15041 results for "cancer studies using rna-seq"

in 48.82 milliseconds.

• SIGi001-A-8 / SAMEA4448777 WGS data

  The iPSC line SIGi001-A-8 / SAMEA4448777 has undergone whole genome sequencing. Whole genome sequencing was done using Illumina HiSeq X Five platform with a reference genome of GRCh38. Raw data as FASTQ files and analysed data as CRAM files are available for this sample, in this dataset. The iPSC line SIGi001-A-8 is available for research use at www.EBiSC.org.

  Dataset EGAD50000001093

• SIGi001-A-9 / SAMEA4447499 WGS data

  The iPSC line SIGi001-A-9 / SAMEA4447499 has undergone whole genome sequencing. Whole genome sequencing was done using Illumina HiSeq X Five platform with a reference genome of GRCh38. Raw data as FASTQ files and analysed data as CRAM files are available for this sample, in this dataset. The iPSC line SIGi001-A-9 is available for research use at www.EBiSC.org.

  Dataset EGAD50000001095

• Whole Exome Sequencing of paired gDNAs and PPGL tumor DNA from patients with cyanotic congenital heart disease

  Fastq files from Whole Exome Sequencing of 12 paired germline DNA (from blood/saliva) and 14 PPGL tumor DNA (from formalin-fixed paraffin-embedded (FFPE) blocks from surgery) from patients with cyanotic congenital heart disease (CCHD) and pheochromocytoma and paraganglioma (PPGL). Sequencing was performed using the Illumina HiSeq4000.

  Dataset EGAD50000001201

• 10x Visium Spatial Transcriptomics of 61 Human Hepatocellular Carcinoma Samples

  This dataset contains spatial transcriptomics sequencing data from 61 hepatocellular carcinoma (HCC) tissue samples profiled using the 10x Genomics Visium platform. The cohort includes 38 resected tumors and 23 tumors from patients treated with atezolizumab plus bevacizumab. Sequencing data are provided as paired-end FASTQ files. These data support the analysis of intra-tumoral heterogeneity and its association with clinical outcomes.

  Dataset EGAD50000002122

• Neuroblastoma cell-lines and healthy cfDNA used for the benchmarking study

  This dataset comprises nine neuroblastoma cell lines used to construct the reference matrix for the RRBS-CL dataset in the corresponding benchmarking study. In addition, it includes one extra neuroblastoma cell line and a pooled cfDNA sample from multiple donors, which were used to generate the in silico mixtures. All the samples were profiled using DNA methylation sequencing.

  Dataset EGAD50000002199

• Single-cell DNA sequencing dataset of aplastic anemia and RCC (31 samples)

  This dataset contains raw single-cell DNA sequencing data generated from 31 patients with aplastic anemia using the Mission Bio Tapestri platform. Libraries were prepared with a targeted DNA amplicon panel and sequenced on an Illumina platform. These raw data capture single-cell variant profiles and clonal architecture and serve as the basis for downstream analysis of somatic mutations and clonal hematopoiesis.

  Dataset EGAD50000002189

• Reference single cell SNP array dataset from Coriell for training and validation of method for accurate single cell genotyping

  This dataset contains DNA from B-lymphocytes from 2 Coriell families and 4 individuals hybridized to HumanKaryomap BeadChip Array. Single cells from subjects GM12878 and GM7228 were amplified using multiple displacement amplification (SureMDA) according to Infium Karyomapping Assay Guide. Bulk DNA was processed and hybridized to an array for subject GM12878, GM07224 and GM07225.

  Dataset EGAD00001006376

• V(D)J and 5' Gene Expression data on patients with aplastic anemia

  Chromium V(D)J and 5' Gene Expression platform (10X Genomics) was used to study patients with aplastic anemia. CD45+ cells from two patients (patient AA-3: 3 longitudinal samples from bone marrow and patient AA-4: 3 longitudinal samples from peripheral blood) were analysed. The raw data was processed using Cell Ranger 3.0.1 pipelines.

  Dataset EGAD00001006937

• Whole-exome sequencing of P2RY8-CRLF2-positive ALL on Illumina HiSeq 2000, 100 bp paired-end

  Genomic DNA from leukemic and remission bone marrow mononuclear cells was isolated with the QIAamp DNA Blood Extraction Kit (Qiagen, Venlo, The Netherlands). Libraries were prepared using Nextera Rapid Capture Exome Kit (Illumina, San Diego, USA). Paired-end sequencing of 100 bp reads was performed on a HiSeq 2000 (Illumina) to obtain at least a 50 x coverage.

  Dataset EGAD00001002666

• Enhanced reduced representation bisulfite sequencing (eRRBS) on 45 multiple myeloma samples and 3 normal plasma cell

  Enhanced reduced representation bisulfite sequencing (eRRBS) on 45 multiple myeloma samples and 3 normal plasma cell. Enhanced reduced representation bisulfite sequencing (eRRBS) on 45 multiple myeloma samples and 3 normal plasma cell. Libraries were sequenced on a HiSeqTM4000 Illumina machine using 75bp paired-end reads

  Dataset EGAD00001007822

• WES data of central nervous system neoplasm patients

  Dataset containing 2068 WES tumor and control samples of central nervous system neoplasm patients. The data was sequenced on a Illumina NextSeq 500 using a NPHD2015A kit. The sequencing was always paired.

  Dataset EGAD00001009855

• Paired Exome sequencing of 34 samples (tumors and controls) of different tumors

  Paired Exome sequencing of 34 samples (tumors and controls) of different tumors. The samples were prepared using Agilent SureSelect V5+UTRs, the sequencing was done on Illumina HiSeq 4000.

  Dataset EGAD00001009705

• ctDNA whole exome genome sequencing dataset

  Dataset contains all available exome sequencing paired-end fastq files from our study "A generalizable machine learning framework for classifying DNA repair defects using ctDNA exomes"

  Dataset EGAD00001010069

• WGS Fastq files from the CPC-Gene project in support of PRAD-CA, DCC Release 26

  This dataset contains fastq files with Whole genome sequencing data for the CPC-Gene Project. Data from each sample was generated using multiple whole genome libraries and sequenced across multiple runs

  Dataset EGAD00001003761

• Genome Denmark Phase II - alignments

  Alignment of Genome Denmark Phase II dataset to GRCh38. The dataset consists of 150 Danish individuals (50 trios) sequenced to 80X. The BAM-file contains data from multiple libraries created from one individual with libraries of 180, 500, 800, 2000, 5000, 10000 and 20000 bp. The libraries were created using standard Illumina protocols for paired end reads (180-800bp libraries) and mate pair libraries (2kb-20kb).

