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• The genomic and radiomic complexity of multifocal prostate cancer

  Multiparametric magnetic resonance imaging (mpMRI) and molecular prognostic tests are emerging to guide screening and prostate cancer (PCa) diagnosis, however their efficacy and cross validation requires further assessment in the context of intraprostatic heterogeneity and patient prognosis. To evaluate the molecular features that make prostate tumors visible to mpMRI, we established an mpMRI-blind multicore collection and performed low pass whole genome, exome, transcriptome and methylation profiling of 14 lesions and 23 representative cores from 6 PCa patients. Our results show that diagnosis based on mpMRI does not capture the genomic complexity of tumors, and reveal that commercial prognostic signature results based on single-biopsy assessments are insufficient to define risk of progression. Altogether, our study supports the use of a multi-biopsy assessment in both mpMRI visible and non-visible areas in order to provide a truly personalised diagnosis

  Study EGAS00001002767

• VIKING Health Study - Shetland

  The Viking Health Study – Shetland, together with ORCADES collectively termed VIKING, aims to identify genes influencing risk factors for common diseases such as heart disease, diabetes, glaucoma and stroke. The genetic research cohort study in Shetland was established to identify genetic variants, both common and rare, increasing risk of disease. This isolated population has a number of characteristics, the most important being the very large number of distant relatives, which are favourable for the identification of rare variants influencing disease risk. This study describes PCR-free paired end whole genome sequencing (TruSeq DNA PCR-Free, Illumina) run on a HiSeqX platform at 30X coverage on 500 individuals from VIKING. Unrelated individuals from the largest families were selected first, followed by those from smaller families, until eventually related individuals were selected to best represent the variation in the full cohort.

  Study EGAS00001003872

• Accurate mapping of mitochondrial DNA deletions and duplications using deep sequencing

  Deletions and duplications in mitochondrial DNA (mtDNA) cause mitochondrial disease and accumulate in conditions such as cancer and age-related disorders, but validated high-throughput methodology that can readily detect and discriminate between these two types of events is lacking. Here we present MitoSAlt, a computational method for accurate identification, quantification and visualization of mtDNA deletions and duplications from whole genome, whole exome or transcriptome sequencing data. MitoSAlt was tested on simulated sequencing reads and human patient samples with single deletions and duplications to verify its accuracy. Application to mouse models of mtDNA maintenance disease further demonstrated the ability to detect deletions and duplications even at low levels of heteroplasmy. MitoSAlt paves the way for simple and reliable determination of mtDNA deletions and duplications across a wide range of relevant conditions and available sequencing datasets.  

  Study EGAS00001004380

• Single-cell analysis reveals fibroblast clusters linked to immunotherapy resistance in cancer

  A subset of Cancer-Associated Fibroblasts (CAF-S1) mediates immunosuppression in breast cancers (BC), but its heterogeneity and its impact on immunotherapy response remain unknown. Here, we identify 8 CAF-S1 clusters by analyzing more than 18000 single CAF-S1 fibroblasts from BC. We validate the 5 most abundant clusters by flow cytometry and in silico analyses in other cancer types, highlighting their relevance. Myofibroblasts from clusters 0 and 3, characterized by extra-cellular matrix proteins and TGF signaling respectively, are indicative of primary resistance to immunotherapies. Cluster 0 up-regulates PD-1 and CTLA-4 protein levels in regulatory T lymphocytes (Tregs), which in turn increases CAF-S1 cluster 3 cellular content. Thus, our study highlights a positive feedback loop between specific CAF-S1 clusters and Tregs and uncovers their role in immunotherapy resistance.

  Study EGAS00001004030

• Multi-omic single-cell profiling of peripheral blood immune cells from COVID-19 patients and controls.

  The COVID-19 pandemic, caused by SARS coronavirus 2 (SARS-CoV-2), has resulted in excess morbidity and mortality as well as economic decline. To characterise the systemic host immune response to SARS-CoV-2, we performed single-cell RNA-sequencing coupled with analysis of cell surface proteins, providing molecular profiling of over 800,000 peripheral blood mononuclear cells from a cohort of 130 patients with COVID-19. Our cohort, from three UK centres, spans the spectrum of clinical presentations and disease severities ranging from asymptomatic to critical. Three control groups were included: healthy volunteers, patients suffering from a non-COVID-19 severe respiratory illness and healthy individuals administered with intravenous lipopolysaccharide to model an acute inflammatory response. Full single cell transcriptomes are coupled with quantification of 188 cell surface proteins, and T and B lymphocyte antigen receptor repertoires.

