10161 results for "cancer rna-seq"

in 41.75 milliseconds.

• 18 Whole Exome Sequencing for Radiation Induced-Meningiomas

  Purpose: Majority of pediatric cancers require the irradiation of the central nervous system (CNS), and as more patients survive into adulthood from improved oncological therapy the sequelae of brain radiation are increasing in prevalence. Radiation-induced meningiomas (RIMs), one such secondary effect, demonstrate a clinically more aggressive behaviour than sporadic meningiomas (SMs). We aimed to describe the genomic mutational landscape of RIMs.Methods: We analyzed a principal cohort of 18 RIMs, with 31 RIMs overall, from patients who received childhood radiation therapy and 30 SMs, as a comparator population. We performed a multiplatform integrative genomic analysis; including methylation, whole exome and RNA sequencing. Results: RIMs exhibited a five-fold increase in copy number alterations, commonly the loss of chromosome 1p (17/18 RIMs) and 22q (17/18 RIMs), which was significantly more than observed in sporadic meningiomas. Furthermore, RNA sequencing data revealed an NF2 gene fusion event in 35.3% of RIMs. In all 6 cases, there was a complete NF2 exon spliced into a complete exon of a reciprocal gene, suggesting that the breakpoints of genomic rearrangement are intronic. All tumours with the NF2 fusion also possessed monosomy of chromosome 22q, rendering the cells with homozygous disruption of NF2. Clinically, RIMs with the NF2 fusion exhibited ill-defined borders and a tendency to develop in anatomic frontal location. Also, targeted sequencing panel confirmed that RIMs had fewer nonsynonymous NF2 mutations (6.5% vs. 30% in SM) and absence of mutations in TRAF7, SMO, KLF4, PIK3CA and AKT1, genes traditionally involved in SMs.Conclusion: Our study demonstrates that RIMs have distinct genomic drivers of oncogenesis as compared to SMs, specifically NF2 inactivation through fusion event. Radiation therapy possibly triggers genomic structural rearrangements through error-prone repair of double-stranded DNA breaks.

  Study EGAS00001002317

• NINDS Deep Sequencing for the Detection of Viral Sequences in Primary Progressive Multiple Sclerosis Brains

  Deep sequencing allows for a rapid, accurate characterization of microbial DNA and RNA sequences in many types of samples. Deep sequencing (also called next generation sequencing or NGS) is being developed to assist with the diagnosis of a wide variety of infectious diseases. In this study, seven frozen brain samples (n = 7) from deceased subjects with recent encephalitis were investigated. RNA from each sample was extracted, randomly reverse transcribed, and sequenced. The sequence analysis was performed in a blinded fashion and confirmed with pathogen-specific PCR. This analysis successfully identified measles virus sequences in two brain samples and herpes simplex virus type-1 sequences in three brain samples. No pathogen was identified in the other two brain specimens. These results were concordant with pathogen-specific PCR and partially concordant with prior neuropathological examinations, demonstrating that deep sequencing can accurately identify viral infections in frozen brain tissue (Chan et al., 2014). Data from the primary progressive multiple sclerosis (PPMS) brain specimens (n = 14) and Normal Control brain specimens (n = 14) are also submitted here. All the subjects studied here (encephalitis, PPMS, and controls) were selected from existing collections at the Rocky Mountain and UCLA brain banks. These selections were performed by the directors at the two centers (Dr. Corboy at RM and Nagra at UCLA) based on clinic information provided at the time of collection. All the specimens are from deidentified deceased individuals. The submitting investigators have no identifying information on any of these subjects. To avoid confusion, the dbGaP Subject IDs are identical to the brain bank identifying numbers.

  Study phs000715

• Integration of Genomics and Transcriptomics in unselected Twins and in Major Depression

  Our goals are to develop a comprehensive understanding of the genomics of transcription in a population based unselected sample and to discover DNA and RNA biomarkers for major depressive disorder (MDD). This work is essential to developing a more complete understanding of the biological basis of MDD, a common complex trait associated with considerable morbidity, mortality, and personal/societal cost. All biological samples have been collected from well-defined populations, and are now available. First, we conduct a "genetical genomics" or eQTL study of ~800 MZ and ~800DZ twin pairs. Each subject has been assayed for genome-wide SNPs and CNVs and gene expression from peripheral blood sampled under standardized conditions. We determine the genetic architecture (genetic and non-genetic proportions of variance via twin analyses) for every transcript, and the genome-wide associations (i.e., SNP-transcript eQTL pairs). These analyses will be expanded to consider transcriptional modules. The key deliverable is a detailed catalogue of the general and specific architecture of transcription plus raw intensity files. Second, we seek to discover DNA and RNA biomarkers relevant to MDD, capitalizing on the results of a large MDD study with repeated clinical and biological assessments; we have previously shown that PB is a reasonable proxy for CNS expression and employ an advanced modelling framework: (a) Using baseline data, we identify biomarkers for MDD by comparing ~1000 controls with ~1400 MDD cases via comparisons of SNP, CNV, expression transcripts, and transcriptional modules. (b) Using longitudinal data, we contrast gene expression signatures assessed at baseline and two years later in ~200 controls and ~500 MDD cases.