  Dataset EGAD00001003157

• Australia and New Guinea haplotype phasing (2017-06-27)

  Whole-genome sequencing and phasing of admixed Aboriginal Australian genomes and Papua New Guinean genomes using 10x Genomics Chromium technology. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/ This dataset contains all the data available for this study on 2017-06-27.

  Dataset EGAD00001003407

• Whole genome sequencing data of tumor/normal pairs from 20 patients with hepatoblastoma

  This dataset provides whole genome sequencing data of tumor/normal pairs from 20 patients with hepatoblastoma using the illumina Novaseq sequencing system. It includes 40 samples (20 normals and 20 hepatoblastoma tumors). Our comprehensive analysis identified somatic mutations, structural variations, copy number variations and non-coding variants in hepatoblastoma.

  Dataset EGAD00001003914

• Whole exome analysis of adult type ovarian granulosa cell tumors

  Whole exome data from tumor/normal pairs for adult type ovarian granulosa cell tumor sequencing project. This data set contains 24 tumor whome exomes and 20 matched normal whole exomes generated using the Agilent V4 exome hybrid capture platform, with sequencing performed on an Illumina HiSeq 2000. This dataset contains BAM files generated by aligning paired-end reads to the hg19 reference genome.

  Dataset EGAD00001003961

• Understanding population genetics and patterns of genome-wide heterozygosity in a sample of the Croatian isolated populations (ESGIDalmatians)

  Using high-throughput sequencing technologies and analytical tools, we conduct an exome sequencing study that will help understand the population genetics of a Croatian island isolate, in a sample of 200 subjects from the Adriatic island of Vis who were selected to reflect islanders with at least four known ancestors in grandparental line who are original islanders.

  Dataset EGAD00001001387

• The Chinese University of Hong Kong Hereditary Spastic Paraplegia Data

  The dataset contains the whole genome sequencing data of a family with two unaffected parents and two probands that showed Hereditary spastic paraplegias symptoms. Sequencing reads were aligned to human genome (GRCh38) using BWA-MEM, followed by indel-realignment and PCR-duplicates marking. Alignment results are available for download in BAM format.

  Dataset EGAD00001002146

• Genotype data

  This dataset contains the imputed genotypes for 197 individuals. All individuals were genotyped with the Illumina HumanCoreExome-24 array. The individuals were phased with SHAPEIT and imputed to the 1000 Genomes Project Phase III using IMPUTE2. This dataset was generated as part of the following study: Panousis et al (2019). Combined genetic and transcriptome analysis of patients with SLE: Distinct, targetable signatures for susceptibility and severity

  Dataset EGAD00001005038

• DAC of The polarity and specificity of antiviral T lymphocyte responses determine susceptibility to SARS-CoV-2 infection in cancer patients and healthy individuals

  Dac EGAC00001002517

• Early on-treatment changes in circulating tumor DNA fraction and response to enzalutamide or abiraterone in metastatic castration-resistant prostate cancer - Data Access Committee

  Dac EGAC00001003128

• EGAD00000000048

  Sequencing data from oestrogen-receptor-alpha-positive metastatic lobular breast cancer sample

  Dataset EGAD00000000048

• Transcriptome sequencing of Gingivo-buccal Cancer : ICGC-India Project_2020

  Dataset EGAD00001006003

• BreastCancer_Miroarrays

  Genotyping array data for breast cancer and matched normal mammary gland samples

  Dataset EGAD00010002251

• High throughput profiling of undifferentiated pleomorphic sarcomas identifies two main subgroups with distinct immune contexture, clinical outcome and sensitivity to targeted therapies

  Study EGAS00001004612

• Mutation and Microsatellite Burden Predict Response to PD-1 Inhibition in Children with Germline DNA Replication Repair Deficiency: An Observational Registry Study

  Study EGAS00001005579

• Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths

  Study EGAS00001007402

• Cloning_of_the_breakpoint_of_a_novel_translocation_associated_with_T_acute_lymphoblastic_leukaemia

  Single case of T-ALL carrying t(4;6), a novel translocation.

  Study EGAS00001000520

• MDS 5q- exome reads

  Cancer exome reads consisting of FASTQ paired end reads from bone marrow samples

  Dataset EGAD00001001058

• WGS of Asian lung cancers

  VCF files of somatic variants from tumor-normal pairs of Asian lung cancer patients

  Dataset EGAD00001001240

• Microsatellite unstable colorectal cancers

  Mapped data for 10 Colon MSI cancer samples

  Dataset EGAD00001004500

• Global Anaplastic Thyroid Cancer Initiative

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

  Dataset EGAD00001003236

• RPPA analysis + clinical data

  RPPA analysis from FAIRLANE Trial of Neoadjuvant Ipatasertib Plus Paclitaxel for Triple-Negative Breast Cancer.

