Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment
Study
EGAS00001003886
WGS, DuplexSeq and NanoSeq genomic data from histologically normal tissue in cancer patients
The extent to which mutagenic and non-mutagenic processes, including cancer treatment, contribute to somatic evolution in histologically normal tissue remains unclear. We subjected 168 cancer-free normal samples representing 16 different organs from 22 patients with metastatic cancer enrolled in the PEACE research autopsy study to high-depth duplex panel sequencing (coverage >20,000x). In every sample we identified somatic mutations (range 170 - 2,978) at exceedingly low variant allele frequencies (median VAF 0.0000323), consistent with a patchwork of mutated cells in normal tissue. By analysing the mutational spectra of each sample, we extracted 16 distinct single base substitution mutational signatures, reflecting somatic mutational processes that have moulded the genomes of normal cells. Signatures were found to be associated with diverse aetiologies, including alcohol-related mutation acquisition in liver tissue, smoking-induced mutagenesis in lung and cardiac tissue, and multiple distinct treatment-induced processes, which correlated with treatment and its duration. On average, in this cohort in which patients had each received several lines of anti-cancer therapy, exogenous sources, including treatment-related mutagenesis, underpinned >40% of mutations in liver samples, yet <10% in brain samples. Finally, we observed clear differences in the extent and effects of selection in different tissues, with positive selection in certain tissues, including lung (TP53, EGFR and PIK3CA), liver (NF2L2) and spleen (BRAF, NOTCH2), and limited selection in others, such as brain and cardiac. Over 25% of driver mutations in normal tissue exposed to systemic anti-cancer therapy, including mutations in TP53, could be attributed to treatment-induced mutagenesis. Immunotherapy, while not associated with mutagenesis, was linked to an excess of driver mutations in PPM1D and TP53, illustrating how non-mutagenic treatment can sculpt somatic evolution. Our study reveals the rich tapestry of mutational processes and driver mutations in cancer-free normal tissue, and the profound impact of cancer therapeutic and life-time environmental exposures on normal tissue somatic evolution.
Study
EGAS00001008326
Exceptional Outcomes in a Phase Ib Study Combining PARP and MEK Inhibition, With or Without Anti-PD-L1, for BRCA-Wildtype Platinum-Sensitive Recurrent Ovarian Cancer
To evaluate regimens combining PARP and MEK inhibition, with or without PD-L1 inhibition, for BRCA-wildtype platinum-sensitive recurrent ovarian cancer (PSROC).
Study
EGAS00001007496
Molecular Classification of Hormone Sensitive and Castration Resistant prostate cancer, using non-negative matrix factorization molecular subtyping
We aim to identify molecular subtypes of prostate cancer using consensus non-negative matrix factorization and correlate these with existing biomarkers to inform future immunotherapeutic strategies.
Study
EGAS00001006204
Genomic evolution of pancreatic cancer at single-cell resolution
This project assesses genomic evolution of pancreatic cancer using the Mission Bio Tapestri platform and Whole Exome Sequencing. The Mission Bio Tapestri platform is a single-cell DNA sequencing platform using a targeted gene panel to assess SNV/CNV. Several samples, including primary and metastatic tissue, were used to investigate changes at single-cell resolution.
Study
EGAS50000001351
Comprehensive NGS Profiling to Enable Detection of ALK Gene Rearrangements and MET Amplifications in Non-Small Cell Lung Cancer
We evaluate the analytical performance of the PGDx™ elio™ tissue complete assay, a 505 gene next-generation sequencing (NGS) tissue-based assay, that has now been FDA-cleared for use by physicians to help guide treatment decisions for cancer patients, using a NSCLC cohort of 38 patients.
Study
EGAS50000000010
Single-cell RNA-seq profiling of patient derived organoids
The aim of this study was to profile developement of resistance to cancer treatments using organoids. Two patient derived colorectal cancer organoids were profiled using single cell RNAseq after treatment with a combination of different anticancer drugs. The organoids were profiled both after 4 weeks of treatment and after a drug holiday of 2 weeks.
