10161 results for "cancer rna-seq"

in 64.59 milliseconds.

• Dataset for soft_tissue_tumor-RNA

  Rare cancer sequencing data of 243 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008859

• Single cell and whole tissue transcriptomes investigating Barrett's oesophagus

  Data consists of 4,640 RNA-sequencing sample libraries. These libraries were sequenced from four sites of the upper gastro-intestinal tract (Barrett’s oesophagus, proximal normal oesophagus, proximal normal stomach, and duodenum) in two experiments. 4,587 libraries were produced in the first experiment in which whole transcriptomes were isolated single cells dissociated from endoscopic biopsy tissue obtained from the four previously mentioned tissues. The other 53 libraries were produced in the second experiment in which whole transcriptomes were isolated from whole tissue from endoscopic biopsies of the four previously mentioned tissues. The data found here are stored in the raw fastq file format from paired end sequencing.

  Dataset EGAD00001004344

• Orthotopic murine Group 3 medulloblastoma in C57Bl/6 mice treated with sham or craniospinal irradiation

  Mice with medulloblastoma (Group 3) were treated with sham (isofluorane and imaging xray) or CSI as described by Abbas et al (2022). Total RNA was isolated with RNeasy Plus Mini Kit (Qiagen), library preparation (SureSelect, Agilent), rRNA depletion (Ribo-Zero Plus, Illumina) and sequencing were carried out by GenomicsWA or Australian Genome Research Facility. Libraries were sequenced on NovaSeq 6000 S1 flow cells as paired-end 150bp reads (Illumina).

  Dataset EGAD00001008510

• TK-EP862 - Patient-derived xenograft model of Posterior Fossa A Ependymoma - WSG data

  In Vivo Loss of Tumorigenicity in a Patient-Derived Orthotopic Xenograft Mouse Model of Ependymoma. Whitehouse et al. 2023 Frontiers in Oncology. We describe the establishment of a patient-derived orthotopic xenograft (PDOX) model of posterior fossa A (PFA) EPN, derived from a metastatic cranial lesion. Patient and PDOX tumors were analyzed using RNA sequencing. WSG data (paired end) provided here correspond to germline DNA, Surgical sample 4 (described in the above manuscript as a cranial metastasis of PFA ependymoma), and a patient-derived xenograft derived from the patient.

  Dataset EGAD00001010008

• RNA-sequencing of ex vivo exhausted human antigen-specific T cells

  Tumor-specific T cells are frequently exhausted by chronic antigenic stimulation. To explore new pathways for reinvigoration of anti-tumor immune functions, we developed a human ex vivo exhaustion model by repetitive antigenic stimulation of primary CD8 T cells. This results in T cells that resemble patient-derived T cells in tumors on a phenotypic and transcriptional level.

  Study EGAS00001006794

• Placental_mosaicism

  The aim of this study is to survey somatic mutations in human placentas.

  Study EGAS00001003549

• The_mutational_landscape_of_recurrent_Glioblastome_multiforme

  Targeted gene screen of approx 120 patients with primary GBM and recurrent samples.

  Study EGAS00001001764

• MutWP1__CRUK_Grand_Challenge_Mutographs_of_Cancer__pancreas_LCM_

  Samples prepared by LCM - 5 cases for pilot study. Bulk DNA not available.

  Study EGAS00001003197

• DAC for Combined MEK and BCL-2/XL inhibition is effective in high-grade serous ovarian cancer patient-derived xenograft models and BIM levels are predictive of responsiveness

  Dac EGAC00001001250

• Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing

  Dataset EGAD00001000856

• Exome sequencing

  Exome sequencing of peripheral blood from 4 individuals of a family with familial colorectal cancer type X

  Dataset EGAD00001001009

• Chugai colorectal organoid sequencing

  Genomic and transcriptomic characterization of drug-resistant colon cancer stem cell lines.

  Dataset EGAD00001001446

• RTKs in Multiple Myeloma

  Cancer amplicon reads consisting of BAM paired end reads from primary multiple myeloma samples.

  Dataset EGAD00001001935

• OT2_Illumina_WXS_T

  Whole-exome sequencing on Illumina HiSeq2000/2500 of colorectal cancer primary tumor sample (OT2_cohort)

  Dataset EGAD00001003383

• ega_SJLIFE_BMD_nonALL

  A replication cohort consisting of 1428 adult survivors of any non-ALL pediatric cancer

  Dataset EGAD00010001395

• DNA Methylation profiles of colorectal cancer samples

  Illumina 450K DNA methylation profiles of 314 fresh-frozen colorectal mucosa, adenoma or adenocarcinoma samples.

  Dataset EGAD00010001888

• Proteom study primary CRC and LM

  Proteom characterization in primary colorectal cancer and corresponding liver metastasis

  Dataset EGAD00010002237

• RCRF release 1

  Transcriptome sequencing from the Rare Cancer Research Foundation: leiomyosarcoma, large cell neuroendocrine carcinoma, clear cell carcinoma

  Dataset EGAD00001010198

• Identifying_new_diagnostic_and_treatment_pathways_for_patients_with_unclassifiable_sarcomas

  Whole genome sequencing of tumour normal pairs of human undifferentiated sarcomas.

  Study EGAS00001001604

• Evolution and clinical impact of genetic epistasis within EGFR-mutant lung cancers

  The current understanding of tumorigenesis is largely centered on a monogenic driver oncogene model. This paradigm is incompatible with the prevailing clinical experience in most solid malignancies: monotherapy with a drug directed against an individual oncogenic driver typically results in incomplete clinical responses and eventual tumor progression1-7. By profiling the somatic genetic alterations present in over 2,000 cases of lung cancer, the leading cause of cancer mortality worldwide, we show that combinations of functional genetic alterations, i.e. genetic collectives dominate the landscape of advanced-stage disease. We highlight this polygenic landscape and evolution of advanced-stage non-small cell lung cancer (NSCLC) through the spatial-temporal genomic profiling of 7 distinct tumor biopsy specimens and 6 plasma specimens obtained from an EGFR-mutant NSCLC patient at (1) initial diagnosis of early-stage disease, (2) metastatic progression, (3) sequential treatment and resistance to 2 EGFR inhibitors, (4) death. The comprehensive genomic analysis of this case, coupled with circulating free (cf) tumor DNA profiling of additional advanced-stage EGFR-mutant NSCLC clinical cohorts with associated treatment responses uncovered features of evolutionary selection for multiple concurrent gene alterations: including the presence of EGFR inhibitor-sensitive (EGFRL858R;EGFRexon19del) or inhibitor-resistant (EGFRT790M;EGFRC797S) forms of oncogenic EGFR along with cell cycle gene alterations (e.g. in CDK4/6, CCNE1, RB1) and activating alterations in WNT/β-catenin and PI3K pathway genes, which our data suggest can cooperatively impart non-redundant functions to limit EGFR targeted therapy response and/or promote tumor progression. Moreover, evidence of an unanticipated parallel evolution of both EGFR T790M and two distinct forms of oncogenic PIK3CA was observed. Our study provides a large-scale clinical and genetic dataset of advanced-stage EGFR-mutant NSCLC, a rationale for specific polytherapy strategies such as EGFR and CDK4/6 inhibitor co-treatment to potentially enhance clinical outcomes, and prompts a re-evaluation of the prevailing paradigm of monogenic-based molecular stratification for targeted therapy. Instead, our findings highlight an alternative model of genetic collectives that operate through epistasis to drive lung cancer progression and therapy resistance.