  Dataset EGAD00001008507

• The Thrifty Microbiome: The Role of the Gut Microbiota in Obesity in the Amish

  Emerging evidence that the gut microbiota may contribute in important ways to human health and disease has led us and others to hypothesize that both symbiotic and pathological relationships between gut microbes and their host may be key contributors to obesity and the metabolic complications of obesity. Our "Thrifty Microbiome Hypothesis" poses that gut microbiota play a key role in human energy homeostasis. Specifically, constituents of the gut microbial community may introduce a survival advantage to its host in times of nutrient scarcity, promoting positive energy balance by increasing efficiency of nutrient absorption and improving metabolic efficiency and energy storage. However, in the presence of excess nutrients, fat accretion and obesity may result, and in genetically predisposed individuals, increased fat mass may result in preferential abdominal obesity, ectopic fat deposition (liver, muscle), and metabolic complications of obesity (insulin resistance, hypertension, hyperlipidemia). Furthermore, in the presence of excess nutrients, a pathological transition of the gut microbial community may occur, causing leakage of bacterial products into the intestinal lymphatics and portal circulation, thereby inducing an inflammatory state, further aggravating metabolic syndrome traits and accelerating atherosclerosis. This pathological transition and the extent to which antimicrobial leakage occurs and causes inflammatory and other maladaptive sequelae of obesity may also be influenced by host factors, including genetics. In the proposed study, we will directly test the Thrifty Microbiome Hypothesis by performing detailed genomic and functional assessment of gut microbial communities in intensively phenotyped and genotyped human subjects before and after intentional manipulation of the gut microbiome. To address these hypotheses, five specific aims are proposed: (1) enroll three age- and sex-matched groups from the Old Order Amish: (i) 50 obese subjects (BMI > 30 kg/m2) with metabolic syndrome, (ii) 50 obese subjects (BMI > 30 kg/m2) without metabolic syndrome, and (iii) 50 non-obese subjects (BMI < 25 kg/m2) without metabolic syndrome and characterize the architecture of the gut microbiota from the subjects enrolled in this study by high-throughput sequencing of 16S rRNA genes; (2) characterize the gene content (metagenome) to assess the metabolic potential of the gut microbiota in 75 subjects to determine whether particular genes or pathways are correlated with disease phenotype; (3) characterize the transcriptome in 75 subjects to determine whether differences in gene expression in the gut microbiota are correlated with disease phenotype, (4) determine the effect of manipulation of the gut microbiota with antibiotics on energy homeostasis, inflammation markers, and metabolic syndrome traits in 50 obese subjects with metabolic syndrome and (5) study the relationship between gut microbiota and metabolic and cardiovascular disease traits, weight change, and host genomics in 1,000 Amish already characterized for these traits and in whom 500K Affymetrix SNP chips have already been completed. These studies will provide our deepest understanding to date of the role of gut microbes in terms of 'who's there?', 'what are they doing?', and 'how are they influencing host energy homeostasis, obesity and its metabolic complications? PUBLIC HEALTH RELEVANCE: This study aims to unravel the contribution of the bacteria that normally inhabit the human gastrointestinal tract to the development of obesity, and its more severe metabolic consequences including cardiovascular disease, insulin resistance and Type II diabetes. We will take a multidisciplinary approach to study changes in the structure and function of gut microbial communities in three sets of Old Order Amish patients from Lancaster, Pennsylvania: obese patients, obese patients with metabolic syndrome and non-obese individuals. The Old Order Amish are a genetically closed homogeneous Caucasian population of Central European ancestry ideal for genetic studies. These works have the potential to provide new mechanistic insights into the role of gut microflora in obesity and metabolic syndrome, a disease that is responsible for significant morbidity in the adult population, and may ultimately lead to novel approaches for prevention and treatment of this disorder.

  Study phs000258

• Center for Common Disease Genomics [CCDG] - Inflammatory Bowel Disease (IBD) - Global Microbiome Conservancy Host Exomes

  The human body is a complex ecosystem, hosting tens of billions of bacteria, primarily in the gut. This community, known as the 'gut microbiome', is vital to human health, affecting functions ranging from metabolism, immunity, and development, to behavior. Conversely, reduced microbiome diversity and other imbalances of the gut community (dysbiosis) are associated with many diseases of the industrialized world, such as metabolic syndrome, asthma, and inflammatory bowel diseases among others. Microbiome-based interventions thus hold the potential to revolutionize our understanding of, and therapeutic approaches to, many aspects of human health and disease. Despite many advances, current understanding of the human microbiome is largely limited to majority ethnic groups in industrialized nations, and does not reflect the full diversity of human commensal microbiota. In addition to the scientific ramifications of minority underrepresentation, there are significant translational and ethical implications as well: First, failing to capture the full diversity of healthy human microbiota may limit our ability to understand and generate effective therapeutics for many microbiome-associated diseases. Second, underrepresented groups are less likely to benefit from microbiome-based medical advances tailored to well-studied populations, propagating healthcare inequities. The window of opportunity to characterize human microbiome diversity is closing rapidly. Human gut microbial diversity is diminishing around the globe, due to the spread of Westernized diets and lifestyles, which are associated with reduced microbiome biodiversity. The Global Microbiome Conservancy (GMbC) is a non-profit collaboration between scientists and communities around the world that aims to 1) preserve the full biodiversity of the human gut microbiome, 2) characterize its evolution across populations and host lifestyles and 3) investigate its interactions with the human host. We are collecting gut microbiome and human DNA samples from diverse populations around the world, from isolated groups to urbanized populations, to culture and study this essential biodiversity and to preserve it in a living "seed bank" as a long-term safeguard against future extinctions. The National Human Genome Research Institute (NHGRI) has funded a collaborative large-scale genome sequencing effort to comprehensively identify rare risk and protective variants contributing to multiple common disease phenotypes. Called the Centers for Common Disease Genomics (CCDG), this initiative will explore a range of diseases with the ultimate goal of: Undertaking variant discovery for enough different examples of disease architectures and study designs to better understand the general principles of the genomic architecture underlying common, complex inherited diseases. Understanding how best to design rare variant studies for common disease. Developing resources, informatics tools, and innovative approaches and technologies for multiple disease research communities and the wider biomedical research community. The initial focus of the CCDGs will be in cardiovascular disease (early-onset coronary artery disease, atrial fibrillation, hemorrhagic stroke), neuropsychiatric disease (epilepsy, autism), and autoimmune/inflammatory disease (type 1 diabetes, inflammatory bowel disease). The Broad Institute is one of four selected CCDG project centers. Both exome and genotyping information of GMbC participants will help understanding how recruited human populations are structured and genetically related. This human genetic structure will be analyzed in light of gut microbiome compositional and genomic differences to illuminate associations between specific microbiome traits and human groups and the evolutionary processes involved in the co-evolution of human hosts and their gut microbiome. It will also provide variant information for critical genes shaping the composition of microbiomes, such as genes involved in innate and adaptive immunity (e.g. antimicrobial peptides) or in the regulation of the immune response (e.g. Nod2). Association studies between specific variants in these genes and microbiome features will be performed, which will then be validated with in vitro and in vivo experiments. Human data from GMbC cohorts will also increase the genetic diversity of human populations, providing additional variant information for many susceptible loci that were found to be associated with Crohn's disease and ulcerative colitis. The whole genome sequencing data generated is comprised of samples from diverse and indigenous populations. Raw sequencing data, metadata, vcf and phenotype data at the individual level for a subset of the cohort's samples are available at https://anvilproject.org/data. For questions about availability, contact help@lists.anvilproject.org. Microbiome data for the samples sequenced in this study can be found in phs002235 Global Microbiome Conservancy Sequence Data.