  Study phs000486

• Prediction of HLA genotypes using NGS data

  High-precision human leukocyte antigen (HLA) genotyping is crucial for anti-cancer immunotherapy, but existing tools predicting HLA genotypes using next-generation sequencing (NGS) data are insufficiently accurate.

  Study EGAS00001005274

• Breast Cancer Sequential Sampling Targeted Capture

  This study aims to target capture sequence regions of interest from DNA derived from breast cancer patients who received neo-adjuvant chemotherapy. All patients had multiple biopsies performed before chemotherapy. Patients who had residual disease after the course of treatment underwent a further biopsy. We aim to characterise the mutations involved.

  Dataset EGAD00001000784

• 2014 sequenced WGS-Lung Cancer sample 30 pair

  This data is belong to WGS-Lung Cancer patients' genome data which is aligned to human reference(human_g1k_v37.fasta). There are 30 paired tumor/normal samples from Samsung Hospital. All samples has passed QC and recalibration steps while aligning to reference.

  Dataset EGAD00001003978

• 2014 sequenced Korean WES-Lung Cancer sample 36 pair

  This data is belong to WES-Lung Cancer patients' genome data which is aligned to human reference(human_g1k_v37.fasta). There are 36 paired tumor/normal samples from Samsung Hospital. All samples has passed QC and recalibration steps while aligning to reference.

  Dataset EGAD00001004027

• Breast Cancer -Very young women with ER+ tumor

  Corresponding data set is composed of whole exome sequencing of Korean ER positive breast cancer under 35. This set provides 100 alignment files from normal-tumor paired whole exome sequencing of 50 patients. This is a part of total project data set.

  Dataset EGAD00001002256

• Combination Therapies for Personalised Cancer Medicine in drug resistant EGFR mutant lung cancer (2019-06-10)

  This study involves mutagenizing a range of different cell lines with ENU to identify those mutations which engender resistance to targeted treatment. . This dataset contains all the data available for this study on 2019-06-10.

  Dataset EGAD00001005080

• Whole exome sequencing analysis on patient-derived cervical cancer tissues and respective tumoroids

  Whole exome sequencing (WES) was performed on the matched tumor and organoid pairs from 7 cervical cancer patients. The DNA was sequenced on NovaSeq6000 platform with 8Gb sequencing coverage. WES data was mapped against human reference genome GRCh38 by using BWA (v0.7.5) mapping tool.

  Dataset EGAD00001006166

• Copy number profiling of tissue and plasma samples from high grade serous epithelial ovarian cancer patients

  This dataset includes 289 samples from 46 high grade serous epithelial ovarian cancer patients. Data are from both tissue samples (either primary tumor, or synchronous metastases) and circulating cell-free DNA (cfDNA) of plasma samples taken during therapy and follow-up.

  Dataset EGAD00001006422

• Early breast cancer (WES)

  Whole-exome sequencing of 30 early breast cancer samples.

  Dataset EGAD00001007057

• Spatial transcriptome sequence data from prostate cancer needle biopsies

  Spatial transcriptome sequencing data from prostate cancer needle biopsies. Dataset contains biopsies from before and after androgen deprivation therapy of 3 patients with 8 biopsies per patient in total. 2 sections (replicates) are taken from each biopsy.

  Dataset EGAD00001008636

• Spectrum of Response to Platinum and PARP Inhibitors in Germline BRCA Associated Pancreatic Cancer in the Clinical and Pre-clinical Setting

  Whole genome sequencing data for germline BRCA pancreatic cancer

  Dataset EGAD00001011129

• Whole genome sequence analysis in patients with primary central nervous system lymphomas

  We performed target amplicon sequencing analysis in 28 patients with primary central nervous system lymphomas using target capture technology (NGS) on Cancer Panel to explore molecular targets.