  Study EGAS00001002604

• Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets

  Untreated prostate cancers rely on androgen receptor (AR) signaling for growth and survival, forming the basis for the initial efficacy of androgen deprivation therapy (ADT). Yet, the disease can relapse and progress to a lethal stage termed castration-resistant prostate cancer (CRPC). Reactivation of AR signaling represents the most common driver of CRPC growth and next generation AR signaling inhibitors (ARSIs) are now used in combination with ADT as a first line therapy. However, ARSIs can result in selective pressure generating AR-independent tumors. The transition from AR-dependence frequently accompanies a change in phenotype resembling developmental trans-differentiation or ‘lineage plasticity’. Neuroendocrine prostate cancer, which lacks a defined pathologic classification, is the most studied type of lineage plasticity. However, most AR-null tumors do not exhibit neuroendocrine features and are classified as ‘double-negative prostate cancer’, the drivers of which are poorly defined. Lineage plasticity studies in CRPC are limited by the lack of genetically defined patient-derived models that recapitulate the disease spectrum. To address this, we developed a biobank of organoids generated from patient biopsies to study the landscape of metastatic CRPC and allow for functional validation assays. Proteins called transcription factors (TFs) are drivers of tumor lineage plasticity. To identify the key TFs that drive the growth of AR-independent tumors, we integrated epigenetic and transcriptomic data generated from CRPC models. By presenting a map of the chromatin accessibility and transcriptomic landscape of CRPC using a diverse biobank of organoids, PDXs and cell lines that recapitulate the heterogeneity of metastatic prostate cancer, we validate CRPC-AR and CRPC-NE subtypes and reveal two subtypes of AR-negative/low samples as well as their respective masterTFs. Additional analysis revealed a model in which YAP, TAZ, TEAD and AP-1 function together and drive oncogenic growth in CRPC-SCL samples. Overall, we show here how an approach to stratify CRPC patients into four subtypes using their transcriptomic signatures can potentially inform upon appropriate clinical decisions.

  Study EGAS00001006059

• Influence of Genomic Landscape on Cancer Immunotherapy for Newly Diagnosed Ovarian Cancer: Biomarker Analyses from the IMagyn050 Randomized Clinical Trial

  The IMagyn050 trial (NCT03038100), which evaluated the efficacy of Atezo vs placebo (Pla) with carboplatin, paclitaxel and bevacizumab (CPB) in front line ovarian cancer patient (pts), did not meet its co-primary endpoints of PFS in ITT or PD-L1+ (Moore et al. JCO 2021). The aim of this exploratory study was to evaluate whether patients with BRCA1/2-mutated or homologous recombination-deficient (HRD) ovarian cancers benefitted from atezolizumab in the phase III IMagyn050 (NCT03038100) trial. Methods: Patients with newly diagnosed ovarian cancer were randomized to either atezolizumab or placebo with standard chemotherapy and bevacizumab. PD-L1 status of tumor-infiltrating immune cells was determined centrally (VENTANA SP142 assay). Genomic alterations, including deleterious BRCA1/2 alterations, genomic loss of heterozygosity (gLOH), tumor mutation burden (TMB), and microsatellite instability (MSI), were evaluated using the FoundationOne assay. HRD was defined as gLOH ≥16%, regardless of BRCA1/2 mutation status. Potential associations between progression-free survival (PFS) and genomic biomarkers were evaluated using standard correlation analyses and log-rank of Kaplan-Meier estimates. Results Among biomarker-evaluable samples, 22% (234/1050) harbored BRCA1/2 mutations and 46% (446/980) were HRD. Median TMB was low irrespective of BRCA1/2 or HRD. Only 3% (29/1024) had TMB ≥10 mut/Mb and 0.3% (3/1022) were MSI-high. PFS was better in BRCA2-mutated versus BRCA2-non-mutated tumors and in HRD versus proficient tumors. PD-L1 positivity (≥1% expression on immune cells) was associated with HRD but not BRCA1/2 mutations. PFS was not improved by adding atezolizumab in BRCA2-mutated or HRD tumors; there was a trend toward enhanced PFS with atezolizumab in BRCA1-mutated tumors. Conclusion Most ovarian tumors have low TMB despite BRCA1/2 mutations or HRD. Neither BRCA1/2 mutation nor HRD predicted enhanced benefit from atezolizumab. This is the first randomized double-blind trial in ovarian cancer demonstrating that genomic instability triggered by BRCA1/2 mutation or HRD is not associated with improved sensitivity to immune checkpoint inhibitors.

  Study EGAS00001006838

• Combination Therapies for Personalised Cancer Medicine in 11-18

  This study involves mutagenizing 11-18 with ENU to identify those mutations which engender resistance to targeted treatment. In the last decade we have begun to move towards the use of targeted therapeutics in the clinic, often resulting in dramatic response rates in cancer patients. However, clinical experience has demonstrated time and time again that such responses are invariably followed by the development of drug resistance. Identification of the underlying mechanisms may enable us to reverse such resistance. Traditional methods of modelling this resistance in vitro can lead to a plethora of potential resistance mechanisms that can be difficult to decipher.

  Study EGAS00001002579

• MutWP5__CRUK_Mutographs_of_Cancer__Lung__PD38234__Targeted_

  Sequencing of LCM-derived microbiopsies from explanted lung from pulmonary fibrosis patient. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Deep sampling throughout multiple regions of the lung will determine whether there are differences in smoking-related mutation burden in different portions of the lung. Targeted sequencing will be conducted on samples to identify drivers of interest and clonality of the samples, well-performing samples will be sent for subsequent whole-genome sequencing. Results from this portion of the study will be compared to other individuals with smoking-related diseases (COPD, pulmonary fibrosis, lung cancer), and normal, non-smoking lungs.

  Study EGAS00001003325

• Use_of_Deep_Sequencing_to_Dectect_Clonal_Mutations_In_Sun_Exposed_Skin_Epidermis

  This study aims to define the landscape of somatic mutations in sun exposed human skin by deep sequencing, analyse their frequency and use the data to infer the effect of mutations on proliferating cell behaviour. The frequency of each mutation will reflect the size of the clone of cells in the tissue sample. By analyzing small samples, clones with as few as 100 cells will be detectable. Allele frequency distributions for each mutation will be used to infer cell fate using published methods (Klein et al. 2010). This study will shed unprecedented light on the early clonal events that lead to the emergence of cancer.