  Study phs002205

• Idiopathic Pulmonary Fibrosis Network AntiCoagulant Effectiveness in Idiopathic Pulmonary Fibrosis (IPFNet-ACE-IPF-BioLINCC)

  Data Access NOTE: Please refer to the "Authorized Access" section below for information about how access to the data from this accession differs from many other dbGaP accessions. Objectives: The ACE-IPF trial tested the hypothesis that treatment with warfarin at recognized therapeutic doses would reduce rates of mortality, hospitalization, and declines in Forced Vital Capacity (FVC) in subjects with Idiopathic pulmonary fibrosis (IPF).Background: IPF is a chronic, progressive lung disease of unknown cause characterized by the histopathologic pattern of usual interstitial pneumonia. The median survival of patients with IPF after the onset of symptoms is 2 to 5 years. Prior animal and human studies in pulmonary fibrosis provide a compelling rationale to examine anticoagulation as a therapeutic approach in IPF. Large epidemiologic studies link IPF with thrombosis-related clinical events, such as an increased risk of acute coronary syndrome and deep vein thrombosis. The suspected causal relationship may extend beyond simple coagulation cascade-induced thrombus formation, as procoagulant enzymes may directly stimulate fibrosis via cell surface receptor - mediated responses.Participants: Patients aged 35 to 80 years with progressive IPF were potentially eligible. Progressive IPF was defined as a history of (1) worsening of dyspnea, or (2) physiologic deterioration defined as an absolute decline of either FVC greater than or equal to 10% or DlCO greater than or equal to 15%, a reduction in arterial oxygen saturation of greater than or equal to 5%, or progression of radiographic findings. Between December 14, 2009 and April 1, 2011, 145 subjects were enrolled: 72 in the warfarin group and 73 in the placebo group. The mean age for the population was 67 years. 27% of the subjects were women and 92% were white.Participants were excluded if they met any of the following criteria: current indication for, or treatment with, warfarin, prasugrel, or clopidogrel combined with aspirin; the presence of an increased risk of bleeding; a recent cerebral vascular accident or gastrointestinal bleeding; any current signs or symptoms of severe, progressive, or uncontrolled comorbid illness; and their presence on the active list for lung transplantation. Design: ACE-IPF was a double-blind, randomized, placebo-controlled trial of warfarin targeting an international normalized ratio (INR) of 2.0 to 3.0 in patients with IPF. Subjects were randomized in a 1:1 ratio to warfarin or matching placebo for a planned treatment period of 48 weeks. Study subjects were provided two strengths of warfarin tablets (1 mg and 2.5 mg) or matching placebos. Subjects measured their INR with encrypted meters at least weekly. Participants were seen at screening, baseline, and at 16, 32, and 48 weeks after enrollment. Home monitoring was validated by plasma INR measurement at the week 1 and 16 visits.The primary outcome was a composite endpoint based on the time to all-cause mortality; nonelective, nonbleeding hospitalization; or a decrease in the absolute FVC greater than or equal to 10% from baseline value. Secondary outcome measures included rates of mortality, hospitalization, respiratory-related hospitalization, acute exacerbation, bleeding, cardiovascular events, and changes over time in FVC, 6-minute walk test distance, DlCO, plasma fibrin D-dimer levels, and quality of life (QOL).Conclusions: The study did not show a benefit for warfarin in the treatment of patients with progressive IPF and was terminated due to excess mortality in the warfarin treatment group. Treatment with warfarin was associated with an increased risk of mortality in an IPF population who lacked other indications for anticoagulation.Reported causes of death indicated 11 of the 14 were respiratory-related in the warfarin group versus three of the three in the placebo group. There were also three cardiovascular deaths in the warfarin group versus none in the placebo group. No deaths were attributed to bleeding. The warfarin group also demonstrated an increased rate of combined all-cause hospitalization and all-cause mortality. (Am J Respir Crit Care Med. 2012 Jul 1;186(1):88-95.)

  Study phs004070

• Tumor-associated preferred end coordinates and somatic variants as signatures of circulating tumor DNA

  Cell-free DNA fragmentation is a nonrandom process. We showed that cell-free DNA fragments with ends at certain genomic coordinates had higher likelihoods of being derived from hepatocellular carcinoma. Other coordinates were associated with cell-free DNA molecules originating from the liver. Quantitative assessment of cell-free DNA molecules bearing these respective groups of end signatures correlated with the amounts of tumor-derived or liver-derived DNA in plasma. There were millions of tumor-associated plasma DNA end coordinates across the genome. Due to their high prevalence, they were more readily detectable than somatic mutations as a cancer signature in plasma. Hence, detection of tumor-associated plasma DNA ends may offer a cost-effective means of capturing evidence for the presence of cancer through liquid biopsy assessment.

  Study EGAS00001003160

• Germline variant analysis in childhood AML

  Analysis of rare germline variants in childhood AML in a large panel of cancer predisposition genes (n=216) compiled from literature review, and including genes involved in familial hematological malignancies (HM) and bone marrow failure (BMF) syndromes. The prevalence of extremely rare variants in the combined childhood AML cohort (n=72) was compared to that in the Medical Genome Reference Bank (MGRB; n=2570) comprising individuals aged at least 70 years with no history of cardiovascular disease, dementia or cancer. This showed a significant increase of rare alleles in childhood AML for 100% of subset comparisons. Next additional stringent filtering was applied to determine predicted damaging germline predisposition variants. Overall, 21% of the Australian cohort and 25% of the TARGET cohort presented germline variants predicted to be damaging predisposition variants.

  Study EGAS00001006276

• Neoadjuvant Trastuzumab Response in Breast Cancer

  HER2 (ERBB2) gene amplification and overexpression are present in 15-30% of invasive breast cancers. While HER2-targeted agents such as trastuzumab are effective treatments, therapeutic resistance remains a concern in HER2-positive breast cancer with 40-50% of patients having residual disease after neoadjuvant treatment with chemotherapy and trastuzumab. To investigate features that may make it possible to predict at diagnosis which cancers will be responsive to trastuzumab and chemotherapy, 48 tumor/normal DNA pairs extracted from pretreatment tumor biopsies and blood of HER2-positive breast cancer cases treated with neoadjuvant chemotherapy and trastuzumab were sequenced. Whole genome and exome sequence from tumor (average depth 49x and 71x) and normal (average depth 33x and 69x) DNA are included here as well as RNAseq data for 42 of the tumors. The study cohort was equally divided between patients who experienced pathological complete response and those with residual disease. Samples were obtained from the American College of Surgeons Oncology Group Z1041 trial (NCT00513292) and a local single-institution study (NCT00353483).