Study
EGAS50000001025
CDK4/6 inhibition in advanced chordoma: final results of the NCT PMO-1601
Background. Chordoma is a rare bone tumor with no approved systemic therapy. Inactivation of the tumor suppressor p16 (encoded by CDKN2A) leads to aberrant cyclin D-CDK4/6-RB pathway activity, which can be inhibited by palbociclib in chordoma cell lines.
Patients and Methods. We conducted a phase II single-arm, open-labeled trial on palbociclib in adult patients with advanced chordomas with p16 loss (by immunohistochemistry) or CDKN2A loss (by genomic analysis) and CDK4/6 and RB1 presence (by immunohistochemistry or RNA-Sequencing). Patients received 125mg palbociclib once daily for 21 days in a 28-day cycle. The study used a Simon optimal 2-stage design. The primary endpoint was disease control rate after six cycles. Response was evaluated according to Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1. Secondary endpoints included progression-free survival, overall survival, and biomarker analysis. The study was considered positive if 25% of patients reached the primary endpoint.
Results. Between December 2017 and April 2023, 28 patients (median age 60 years, range 31-84) were enrolled. After a median follow-up of 28 months, the disease control rate was 39%, with 11 out of 28 patients achieving stable disease. No objective responses were observed. The median progression-free survival was 5.6 months, and the median overall survival was 24.6 months. Treatment was well tolerated without new safety signals. CDKN2A deletions were the most common genomic alterations underlying p16 loss and were accompanied by MTAP co-deletion. There was no correlation between responder phenotypes by immunohistochemistry and outcome. RNA-based analysis showed heterogeneous pathways deregulation at study entry suggesting underlying primary resistance mechanisms
Conclusion. This trial met its primary endpoint with a 39% disease control rate, though antitumor activity was modest. Molecularly tailored combination therapies should be considered to improve efficacy. (ClinicalTrials.gov number, NCT03110744).
Study
EGAS00001007985
analysis of immune infiltration in colorectal cancer metastasis
Metastatic colorectal cancer (mCRC) is the main cause of CRC mortality, with limited treatment options. Although immunotherapy has benefited some cancer patients, mCRC typically lacks the molecular features that respond to this treatment. However, recent studies indicate that the immune microenvironment of mCRC may be modified to enhance the effect of immune checkpoint inhibitors. This study aimed to explore the metastatic immune microenvironment by comparing immune cell populations in colorectal liver (CLM), lung (mLu) and peritoneal (PM) metastases.
Study
EGAS50000000652
Mutations conferring differential treatment response in breast cancer
Poor prognosis primary breast cancer patients usually receive cytotoxic chemotherapy as a component of treatment, but despite this aggressive therapy recurrences remain common. Improved understanding of chemoresistance pathways would allow better stratification of chemotherapy using predictive markers, and may allow therapeutic inhibition of resistance mechanisms in order to chemosensitise tumours. We aimed to identify molecular pathways that define chemoresponse using the novel approach of examining the selection exerted by neoadjuvant chemotherapy on sub-clonal somatic mutational profiles of cancer cells.
Study
EGAS00001003626
Defining structural variation associated with breast cancer susceptibility by long-read genome sequencing
Germline structural variants (SVs) are challenging to identify by conventional genetic testing assays. Long-read sequencing has improved the global characterization of SVs, but its sensitivity at genetic loci associated with high- and moderate-penetrance cancer susceptibility has not been reported. This study used long-read genome sequencing performed on the Oxford Nanopore Technologies' PromethION to resolve variants underlying breast cancer susceptibility in sixteen individuals with pathogenic germline SVs in BRCA1, BRCA2, CHEK2 or PALB2.
Study
EGAS00001005872
Deep whole genome sequencing identifies recurrent genomic alterations in breast cancer cell lines and patient derived xenograft models
Breast cancer cell lines (BCCLs) and patient-derived xenografts (PDX) are the most frequently used models in breast cancer research. Despite their widespread usage, genome sequencing of these models is incomplete, with previous studies only focusing on targeted gene panels, whole exome or shallow whole genome sequencing. Here we describe deep whole genome sequencing (WGS) of commonly used BCCL and PDX models using the Illumina X10 platform with an average ~ 60x coverage.