  Study EGAS00001000515

• Use_of_Deep_Sequencing_to_Dectect_Clonal_Mutations_In_Sun_Exposed_Skin_Epidermis_PART2

  This study aims to define the landscape of somatic mutations in sun exposed human skin by deep sequencing, analyse their frequency and use the data to infer the effect of mutations on proliferating cell behaviour. The frequency of each mutation will reflect the size of the clone of cells in the tissue sample. By analyzing small samples, clones with as few as 100 cells will be detectable. Allele frequency distributions for each mutation will be used to infer cell fate using published methods (Klein et al. 2010). This study will shed unprecedented light on the early clonal events that lead to the emergence of cancer.

  Study EGAS00001000603

• Mutational signatures in head and neck cancer (H019)

  Genomic alterations are a driving force in the multistep process of head and neck cancer (HNC) and result from the interaction of exogenous environmental exposures and endogenous cellular processes. Each of these processes leaves a characteristic pattern of mutations on the tumor genome providing the unique opportunity to decipher specific signatures of mutational processes operative during HNC pathogenesis and to address their prognostic value. Computational analysis of whole exome sequencing data of the HIPO-HNC (n=83) and TCGA-HNSC (n=506) cohorts revealed five common mutational signatures (COSMIC signature 1, 2, 3, 13 and 16), and demonstrated their significant association with etiological risk factors (tobacco, alcohol and HPV16).

  Study EGAS00001004588

• Inter and intra - tumor heterogeneity in Colorectal Cancer

  We used high depth massive parallel sequencing analyses to study 27 CRC (colorectal cancer) patients, with a total of 97 tumors (both primary and matched metastases) in addition to healthy control samples. We found inter-tumor concordance for coding mutations; in contrast, gene copy numbers were found to be highly discordant between primary tumors and metastases as validated by fluorescent in-situ hybridization. in a further step, we dissected a single tumor into 68 spatially defined samples and sequenced them separately. Here we identify evenly distributed coding mutations in APC and TP53 in all tumor areas, yet highly variable gene copy numbers in numerous genes.

  Study EGAS00001002150

• Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks

  The identification of functional non-coding mutations is a key challenge in the field of genomics. Here we introduce μ-cisTarget to filter, annotate and prioritize cis-regulatory mutations based on their putative effect on the underlying ‘personal’ gene regulatory network. We validated μ-cisTarget by re-analyzing the TAL1 and LMO1 enhancer mutations in T-ALL, and the TERT promoter mutation in melanoma. Next, we re-sequenced the full genome of ten cancer cell lines and used matched transcriptome data and motif discovery to identify master regulators with de novo binding sites that result in the up-regulation of nearby oncogenic drivers.

  Study EGAS00001002571

• Exome array analysis of adverse reactions to fluoropyrimidine-based therapy for gastrointestinal cancer

  Fluoropyrimidines, including 5-fluororacil (5FU) and its pro-drug Capecitabine, are the common treatment for colorectal, breast, neck and head cancers – either as monotherapy or in combination therapy. Adverse reactions (ADRs) to the treatment are common and often result in treatment discontinuation or dose reduction. Factors contributing to ADRs, including genetic variation, are poorly characterized. We performed exome array analysis to identify genetic variants that contribute to adverse reactions.Our final dataset consisted of 504 European ancestry individuals undergoing fluoropyrimidine-based therapy for gastrointestinal cancer. A subset of 254 of these were treated with Capecitabine. All individuals were genotyped on the Illumina HumanExome Array.

  Study EGAS00001002763

• Rapid response of APC/TP53/KRAS mutated stage IV colorectal cancer under FOLFIRI + Bevacizumab detected by liquid biopsy: a case report

  In our non-interventional liquid biopsy study, a male patient in his fifties diagnosed with stage IV colorectal cancer and polytope liver metastases rapidly progressed after completing chemotherapy and deceased 8 months after diagnosis. Retrospective cell free DNA testing showed that the APC/TP53/KRAS major clone responded quickly after 3 cycles of FOLFIRI + Bevacizumab. Retrospective exome sequencing of pre-chemotherapy and post-chemotherapy tissue samples including metastases confirmed that the APC/TP53/KRAS and other major clonal mutations (GPR50, SLC5A, ZIC3, SF3A1 and others) were present in all samples. After the last chemotherapy cycle,

  Study EGAS00001004088

• BAM files of targeted next-generation DNA sequencing data of 13 chordoid gliomas of the third ventricle

  BAM files of targeted next-generation DNA sequencing data of 13 chordoid gliomas of the third ventricle (2 paired tumor-normal samples and 11 tumor-only samples). Genomic DNA was extracted from formalin-fixed, paraffin-embedded blocks of tumor tissue from 13 patients with chordoid glioma of the third ventricle using the QIAamp DNA FFPE Tissue Kit (Qiagen). Genomic DNA was also extracted from leukocytes in a peripheral blood sample from one of the patients and a non-neoplastic gastric biopsy specimen from one of the patients. Capture-based next-generation DNA sequencing was performed at the University of California, San Francisco Clinical Cancer Genomics Laboratory, using an assay that targets all coding exons of approximately 500 cancer-related genes, select introns of 47 genes, and TERT promoter with a total sequencing footprint of 2.8 Mb (UCSF500 Cancer Panel). Sequencing libraries were prepared from genomic DNA, and target enrichment was performed by hybrid capture using a custom oligonucleotide library (Nimblegen SeqCap EZ Choice). Captured libraries were sequenced as paired-end 100 bp reads on an Illumina HiSeq 2500 instrument. Duplicate sequencing reads were removed computationally to allow for accurate allele frequency determination and copy number calling.

  Dataset EGAD00001003818

• Field effect of healthy and diseased livers (2019-04-08)

  Recent work in the Campbell group has revealed somatic mutations present in normal, non-cancerous human skin. A subset of the mutations conferred selective advantages to the host cells, leading to clonal expansions and raising the risk for future cancer development. Capturing such somatic mutations in normal tissue is important to advance our understanding about carcinogenesis and could provide prospective medical insights. In this project, our goal is to detect somatic mutations in normal (pre-cancerous) liver tissue. Using Laser Microdissection technology, we will dissect individual liver lobules from patient samples and submit these to sequencing. For each patient sample, we aim to sequence multiple lobules to characterise the mutagenic burden. Samples will be taken from patients with different liver disease aetiologies, including alcoholism and obesity, with a view on distinguishing the prevalent mutation types occurring in each disease context. We will perform targeted sequencing, initially using the WTSI cancer panel. Later we aim to use a novel bait set that captures both cancer genes as well as genes relevant to the non-cancerous samples (ie. genes implicated in hereditary disorders, immune sequences). . This dataset contains all the data available for this study on 2019-04-08.