  Study JGAS000258

• Colon adenomas and adenocarcinomas and matched mucosae

  Whole exome sequencing in sporadic colorectal cancers (CRC) and advanced adenomas (Ad-As), and their paired healthy mucosa, for a deeper understanding of the biology of this cancer.

  Study EGAS00001007255

• Prediction of plasma ctDNA fraction and prognostic implications of liquid biopsy in advanced prostate cancer

  Targeted cfDNA and WBC sequencing data from patients profiled in the study "Prediction of plasma ctDNA fraction and prognostic implications of liquid biopsy in advanced prostate cancer". Note that 'Exome sequencing' is listed under Dataset Type since there is no option for targeted panel sequencing.

  Dataset EGAD50000000303

• Norwegian Institute of Public Health – Cancer Registry of Norway Data Access Policy for JanusRNA transcriptomics datasets archived in Federated EGA Norway

  JanusRNA transcriptomics datasets are generated from biobank samples from the Janus Serum bank of the Cancer Registry of Norway/National Institute of Public Health. This Data Access Committee has been appointed to govern controlled access to these datasets archived in Federated EGA Norway.

  Dac EGAC50000000192

• Clinical and molecular features of early onset pancreatic cancer

  A retrospective cohort study on the clinical and molecular features of early onset pancreatic cancers (i. e. diagnosed at <50 years old) in comparison with later onset tumors.

  Study EGAS50000000362

• XClone for analyzing somatic copy number alterations

  Somatic copy number alterations (CNAs) are major mutations that contribute to the development and progression of various cancers. Despite a few computational methods proposed to detect CNAs from single-cell transcriptomic data, the technical sparsity of such data makes it challenging to identify allele-specific CNAs, particularly in complex clonal structures. In this study, we present a statistical method, XClone, that strengthens the signals of read depth and allelic imbalance by effective smoothing on cell neighborhood and gene coordinate graphs to detect haplotype-aware CNAs from scRNA-seq data. By applying XClone to multiple datasets with challenging compositions, we demonstrated its ability to robustly detect different types of allele-specific CNAs and potentially indicate whole genome duplication, therefore enabling the discovery of corresponding subclones and the dissection of their phenotypic impacts.

  Study EGAS00001007854

• Prediction of Resistance and Sensitivity to HER2 Targeted Therapy in the Neoadjuvant Setting

  Women with breast cancers that overexpress HER2 are at greater risk for disease progression and death than women whose tumors do not overexpress HER2. Trastuzumab, a recombinant humanized monoclonal antibody against the extracellular domain of the HER2 protein blocks downstream signaling of HER2 and substantially improves the efficacy of chemotherapy in women with metastatic and early-stage HER2-positive breast cancers. Because resistance to trastuzumab eventually results in progressive disease in the metastatic setting and contributes to recurrence following adjuvant trastuzumab-based therapy, it is important to develop agents other than trastuzumab that target HER2 signaling through different mechanisms of action. Lapatinib is an oral, small molecule, dual tyrosine kinase inhibitor of HER2 and EGFR. Lapatinib has shown a lack of cross-resistance with trastuzumab in preclinical studies and activity in women with HER2-positive, metastatic breast cancer that has progressed during trastuzumab treatment. Trastuzumab blocks the downstream signaling of HER2 by binding to the extracellular domain of the receptor. Lapatinib binds to the intracellular domains of HER2 and EGFR and prevents activation of downstream signaling pathways. Because of this different mechanism of action, lapatinib may be effective in trastuzumab-resistant disease. The study will also provide important safety information on trastuzumab and lapatinib combinations immediately following anthracycline exposure, and also provide an initial direct comparison of cardiac effects of trastuzumab and lapatinib when incorporated into a standard sequential adriamycin and cyclophosphamide (AC) followed by weekly paclitaxel neoadjuvant regimen. Availability of a second agent that can interrupt HER2-signaling pathways through completely different mechanisms than those of trastuzumab offers the potential for further improvement in the management of patients with HER2-overexpressing breast cancer in both the adjuvant and metastatic setting. Co-administration of both trastuzumab and lapatinib with chemotherapy may be important in improving outcomes in subsets of HER2-positive breast cancers. However, use of two inhibitors of the HER2 pathway will increase costs and may increase toxicity, so it will be important to identify the subsets of patients who would benefit from the dual therapy. Inhibition of HER2 with a single agent clearly is sufficient for many patients as evidenced by the results of the trastuzumab trials. Therefore, co-administration to unselected populations of women with HER2-positive breast cancers would not represent an optimal approach. Given the activity of lapatinib, it is likely that it will also be sufficiently active in inhibiting HER2-pathway activation in some patients to allow for its use as the sole inhibitor of the HER2 pathway. Different populations may also derive greater benefit from one of the HER2-blocking agents relative to the other. Identification of potential predictive factors for pathologic complete response to the combination or to either agent administered alone in neoadjuvant trials would provide important information for adjuvant trials designed to definitively address these important issues. This study will compare 3 combined chemotherapy regimens: AC followed by paclitaxel plus trastuzumab and lapatinib, AC followed by paclitaxel plus lapatinib, and AC followed by paclitaxel plus trastuzumab given before surgery to patients with HER2-positive breast cancer.Tumor samples were collected prior to treatment and RNA sequencing was performed with this version.