Study
EGAS00001006285
Whole Genome Sequencing Data of High Grade Serous Ovarian Cancer
Longitudinal whole genome sequencing data to study chemoresponse in ovarian cancer. These samples belong to an ongoing sample collection and the data already includes hundreds of samples from over 200 patients. Samples are from primary and metastatic tissues and ascites. All patients have been treated with platinum-taxane based chemotherapy and majority of them are diagnosed with high-grade serous ovarian cancer.
Study
EGAS00001006775
WES of breast cancer patients and controls
This study assessed the variant profiles of 408 samples from 126 breast cancer patients with various survival outcomes, including paired uninvolved mammary gland samples collected at proximal distances from primary lesions. As a reference, control samples from 15 mammoplasty individuals without cancer history were studied. Whole exome sequencing was performed to identify post-zygotic and germline variants present in the studied samples. Variant annotation in known databases, interpretation, and statistical analyses followed to discern the clinical relevance of called variants.
Study
EGAS50000000539
Identification_and_functional_validation_of_driver_mutations_in_colorectal_cancer
Targeted exome sequencing of human colorectal cancers for the identification of novel cancer drivers.
Study
EGAS00001000044
Whole_Genome_sequencing_of_rhabdomyosarcoma_tumour_tissue
The aim of this study is to investigate the genomic landscape of human cancer.
Study
EGAS00001008280
Single_cell_RNA_sequencing_of_rhabdomyosarcoma_tumour_tissue
The aim of this study is to investigate the genomic landscape of human cancer.
Study
EGAS00001008281
Single_cell_ATAC_sequencing_of_rhabdomyosarcoma_tumour_tissue
The aim of this study is to investigate the genomic landscape of human cancer.
Study
EGAS00001008283
Bulk_RNA_sequencing_of_rhabdomyosarcoma_tumour_tissue
The aim of this study is to investigate the genomic landscape of human cancer.
Study
EGAS00001008278
Bulk_RNA_sequencing_of_rhabdomyosarcoma_tumour_tissue
The aim of this study is to investigate the genomic landscape of human cancer.
Study
EGAS00001008282
Single_cell_ATAC_sequencing_of_rhabdomyosarcoma_tumour_tissue
The aim of this study is to investigate the genomic landscape of human cancer.
Study
EGAS00001008279
Breast_Cancer_Matched_Pair_Cell_Line_Whole_Genomes
We propose to definitively characterise the somatic genetics of matched pair breast cancer cell lines through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.
Study
EGAS00001000166
Y_chromosome_mis_segregation_in_the_DLD_1_cell_line
Study of the well-established DLD-1 colorectal cancer cell line, engineered with an inactivatable Y centromere that leads to mis-segregation. The goal is to gain insights into the mechanism of chromothripsis due to chromosome mis-segration.
Study
EGAS00001002551
Triple_Negative_Breast_Cancer_Whole_Genomes
We propose to definitively characterise the somatic genetics of Triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.
Study
EGAS00001000092
Transcriptome_Sequencing_of_Cancer_Cell_Lines
In this study we will sequence the transcriptome of Verified Cancer Cell lines. This will be married up to whole exome and whole genome sequencing data to establish a full catalog of the variations and mutations found.
Study
EGAS00001000261
Colorectal cancer genomics with primary and metastatic samples
We performed whole genome sequencing of metastatic colorectal cancer from 16 patients. Normal adjacent tissue, primary tissue, and metastatic tissue were analyzed to uncover metastatic progression and difference between primary and distant metastatic lesions.
Study
EGAS00001006465
Colorectal cancer transcriptomics with primary and metastatic samples
We performed RNAseq analysis of metastatic colorectal cancer from 16 patients. Normal adjacent tissue, primary tissue, and metastatic tissue were analyzed to uncover metastatic progression and difference between primary and distant metastatic lesions.