  Dataset EGAD00001004941

• Genomic Resistance Patterns to Second Generation Androgen Blockade in Paired Tumor Biopsies of Metastatic Castrate-Resistant Prostate Cancer

  We examined genetic resistance to second generation androgen targeting therapies (abiraterone acetate or enzalutamide) by analyzing whole exome sequencing of patient-matched pre-treatment and post-resistance tumors from a series of castrate-resistant prostate cancer (CRPC) patients. Abiraterone resistant tumors harbored alterations in AR and MYC, whereas patients treated with enzalutamide had acquired alterations in the cell cycle pathway. We experimentally confirmed expression of cell-cycle kinases sufficed to drive enzalutamide resistance, which was mitigated through CDK4/6 blockade. These observations link genetic resistance to specific therapeutic agents to inform strategies in genomically selected advanced CRPC.

  Study phs001447

• Radiation-Related Genomic Profile of Papillary Thyroid Cancer after the Chernobyl Accident

  The April 26, 1986 accident at the Chernobyl nuclear power plant in northern Ukraine resulted in the release of radioactive contaminants, which were deposited in the surrounding areas in Ukraine, Belarus, and Russia. The main radiation-related health effect resulting from these exposures is the increased occurrence of thyroid cancer among individuals who were children at the time of the accident or born shortly thereafter. The purpose of this study was to conduct a comprehensive genomic landscape analysis of papillary thyroid tumors arising in individuals who were exposed as children to radioactive iodine (I-131) from the Chernobyl nuclear power plant accident.

  Study phs001134

• plasma DNA LINE-1 targeted bisulfite sequencing: a new non-invasive multi-cancer detection marker

  The detection of circulating tumor DNA, which allows non-invasive tumor molecular profiling and disease follow-up, promises optimal and individualized management of patients with cancer. However, detecting small fractions of tumor DNA released when the tumor burden is reduced remains a challenge. We developed a PCR-based targeted bisulfite method coupled to deep sequencing to detect methylation patterns of L1PA elements,which we named DIAMOND (for Detection of Long Interspersed Nuclear Element Altered Methylation ON plasma DNA). We used sodium bisulfite chemical conversion to achieve base-pair resolution analysis and designed a multiplexed PCR based on 8 amplicons covering L1PAs .

  Study EGAS50000000446

• Sensitive urothelial cancer detection via high volume urine DNA analysis

  Cystoscopy and imaging are the gold standard for urothelial cancer (UC) detection and surveillance, but cystoscopy is an uncomfortable procedure associated with adverse effects and a low diagnostic yield as only 10% of hematuria patients have UC. Urine tumor DNA (utDNA) is a non-invasive UC biomarker that has suffered from poor sensitivity for Ta stage tumors (<80%). We hypothesized that high urine volume analysis with a multi-gene panel could overcome these limitations, and developed a 100 mL utDNA laboratory platform (UroScout) that analyzes 25 commonly mutated UC genes and 8 copy number-altered loci for somatic alterations to detect UC.

  Study EGAS50000000630

• Placental_genomics

  The aim of this study is to define the mutational landscape of placentas.

  Study EGAS00001003297

• Aggressive PDACs show hypomethylation of repetitive elements and the execution of an intrinsic IFN program linked to a ductal cell-of-origin

  Study EGAS00001004660

• EGAD00010000266

  Metabric breast cancer samples (Genotype raw data)

  Dataset EGAD00010000266

• ICGC Prostate Cancer Whole Genome Sequencing

  A small subsample of EGAD00001000689. Please do not use.

  Dataset EGAD00001000263

• Illumina_WXS_T

  Whole-exome sequencing on Illumina HiSeq2000/2500 of colorectal cancer primary tumor sample

  Dataset EGAD00001002099

• OT2_Illumina_WGS_T

  Whole-genome sequencing on Illumina HiSeq2000/2500 of colorectal cancer primary tumor sample (OT2_cohort)

  Dataset EGAD00001003375

• OT2_Illumina_WXS_MET

  Whole-exome sequencing on Illumina HiSeq2000/2500 of colorectal cancer metastasis sample (OT2_cohort)

  Dataset EGAD00001003379

• Whole exome sequencing of bulk primary tumor (and one lymph node metastasis) and matched blood of six non-metastatic breast cancer patients

  Dataset EGAD00001002746

• Mapping the breast cancer metastatic cascade onto circulating tumour DNA using genetic and epigenetic clonal tracking

  Dataset EGAD00001005507

• RNASeq files for GenomePaint paper

  RNASeq files for GenomePaint paper titled "Exploration of coding and non-coding variants in cancer using GenomePaint."

  Dataset EGAD00001006680

• methylation_ec

  Raw methylation data from cervical samples in individuals with endometrial cancer.

  Dataset EGAD00010002084

• methylation_oc

  Raw methylation data from cervical samples in individuals with ovarian cancer.

  Dataset EGAD00010002086

• VCF dataset of Colorectal Cancer Synthetic genomes

  This dataset contains genomic variants data from VCF files of four patients synthetically generated in the EOSC4Cancer project

  Dataset EGAD50000000314

• Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis

  Monozygotic (MZ) twins have been widely employed for dissection of the relative contributions of genetics and environment in disease. In multiple sclerosis (MS), an autoimmune demyelinating disease that commonly causes neurodegeneration and disability in young adults, disease discordance in MZ twins has been interpreted to indicate environmental importance in pathogenesis. However, genetic and epigenetic differences between MZ twins have been described, challenging the accepted experimental paradigm in disambiguating effects of nature and nurture. Here, we report the genome sequences of one MS-discordant MZ twin pair and messenger RNA (mRNA) transcriptome and epigenome sequences of CD4+ lymphocytes from three MS-discordant, MZ twin pairs. No reproducible differences were detected between co-twins among ~3.6 million single nucleotide polymorphisms (SNPs) or ~0.2 million insertion-deletion polymorphisms (indels). Nor were any reproducible differences observed between siblings of the three twin pairs in HLA haplotypes, confirmed MS-susceptibility SNPs, copy number variations, mRNA and genomic SNP and indel genotypes, or expression of ~19,000 genes in CD4+ T cells. Only two to 176 differences in methylation of ~2 million CpG sites were detected between siblings of the three twin pairs, in contrast to ~800 differences in methylation between T cells of unrelated individuals and several thousand differences between tissues or normal and cancerous tissues. In the first systematic effort to estimate sequence variation among MZ co-twins, we did not find evidence for genetic, epigenetic or transcriptome differences that explained disease discordance. These are the first female, twin and autoimmune disease genome sequences reported.

  Study phs000239

• Sequencing_Acute_Myeloid_Leukaemia_

  This project will aim at sequencing and analysing three samples from a patient with acute myeloid leukaemia (AML) with t(15;17) translocation (acute promyelocytic leukaemia). The patient was treated with standard chemotherapy and samples (blood and bone marrow) taken for minimal residual disease measured during and after chemotherapy. 2-3years later the patient presented a second AML containing inv (16).In this project we will sequence both AML and normal genomes to find associated mutations This will allow unprecedented insights into the dynamics of appearance of secondary AML, since we will be able to use the MRD samples to track the emergence of the inv(16) leukaemia. We will also be able to distinguish whether the 2 leukaemias are clonally related or not. This project will entail sequencing and analysis of three samples (whole genome 30x coverage) using Hi-Seq. The funds from this grant will cover the cost of sequencing 9 lanes from the AML t(15;17) sample, 9 lanes from AML inv(16) sample and 8 lanes from the normal genome.

