to the original CRISPR-KO v1.1 library to reveal genes essential for HaCaT survival and growth. . This dataset contains all the data available for this study on 2019-08-14.

  Dataset EGAD00001005252

• The identification of genetic vulnerabilities in head and neck cancers for the development of novel treatments. (2019-06-10)

  Exome Sequencing in a set of Asian Head and Neck cancer cell lines, to identify mutations that can be used to genomically classify the cell lines. . This dataset contains all the data available for this study on 2019-06-10.

  Dataset EGAD00001005082

• Whole genome sequencing raw data for fragile X associated unmethylated expansion carrier 1

  Whole genome sequencing raw data for fragile X associated unmethylated expansion carrier 1. DNA was sequenced using the illumina NovaSeq6000 system. 8x paired end FASTQ files from one DNA sample (UFM 1), 4x R1 files and 4x R2 files.

  Dataset EGAD50000000917

• Whole genome sequencing raw data for fragile X associated unmethylated expansion carrier 2

  Whole genome sequencing raw data for fragile X associated unmethylated expansion carrier 2. DNA was sequenced using the illumina NovaSeq6000 system. 8x paired end FASTQ files from one DNA sample (UFM 2), 4x R1 files and 4x R2 files.

  Dataset EGAD50000000921

• RNA-seq data for genomic determinants of response and resistance to inotuzumab in B-ALL

  RNA-seq data for 101 samples with B-cell acute lymphoblastic leukemia

  Dataset EGAD50000000095

• WGS data for genomic determinants of response and resistance to inotuzumab in B-ALL

  Whole genome sequencing data for 45 samples with B-cell acute lymphoblastic leukemia

  Dataset EGAD50000000096

• High-throughput sequencing data for prostate methylome analysis

  Paired-end 150 (PE150) high-throughput sequencing data from 19 PCA, 29 BPH, and 19 BCA tissue samples. MeDIP-seq was employed to specifically enrich methylated DNA fragments across the genome, followed by methylation amplicon sequencing for further validation.

  Dataset EGAD50000002747

• GenomeDenmark Phase 2 - variants called on chrY for 62 males.

  Variants on the Y chromosome for 62 danish males in VCF format from the GenomeDenmark Phase 2 cohort. Variants were called using reference based approaches such as the haplotype-caller module from GATK and using alignment of denovo assemblies to the reference using ASMvar.

  Dataset EGAD00001003186

• V4 panel bait design test (2018-03-07)

  Targeted gene screen of FFPEs, cell lines and primary CRC tumours for testing the new V4 Colorectal gene panel. . This dataset contains all the data available for this study on 2018-03-07.

  Dataset EGAD00001004001

• Carcinoid study - WGS dataset

  Fernandez-Cuesta et al., 2014, Nature Communication, Whole genome sequencing was performed using a read length of 2x100 bp for all samples. On average, 110 Gb of sequence were produced per sample, aiming a mean coverage of 30x for both tumour and matched normal.

  Dataset EGAD00001000813

• H3Africa ReMAC Shotgun Metagenomic Phenotype

  Phenotype data for shotgun metagenomic sequencing data of nasopharyngeal fluid for studying nasopharyngeal colonization dynamics with Streptococcus pneumoniae and associated antimicrobial-resistance in a South African birth cohort. https://www.ebi.ac.uk/ena/data/view/PRJEB37312

  Dataset EGAD00001006244

• A Single-cell Atlas of Progressive TKI Resistance in Chronic Myeloid Leukemia

  57 Bone marrow specimens for 5 healthy bone marrow and 24 CML samples profiled with 10X scRNA-seq 5' upon separation using MACS for CD34.

  Dataset EGAD00001007946

• CBD-RAW-REPERTOIRE-B: B cell bulk repertoire sequence files

  fastq and filtered fasta files for B-cell receptor sequencing. For further information regarding this dataset, please contact Rachael Bashford-Rogers at contact@combat.ox.ac.uk.