Study
EGAS00001006464
Whole exome sequencing of 103 pairs BLCA-CN
We sequenced 50M exomes of 103 pairs bladder cancer of chinese
Study
EGAS00001000677
Single_cell_RNA_sequencing_of_rhabdomyosarcoma_tumouroids
The aim of this study is to investigate the genomic landscape of human cancer.
Study
EGAS00001008273
Single_cell_RNA_sequencing_of_rhabdomyosarcoma_tumour_tissue
The aim of this study is to investigate the genomic landscape of human cancer.
Study
EGAS00001008275
Single_cell_ATAC_sequencing_of_rhabdomyosarcoma_tumour_tissue
The aim of this study is to investigate the genomic landscape of human cancer.
Study
EGAS00001008276
The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer
Reactivation of telomerase reverse transcriptase (TERT) expression enables cells to overcome replicative senescence and escape apoptosis, fundamental steps in the initiation of human cancer. Multiple cancer types, including up to 83% of glioblastomas (GBM), harbor highly recurrent TERT promoter mutations of unknown function but specific to two nucleotide positions. We identify the functional consequence of these mutations in GBM to be recruitment of the multimeric GABP transcription factor specifically to the mutant promoter. Allelic recruitment of GABP is consistently observed across four cancer types, highlighting a shared mechanism underlying TERT reactivation. Tandem flanking native ETS motifs critically cooperate with these mutations to activate TERT, likely by facilitating GABP heterotetramer binding. GABP thus directly links TERT promoter mutations to aberrant expression in multiple cancers.
Study
EGAS00001001242
Patient-derived organoids as a novel tool to study cervical cancer
Cervical cancer is the most prevalent gynecological malignancy worldwide, often caused by infection with a high-risk human papillomavirus. Currently, there are only limited number of human-derived culture systems available that enable to study the viral infection for short-term. Here, we report on establishment of long-term human-derived organoid cultures from both healthy ecto- and endocervical epithelia that closely recapitulate the tissues of origin by maintaining the authentic histological and tissue-specific gene expression profiles. Additionally, using material from patients’ Pap-brush material, a successful panel of long-term patient-derived cancer organoids was established that maintain the causative viral infection in vitro and show differential response to common chemotherapy regimens. This study provides a promising platform for cervical cancer research and studying direct virus-host interactions.
Study
EGAS00001004439
Whole_genome_sequencing_of_rhabdomyosarcoma_tumouroids
The aim of this study is to investigate the genomic landscape of human cancer.
Study
EGAS00001008270
Whole_Genome_sequencing_of_rhabdomyosarcoma_tumour_tissue
The aim of this study is to investigate the genomic landscape of human cancer.
Study
EGAS00001008274
PARADIGM: Combined ctDNA and serum PSA for dynamic monitoring of metastatic prostate cancer starting first-line treatment
The prognosis of newly-diagnosed metastatic prostate cancer is highly variable. The PARADIGM prospective cohort study evaluated predictors of survival in blood collected at the start of each of the first six treatment cycles from 114 high-volume metastatic patients starting androgen deprivation therapy combined with docetaxel or an androgen receptor pathway inhibitor.
Study
EGAS50000001357
Cancer_Genome_Libraries_Tests
Testing library production.Genomic libraries (500 bps) will be generated from total genomic DNA derived from commomon epithelial cancer samples and subjected to paired end sequencing on the llumina plateforms. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.
Study
EGAS00001000208
Sensitive neoantigen discovery by real-time mutanome-guided immunopeptidomics - WES
Targeting cancer-specific HLA-peptide complexes is a promising immunotherapy approach, with mutated neoantigens offering high value for their immunogenicity and cancer-specificity. Selecting immunogenic targets requires personalized prioritization of cancer-specific immunopeptides. Mass spectrometry (MS)-based immunopeptidomics supports this process by directly identifying cancer-specific antigens and informing global presentation patterns to refine immunogenicity predictions. Clinical pipelines, however, must balance global depth and target sensitivity compounded by low input samples and time constraints. Here, we present NeoDiscMS, an extension of the NeoDisc pipeline, enabling personalized immunopeptidomics data acquisition. By leveraging real-time NGS-guided spectral acquisitions, NeoDiscMS maximizing sensitivity with minimal loss of global depth. NeoDiscMS improves TAA-derived peptide detection up to 20% and enhances neoantigen identification confidence compared to the clinical gold standard method. Designed for effectiveness and ease of use, it requires minimal effort for implementation. NeoDiscMS advances personalization in clinical antigen discovery by enabling more sensitive neoantigen detection while seamlessly integrating into existing workflows.