  Study phs003275

• Validation of SNVs found by Exome-seq in S2-SF1, -SF5 and -SF9 hiPSCs

  PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001000631

• Pervasive H3K27 acetylation and ERV expression in H3.3K27M gliomas present a therapeutic vulnerability

  We sequenced a total of 2 H3.3K27WT (pcGBM2, G477; 3 replicates total) and 2 H3.3K27M (DIPGVI, DIPGXIII; 6 replicates total) patient-derived cell lines as well as Crispr/Cas9 H3.3K27M-KO clones for one of the cell lines (3 replicates total; DIPGXIII-KO) using ATAC-Seq. P-XX designates passages of replicates. These samples can be found at GEO under accession number GSE128744. This repository contains 1 replicate of G477 to be released under controlled access.

  Dataset EGAD00001004961

• McGill Sperm Methylome Sequencing Data

  The study includes NGS-based WGBS on one sperm DNA sample pooled from 30 participants, and methylC-capture sequencing (MCC-Seq) on the same pooled sperm sample as well as 45 sperm DNA samples derived from both fertile and infertile individuals in two cohorts (Toronto, a fertile cohort; Montreal, an idiopathic infertility cohort). All the data were generated with 100bp paired-end reads using the Illumina HiSeq2000 or 4000 systems.

  Dataset EGAD00001004978

• Epigenome mapping in purified cells of the digestive and urogenital organs: Participation in International Human Epigenome Consortium (IHEC) (ChIP-seq)

  The aim of this study is to participate in International Human Epigenome Consortium (IHEC, http://ihec-epigenomes.org/), through disclosure of quality epigenome profiles of various normal cell lineages and diseased cells purified from surgically resected materials of multiple Japanese people.

  Study JGAS000027

• Gene expression matrix for Smart-seq2 data of peripheral blood B cells

  The dataset contains scRNA-seq gene expression matrix (csv file) and metadata (csv file) after quality control filtering for data generated with the Smart-seq2 protocol. Transcript expression was quantified with Salmon v0.11.3 using cDNA sequences from GRCh38.94 and k-mer length 25, and was aggregated to gene level and transcript-length-corrected using tximport v1.8.0. The dataset comprises IgA+ transglutaminase 2-specific and other IgA+ B cells from the peripheral blood of 355 cells from two untreated celiac disease patients.

  Dataset EGAD50000000338

• Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells

  Mitochondrial genomes are separated from the nuclear genome for most of the cell cycle by the nuclear double membrane, intervening cytoplasm and the mitochondrial double membrane. Despite these physical barriers we show that somatically acquired mitochondrial-nuclear genome fusion sequences are present in cancer cells. Most occur in conjunction with intranuclear genomic rearrangements and the features of the fusion fragments indicate that non-homologous end joining and/or replication-dependent DNA double strand break repair are the dominant mechanism involved. This study includes 12 pairs of whole-genome sequences (tumour and paired-normal), which present somatic mitochondrial DNA integrations in tumour genomes. Reference: Young Seok Ju et al., Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells, Genome Research (2015).

  Study EGAS00001001234

• A benchmarking resource for NGS testing of cancer predisposition genes

  A benchmarking resource of 639 individuals, to assess the analytical sensitivity of cancer predisposition gene (CPG) testing.The dataset includes sequencing data generated using the TruSight Cancer Panel (TSCP) a targeted NGS assay for analysis of CPGs and orthogonally generated data supporting at least one pathogenic variant in a CPG for a total of 645 pathogenic CPG variants.The set of pathogenic CPG variants includes strong representation of some of the most challenging types of pathogenic variants, with 339 indels, including 16 complex indels and 24 insertions or deletions with length greater than 5bp, and 74 exon CNVs, including 23 single exon CNVs. There are 502 pathogenic variants in BRCA1 or BRCA2, making this an important first-line validation dataset for laboratories performing NGS testing of BRCA1 and BRCA2.