  Study EGAS00001005465

• Hereditary Cancer Diagnostics with I2HCP gene panel

  This dataset contains targetted DNA sequencing data generated in the context of genetic diagnostics of hereditary cancer. Target enrichment was performed with the I2HCP, a custom hereditary cancer gene panel based in Agilent SureSelect and developed by the Germans Trias i Pujol Research Institute (IGTP, Badalona, Catalonia, Spain) and the Catalan Institute of Oncology (ICO, L'Hospitalet de Llobregat, Catalonia, Spain). After the enrichment, 108 samples were sequenced in Illumina HiSeq machines and 130 in MiSeq machines. Some of the samples were sequenced on both platforms. The dataset also includes MLPA validation data for all identified copy-number alterations, annotated with exon resolution and information about negative MLPA results. All this data was generated in the context of routine diagnostics and compiled together with MPLA validation data for a genetic diagnostics oriented benchmark of germline CNV calling tools.

  Study EGAS00001004316

• Conserved interferon-gamma signaling and decreased immune exclusion programs in responses to immune checkpoint blockade therapy

  We analyzed baseline and on-therapy tumor biopsies from 101 patients with advanced melanoma treated with nivolumab (anti-PD-1) alone or combined with ipilimumab (anti-CTLA-4). Analysis of whole transcriptome data showed that T cell infiltration and interferon-gamma signaling signatures corresponded most highly with clinical response to therapy, with a reciprocal decrease in cell cycle and WNT signaling pathways in responding biopsies. Clinical outcome differences were likely not due to differential melanoma cell responses to interferon-gamma, as 57 human melanoma cell lines exposed in vitro to this cytokine showed a conserved interferon-gamma transcriptome response unless they had mutations that precluded signaling from the interferon-gamma receptor. Therefore, the magnitude of the antitumor T cell response and the corresponding downstream interferon-gamma signaling are the main drivers of clinical response or resistance to immune checkpoint blockade therapy.

  Study EGAS00001004545

• POPCOL: population-based colonoscopy.

  PopCol is a cohort study in Stockholm, Sweden that includes a data-rich set of individuals with data available from bowel symptoms questionnaires, gastroenterology visits and biospecimens (genotype and 16S sequencing from blood and stool samples, respectively). Genotyping was carried out using the Illumina HumanOmniExpressExome-8v1 arrays at the SciLifeLab NGI facility in Uppsala, Sweden. Fecal DNA was extracted from samples kept at -80°C using Qiagen 5 QIAamp DNA Stool Mini Kits and analyzed using 16S rRNA gene amplicon sequencing (in the V1-V2 hypervariable region). This was performed on the Illumina MiSeq platform at the Institute of Clinical Molecular Biology (IKMB) in Kiel, Germany. Of these, six PopCol participants were PPI users and 12 used antibiotics. The study was approved by the local Committee of Research Ethics (Forskningskommitté Syd) at Karolinska Institutet, Stockholm, in November 2001. Written informed consent was obtained from all participants

  Study EGAS00001004869

• Oncogenic chimeric transcription factors drive tumor-specific transcription, processing, and translation of silent genomic regions

  Many cancers are characterized by gene fusions encoding oncogenic chimeric transcription factors (TFs) such as EWS::FLI1 in Ewing sarcoma (EwS). Here, we find that EWS::FLI1 induces the robust expression of a specific set of novel spliced and polyadenylated transcripts within otherwise transcriptionally silent regions of the genome. These neogenes (NGs) are virtually undetectable in large collections of normal tissues or non-EwS tumors and can be silenced by CRISPR interference at regulatory EWS::FLI1-bound microsatellites. Ribosome profiling and proteomics further show that some NGs are translated into highly EwS-specific peptides. More generally, we show that hundreds of NGs can be detected in diverse cancers characterized by chimeric TFs. Altogether, this study identifies the transcription, processing, and translation of novel, specific, highly expressed multi-exonic transcripts from otherwise silent regions of the genome as a new activity of aberrant TFs in cancer.