  Study phs001291

• Analysis of Epigenomes and Genome Topology in Colorectal Cancer

  When diagnosing cancer, pathologists use nuclear morphology as a hallmark of tumor cells, but the topological changes linked to alterations in the shape of the nucleus were poorly understood. To uncover the molecular changes that occur in the 3D structure of cancer genomes, we integrated topological maps for colon tumors and normal colon tissues with epigenetic, transcriptional, and imaging data. We characterized tumor-associated changes in chromatin loops, topologically associated domains (TADs), and large-scale compartments. We found that chromatin loop rewiring contributes to oncogenic gene expression programs. Whereas TAD structures are largely stable, the spatial partitioning of the open and closed genome compartments is compromised in tumors and is accompanied by hypomethylation and histone mark rearrangements. We also identified a compartment that is reorganized in tumors and is at the interface between the canonical A and B compartments. Similar changes were evident in non-malignant cells that had accumulated excessive cellular divisions. Our analyses suggest that these compartment changes repress stemness and invasion programs while inducing immunity genes, and they may therefore restrain malignant progression.

  Study phs002288

• Mutational signature in colorectal cancer induced by genotoxic pks+ E. coli

  Various species of the intestinal microbiota have been associated with the development of colorectal cancer (CRC), yet a direct role of bacteria in the occurrence of oncogenic mutations has not been established. Escherichia coli can carry the pathogenicity island pks, which encodes a set of enzymes that synthesize colibactin. This compound alkylates DNA on adenine residues and induces double strand breaks in cultured cells. Here, we exposed human intestinal organoids to genotoxic pks+ Escherichia coli by repeated luminal injection over a period of 5 months. Whole genome sequencing (WGS) of clonal organoids before and after this exposure reveals a distinct mutational signature, absent from organoids injected with isogenic pks-mutant bacteria. The same mutational signature is detected in a subset of 3668 human metastatic cancer genomes, predominantly in a subset of CRC cases. Our study describes a distinct mutational signature in CRC and implies that the underlying mutational process directly results from past exposure to bacteria carrying the colibactin-producing pks pathogenicity island.

  Study EGAS00001003934

• Multi-focal genomic dissection of synchronous primary and metastatic tissue from de novo metastatic prostate cancer

  De novo metastatic prostate cancer is highly aggressive, but the paucity of routinely-collected tissue in this setting has hindered genomic stratification and jeopardizes precision oncology efforts. Here, we leveraged a rare study of surgical intervention in 43 de novo metastatic prostate cancers to assess somatic genotype across 607 synchronous primary and metastatic tissue foci plus circulating tumor DNA. Intra-prostate heterogeneity was pervasive and impacted clinically-relevant genes, resulting in frequent discordance between select primary-restricted foci and synchronous metastases. Additional complexity was driven in several instances by polyclonal metastatic seeding from the reservoir of phylogenetically-related primary populations. When simulating standard clinical practice relying on a single tissue focus, genomic heterogeneity plus highly variable per-sample tumor fraction caused false genotyping of dominant disease. However, in silico modeling demonstrated that analysis of multiple biopsy cores can rescue misassigned somatic genotypes. Our results define the relationship between synchronous treatment-naive primary and metastatic lesions in de novo metastatic prostate cancer and provide a framework for implementing genomics-guided patient management.

  Study EGAS00001006466

• Structural Expression of BMMF in tissues of colorectal, lung and pancreatic cancer patients

  Chronic inflammation, linked to the presence of bovine milk and meat factors (BMMF) and specific subsets of macrophages, results in oxygen radical synthesis and induction of mutations in DNA of actively replicating cells and replicating single stranded DNA (zur Hausen et al., 2017). Cancers arising from this process have been characterized as indirect carcinogenesis by infectious agents (without persistence of genes of the agent in premalignant or cancers cells). Here we investigate structural properties of pleomorphic vesicles, regularly identified by staining peritumour tissues of colorectal, lung and pancreatic cancer for expression of BMMF Rep. The latter represents a subgroup of BMMF1 proteins involved in replication of small single-stranded circular plasmids of BMMF, but most likely also contributing to pleomorphic vesicular structures found in the periphery of colorectal, lung and pancreatic cancers. Structurally dense regions are demonstrated in preselected areas of colorectal cancer, after staining with monoclonal antibodies against BMMF1 Rep. Similar structures were observed in human embryonic cells (HEK293TT) overexpressing Rep. These data suggest that Rep or Rep isoforms contribute to the structural formation of vesicles.

  Study EGAS00001006744

• LLDeep DAG2+ scRNA-seq in PBMCs

  Single cell transcriptomics of PBMCs of 47 donors from the Lifelines Deep cohort (general population, Northern part of the Netherlands). Cells of five or six different donors were pooled together in one sample pool, resulting in eight different sample pools. In total, 28.855 cells were captured and their transcriptomes were sequenced to an average depth of 74k. Genotype data was available for each donor, which allowed us to use the Demuxlet method that uses variable SNPs between the pooled individuals to determine which cell belongs to which individual. Since genotype information is lacking of 2 individuals, the transcriptome of only 45 individuals could be retrieved.

  Dataset EGAD00010001315

• Single Cell RNASeq for ARMS tumors

  6 samples from 3 mice related to Alveolar Rhabdomysarcoma. In this study, we employ scRNA-seq to analyze ARMS tumors from a conditional mouse model of ARMS. The conditional knock-in mouse model of ARMS, in which the Pax3-Foxo1 allele is activated in the skeletal muscle cell lineage via Myf6Cre (Myf6CrePax3P3Fm/P3FmTrp53F2-10/F2-10; referred to hereafter as GEMM-ARMS) has been described previously23,24. These mice also carry Cre-activated reporters, eYFP to label Pax3::Foxo1-expressing cells and dsRED2 to labels Myh2-expressing cells. Some tumors are derived from GEMM-ARMS mice, and some are allografts of GEMM-ARMS tumors into immunodeficient mice

  Dataset EGAD50000002241

• ATAC-seq of uncultured CD112high and CD112low long-term(LT) human hematopoietic stem cells (HSC) from umbilical cord blood

  ATAC-sequencing was performed to establish chromatin accessibility signatures that underlie the differential in vitro priming and regeneration phenotypes of CD112high and CD112low LT-HSC. CD112high and CD112low LT-HSC from 2-3 independent human umbilical cord blood pools were prospectively isolated for DNA extraction, library preparation and sequencing.