  Dataset EGAD00001007960

• RNA-seq for identification of neotranscripts

  This dataset contains RNA-seq data (Fastq files of paired-end data) of 18 patient tumors used for identification of neotranscripts in 18 different types of fusion-driven sarcomas and other cancers as described in Vibert et al., Mol Cell 2022 (PMID: 35550257)

  Dataset EGAD00001008832

• Targeted Myeloid DNA-Panelsequencing, DKFZ

  Targeted myeloid DNA-Panelsequencing from purified bone marrow blasts of 104 treatment naive AML patients from the discovery cohort. For more details, we refere to Jayavelu, Wolf, Buettner et al. Libraries were prepared from 40 ng DNA using the QIASeq Human Myeloid Neoplasms Panel (Qiagen) according to the manufacturer’s protocol. Samples were tagged with the QIAseq 96-Unique Dual Index Set A for Illumina platforms (Qiagen) to yield unique combinations of i5 and i7 barcodes for each sample. Sample fragment size distribution and concentration was estimated using the Agilent High Sensitivity DNA kit on a 2100 Bioanalyzer (Agilent). Samples were pooled in an equimolar fashion, denatured, and diluted to 1.5 pM according to Illumina’s recommendations. The diluted library was sequenced on a NextSeq 500 benchtop sequencer (Illumina) using NextSeq High Output cartridges. Demultiplexing was performed using the BaseSpace cloud platform (Illumina).

  Dataset EGAD00001008501

• Familial breast cancer targeted sequencing with ONT

  A large cohort of 600 cases with familial breast cancer as classified by the Spanish Society of Medical Oncology (SEOM) Clinical Guidelines Update that were recruited during 6 years at Hospital Universitario Morales Meseguer (Murcia, Spain) were retrospectively evaluated to select 16 cases with no positive finding in NGS analysis of 20 genes implicated in this disease. These 16 cases were selected for further investigation using nanopore sequencing. This method involved the use of adaptive sampling enrichment, targeting a panel of 18 human genome regions, which contained the 20 genes (PTEN, ATM, BRCA2, PALB2, CDH1, TP53, NF1, RAD51D, BRCA1, RAD51C ,BRIP1, STK11, CHEK2, EPCAM, MSH2, MSH6, BARD1, MLH1, PMS2, NBN). In 5 samples (P1, P2, P4, P15 and P16) no selection of long reads was performed. Additionally, in 3 samples (P7, P9 and P10), both procedures were performed in two independent runs, and for the second run of P7, the DNA was previously fragmented using g-TUBE Covaris® (ref 520079) according to the protocol for 6 kb fragments.

  Dataset EGAD00001011106

• Epigenetic profiling of primary human thymocyte subsets

  Dynamic changes of the DNA methylation (DNAmeth) landscape drive differentiation of mature T lymphocytes. However, the role of DNAmeth-mediated regulation in thymocyte development remains unclear. Thus, we generated genome-wide DNAmeth and transcriptomic profiles of eight defined, ex vivo isolated primary human thymocyte subsets, to assess the epigenetic remodling taking place during human thymic T cell development. The generated data may also serve as a reference for the analysis of T cell-based inborn errors of immunity or for quality control purposes of in vitro generated T cell populations.

  Study EGAS50000001106

• Whole Exome sequencing of colorectal cancer patients (SG-BULK)

  The study was approved by the institutional review board of Singhealth (2018-2795). Ten 5-µm tissue sections were cut using standard microtomy techniques. Each collected cell population was then extracted using the allprep kit. Extracted material was then quantified using a Qubit fluorometer. DNA-seq libraries were captured to exome regions using xGen Exome Research Panel v1.0 (IDT), and libraries were prepared using the KAPA Hyper prep kit. DNA libraries were sequenced to a target depth of ×200 for tumor sample, ×100 for normal samples on the Illumina HiSeq platform.