  Study EGAS00001006293

• Genomic landscape and molecularly-informed therapy in thymic carcinoma and other advanced thymic epithelial tumors (H021, HIPO)

  The molecular landscape of malignant thymic epithelial tumors (TET) is largely unknown. To better understand and target these clinically challenging entities, we characterize 81 patients harboring 46 thymus carcinomas (TC), 8 neuroendocrine tumors of the thymus (NET) and 27 thymomas using WGS/WES, transcriptome and methylome analysis. TC harbor different molecular alterations compared to thymoma and NET and have higher tumor mutational burden than thymomas. 14/76 TET patients show (likely) pathogenic germline alterations. Composite biomarker analysis indicates homologous repair deficiency in a subset of patients. We identify immunologically hot and cold TC. Cold TC show significantly shorter overall survival. 71/81 patients receive molecularly-informed therapy recommendations, which are applied in 28/71 cases leading to a DCR of 60% and an ORR of 24% (both n=25). 8/23 patients reach PFS ratios > 1.3, seven of them having TC.

  Study EGAS00001006408

• DNA methylation-based classification of sinonasal tumors [Proteomics data]

  The diagnosis of sinonasal tumors is challenging due to a heterogeneous spectrum of various differential diagnoses as well as poorly defined, disputed entities such as sinonasal undifferentiated carcinomas (SNUCs). In this study, we apply a machine learning algorithm based on DNA methylation patterns to classify sinonasal tumors with clinical-grade reliability. We further show that sinonasal tumors with SNUC morphology are not as undifferentiated as their current terminology suggests but rather reassigned to four distinct molecular classes defined by epigenetic, mutational and proteomic profiles. This includes two classes with neuroendocrine differentiation, characterized by IDH2 or SMARCA4/ARID1A mutations with an overall favorable clinical course, one class composed of highly aggressive SMARCB1-deficient carcinomas and another class with tumors that represent previously misclassified adenoid cystic carcinomas. The repository includes the raw mass spectrometry-based proteomics data

  Study EGAS00001006712

• single nuclei RNASeq of 5 regions of the human prenatal brain

  Data generated through single nuclei RNA sequencing on 5 regions of the brain (frontal cortex, ganglionic eminence, hippocampus, thalamus and cerebellum) from 3 fetuses (two of 14 and one of 15 post-conception weeks, all female). Tissue was acquired from the MRC-Wellcome Trust Human Developmental Biology Resource (HDBR) with ethical approval. snRNA-seq libraries were prepared from ∼10,000 nuclei from each sample using Chromium Single Cell 3ʹ (v3) reagents (10X Genomics). Quality control of libraries was performed using the Agilent 5200 Fragment Analyzer before sequencing on an Illumina NovaSeq 6000 to a depth of at least 865 million (median = 1.01 billion) read pairs per library. Raw sequencing data were converted into FASTQ files. For a full description of data generation, please see Cameron et al, Biological Psychiatry 2022, https://doi.org/10.1016/j.biopsych.2022.06.033.

  Study EGAS00001006537

• Identification of neoantigen from MSI-CRC patient derived organoids and its application for targeting by autologous T cells

  Targeting neoantigens expressed only by tumor cells enable tumor destruction without unexpected damages to healthy tissues. Here, we identified neoantigens from microsatellite instable (MSI) colorectal cancer (CRC) patient-derived organoids by genomics and immunopeptidomics approches. The neoantigens in this study were predicted from frame-shift mutation by whole-genome sequencing and confirmed its presentation on organoids surface class I HLA molecules by mass spectrometry. We utilized these neoantigens to isolate neoantigen-specific CD8 T cells from autologous PBMC, and proved tumor organoids killing ability of the CD8 T cells, whereas it did not attack normal organoids. This study provides a platform to identify neoantigen from patient-derived cancer organoids and a model to validate T cell recognition, which could be useful for adoptive CD8 T cell transfer treatment for MSI-CRC patient.

  Study EGAS00001006633

• DNA methylation-based classification of sinonasal tumors [DNA sequencing]

  The diagnosis of sinonasal tumors is challenging due to a heterogeneous spectrum of various differential diagnoses as well as poorly defined, disputed entities such as sinonasal undifferentiated carcinomas (SNUCs). In this study, we apply a machine learning algorithm based on DNA methylation patterns to classify sinonasal tumors with clinical-grade reliability. We further show that sinonasal tumors with SNUC morphology are not as undifferentiated as their current terminology suggests but rather reassigned to four distinct molecular classes defined by epigenetic, mutational and proteomic profiles. This includes two classes with neuroendocrine differentiation, characterized by IDH2 or SMARCA4/ARID1A mutations with an overall favorable clinical course, one class composed of highly aggressive SMARCB1-deficient carcinomas and another class with tumors that represent previously misclassified adenoid cystic carcinomas. This repository includes the results from DNA sequencing and mass spectrometry-based proteomics.