Study
EGAS50000000976
Sensitive neoantigen discovery by real-time mutanome-guided immunopeptidomics - RNAseq
Targeting cancer-specific HLA-peptide complexes is a promising immunotherapy approach, with mutated neoantigens offering high value for their immunogenicity and cancer-specificity. Selecting immunogenic targets requires personalized prioritization of cancer-specific immunopeptides. Mass spectrometry (MS)-based immunopeptidomics supports this process by directly identifying cancer-specific antigens and informing global presentation patterns to refine immunogenicity predictions. Clinical pipelines, however, must balance global depth and target sensitivity compounded by low input samples and time constraints. Here, we present NeoDiscMS, an extension of the NeoDisc pipeline, enabling personalized immunopeptidomics data acquisition. By leveraging real-time NGS-guided spectral acquisitions, NeoDiscMS maximizing sensitivity with minimal loss of global depth. NeoDiscMS improves TAA-derived peptide detection up to 20% and enhances neoantigen identification confidence compared to the clinical gold standard method. Designed for effectiveness and ease of use, it requires minimal effort for implementation. NeoDiscMS advances personalization in clinical antigen discovery by enabling more sensitive neoantigen detection while seamlessly integrating into existing workflows.
Study
EGAS50000000977
MutWP6__CRUK_Grand_Challenge_Mutographs_of_Cancer__alkylating_agents
The Mutographs project aims to advance our understanding of the causes of cancer through studies of mutational signatures. Led by Mike Stratton, together with Paul Brennan, Ludmil Alexandrov, Allan Balmain, David Phillips and Peter Campbell, this large-scale international research endeavour was awarded a Cancer Research UK Grand Challenge.
Within Mutographs, work lead by the Sanger Institute will investigate whether detection of somatic mutations and mutational signatures in circulating white blood cells can be developed into a practical, generic system for surveying and monitoring multiple different endogenous and exogenous exposures, providing an ‘observatory’ on somatic mutational processes in humans.
Whole genome sequences are generated at the Wellcome Sanger Institute (Illumina HiSeqX). Somatic mutational signatures are subsequently extracted by non-negative matrix factorisation methods.
Through an enhanced understanding of cancer aetiology, Mutographs unprecedented effort is anticipated to outline modifiable risk factors, lead to new approaches to prevent cancer, and provide opportunities to empower early detection, refine high-risk groups and contribute to further therapeutic development.
Study
EGAS00001003637
GENOMIC MUTATION LANDSCAPE OF SKIN CANCERS FROM DNA REPAIR-DEFICIENT XERODERMA PIGMENTOSUM PATIENTS
Xeroderma pigmentosum (XP) is a genetic disorder caused by mutations in genes of the Nucleotide Excision Repair (NER) pathway (groups A-G) or in Translesion Synthesis (TLS) DNA polymerase η (group V). XP is associated with an increased skin cancer risk, reaching, for some groups, several thousand-fold compared to the general population. Here, we analyzed 38 skin cancer genomes from five XP groups. We found that the activity of NER determines heterogeneity of the mutation rates across skin cancer genomes and that transcription-coupled NER extends beyond the gene boundaries reducing the intergenic mutation rate. Mutational profile in XP-V tumors revealed the role of polymerase η in the error-free bypass of (i) rare TpG and TpA DNA lesions, (ii) 3’ nucleotides in pyrimidine dimers, and (iii) TpT photodimers. Our study unravels the genetic basis of skin cancer risk in XP and provides insights into the mechanisms reducing UV-induced mutagenesis in the general population.