  Study EGAS00001006006

• Malnutrition and Enteric Disease Network (Mal-ED) Case-Control Study in Brazil

  The Malnutrition and Enteric Disease Network (Mal-ED) Case-Control Study enrolled children in the age range 6-24 months between 2010 and 2014 in Fortaleza, Ceará, Brazil.The aim of the study was to understand the etiology and pathogenesis of malnutrition. Children were prospectively enrolled cases defined as weight for age Z Score (WAZ) <-2 and age and neighborhood matched controls defined as WAZ>-1.This submission includes genetic and associated phenotypic data on a subset of 336 participants. More information on this project and its related projects can be found here: Studies of diarrheal susceptibility, growth, and development, in pediatric populations in Northeastern Brazil

  Study phs003173

• Malnutrition and Enteric Disease Network (Mal-ED) Birth Cohort in Brazil

  The Malnutrition and Enteric Disease Network (Mal-ED) Birth Cohort in Brazil enrolled 242 children between 2010 and 2014; an additional 101 infants recruited under the ICIDR (International Center for Infectious Disease Research) program and evaluated by the same procedures as Mal-ED were included in the cohort. The aim of the study was to evaluate the role of enteropathogens in causing intestinal inflammation and a failure of growth and development.This submission includes genetic and corresponding anthropometric data on a subset of 279 participants. More information on this project and its related projects can be found here: Studies of diarrheal susceptibility, growth, and development, in pediatric populations in Northeastern Brazil

  Study phs003172

• MCO colorectal cancer genomics at UNSW

  This dataset contains DNA sequencing data from 95 colorectal cancer and matched-normal samples. The dataset contains targeted deep sequencing of selected regulatory elements in 95 cancer and matched-normal samples, and data for one sample that was additionally whole-genome sequenced (cancer and matched-normal).

  Dataset EGAD00001004582

• IBD-dysplasia

  This data set concerns DNA copy number alterations and mutation data from 30 IBD-associated dysplastic lesions and 13 IBD-associated cancers. DNA was isolated from formalin-fixed, paraffin-embedded material. Whole-genome shallow seq and Truseq amplicon cancer panel (Illumina) were used for detection of DNA copy number alterations and gene mutations, respectively.

  Dataset EGAD00001005196

• Longitudinal evaluation of serum microRNAs as biomarkers for neuroblastoma burden and therapeutic p53 reactivation

  Small RNA sequencing data (TruSeq small RNA library preparation kit v2) from serum samples and tumor tissue of orthotopically injected mice (SH-SY5Y cell line) and unengrafted mice, treated with idasanutlin, temsirolimus and vehicle control.

  Dataset EGAD00001009625

• Comparison of 133/144bp dominant phenotype vs 166bp dominant phenotype.

  Background: Previous studies found that cell-free DNA (cfDNA) generated from tumors was shorter than that from healthy cells, and selecting short cfDNA could enrich for tumor cfDNA and improve its usage in early cancer diagnosis and treatment monitoring; however, the underlying mechanism of shortened tumor cfDNA was still unknown, which potentially limits its further clinical application.Results: Using targeted sequencing of cfDNA in a large cohort of solid tumor patient, sequencing reads harboring tumor-specific somatic mutations were isolated to examine the exact size distribution of tumor cfDNA. For the majority of studied cases, 166bp remained as the peak size of tumor cfDNA, with tumor cfDNA showing an increased proportion of short fragments (100-150bp). Less than 1% of cfDNA samples were found to be peaked at 134/144bp and independent of tumor cfDNA purity. Using whole-genome sequencing of cfDNA, we discovered a positive correlation between cfDNA shortening and the magnitude of chromatin inaccessibility, as measured by transcription, DNase I hypersensitivity, and histone modifications. Tumor cfDNA shortening occurred simultaneously at both 5’ and 3’ ends of the DNA wrapped around nucleosomes. Conclusions: Tumor cfDNA shortening exhibited two distinctive modes. Tumor cfDNA purity and chromatin inaccessibility were contributing factors but insufficient to trigger a global transition from 166bp dominant to 134/144bp dominant phenotype.