  Study EGAS00001006713

• RNA stability controlled by m6A methylation contributes to X-to-autosome dosage compensation in mammals

  In mammals, X-chromosomal genes are expressed from a single copy since males (XY) possess a single X chromosome, while females (XX) undergo X inactivation. To compensate for this reduction in dosage compared to two active copies of autosomes, it has been proposed that genes from the active X chromosome exhibit dosage compensation. However, the existence and mechanism of X-to-autosome dosage compensation are still under debate. Here, we show that X-chromosomal transcripts are reduced in m6A modifications and more stable compared to their autosomal counterparts. Acute depletion of m6A selectively stabilises autosomal transcripts, resulting in perturbed dosage compensation in mouse embryonic stem cells. We propose that higher stability of X-chromosomal transcripts is directed by lower levels of m6A, indicating that mammalian dosage compensation is partly regulated by epitranscriptomic RNA modifications.

  Study EGAS00001007112

• ATAC-Seq of healthy and IBD blood samples

  PBMCs from blood samples of 9 age- and gender-matched healthy subjects and 25 IBD patients were isolated through a Ficoll density gradient and used to isolate live CD4 T cells through a magnetic cell isolation kit (Miltenyi Biotec). Twelve thousand live CD4 T cells were then used to prepare ATAC-Seq libraries. Briefly, crude nuclei of live CD4+ T cells were treated with Tagment DNA buffer and Tagment DNA Enzyme (Nextera DNA Library Prep Kit, Illumina), and then the DNA was purified by MinElute PCR Purification Kit (Qiagen). Transposed DNA fragments were amplified using specific adapters followed by purification with MinElute PCR Purification Kit (Qiagen). Fragments from 240-360pb were selected in the PippinHT system (Sage Science). The quality of the library and its DNA concentration were assessed by Bioanalyzer instruments (Agilent Technologies) and ultimately submitted for sequencing using Illumina HiSeq 2500 sequencer, V4 chemistry.

  Study EGAS00001007343

• Detecting and quantifying clonal selection in somatic mosaicism

  In this study, we introduce a scalable method to identify clonal selection in an individual tissue, agnostic of the underlying mutations. To study clonal selection in the haematopoietic system, we performed whole genome sequencing on bone marrow CD34+ haematopoietic stem and progenitor cells from 22 non-leukemic individuals, 30-89 years of age. We performed 90x whole genome sequencing for all samples and re-sequenced 19 samples with sufficient DNA to a total target coverage of 270x. Whole genome sequencing of hair follicle DNA from the same individuals was used as germline control. In addition, we sequenced unseparated bone marrow mononuclear cells, CD3-CD34- bone marrow mononuclear cells, and peripheral blood granulocytes from 14 samples. Samples were collected from individuals undergoing hip replacement surgery as part of the Mechanisms of Age-Related Clonal Haematopoiesis (MARCH) Study (REC Ref: 17/YH/0382).

  Study EGAS00001007558

• Genetic origins of the Kiritimati population from central-eastern Micronesia

  The migration of Austronesian-speaking populations through Oceania has intrigued researchers for decades. The Kiribati islands, situated along the boundaries of Micronesia and Polynesia, provide a crucial link in this migration. We analyzed the genome-wide data of the Kiritimati population of Kiribati to uncover their genetic origins and connections with other Oceanian groups. Our study reveals that the Kiritimati population primarily exhibits Remote Oceanian-related ancestry associated with ancient Lapita and present-day Polynesian populations. In addition, our identity-by-descent analysis identifies populations from Philippines as their closest relatives in Island Southeast Asia. The genetic links between Kiritimati, ancient Lapita, and modern Polynesians underscore the shared ancestry and continuous gene flow across these regions. This genetic continuity and ongoing links are supported by linguistic and cultural evidence, illustrating a complex history of migration and admixture in Oceania.