  Study EGAS00001002993

• Comprehensive Molecular Analysis of Colon Cancer for the Identification and Validation of New Biomarkers

  This study aims to identify diagnostic and prognostic biomarkers in colon cancer and to study understand the complex genomic, genetic and epigenetic relationships with a multiomic approach. The study includes tumor and paired normal mucosa of 100 colon cancer patients diagnosed at stage II, untreated and with microsatellite stable tumours. Also 50 normal mucosa samples from healthy donors are included as reference. The samples have been analysed for gene expression with Affymetrix U219 array (available at GEO GSE44076), SNP/CNV with the Affymetrix 6.0 Human SNP array, for DNA methylation with the Illumina 450K array. Small RNAs were sequenced with the Solid technology and 42 of the tumours and paired normal mucosa DNA were whole exome sequenced with Illumina Genome Analyzer.

  Study EGAS00001002453

• Longitudinal monitoring of cell-free DNA methylation in ALK-positive non-small cell lung cancer patients

  Here, we performed genome-wide 5-mC profiling in plasma of metastatic ALK-rearranged non-small cell lung cancer (NSCLC) patients receiving tyrosine kinase inhibitor therapy. We established a strategy to identify ALK-specific 5-mC changes from cfDNA and demonstrated the suitability of the identified markers for cancer detection, prognosis and therapy monitoring. Longitudinal plasma samples (n = 79) of 21 ALK-positive NSCLC patients and 13 healthy donors were collected alongside 15 ALK-positive tumor tissue and 10 healthy lung tissue specimens. All plasma and tissue samples were analyzed by cell-free DNA methylation immunoprecipitation sequencing to generate genome-wide 5-mC profiles. Information on genomic alterations (i.e., somatic mutations/fusions and copy number alterations) determined in matched plasma samples were available from previous studies.

  Study EGAS00001006573

• The KATHERINE study of adjuvant trastuzumab emtansine in HER2-positive breast cancer: analysis of patients with HER2-negative residual invasive disease on re-testing

  Following chemotherapy and human epidermal growth factor 2 (HER2)-targeted neoadjuvant therapy for HER2-positive early breast cancer, residual invasive breast cancer at surgery may be HER2-negative on retesting in some patients. We evaluated outcomes with T-DM1 and trastuzumab in patients randomized in the phase III KATHERINE trial based on HER2-positive central testing of the core biopsy with HER2-negative central testing on their corresponding surgical specimen. In the 70/845 (8.3%) patients with HER2-negative residual disease on retesting at surgery, there were 11 IDFS events in the 42 trastuzumab-treated patients (26.2%) and none in the 28 T-DM1-treated patients, suggesting that T-DM1 should not be withheld in this patient population.

  Study EGAS00001006037

• The assessment of genetic and immunological backgrounds in advanced NSCLC patients treated with immunotherapy

  Non-small-cell lung cancer treatment relies greatly on immunotherapy. Both programmed death ligand 1 expression on tumour cells and tumour mutational burden are used to predict the response to such treatment and qualify patients for the therapy, but in some cases, those biomarkers do not perform well enough. Discovering new markers indicating resistance or response to immunotherapy would therefore allow clinicians to modify therapy course for the benefit of the patient. This paper is aimed at describing the genetic and immunological background of immunotherapy courses and discovering factors possibly related to clinical benefit or lack of response, using next-generation sequencing of tumour tissue and flow cytometry analysis of lymphocyte subpopulations in peripheral blood of non-small cell lung cancer patients.

  Study EGAS50000000180

• Clinical Cancer Sequencing

  Translating whole exome sequencing (WES) for prospective clinical use may impact the care of cancer patients; however, multiple innovations are necessary for clinical implementation. These include: (1) rapid and robust WES from formalin-fixed paraffin embedded (FFPE) tumor tissue, (2) analytical output similar to data from frozen samples, and (3) clinical interpretation of WES data for prospective use. In this study, we describe a prospective clinical WES platform for archival FFPE tumor samples. The platform employs computational methods for effective clinical analysis and interpretation of WES data. When applied retrospectively to 511 exomes, the interpretative framework revealed a "long tail" of somatic alterations in clinically important genes. Prospective application of this approach identified clinically relevant alterations in 15/16 patients. Overall, this methodology may inform the widespread implementation of precision cancer medicine.