  Study EGAS00001004135

• Drug-perturbation-based stratification of blood cancer

  As new generations of targeted therapies emerge and tumor genome sequencing discovers increasingly comprehensive mutation repertoires, the functional relationships of mutations to tumor phenotypes remain largely unknown. Here, we measured ex vivo sensitivity of 246 blood cancers to 63 drugs alongside genome, transcriptome, and DNA methylome analysis to understand determinants of drug response. We assembled a primary blood cancer cell encyclopedia data set that revealed disease-specific sensitivities for each cancer. Within chronic lymphocytic leukemia (CLL), responses to 62% of drugs were associated with 2 or more mutations, and linked the B cell receptor (BCR) pathway to trisomy 12, an important driver of CLL. Based on drug responses, the disease could be organized into phenotypic subgroups characterized by exploitable dependencies on BCR, mTOR, or MEK signaling and associated with mutations, gene expression, and DNA methylation. Fourteen percent of CLLs were driven by mTOR signaling in a non–BCR-dependent manner. Multivariate modeling revealed immunoglobulin heavy chain variable gene (IGHV) mutation status and trisomy 12 as the most important modulators of response to kinase inhibitors in CLL. Ex vivo drug responses were associated with outcome. This study overcomes the perception that most mutations do not influence drug response of cancer, and points to an updated approach to understanding tumor biology, with implications for biomarker discovery and cancer care.

  Study EGAS00001001746

• Gene Expression Signature in Normal Mammary Gland from 83 Breast Cancer Patients Indicates Pre-tumorous Changes and Adverse Outcomes

  This study assessed the transcriptomic profiles of 242 samples from 83 breast cancer patients with unfavorable outcomes, including paired uninvolved mammary gland samples collected at varying distances from primary lesions. As a reference, control samples from 53 mammoplasty individuals without cancer history were studied. A custom panel of 634 genes linked to breast cancer progression and metastasis was employed for expression profiling (targeted RNA sequencing), followed by whole-transcriptome (RNA sequencing) verification experiments and statistical analyses to discern molecular signatures and their clinical relevance.

  Study EGAS50000000011

• Single-cell RNA sequencing of control and Notch inhibitor treated HCC PDX model

  We generated single-cell RNA-seq data for anti-Notch2 (n=3), anti-JAG1 (n=1) and anti-gD (n=4) treated LIV78 tumors. NCR nude mice bearing similarly sized LIV78 tumors (volumes between 300-900mm3) were injected intravenously with 30mg/kg body weight of either anti-Notch2, anti-Jag1 or anti-gD control antibody 72hrs prior to tumor harvest and tumor cell isolation. Following the depletion of CD45+ and Ter119+ cells, the samples were processed for single-cell RNA-seq (scRNAseq) as described previously (Long et al., 2019) using the Chromium Single Cell 3’ Library and Gel bead kit v2, following the manufacturer’s manual. cDNAs and libraries were prepared following the manufacturer’s manual (10X Genomics). Libraries were profiled by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies) and quantified using Kapa Library Quantification Kit (Kapa Biosystems, Wilmington, MA). Each library was sequenced in one lane of HiSeq 2500 (Illumina) following the manufacturer’s sequencing specification (10X Genomics) to produce the resulting FASTQ files.

  Dataset EGAD50000000738

• Independent development of lymphoid and histiocytic malignancies from a shared early precursor

  Recent reports have described lineage flexibility in patients with recurrent hematologic malignancies. We encountered a boy with T-lineage acute lymphoblastic leukemia, non-Langerhans cell histiocytosis and histiocytic sarcoma. All tumors showed identical T-cell receptor rearrangements, but SNP arrays and whole exome sequencing revealed unique aberrations in each tumor. From the genetic data we conclude that the tumors were derived from a precursor cell with lineage plasticity for both lymphoid and myeloid development. From this precursor cell, the tumors evolved with independent genetic progression in a non-linear manner.

  Study EGAS00001001353

• Circulating tumour DNA abundance and potential utility in de novo metastatic prostate cancer

  Several systemic therapeutic options exist for metastatic castration sensitive prostate cancer (mCSPC). Circulating tumour DNA can profile metastatic castration resistant prostate cancer and influence treatment decisions, but remains untested in mCSPC. We set out to determine ctDNA abundance at de novo mCSPC diagnosis and whether ctDNA provides complementary clinically relevant information to a prostate biopsy. We collected and sequenced 77 plasma cell-free DNA samples from 53 newly diagnosed patients with mCSPC. Targeted sequencing was also performed on DNA from 48 diagnostic prostate tissue samples.