  Study EGAS00001008060

• PDX_models_from_Latin_America_RNAseq

  Acral melanoma (AM) is a subtype of cutaneous melanoma that occurs on glabrous skin of the hands and feet (palms, soles and nail apparatus) and which is relatively more common in non-European descent populations such as those of Latin America. Compared to other subtypes, it is poorly studied and experimental models that faithfully reproduce human AM features are urgently needed. We report the generation and preliminary characterisation of a collection of patient-derived xenografts of acral melanomas (AM-PDX) from Latin-American patients. PDX came from Brazilian and Mexican patients cared for at the Instituto Nacional de Câncer (INCA) and the Instituto Nacional de Cancerologia (INCan). The majority of the samples are acral lentiginous melanomas, ulcerated, with > 4mm Breslow depth and > 2 mitosis / mm2. Samples were mechanically fragmented and subcutaneously implanted in NSG mice and then collected for molecular analysis.

  Study EGAS00001008150

• PDX_models_from_Latin_America_Xenofiltered_WES

  Acral melanoma (AM) is a subtype of cutaneous melanoma that occurs on glabrous skin of the hands and feet (palms, soles and nail apparatus) and which is relatively more common in non-European descent populations such as those of Latin America. Compared to other subtypes, it is poorly studied and experimental models that faithfully reproduce human AM features are urgently needed. We report the generation and preliminary characterisation of a collection of patient-derived xenografts of acral melanomas (AM-PDX) from Latin-American patients. PDX came from Brazilian and Mexican patients cared for at the Instituto Nacional de Câncer (INCA) and the Instituto Nacional de Cancerologia (INCan). The majority of the samples are acral lentiginous melanomas, ulcerated, with > 4mm Breslow depth and > 2 mitosis / mm2. Samples were mechanically fragmented and subcutaneously implanted in NSG mice and then collected for molecular analysis.

  Study EGAS00001008231

• PDX_models_from_Latin_America_RNAseq_Xenofiltered

  Acral melanoma (AM) is a subtype of cutaneous melanoma that occurs on glabrous skin of the hands and feet (palms, soles and nail apparatus) and which is relatively more common in non-European descent populations such as those of Latin America. Compared to other subtypes, it is poorly studied and experimental models that faithfully reproduce human AM features are urgently needed. We report the generation and preliminary characterisation of a collection of patient-derived xenografts of acral melanomas (AM-PDX) from Latin-American patients. PDX came from Brazilian and Mexican patients cared for at the Instituto Nacional de Câncer (INCA) and the Instituto Nacional de Cancerologia (INCan). The majority of the samples are acral lentiginous melanomas, ulcerated, with > 4mm Breslow depth and > 2 mitosis / mm2. Samples were mechanically fragmented and subcutaneously implanted in NSG mice and then collected for molecular analysis.

  Study EGAS00001008232

• Mutational signatures of environmental carcinogens in human tissue organoids

  Whole genome sequencing of human tumours has revealed distinct patterns (signatures) of mutations that provide clues to the causative origins of cancer. Some signatures have been attributed to endogenous processes, some to exogenous agents, while a substantial proportion are of unknown origin. Generation of mutational signatures induced in experimental systems can verify the signature assignments and shed light on their origins and mechanisms. We have investigated mutational signatures of environmental carcinogens in human tissue organoid cultures. These 3-dimensional systems retain some of the architecture and functions of the organs from which they are derived, affording the opportunity to observe the effects of carcinogens in both target and non-target organs. There was a lesser requirement for an exogenous metabolizing system, as the cultures were, in most cases, capable of activating test agents. Duplex sequencing eliminated PCR amplification errors from mutational profiles and removed the need to clone carcinogen-treated cultures. Gastric, colon, liver, pancreas and kidney organoids were exposed to benzo[a]pyrene (BaP), aflatoxin B1 (AFB1), aristolochic acid (AAI) and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP). All four agents induced single-base substitution (SBS) signatures, BaP and AAI induced double-base substitution (DBS) signatures and indel (ID) signatures, and PhIP also induced an ID signature. These signatures were the same in all five organoid types, although there were quantitative differences. A further 13 environmental carcinogens were investigated in human gastric organoids, and signatures were obtained for seven of them: ethylnitrosourea (ENU), methylazoxymethanol acetate (MAM), N-methyl-N′-nitro-N-nitrosoguanidine (MMNG), potassium bromate, glycidamide, styrene oxide and propylene oxide, providing additional insights into processes underlying the causes of human cancer.