  Study EGAS00001000035

• Genes associated with pancreas development and function maintain open chromatin in iPSCs generated from human pancreatic beta cells

  Current in-vitro islet differentiation protocols suffer from heterogeneity and low efficiency. Induced-pluripotent stem cells (iPSCs) derived from pancreatic beta-cells (BiPSCs) preferentially differentiate towards endocrine pancreas-like cells versus those from fibroblasts (FiPSCs). We interrogated genome-wide open chromatin in BiPSCs and FiPSCs via ATAC-seq, and identified ~8.3k significant, differential open chromatin sites (DOCS) between the two iPSC subtypes (FDR&lt;0.05). DOCS where chromatin was more accessible in BiPSCs (Bi-DOCS) were significantly enriched for known regulators of endodermal development, including bivalent and weak enhancers, and FOXA2 binding sites (FDR&lt;0.05). Bi-DOCS were associated with genes related to pancreas development and beta-cell function, including transcription factors mutated in monogenic diabetes (PDX1, NKX2-2, HNF1A; FDR&lt;0.05). Moreover, Bi-DOCS correlated with enhanced gene expression in BiPSC-derived definitive endoderm and pancreatic progenitor cells. Bi-DOCS therefore highlight genes and pathways governing islet-lineage commitment, which can be exploited for differentiation protocol optimisation, diabetes disease modelling, and therapeutic purposes.

  Study EGAS00001002591

• FFPE_normals_v2_gbm_wtsi_panel

  Targeted pulldown of approx 60 ffpe normal samples to use as normal controls

  Study EGAS00001002124

• Childhood_arthritis_DNA

  The aim of this study is to describe the transcriptome of single arthritic cells.

  Study EGAS00001002652

• Human_Developmental_Cell_Atlas_HDCA___WGS

  Single cell + bulk genomics study for immune and hematopoietic organs during human fetal development

  Study EGAS00001002929

• Biomarker Data from KATHERINE: A Phase III Study of Adjuvant Trastuzumab Emtansine versus Trastuzumab in Patients with Residual Invasive Disease after Neoadjuvant Therapy for HER2-Positive Breast Cancer

  Study EGAS00001006229

• EGAD00010000270

  Metabric breast cancer samples (Images)

  Dataset EGAD00010000270

• BASIS Genome Validation Study

  Bespoke validation experiments will be performed on ER+ Breast Cancer cases to confirm the presence of mutations found in whole genome sequencing.

  Dataset EGAD00001000661

• SCCOHT

  Exome sequencing of familial and sporadic small cell cancer of ovary cases.

  Dataset EGAD00001000791

• Illumina_WGS_T

  Whole-genome sequencing on Illumina HiSeq2000/2500 of colorectal cancer primary tumor sample

  Dataset EGAD00001002088

• OT2_Illumina_RNA_T

  RNAseq on Illumina HiSeq2000/2500 of colorectal cancer primary tumor sample (OT2_cohort)

  Dataset EGAD00001003367

• OT2_Illumina_WGS_MET

  Whole-genome sequencing on Illumina HiSeq2000/2500 of colorectal cancer metastasis sample (OT2_cohort)

  Dataset EGAD00001003372

• OT2_Solid_WXS_T

  Whole-exome sequencing on AB 5500xl Genetic Analyzer of colorectal cancer primary tumor sample (OT2_cohort)

  Dataset EGAD00001003386

• Hipo-032 Metastasome of Colorectal Cancer

  Whole genome sequencing of Control (blood), Tumor and metastasis triplets for 12 samples.

  Dataset EGAD00001003965

• Prostate cancer datasets WES

  WES: 48 samples (5 blood samples from 6 patient data): 22 Tumour cores and 26 normal/benign cores (HiSeq)

  Dataset EGAD00001004467

• WGS files for Zhang GenomePaint paper

  WGS files for GenomePaint paper titled "Exploration of coding and non-coding variants in cancer using GenomePaint."

  Dataset EGAD00001006679

• cfDNA dataset for cfDNA cohort

  Cell free DNA sequencing data for 233 samples across multiple cancer types for cfDNA cohort

  Dataset EGAD50000000104

• SPECIAL: scRNA-seq

  Tumour biopsies were collected from twenty-three patients (46 samples) (of which 20 were matched) with locally advanced or metastatic melanoma (stage IIIB – stage IV). Library construction was done either with the Chromium Single Cell 3ʹ GEM, Library &amp; Gel Bead Kit v3 (n = 16; 10x genomics, Cat#1000092) or the Chromium Single Cell A Chip Kit and 5’ Library &amp; Gel Bead Kit (10x genomics, Cat#1000014). All libraries were sequenced on Illumina NextSeq, HiSeq4000 or NovaSeq6000 until sufficient saturation was reached (60% on average). The reference genome used in this study was GRCh38.

  Dataset EGAD00001009291

• Transcriptome and epigenome characterization of BMP signaling effects on H3.3K27M DIPG

  We profiled transcriptome and epigenome of BMP signaling effects on H3.3K27M DIPG.

  Dataset EGAD00001007768

• Origins and functional consequence of somatic mitochondrial DNA mutations

  Recent sequencing studies have extensively explored the somatic alterations present in the nuclear genomes of cancers. Although mitochondria control energy metabolism and apoptosis, the origins and impact of cancer-associated mutations in mitochondrial DNA (mtDNA) are unclear. Here, we analysed somatic alterations in mtDNA from 1,675 tumors across 31 histologies. We identified 1,907 somatic substitutions, which exhibited dramatic replicative strand bias, predominantly C&gt;T and A&gt;G on the mitochondrial heavy strand. This strand-asymmetric signature differs from those found in nuclear cancer genomes but matches the inferred germline process shaping primate mtDNA sequence content. Numbers of mtDNA mutations showed considerable heterogeneity across tumor types. Missense mutations were selectively neutral and often gradually drifted towards homoplasmy over time. In contrast, mutations resulting in protein truncation undergo negative selection and were almost exclusively heteroplasmic. Our findings indicate that the endogenous mutational mechanism has far greater impact than any other external mutagens in mitochondria, and is fundamentally linked to mtDNA replication.

  Study EGAS00001000968

• A biobank of patient-derived pediatric brain tumor models

  Brain tumors are the leading cause of cancer-related death in children. Genomic studies have provided insights into molecular subgroups and oncogenic drivers of pediatric brain tumors that may lead to novel therapeutic strategies. To evaluate new treatments, better preclinical models adequately reflecting the biological heterogeneity are needed. Through the Children’s Oncology Group ACNS02B3 study, we have generated and comprehensively characterized 30 patient-derived orthotopic xenograft models and 7 cell lines representing 14 molecular subgroups of pediatric brain tumors. Patient-derived orthotopic xenograft models were found to be representative of the human tumors they were derived from in terms of histology, immunohistochemistry, gene expression, DNA methylation, copy number, and mutational profiles. In vivo drug sensitivity of targeted therapeutics was associated with distinct molecular tumor subgroups and specific genetic alterations. These models and their molecular characterization provide an unprecedented resource for the cancer community to study key oncogenic drivers and to evaluate novel treatment strategies.