  Study EGAS00001003351

• The scRNA dataset for TIGIT in MCL with CART

  We collected longitudinal samples from 15 patients with MCL at various clinical time points before and after CAT-T therapy brexucabtagene autoleucel (BA) infusion. The patients were grouped into three categories based on their clinical responses after BA treatment: 1) responsive (n = 9), 2) relapsed (n = 5), and 3) refractory (n = 1). All patients in category #1 and #2 had initially attained a complete response (CR) after BA therapy. The responsive group maintained CR with no relapse at the time of last follow up, while the relapsed group achieved initial CR but eventually relapsed. The 10x Chromium™ Single-Cell 5′ Reagent Kit v2 (PN-1000190, 10x GENOMICS) and Chromium Single-Cell Human TCR amplification Kit (PN-1000252, 10x GENOMICS) were used to perform single-cell separation, cDNA amplification, and library construction for gene expression and TCR repertoire following the manufacturer’s guidelines. Thirty-nine samples passed quality control and underwent single-cell transcriptome profiling with simultaneous single-cell T-cell receptor (TCR) repertoire analysis.

  Dataset EGAD00001010180

• Development of molecular targeted therapy for small cell lung cancer by comprehensive genome analysis

  Aims: Identifying new therapeutic targets of small cell lung cancer (SCLC), genome-wide mutation analysis has been performed. Methods: Genomic DNA was extracted from formalin-fixed or methanol-fixed tissue samples. 71 Mb of DNA fragments containing whole coding exons were concentrated using SureSelect Human All Exon V4+UTRs Kit (Agilent Technologies) followed by 100-bp paired end sequencing by HiSeq 2000 (Illumina). Participants/Materials: 51 of 1042 cases of pathologically diagnosed small seen lung cancer that were registered to National Cancer Hospital East Lung Cancer Database in 1992-2012, and which surgically resected or biopsy samples were suitable for DNA extraction for further analyses.

  Study JGAS000037

• Response to tumor-infiltrating lymphocyte adoptive therapy is associated with preexisting CD8+ T-myeloid cell networks in melanoma

  Adoptive cell therapy (ACT) using ex vivo–expanded tumor-infiltrating lymphocytes (TILs) can eliminate or shrink metastatic melanoma, but its long-term efficacy remains limited to a fraction of patients. Using longitudinal samples from 13 patients with metastatic melanoma treated with TIL-ACT in a phase 1 clinical study, we interrogated cellular states within the tumor microenvironment (TME) and their interactions. We performed bulk and single-cell RNA sequencing, whole-exome sequencing, and spatial proteomic analyses in pre- and post-ACT tumor tissues, finding that ACT responders exhibited higher basal tumor cell–intrinsic immunogenicity and mutational burden. Compared with nonresponders, CD8+ TILs exhibited increased cytotoxicity, exhaustion, and costimulation, whereas myeloid cells had increased type I interferon signaling in responders. Cell-cell interaction prediction analyses corroborated by spatial neighborhood analyses revealed that responders had rich baseline intratumoral and stromal tumor–reactive T cell networks with activated myeloid populations. Successful TIL-ACT therapy further reprogrammed the myeloid compartment and increased TIL-myeloid networks. Our systematic target discovery study identifies potential T-myeloid cell network–based biomarkers that could improve patient selection and guide the design of ACT clinical trials.