  Dataset EGAD00001015616

• Mutational signatures of environmental carcinogens in human tissue organoids – WGS Bulk Normals

  Whole genome sequencing of human tumours has revealed distinct patterns (signatures) of mutations that provide clues to the causative origins of cancer. Some signatures have been attributed to endogenous processes, some to exogenous agents, while a substantial proportion are of unknown origin. Generation of mutational signatures induced in experimental systems can verify the signature assignments and shed light on their origins and mechanisms. We have investigated mutational signatures of environmental carcinogens in human tissue organoid cultures. These 3-dimensional systems retain some of the architecture and functions of the organs from which they are derived, affording the opportunity to observe the effects of carcinogens in both target and non-target organs. There was a lesser requirement for an exogenous metabolizing system, as the cultures were, in most cases, capable of activating test agents. Duplex sequencing eliminated PCR amplification errors from mutational profiles and removed the need to clone carcinogen-treated cultures. Gastric, colon, liver, pancreas and kidney organoids were exposed to benzo[a]pyrene (BaP), aflatoxin B1 (AFB1), aristolochic acid (AAI) and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP). All four agents induced single-base substitution (SBS) signatures, BaP and AAI induced double-base substitution (DBS) signatures and indel (ID) signatures, and PhIP also induced an ID signature. These signatures were the same in all five organoid types, although there were quantitative differences. A further 13 environmental carcinogens were investigated in human gastric organoids, and signatures were obtained for seven of them: ethylnitrosourea (ENU), methylazoxymethanol acetate (MAM), N-methyl-N′-nitro-N-nitrosoguanidine (MMNG), potassium bromate, glycidamide, styrene oxide and propylene oxide, providing additional insights into processes underlying the causes of human cancer.

  Dataset EGAD00001015630

• Single cell characterization of T-cell lymphoma: RNA (2025-07-31)

  Lymphomas are types of blood cancer derived from lymphocytes, and can be classified into two main categories, Hodgkin's lymphomas (HL) and non-Hodgkin lymphomas (NHL). T-cell lymphoma is a type of NHL that develops from T lymphocytes and accounts for 10-15% of total NHL cases. As a rare disease, T-cell lymphoma is functionally, pathologically, and clinically complex and heterogeneous. The 2016 revision of the WHO classification has listed 29 subtypes of mature T/NK-cell neoplasms, among which over 25 are T lymphocyte in origin. These subtypes of T-cell lymphomas have different biological behaviours and clinical prognosis. Clinically, T-cell lymphoma ranges from indolent (slow-growing) to aggressive (fast-growing and spreading) disease. According to the guideline booklet provided by the Lymphoma Research Foundation (https://lymphoma.org/aboutlymphoma/nhl/), indolent T-cell lymphoma subtypes include adult T-cell leukaemia/lymphoma (ATLL), cutaneous T-cell lymphoma (CTCL), and mycosis fungoides (MF), while the aggressive subtypes include anaplastic large cell lymphoma (ALCL), angioimmunoblastic T-cell lymphoma (AITL), peripheral T-cell lymphoma (PTCL), and T lymphoblastic lymphoma (TLBL). PTCL and ALCL represent the most common subtypes of aggressive T-cell lymphoma whereas TLBL is a rare and aggressive subtype mostly diagnosed in children. In this study, we will use single cell RNA sequencing and single cell multiomic methods three aggressive T-cell lymphoma subtypes (ALCL, PTCL and TLBL) and try to gain a deeper insight into the genotypic and phenotypic features of these T-cell lymphomas. . This dataset contains all the data available for this study on 2025-07-31.

  Dataset EGAD00001015669

• Molecular risk stratification in patients with T1 colorectal cancer_WES

  The introduction of bowel cancer screening has led to a significant increase in the proportion of patients being diagnosed with asymptomatic, early-stage colorectal cancer (CRC). Although the majority of these patients are successfully treated with surgery alone, a small proportion of patients have 'born-to-be-bad' aggressive lesions with early dissemination leading to distant metastases. Current standard of care histological assessment is unable to distinguish between these aggressive versus non-aggressive early lesions which is essential to provide appropriate clinical management decisions. This study aims to carry out molecular and histological profiling of approximately 300 T1 CRCs in order to develop a molecular stratifier based on the risk of relapse in early-invasive CRC. This novel T1 cohort will represent the world's largest molecularly characterised T1 cohort of samples, with digital pathology assessment alongside whole exome sequencing, copy number variation analysis and 3' RNA-seq. This data will be used to generate a robust panel of molecular and/or histological markers applicable to formalin-fixed paraffin embedded (FFPE) archival tissue which discriminates between T1 lesions based on risk of relapse, which will ultimately be used to inform clinical management of CRC at the earliest stages of the disease.

  Dataset EGAD00001010890