  Study EGAS00001002536

• A novel TP53-KPNA3 translocation defines a de novo treatment-resistant clone in osteosarcoma

  Osteosarcoma is the most common primary bone cancer. It can be cured by aggressive surgery and chemotherapy, but outcomes for metastatic or chemoresistant disease remain dismal. Cancer sequencing studies have shown that the p53 pathway is dysregulated in nearly every case, often by translocation; however, no studies of osteosarcoma evolution or intratumor heterogeneity have been done to date. We studied a patient with chemoresistant, metastatic disease over the course of three years. We performed exome sequencing on germline DNA and DNA collected from tumor at three separate timepoints. We compared variant calls and variant allele frequencies between different samples. We identified subclonal driver mutations in several different genes in the primary tumor sample and found that one particular subclone dominated subsequent tumor samples at relapse. This clone was marked by a novel TP53-KPNA3 translocation and loss of the opposite-strand wild-type TP53 allele. Future research must focus on functional significance of such clones and strategies to eliminate them.

  Study EGAS00001001805

• Impact of mutational profiles on response of primary oestrogen receptor-positive breast cancers to oestrogen deprivation

  Presurgical studies allow study of the relationship between mutations and response of estrogen receptor positive (ER+) breast cancer to aromatase inhibitors (AIs) but have been limited to small biopsies. Here in Phase I of this study, we perform exome sequencing on baseline, surgical core-cuts and blood from 60 patients (40 AI treated, 20 Controls). In poor responders (based on Ki67 change) we find significantly more somatic mutations than good responders. Subclones exclusive to baseline or surgical cores   occur in approximately 30% of tumours. In Phase II we combine targeted sequencing on another 28 treated patients with Phase I. We find six genes frequently mutated: PIK3CA, TP53, CDH1, MLL3, ABCA13 and FLG with 71% concordance between paired cores. TP53 mutations are associated with poor response. We conclude that multiple biopsies are essential for confident mutational profiling of ER+ breast cancer and TP53 mutations are associated with resistance to oestrogen deprivation therapy.

  Study EGAS00001001940

• Comparing nodal versus bony metastatic spread using tumour phylogenies

  The role of lymph node metastases in distant prostate cancer dissemination and lethality is ill defined. Patients with metastases restricted to lymph nodes have a better prognosis than those with distant metastatic spread, suggesting the possibility of distinct aetiologies. To explore this, we traced patterns of cancer dissemination using tumour phylogenies inferred from genome-wide copy-number profiling of 48 samples across 3 patients with lymph node metastatic disease and 3 patients with osseous metastatic disease. Our results show that metastatic cells in regional lymph nodes originate from evolutionary advanced extra-prostatic tumour cells rather than less advanced central tumour cell populations. In contrast, osseous metastases do not exhibit such a constrained developmental lineage, arising from either intra or extra-prostatic tumour cell populations, at early and late stages in the evolution of the primary. Collectively, this comparison suggests that lymph node metastases may not be an intermediate developmental step for distant osseous metastases, but rather represent a distinct metastatic lineage.

  Study EGAS00001001801

• Whole-exome sequencing reveals the origin and evolution of Hepato-Cholangiocarcinoma

  Hepatocellular-cholangiocarcinoma (H-ChC) is a rare subtype of liver cancer with clinicopathological features of both hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA). To date, molecular mechanisms underlying the co-existence of HCC and iCCA components in a single tumor remain elusive. Here we show that H-ChC samples contain substantial private mutations from WES analyses, ranging from 33.1% to 86.4%, indicative of substantive intratumor heterogeneity (ITH). However, on the other hand, numerous ubiquitous mutations shared by HCC and iCCA suggest the monoclonal origin of H-ChC. Mutated genes identify herein e.g. VCAN, ACVR2A and FCGBP are speculated to contribute to distinct differentiation of HCC and iCCA within H-ChC. Moreover, immunohistochemistry demonstrate that EpCAM is highly expressed in 80% of H-ChC implying the stemness of such liver cancer. In summary, our data highlight the monoclonal origin and stemness of H-ChC, as well as substantial intratumoral heterogeneity.

  Study EGAS00001002783

• Automated image-based profiling of complex drug induced phenotypes in patient-derived organoids

  We established a platform for high-throughput confocal fluorescence microscopy and automated image analysis to perform large-scale drug response profiling with patient derived organoids (PDOs). Using PDO lines newly established from colorectal cancer patients with a standardized workflow, we performed chemical perturbations with more than 500 experimental and clinically used compounds. Subsequently, we captured approx. six million images by confocal microscopy. To analyze drug-induced PDO re-organization on a single organoid level we developed SCOPE, a software framework for automated PDO high-throughput image analysis. We observed a rich variety of divergent and reoccurring compound induced phenotypes in organoids. Perturbation of cellular processes, including signaling by MEK, GSK3β, cyclin dependent kinases (CDKs) and others, led to recurring and distinct architectural changes. Highlighting the clinical relevance, PDO viability was heterogeneous after perturbation with anticancer drugs and matched clinical response of corresponding colorectal cancer patients. Our work opens new avenues for image-based profiling for accelerated drug discovery and clinical decision-making.

  Study EGAS00001003140

• Whole genome sequencing of breast cancer and related clones

  Paired WGA (whole-genome amplificated) samples from 65 single cell-derived organoids and six fresh single cell-derived organoid samples both of which were established from normal mammary epithelial cells, 84 FFPE LCM (laser-capture microdissection) samples of breast cancer and related clones, 79 fresh-frozen LCM samples of non-cancer lobules of breast cancer patients, and 36 matched germline controls were subjected to whole genome sequencing using NovaSeq 6000 system (Illumina) or DNBSEQ-G400RS (MGI Tech).

  Dataset EGAD00001010833

• Single molecule molecular inversion probe capture developed using the CIViC database

  This study evaluated the use of the Clinical Interpretations of Variants in Cancer database (CIViC) to develop an Open-sourced CIViC Annotation Pipeline (OpenCAP). OpenCAP is a resource that allows users to develop a clinical capture panel that can be linked back to clinical summaries within the CIViC database. This method for capture panel development and variant annotation was tested using 27 cancer samples from 5 tumor subtypes with original exome or genome sequencing. Specifically, using OpenCAP, 111 variants were identified as relevant for the capture panel and 2,027 smMIPs were designed to target these variants. The smMIPs panel design was employed on all samples to validate the capture panel design. When compared to original sequencing, the CIViC smMIPs capture panel demonstrated a 95% sensitivity for variant detection (n = 61 variants). Additionally, the CIViC smMIPs capture panel identified 182 additional clinically relevant variants that had been missed on original sequencing.