  Study EGAS50000001217

• Clinical and genetic factors associated with tumor response to neoadjuvant (chemo)radiotherapy, survival and recurrence risk in rectal cancer

  Rectal cancer poses challenges in preoperative treatment response, with up to 30% achieving a complete response (CR). Personalized treatment relies on accurate identification of responders at diagnosis. This study aimed to unravel CR determinants, overall survival (OS), and time to recurrence (TTR) using clinical and targeted sequencing data. Analyzing 402 patients undergoing preoperative treatment, tumor stage, size, and treatment emerged as robust response predictors. CR rates were higher in smaller, early-stage, and intensively treated tumors. Targeted sequencing analyzed 216 cases, while 120 patients provided hotspot mutation data. KRAS mutation dramatically reduced CR odds by over 50% (odds ratio [OR]=0.3 in the targeted sequencing and OR=0.4 hotspot cohorts, respectively). In contrast, SMAD4 and SYNE1 mutations were associated with higher CR rates (OR=6.0 and 6.8, respectively). Favorable OS was linked to younger age, CR, and low baseline carcinoembryonic antigen levels. Notably, CR and an APC mutation increased TTR, while a BRAF mutation negatively affected TTR. Beyond tumor burden, SMAD4 and SYNE1 mutations significantly influenced CR. KRAS mutations independently correlated with radiotherapy resistance, and BRAF mutations heightened recurrence risk. Intriguingly, nonresponding tumors with initially small sizes carried a higher risk of recurrence. These findings offer insights into rectal cancer treatment response, guiding personalized therapeutic strategies. By uncovering factors impacting CR, OS, and TTR, this study underscores the importance of tailored approaches for rectal cancer patients. These findings, based on extensive analysis and mutation data, pave the way for personalized interventions, optimizing outcomes in the challenges of rectal cancer preoperative treatment.

  Study EGAS00001007501

• Dynamics of tumor ecosystems and microbiome in response to neoadjuvant atezolizumab, bevacizumab, and FOLFOX treatment in patients with unresectable colorectal cancer with liver metastasis

  This study aims to explore the effects of neoadjuvant atezolizumab, bevacizumab, leucovorin, 5-fluorouracil, and oxaliplatin (ABFOLFOX) in patients with unresectable colorectal liver metastases (CRLM), focusing on the molecular dynamics of tumor ecosystems (TE) of CRLM and their impact on treatment outcomes. The study comprises two cohorts with CRLM tissue samples analyzed with RNA sequencing and immunohistochemical staining: cross-sectional cohort A (n = 60, CRLM treated with or without neoadjuvant chemotherapy) and prospective cohort B (n = 20 with serial sampling and treated with ABFOLFOX). Shotgun metagenomic sequencing was done for stool samples from cohort B.

  Study EGAS50000000677

• NHLBI TOPMed: Determining the Association of Chromosomal Variants with Non-PV Triggers and Ablation-Outcome in AF (DECAF)

  The DECAF trial was conducted at the Texas Cardiac Arrhythmia Institute (TCAI) in 2013 in collaboration with the University of Texas at Austin. Four hundred consecutive AF patients undergoing catheter ablation were enrolled. All participants provided voluntary informed consents. Blood samples were collected before the ablation procedure and labeled with anonymous patient identifier. The researchers at UT Austin responsible for DNA extraction and genetic analysis were blinded about the clinical characteristics and identification of the study participants. AF cases included adults >18 years of age from both sex and all AF types.

  Study phs001546

• Enabling sensitive and precise detection of ctDNA through somatic copy number aberrations in breast cancer

  Cell-free DNA (cfDNA) extracted from peripheral blood has emerged as a crucial biomarker source in oncology research. To enhance the detection of somatic copy number alterations (SCNAs) and circulating tumor DNA (ctDNA), we developed eSENSES, a 2Mb breast cancer-targeted NGS panel. It includes 15,000 genome-wide SNPs, 500 focal SNPs in breast cancer driver regions, and exons from 81 commonly altered genes, alongside a custom computational approach. eSENSES provides a reliable, powerful and cost-effective tool for monitoring disease progression and guiding therapeutic decisions in breast cancer patients.