  Study EGAS00001005121

• scRNA-seq to study interactions between HSPCs, BMSCs and immune microenvironment

  Mechanisms of clonal evolution in myeloid neoplasms remain incompletely understood. Darwinian theory predicts that the (micro)environment of clone-propagating stem cells may contribute to clonal selection. Here, we provide data fitting this model, establishing a relationship between stromal niche inflammation, inflammatory stress in HSPCs, clonal resistance and leukemic evolution in human MDS.

  Study EGAS00001008181

• mRNA and T cell receptor sequencing of patients with Pandemrix-associated narcolepsy type 1

  PBMCs isolated from 27 individuals (11 narcolepsy type 1 patients, 16 healthy controls) were stimulated with the peptide Neuroaminidase 175-189 or Protein-O-mannosyl transferase 1 (POMT1) 675-689 or media as control. FACS sorted CD4+ and CD8+ lymphocytes from one patient were subjected to the same stimulation. Transcriptome profiling was done with a 3' tagging protocol. T cell receptor repertoires were profiled with amplicon sequencing (Rep-seq). The dataset contains FASTQ files with sequencing reads, transcript count matrices and TCR clonotypes.

  Dataset EGAD00001006796

• Single-cell T-cell receptor sequencing data of peripheral blood mononuclear cells obtained from 30 ATL patients, 11 HTLV-1-infected asymptomatic carriers, and 4 healthy donors.

  Single-cell T-cell receptor sequencing (scTCR-seq) data of peripheral blood mononuclear cells (PBMCs) obtained from 30 ATL patients (34 samples including 4 sequential ones), 11 HTLV-1-infected asymptomatic carriers, and 4 healthy donors.

  Dataset EGAD00001007014

• Single-cell multi-omics analysis of COVID-19 patients with pre-existing autoimmune diseases

  Single-cell analysis of the transcriptome, T cell immune receptors, and surface proteome (CITE-seq) from peripheral blood mononuclear cells (PBMCs) of COVID-19 patients with pre-existing autoimmune diseases (rheumatoid arthritis n = 5, psoriasis n = 4, or multiple sclerosis n = 3), as well as COVID-19 patients without pre-existing autoimmunity as controls (n = 10) to investigate altered immune responses.

  Dataset EGAD00001007982

• Paired-end Whole Exome-seq analysis of the 3D evolution of glioma cell populations. Part 2.

  Dataset contains paired-end Whole Exome sequencing data from 257 glioma samples from 28 patients. 26 normal blood samples are also included.

  Dataset EGAD00001009496

• mRNA and T cell receptor sequencing of patients with Pandemrix-associated narcolepsy type 1

  PBMCs isolated from 27 individuals (11 narcolepsy type 1 patients, 16 healthy controls) were stimulated with the peptide Neuroaminidase 175-189 or Protein-O-mannosyl transferase 1 (POMT1) 675-689 or media as control. FACS sorted CD4+ and CD8+ lymphocytes from one patient were subjected to the same stimulation. Transcriptome profiling was done with a 3' tagging protocol. T cell receptor repertoires were profiled with amplicon sequencing (Rep-seq). The dataset contains FASTQ files with sequencing reads, transcript count matrices and TCR clonotypes.

  Dataset EGAD00001006797

• Whole-genome plasma DNA sequencing in CRC patients under anti-EGFR therapy

  In this study we performed whole genome sequencing of plasma DNA (plasma-Seq) of 19 plasma-DNA samples from a total of 10 patients treated with anti-EGFR therapy. We demonstrated that development of resistance to anti-EGFR therapies is frequently associated with focal amplifications of KRAS, MET, and ERBB2. We also showed that focal KRAS amplifications can be acquired in tumor genomes of patients under cytotoxic chemotherapy. Furthermore, we provide evidence that specific chromosomal polysomies, such as overrepresentations of 12p and 7p, harboring KRAS and EGFR, respectively, determine responsiveness to anti-EGFR therapy.

  Dataset EGAD00001000748

• EGAD00000000013

  WTCCC1 project Breast cancer (BC) samples

  Dataset EGAD00000000013

• Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments

  Dataset EGAD00001001602

• Colorectal cancer cells possess an equipotent capacity to enter a developmental pausing-like state to survive chemotherapy

  Dataset EGAD00001006847

• MAF dataset of Colorectal Cancer Synthetic genomes

  This dataset contains genomic variants data in MAF format from four patients synthetically generated

  Dataset EGAD50000000315

• cfDNA whole-genome TAPS data for cancer detection DAC

  80x whole-genome sequencing data from circulating tumour DNA pre-treated with TAPS from 91 patients

  Dac EGAC50000000440

• Integrated Genomic and Transcriptomic Analysis Reveals Unique Characteristics of Hepatic Metastases and Pro-metastatic Role of Complement C1q in Pancreatic Ductal Adenocarcinoma

  Study EGAS00001004821

• CEHM

  Study of the genetic and epigenetic clonal evolution of blood cancers.

  Study EGAS00001002366

• RBtargetedSeq

  Retinoblastoma is a rare childhood cancer of the retina. We studied retinoblastoma by Targeted Sequencing.

  Dataset EGAD00001008004

• Pancreatic Cancer OICR

  ICGC DCC Release 24, PACA-CA Whole Genome sequence merged alignments

  Dataset EGAD00001003270

• Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes

  Aberrant DNA repair processes are a hallmark of human tumours. How these deficiencies variously impact the genomes of ovarian cancer between and within histotypes remains unknown. We studied the whole genome pointmutation and structural variation patterns of 133 tumours (59 high grade serous (HGSC), 35 clear cell (CCOC), 29 endometrioid (ENOC), and 10 adult granulosa cell tumours (GCT)) as a substrate for class discovery in ovarian cancer. Ab-initio clustering of integrated point mutation and structural variation signatures revealed seven novel subgroups, comprising between and within histotype stratification. Prevalence of fold-back inversions (FBI) co-localised with high level amplification events divided HGSC into two prognostically significant subgroups. This finding was recapitulated in two additional independent cohorts (total n=576 cases), and transcended gene based mutation status and gene expression as prognostically relevant features of HGSC. CCOC were divided into one group harbouring a signature reflective of active genome editing via APOBEC enzymes (26%) and a complementary group with an age-relatedmutational signature. ENOC were divided intomicrosatellite instable (MSI) cases (28%) with a distinctmismatch repairmutation signature and an outlying mutation rate, with the remainder of cases distributed amongst the remaining six groups. We suggest the FBI, MSI, and APOBEC groups represent biologic strata that could direct treatment strategies. Taken together, our work establishes the efficacy of the somatic genome as a biomarker to stratify ovarian cancers, simultaneously identifying patients that may benefit from emerging therapeutics and distinct subgroups within classic ovarian cancer histotypes.