  Study phs001890

• Scalable Whole-Exome Sequencing of Cell-Free DNA Reveals High Concordance with Metastatic Tumors

  We performed whole genome sequencing and whole-exome sequencing of cell-free DNA (cfDNA) and whole-exome sequencing of matched tumor biopsies and germline DNA from patients with metastatic cancer. Using ichorCNA, a software tool that quantifies tumor content in ultra-low pass whole genome sequencing (~0.1x) of cfDNA without prior genomic characterization of the tumor, we show genome-wide concordance between cfDNA and tumor biopsies and detectability of high tumor fractions (&gt;0.1) in the cfDNA of many patients with metastatic cancer. We then established that whole-exome sequencing of cfDNA can enable comprehensive profiling of tumors from blood, with high tumor-content cfDNA samples demonstrating concordance of clonal somatic mutations, copy number alterations, mutational signatures, and neoantigens with matched tumor biopsies. This study introduces a new method to identify patients that could be eligible for tumor profiling from cfDNA and sheds light on the concordance between metastatic tissue and blood biopsies.

  Study phs001417

• A Phase II Clinical Trial of the PARP Inhibitor Talazoparib in BRCA1 and BRCA2 Wild-Type Patients

  The Talazoparib Beyond BRCA (TBB), a phase II proof-of-concept clinical trial, was designed to test the efficacy of talazoparib, a potent, orally bioavailable PARP inhibitor, with an established Phase II recommended dose, in the treatment of advanced BRCA wildtype (WT), HER2-negative breast cancer and other solid tumors with homologous recombination (HR) deficiency. Eligible patients had advanced HER2-negative breast cancer or other solid tumors with a germline or somatic mutation in a gene linked to the HR pathway. Patients identified as harboring a deleterious or suspected deleterious germline or somatic mutation in the HR pathway were treated with single agent talazoparib until disease progression. Primary and metastatic tumor samples were sequenced with panel sequencing and exome sequencing to detect commonly mutated genes and those associated with DNA repair deficiency. In addition, ctDNA was sequenced at baseline and progression. Fastq files for tumor and ctDNA sequencing are deposited.&nbsp;

  Study phs002803

• Hi-C Profiling of Solid Tumor Samples

  Structural variants, such as translocations, inversions, duplications, and deletions, have long been recognized as mutations that can contribute to the initiation and progression of cancer. This can occur through a variety of mechanisms, including changes in gene dosage and the generation of fusion genes. In recent years, it is becoming increasingly clear that these events also can alter how genomes are organized in 3D space in the nucleus and contribute to changes in enhancer-promoter regulation. However, it remains poorly understand how often 3D genome structural changes occur in cancers, what genes are affected by these events, and in which tumor types. This study is part of ongoing work to better characterize 3D genome structural changes across a variety of tumor types to better understand where and when 3D genome structure changes as the result of structural variation in cancer genomes and to characterize the genes and tumor types affected.

  Study phs003227

• Gut Microbiome and Types of Colorectal Polyps

  Colorectal cancer is a heterogeneous disease arising from at least two precursors-the conventional adenoma and the serrated polyp. This dataset was used to test the relationship of the gut microbiota to specific colorectal polyp types. We included samples from two independent study populations based at colonoscopy clinics: the Centers for Disease Control and Prevention (CDC) Study of In-home Tests for Colorectal Cancer (SIT), and the New York University (NYU) Human Microbiome and Colorectal Tumor study. Gut microbiota were assessed in 667 colonoscopy-screened adults by 16S rRNA gene sequencing of stool samples, of which 540 were included in our analysis. Participants were categorized as conventional adenoma cases, serrated polyp cases, or polyp-free controls. CA cases were further classified as proximal or distal and as non-advanced or advanced. Serrated polyp cases were further classified as hyperplastic polyp or sessile serrated adenoma. Our results show associations between gut microbiome composition and presence of conventional adenomas, including reduced diversity and alterations in taxon abundance.

  Study phs001381

• The Genomic Landscape of Interval Colorectal Cancers

  Interval colorectal cancers (CRC), cancers diagnosed after a screening/surveillance exam in which no cancer is detected, and before the date of the next recommended exam, reflect an unprecedented challenge in CRC detection and prevention. To better understand this poorly characterized CRC variant, we examined the clinical and mutational characteristics of interval CRCs in comparison to screen-detected CRCs. We used data from the Prostate, Lung, Colorectal and Ovarian (PLCO) cancer randomized controlled trial (RCT) of flexible sigmoidoscopy (FS) screening, which enrolled 154,900 men and women aged 55 to 74 years between 1993 and 2001. Whole Exome Sequencing (WES) was performed on 323 samples from 168 participants (data available through dbGaP). We found colorectal cancers diagnosed between screening exams (interval cancers) had significantly increased risk of death than screen detected cancers although no significant molecular differences were observed between screen-detected and interval CRC at the whole exome sequencing level.

  Study phs003093

• Tumor inflammation and mutational burden are differentially associated with response to nivolumab or nivolumab plus ipilimumab in metastatic colorectal cancer

  Nivolumab alone and in combination with ipilimumab demonstrated durable clinical benefit in patients with previously treated microsatellite instability-high/mismatch repair-deficient metastatic colorectal cancer in the phase 2 CheckMate 142 study. Exploratory biomarker analyses of tumor and microbiome samples from CheckMate 142 were performed to evaluate associations between various biomarkers and the efficacy of nivolumab monotherapy and nivolumab plus ipilimumab combination in these patients. Higher expression of inflammation-related gene expression signatures was associated with improved response per investigator assessment and survival benefit with nivolumab monotherapy. In contrast, higher tumor mutational burden, tumor indel burden and degrees of microsatellite instability were associated with improved response per investigator assessment and survival benefit with nivolumab plus ipilimumab. While interpretation is limited by the exploratory nature of these analyses, they suggest that tumor antigenicity rather than baseline tumor inflammation might be important for the combinatorial efficacy. Validation of these findings in larger, randomized studies is necessary.

  Study EGAS50000000416

• Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution

  We have used next generation sequencing to sequence genomes (>43-fold coverage) and transcriptomes of an oestrogen-receptor-alpha-positive metastatic lobular breast cancer at depth. We found 32 somatic non-synonymous coding mutations present in the metastasis, and measured the frequency of these somatic mutations in DNA from the primary tumour of the same patient.