  Study EGAS50000000793

• Fecal microbiome of T2D patients undergoing semaglutide or empagliflozin treatment

  The gut microbiome has been shown to be affected by the use of many human-targeted medications, and the interaction can be bidirectional. This has been clearly demonstrated for type 2 diabetes medications that have been in clinical use for several decades. However, the bidirectional effects of novel type 2 diabetes drugs semaglutide, empagliflozin, and the gut microbiome have yet to be clearly described. We investigated the effect of semaglutide and empagliflozin initiation on the gut microbiome of type 2 diabetes patients. In addition, we analyzed whether the pre-treatment gut microbiome can predict the treatment efficacy. Twenty subjects (10 women and 10 men) were enrolled in the study between November 2019 and January 2023 from the University of Tartu Hospital, Tartu, Estonia. All participants had been diagnosed with type 2 diabetes. The study group taking semaglutide included 6 women and 4 men, and the group prescribed empagliflozin included 4 women and 6 men. Gut microbiome fecal samples donated at four timepoints (Baseline, Month 1, Month 3; Month 12) were studied using 16S ribosomal RNA gene sequencing and analysis.

  Dataset EGAD50000000756

• WGS and WTS data of patients diagnosed with MEITL.

  WGS from 4 patients, WTS from only 3 patients (insufficient tissue from 4th patient for WTS). Whole-genome sequencing (WGS) was performed for 60 pairs of tumor-normal samples from patients diagnosed with NKTL. Genomic DNA from tumor tissue was extracted with QIAamp DNA Mini Kit. The DNA for the matching normal was obtained from blood or buccal swabs and purified by Blood and Cell Culture DNA Mini kit or E.Z.N.A. Tissue DNA Kit (Omega Bio-tek) according to manufacturer’s instructions. The quantity and quality were assessed by Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen) and agarose gel electrophoresis. All sequencing libraries were prepared using TruSeq Nano DNA Library Prep Kit (Illumina). Paired-end sequencing was performed on Illumina HiSeq 2000. Whole-transcriptome sequencing (WTS): Total RNA from snap frozen EITL tumor samples was extracted using TRIzol (Invitrogen) and purified with RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. The integrity of RNA was determined by electrophoresis using 2100 Bioanalyzer (Agilent Technologies). 500 ng of total RNA was reverse transcribed with iScript cDNA Synthesis Kit (Bio-Rad, Hercules, CA, USA). Quantification was performed using SsoFast EvaGreen Supermix and CFX96 Real-Time PCR System (both Bio-Rad). Sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina) and WTS was performed on Illumina HiSeq 2500 with 2x101 bp read length. Description of prefix used in filenames: T: Tumor samples N: Normal samples (Blood) P: PDX samples

  Dataset EGAD00001005341

• Patient-derived xenograft models of head and neck cancers

  Establishment and characterization of two patient-derived xenograft models from HNSCC patients , initiatlly treatment-naive, and for which cetuximab-acquired resistant model couterparts have been generated. All models have been characterized at genomic level. HNSCC tissues were obtained from surgical resections at Cliniques universitaires St Luc in Brussels (Belgium).

  Dac EGAC50000000502

• Single-cell RNA-sequencing for peripheral blood mononuclear cells from COVID-19 patients and healthy controls of Japanese

  We performed single-cell RNA-sequencing of peripheral blood mononuclear cells obtained from COVID-19 patients and healthy controls.

  Study JGAS000593

• Single-cell RNA-sequencing for peripheral blood mononuclear cells from COVID-19 patients and healthy controls of Japanese

  We performed single-cell RNA-sequencing of peripheral blood mononuclear cells obtained from COVID-19 patients and healthy controls.

  Study JGAS000543

• Bulk RNAseq of FFPE and FF tissues at baseline and on-treatment

  Bulk transcriptomics for investigating transcriptomic biomarkers related to response at baseline and exploring treatment dynamics in transcriptomic signatures to gain a better understanding of the effects of ICB on the urothelial cancer tumor microenvironment (TME).

  Dataset EGAD50000002253

• Ultra-long whole-genome and Cas9-targeted nanopore sequencing of fibroblasts: FSHD, BAMS, healthy controls

  Data from the D4Z4End2End study (Xiao et al. 2025), for genetic and epigenetic analysis of the D4Z4 macrosatellite in health and disease.

  Dataset EGAD50000001551