  Study EGAS00001002390

• Neoantigen responses to Immunotherapy in Prostate Cancer

  To determine whether antigen-specific T cell responses can be elicited following treatment with ICT in cancers that have a low TMB, a clinical trial with ipilimumab (anti-CTLA-4) was conducted in 30 patients with metastatic castration-resistant prostate cancer (CRPC). We identified 2 distinct groups of patients divided by clinical outcomes, which consisted of a cohort with Favorable and Unfavorable outcomes. Compared to the Unfavorable cohort, the patients in the Favorable cohort were more likely to have higher intratumoral CD8 T cell density and/or IFN-γ response gene signature, including five patients who had antigen-specific T cell responses that were only detectable after ipilimumab therapy. Three patients had T cell responses against tumor-associated antigens (PSMA and PAP). Importantly, two patients with a relatively low TMB had T cell responses against unique neoantigens. Collectively, our data indicate that a subset of patients with metastatic prostate cancer benefit from ICTs, particularly those who have immunological biomarkers associated with effector T cell responses. Publication: Sumit K. Subudhi, Luis Vence, Hao Zhao, Jorge Blando, Shalini S. Yadav, Qing Xiong, Alexandre Reuben, Ana Aparicio, Paul G. Corn, Brian F. Chapin, Louis L. Pisters, Patricia Troncoso, Rebecca Slack Tidwell, Peter Thall, Chang-Jiun Wu, Jianhua Zhang, Christopher L. Logothetis, Andrew Futreal, James P. Allison and Padmanee Sharma, 2020, Neoantigen responses, immune correlates, and favorable outcomes after ipilimumab treatment of patients with prostate cancer. Science Translational Medicine, 01 Apr 2020:Vol. 12, Issue 537, eaaz3577DOI: 10.1126/scitranslmed.aaz3577. https://pubmed.ncbi.nlm.nih.gov/32238575/

  Study EGAS00001004050

• ICGC prostate cancer MBD sequencing (DNA methylation)

  Dataset EGAD00001000632

• Nanostring

  Nanostring PanCancer immune profiling data for The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer

  Dataset EGAD00010001515

• Blood dataset - Case-control

  blood-based gene expression from breast cancer cases and age-matched controls

  Dataset EGAD00010001062

• Ovarian carcinoma

  Genome-wide NanoRCS of cfDNA from ascites of Ovarian cancer patients

  Dataset EGAD50000000219

• TCR β-chain repertoire characterization of regulatory and conventional T cells in breast tumors from breast cancer patients.

  Dataset EGAD00001006428

• PanCancer_Phosphoproteomics2024

  Pan-cancer phosphoproteomics profiling data for 1000 retrospective and prospective samples of the MASTER/INFORM cohort,Shotgun proteomics

  Dataset EGAD00010002730

• BAP1_sequence_of_uveal_melanoma_cell_lines

  Detection of BAP1 mutations in DNA from 3 uveal melanoma cell lines.

  Study EGAS00001001520

• Pulldown_DNA_methylation_study_v2

  Pilot study to set up sequencing protocols for targeted pulldown methylation profiling

  Study EGAS00001000979

• Nuclear_single_seq_pilot

  The aim of this study is to analyse the genomes of tumours

  Study EGAS00001003386

• Low_input_LC__ISC_

  R&D project to develop low input library construction methods.

  Study EGAS00001001856

• Somatic_mutation_in_edited_cholangiocyte_organoids_WGS

  Characterisation of mutation rates and patterns in edited human cholangiocyte organoids (WGS)

  Study EGAS00001006326

• Psoriatic_arthritis_WGS

  Whole genome sequencing of immune cells from patients diagnosed with psoriatic arthritis

  Study EGAS00001002822

• Infant_Spindle_Tumour_Study

  We aim to describe the transcriptomic landscape of infant spindle cell tumours.

  Study EGAS00001002935

• MED12L Gene Alterations Define Aggressive BRCA2-Mutant Prostate Cancers

  Aligned sequence data from 14 Prostate cancer samples with BRCA2 mutations

  Dataset EGAD00001002739

• RCRF release 1

  Rare Cancer Research Foundation: leiomyosarcoma, large cell neuroendorcrine carcinoma, clear cell carcinoma

  Dataset EGAD00001010199

• Familial Breast cancer dataset

  Illumina HiSeqXTen platform sequencing data of whole genome libraries prepared from 156 matched tumour-normal samples from 78 donors

  Dataset EGAD00001004494

• 20180221_EGA_OESO

  Illumina platform sequencing of whole genome libraries prepared from normal, Barrett's oesophagus and oesophageal cancer samples from 44 donors

  Dataset EGAD00001003996

• Anaplastic Meningioma V3 cancer gene panel

  Investigation into causal genes underlying anaplastic meningioma

  Dataset EGAD00001001430

• Genetic investigation of 12q-amplified osteosarcomas

  Further investigation and characterisation of 12q-amplified low- and high-grade osteosarcomas with MDM2 and/or CDK4 amplification focusing on SV, copy number and gene fusion analyses. In total, 25 cases (33 samples total due to multi-sampling) were included, with some form of sequencing data available for 27 samples. Mate-pair whole genome sequencing (Illumina) is available for 19 samples, longread whole genome sequencing (PacBio HiFi) on 10 samples and RNA-sequencing (Illumina Truseq) on 21 samples. Data is available as BAM files.

  Dataset EGAD50000000707

• Single nucleus RNA sequencing of squamous cell carcinoma arising from mature teratoma of the ovary

  Squamous cell carcinoma arising from mature teratoma is one of the rare ovarian cancers. Therefore, the detailed molecular background of this disease has not been elucidated. The purpose of this study is to investigate the single-cell transcriptional landscape of this disease.