  Study EGAS00000000054

• ENU-NCI-H508 cetuximab fixed concentration project

  Cetuximab is a targeted monoclonal antibody against the epidermal growth factor receptor (EGFR) which is used therapeutically for the treatment of KRAS wild-type colorectal cancer (CRC). The Cetuximab sensitive KRAS wild-type CRC cell line NCI-H508 has been treated with a fixed concentration of ENU for 24 hours and then selected with Cetuximab until drug resistant clones were ready to be picked and grown up as sub-clones of the parental cell line. These will have genes causally implicated in cancer sequenced to identify common point mutations in multiple independently derived drug resistant clones as a forward genetic screen for mechanisms of resistance to Cetuximab in CRC

  Dataset EGAD00001001948

• ENU-CCK-81 cetuximab pilot project

  Cetuximab is a targeted monoclonal antibody against the epidermal growth factor receptor (EGFR) which is used therapeutically for the treatment of KRAS wild-type colorectal cancer (CRC). The Cetuximab sensitive KRAS wild-type CRC cell line NCI-H508 has been treated with a fixed concentration of ENU for 24 hours and then selected with Cetuximab until drug resistant clones were ready to be picked and grown up as sub-clones of the parental cell line. These will have genes causally implicated in cancer sequenced to identify common point mutations in multiple independently derived drug resistant clones as a forward genetic screen for mechanisms of resistance to Cetuximab in CRC.

  Dataset EGAD00001001947

• ENU-NCI-H508-Cetuximab-SecondRound

  Cetuximab is a targeted monoclonal antibody against the epidermal growth factor receptor (EGFR) which is used therapeutically for the treatment of KRAS wild-type colorectal cancer (CRC). The Cetuximab sensitive KRAS wild-type CRC cell line NCI-H508 has been treated with a fixed concentration of ENU for 24 hours and then selected with Cetuximab until drug resistant clones were ready to be picked and grown up as sub-clones of the parental cell line. These will have genes causally implicated in cancer sequenced to identify common point mutations in multiple independently derived drug resistant clones as a forward genetic screen for mechanisms of resistance to Cetuximab in CRC

  Dataset EGAD00001002065

• Inter and intra - tumor heterogeneity in Colorectal Cancer

  The dataset consists of two main sample groups. 1) The inter-tumour sample group contains a total of 97 samples from 27 patients. Each patient has a single normal and primary sample as well as one or more metastases. All samples were sequenced using IonTorrent PGM and a custom colorectal cancer (CRC) panel. 2) The intra-tumour sample group contains a total of 68 samples from a single tumour as well as a normal tissue sample. All 68 samples were sequenced using IonTorrent PGM and a custom CRC panel. Shallow whole genome sequencing was additionally applied to 10 of the samples using Illumina HiSeq 4000.

  Dataset EGAD00001003131

• Targeted and exome sequencing data from 24 prostate cancer patients with somatic hypermutation

  This dataset contains all available targeted and exome sequencing paired fastq files from our study, "Identification of hypermutation and defective mismatch repair in ctDNA from metastatic prostate cancer". Patient identifiers are denoted by the first three characters of the sample aliases (e.g. "P01"), and additional information is appended to reflect the panel used (targeted 73 gene panel: "PC", or whole-exome panel: "WXS"), and whether the sample represents cell-free DNA ("cfdna") or paired white-blood cell control ("wbc"). Several patients have multiple serial collections available, and these are denoted by the characters "C1, C2, C3," etc. All samples were sequenced using Illumina technology.

  Dataset EGAD00001005474

• MutWP5: CRUK Mutographs of Cancer: Lung: PD37920 (WG) (2020-02-20)

  Sequencing of LCM-derived microbiopsies from explanted lung from COPD patient. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Deep sampling throughout multiple regions of the lung will determine whether there are differences in smoking-related mutation burden in different portions of the lung. Whole-genome sequencing will be conducted on samples identified as promising from the initial targeted data. Results from this portion of the study will be compared to other individuals with smoking-related diseases (COPD, pulmonary fibrosis, lung cancer), and normal, non-smoking lungs. . This dataset contains all the data available for this study on 2020-02-20.

  Dataset EGAD00001005990

• MutWP5: CRUK Mutographs of Cancer: Lung: PD38234 (WG) (2020-02-20)

  Sequencing of LCM-derived microbiopsies from explanted lung from pulmonary fibrosis patient. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Deep sampling throughout multiple regions of the lung will determine whether there are differences in smoking-related mutation burden in different portions of the lung. Whole-genome sequencing will be conducted on samples identified as promising from the initial targeted data. Results from this portion of the study will be compared to other individuals with smoking-related diseases (COPD, pulmonary fibrosis, lung cancer), and normal, non-smoking lungs. . This dataset contains all the data available for this study on 2020-02-20.

  Dataset EGAD00001005991

• 76 cancer and normal whole genomes from eleven SI-NET patients

  This dataset comprises of 76 cancer and normal whole genomes obtained from 11 SI-NET patients, in the form of two fastq files (forward and reverse reads) for each genome containing sequences generated by Illumina NovaSeq 6000 system.

  Dataset EGAD00001006161

• MutWP5: CRUK Mutographs of Cancer: Lung: PD38233 (WG) (2021-02-02)

  Sequencing of LCM-derived microbiopsies from explanted lung from COPD patient. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Deep sampling throughout multiple regions of the lung will determine whether there are differences in smoking-related mutation burden in different portions of the lung. Whole-genome sequencing will be conducted on samples identified as promising from the initial targeted data. Results from this portion of the study will be compared to other individuals with smoking-related diseases (COPD, pulmonary fibrosis, lung cancer), and normal, non-smoking lungs. . This dataset contains all the data available for this study on 2021-02-02.

  Dataset EGAD00001006930

• MutWP5: CRUK Mutographs of Cancer: Lung: PD43291_Novaseq (Exome) (2021-02-02)

  Sequencing of LCM-derived microbiopsies from explanted lung from COPD patient. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Deep sampling throughout multiple regions of the lung will determine whether there are differences in smoking-related mutaiton burden in different portions of the lung. Whole-genome sequencing will be conducted on samples identified as promising from the initial targeted data. Results from this poriton of the study will be compared to other individuals with smoking-related diseases (COPD, pulmonary fibrosis, lung cancer), and normal, non-smoking lungs. . This dataset contains all the data available for this study on 2021-02-02.

  Dataset EGAD00001006932

• Early onset sporadic rectal cancer exome from Indian population

  Paired tumor-normal exome data from 47 Microsatellite stable Early-onset sporadic rectal cancer exome from the Indian population

  Dataset EGAD00001008504

• MutWP5: CRUK Mutographs of Cancer: Lung: PD43291_Novaseq (WG)

  Sequencing of LCM-derived microbiopsies from explanted lung from COPD patient. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Deep sampling throughout multiple regions of the lung will determine whether there are differences in smoking-related mutaiton burden in different portions of the lung. Whole-genome sequencing will be conducted on samples identified as promising from the initial targeted data. Results from this poriton of the study will be compared to other individuals with smoking-related diseases (COPD, pulmonary fibrosis, lung cancer), and normal, non-smoking lungs. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010111

• November 2020 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  November 2020 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001007529

• Analysis of genes related to the oncogenesis, progression or effectiveness of drug therapies of urological tumors .

  To clarify the oncogenesis and the progression mechanism of urological tumors, we continuously collect tumor samples of our patients with high quality. Then we used them to comprehensive analyses such as genome sequencing or epi-genome sequencing. Through these analyses, we aim for elucidating the oncogenesis or for developing newly treatment strategies of each cancer.

  Study JGAS000564