Study
EGAS00001006732
Assessment of cannabidiol and Δ9-tetrahydrocannabiol in mouse models of medulloblastoma
Phytocannabinoids Δ9-tetrahydrocannabinol (THC) and cannabidiol (CBD) have been demonstrated to exhibit anti-cancer activity in preclinical models of brain cancer leading to new clinical trials for adults with glioblastoma. We describe here the first report that has investigated a role for THC and CBD in paediatric brain cancer. Cannabinoids had cytotoxic activity against medulloblastoma and ependymoma cells in vitro, functioning in part through the inhibition of cell cycle progression and the induction of autophagy. Despite these effects in vitro, when tested in orthotopic mouse models of medulloblastoma or ependymoma, no impact on animal survival was observed. Furthermore, cannabinoids neither enhanced nor impaired conventional chemotherapy in a medulloblastoma mouse model. These data show that while THC and CBD do have some effects on medulloblastoma and ependymoma cells, are well tolerated and have minimal adverse effects, they do not appear to elicit any survival benefit in preclinical models of paediatric brain cancer.
Study
EGAS00001004963
Early detection of ovarian cancer using cell-free DNA fragmentomes and protein biomarkers
Ovarian cancer is the leading cause of death from gynecological cancers worldwide. No effective screening methods exist, and tumors are commonly detected at advanced stages where treatment is much less effective. In this study, we used whole-genome cell-free DNA (cfDNA) fragmentome and protein biomarker (CA-125 and HE4) analyses to evaluate 591 women from the European Union or the United States with ovarian cancer, benign adnexal masses, or without ovarian lesions. Using a machine learning model that incorporated multi-analyte fragmentome data and protein measurements, we detected ovarian cancer with high specificity >99% and sensitivity of 72%, 69%, 87%, and 100% for stages I–IV, respectively (AUC=0.96, 95% CI: 0.94-0.99), including 90% of high grade serous ovarian cancers. At the same specificity, CA-125 alone detected 34%, 62%, 63%, and 100% of ovarian cancers for stages I–IV (p=0.001, two-sided test of equal proportions). Additionally, our approach distinguished benign masses from ovarian cancers with high accuracy (AUC of 0.88, 95% CI=0.83-0.92). These results were validated in an independent population. These findings show that integrated cfDNA fragmentome and protein analyses detect ovarian cancers with high performance, enabling a new accessible approach for noninvasive ovarian cancer screening and diagnostic evaluation.
Study
EGAS50000000484
EOSC4Cancer Synthetic Colorectal Cancer Genomic data
In this study there are stored the synthetic datasets produced by partners involved in EOSC4Cancer. The study contains independent datasets available for the research community. The synthetic genomes have been created trying to mimic real cancer data.
Study
EGAS50000000190
Breast Cancer PDTX Encyclopaedia
Molecular data from the collection of PDTX breast cancer models described in Bruna et al, 2016. Cell. It includes whole exome sequencing, shallow whole genome sequencing, expression arrays and reduced bisulfite representation sequencing (RRBS).
Study
EGAS00001001913
BASIS_RNAseq
We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.
Study
EGAS00001000707
Whole_Exome_PC9_and_A375
Drug resistant population of PC9(human non-small cell lung cancer) or A375 (human melanoma) cell lines were used for this study. By exome sequencing, we will analyse mutations of cells in drug tolerent state and after drug holiday.
Study
EGAS00001002493
Breast_Cancer_Whole_Genome_Sequencing
We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.
Study
EGAS00001000210
Harnessing_transposons_for_drug_resistance_gene_discovery_in_cancer
This study involves a forward genetic screen to identify common insertion sites in drug resistant clones. We will be utilising piggybac transposon systems in order to generate multiple drug resistant clones in a range of human cancer cell lines.
Study
EGAS00001000468
Genomic Rearrangements in Pediatric Cancer
This study contains a collection of samples used to determine the role and impact of genomic rearrangements in a pan cancer pediatric cohort.
Study
EGAS00001005312