  Study JGAS000521

• Mapping genetic variants underlying gene regulation in healthy intestinal cell types to identify novel IBD drug targets (2020-05-12)

  Biopsies from the terminal ileum and rectum of healthy individuals are digested on ice to single cells and processed for single-cell RNA-sequencing (10X Genomics and Illumina) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2020-05-12.

  Dataset EGAD00001006139

• Sequencing data for oesophageal and related samples - Scott et al (WGS, RNA)

  Data supporting: "Evidence that polyploidy in esophageal adenocarcinoma originates from mitotic slippage caused by defective chromosome attachments" Scott et al. WGS and RNAseq sequencing data Organoid, tumour and normal samples BAM files

  Dataset EGAD00001006738

• PIVUS study - Longitudinal transcriptomics - Advanced aging

  We performed RNA sequencing in whole-blood from the same 65 individuals from the PIVUS study at ages 70 and 80 (130 samples) to quantify how gene expression, alternative splicing, and their genetic regulation are altered during this 10-year period of advanced aging. Each individual has four fastq files, two for each age. Consecutive sample IDs refer to the sample individual, e.g. PIVUS003 and PIVUS004 are the age 70 and age 80 samples of the first individual.

  Dataset EGAD00001004965

• Single cell study of infant leukemias

  We have performed single cell RNA-sequencing for infant and childhood B-cell acute lymphoblastic leukemias as well as infant acute myeloid leukemias at diagnosis. The sequencing was performed with 10X Chromium single cell 3’ and 5’ chemistry.

  Dataset EGAD00001007854

• Single-cell GoT sequencing from CH, MDS and AML patients with CH mutations

  Single-cell targeted amplicon RNA sequencing from CH (n = 3), MDS (n = 6, MDS02 in 2 replicates) and AML (n =1, in 2 replicates) samples with mutations in splicing factors (SF3B1 - n = 8 [2 -CH, 6 MDS], U2AF1 n = 1) or transcription regulators (DNMT3A - CH04). The transcripts are targeted to detect a particular CH mutation in the listed genes. U2AF1 GoT are full-length cDNA, while the rest follow the 10x 3' V3 protocol.

  Dataset EGAD00001011284

• Neuroblastoma patient WGS data

  Paired tumor and normal WGS of primary neuroblastomas. This is an update of the „Berlin Neuroblastoma Dataset” (EGAS00001004022). This data was used for the analysis of circular RNA expression and regulation in neuroblastoma.

  Dataset EGAD00001008123

• Sequencing data for oesophageal and related samples - Izadi et al (WGS, RNA)

  Data supporting: "Genomic analysis of response to neoadjuvant chemotherapy in esophageal adenocarcinoma" Izadi et al. WGS for tumour and normal samples. RNAseq for tumour samples.

  Dataset EGAD00001007493

• Patient-derived gene and protein expression signatures of NGLY1 deficiency

  Single-end bulk RNA sequencing results of cell lines derived from patients described with NGLY1 deficiency as well as parent and CRISPR edited controls. The cell lines represent 4 different cell types: fibroblasts, lymphoblastoid cells, induced pluripotent stem cells (iPSCs) and neural progenitor cells (NPCs.).

  Dataset EGAD00001008094

• DCM-controls

  DCM-controls (113 human non-DCM samples) human heart biopsies from 113 non-diseased controls were subjected to RNA sequencing in order to assess transcriptome variation. We used Illumina HiSeq2000 technology. Each sample-dataset contains the output from tophat-1.4.1 (one *.bam file with the aligned reads and two *.fq files one with the not aligned forward read and one with the revers unaligned reads). We reveal extensive differences of gene expression and splicing between dilated cardiomyopathy patients and controls.

  Dataset EGAD00001003391

• DCM-cases

  DCM-cases (149 human DCM samples) human heart biopsies from 149 patients with dilated cardiomyopathy (DCM) were subjected to RNA sequencing in order to assess transcriptome variation. We used Illumina HiSeq2000 technology. Each sample-dataset contains the output from tophat-1.4.1 (one *.bam file with the aligned reads and two *.fq files one with the not aligned forward read and one with the revers unaligned reads). We reveal extensive differences of gene expression and splicing between dilated cardiomyopathy patients and controls.

  Dataset EGAD00001003390

• Sequencing data for oesophageal and related samples - Nowicki-Osuch, Zhuang et al (bulk RNA)

  Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. RNAseq (BAM files) 12 Barrett's samples 12 normal oesophageal samples 11 normal gastric cardia samples

  Dataset EGAD00001006882

• SCAT_Osteosarcoma_Validation

  This experiment is to validate putative somatic substitutions and indels identified in an exome screen of ~50 osteosarcoma tumour/normal pairs. It is the first stage in our ICGC commitment to study osteosarcoma. The validation process is an important component of our analysis to clarify the data prior to looking for evidence of new cancer genes, or subverted pathways important in the development of cancer. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001000280

• Exploiting evolutionary steering in cancer therapy

  This dataset contains 9 bam files of exome sequencing for an experiment of evolved resistance. Here a barcoded cell line (HCC827 - POT) has been treated under high concentrations of gefitinib (GEF) and trametinib (TRM) until resistance has evolved, as well as under control conditions (DMSO). The dataset contains exome sequencing of confluent cells for three replicates for each anti-cancer drug as well as two replicates of growth under DMSO conditions. The original barcoded cell line (POT) was also exome sequenced and is included in the cohort. Sequencing was performed on the Illumina NovaSeq platform.

  Dataset EGAD00001005782

• Targeted sequencing (paired) of HR genes in primary and metastatic patient-derived xenografts (PDXs) of colorectal cancer (CRC)

  The dataset includes DNA targeted paired-wise (2 FASTQ per sample) sequencing of a manually curated panel of 44 genes with a documented role in homologous recombination (HR), a pathway of DNA damage response. Sequencing was conducted in 69 tumors from patients with metastatic colorectal cancer after serial passaging in mice (patient-derived xenografts, PDXs). For each PDX model profiled for HR gene mutations, therapeutic annotation of response to FOLFIRI (a chemotherapeutic regimen consisting of the combination of 5-fluorouracil and irinotecan) is available.

  Dataset EGAD50000000107