  Study phs000694

• Evolution of Resistance in ER+ Breast Cancer

  While the combination of endocrine therapy and CDK4/CDK6 inhibitors has been shown to be effective in the metastatic ER+ breast cancer setting, to test whether it is effective in an earlier stage neoadjuvant setting, the FELINE trial (NCT02712723) was established to test the efficacy of letrozole and ribociclib in a ER-positive, HER2-negative patients in a randomized, placebo-controlled, multicenter trial. Patients were randomized to one of three arms: those in Arm A received letrozole and placebo, Arm B letrozole and intermittent ribociclib, and Arm C letrozole and continuous ribociclib. Samples were collected at screening (Day 0), Cycle 1 (Day 14), and end of trial (Day 180). Samples from 24 patients, where cancer cells were present at Day 0 and one additional time point, were subjected to whole-exome sequencing profiling.

  Study phs002287

• TCGA WGS Variants Across 18 Cancer Types

  Even though whole genome sequence (WGS) data has been generated and published in many studies, much of this information is not yet processed for use in down-stream analysis. This study's aim is to provide 1342 WGS normal-tumor paired single nucleotide variations (SNP) over 18 different cancer types provided by The Cancer Genome Atlas (TCGA) project. Individual level data for TCGA can be accessed by requesting access for phs000178. This data includes variations within self-reported white and African-American populations. Variations that exist within the tumor tissue but are absent in associated normal organ tissue (as compared to the human reference genome) are reported. Data published includes SNP and small insertions and deletions, which were generated through a pipeline including the VarScan2 variant calling software.

  Study phs003155

• Primary breast cancers and paired brain metastases sequencing study

  Improving management of brain metastases (BM) from primary breast cancer (PBC) is a challenge in which targeted therapies play a promising role. However this approach is impaired by miss-knowledge of molecular patterns of the metastatic and drug-resistance processes.We performed a differential analysis of copy-number-alterations (CNAs) and mutations profiles by using pan-genomic array-CGH and targeted next-generation-sequencing of 494 cancer-associated genes, in a series of 14 pairs of matched PBC/BM and assessed if the observed genomic alterations may be used as a druggable agent in a clinical trial.

  Study EGAS00001003173

• Somatic mutation and clonal evolution normal breast tissue TGS (2020-01-15)

  Cancer is a genetic disease caused by an accumulation of mutations, however many of these mutations have been identified in pathologically normal tissue. We aim to use laser-capture microscopy (LCM) to sample individual clones from breast tissue to identify whether cancer-associated mutations appear in this normal tissue, assess the mutational burden present, and identify the mutational processes causing these mutations. We will sample from a wide age range of individuals (&lt;20 to &gt;70 years old) to determine whether these processes differ in pre- and post-menopausal women. We will also be comparing the tissue from healthy individuals (samples from breast reduction surgery) to those at elevated risk of breast cancer (mastectomy from BRCA1/2 patients) and those who have breast cancer (adjacent normal, distal normal, and tumour tissue from mastectomy). This will allow us to determine how these processes are different between these groups of individuals, and gain insight into the earliest stages of tumour development. . This dataset contains all the data available for this study on 2020-01-15.

  Dataset EGAD00001005787

• Somatic mutations in facial skin from countries of contrasting skin cancer risk

  The incidence of non-melanoma skin cancer is 17-fold lower in Singapore compared to the UK1, despite Singapore receiving 2-3 times more year-round ultraviolet radiation (UV)2,3. The ageing epidermis of the skin comprises competing somatic mutant clones4,5, from which such cancers develop. We question if differences in keratinocyte skin cancer incidence are reflected in the mutational landscape by comparing ageing facial epidermis from donors of Singapore and the UK. We find UK skin to be a highly competitive, densely mutated landscape with 4-fold greater mutation burden compared to Singaporean skin and differences in clonal selection by country. We disproportionately observe multiple features common to keratinocyte skin cancers6,7,8 in UK skin, such as UV mutagenesis, copy number aberration and hotspot mutations (in particular TP53 R248W). We conclude that keratinocyte skin cancer incidence is reflected in the somatic clones of non-cancerous epidermis. Finally, we re-analyse squamous cell carcinoma exomes from Korea9 to show, even in low incidence populations, carcinogenesis is driven by UV damage.

  Dataset EGAD00001009666

• Somatic mutation and clonal evolution normal breast tissue WGS

  Cancer is a genetic disease caused by an accumulation of mutations, however many of these mutations have been identified in pathologically normal tissue. We aim to use laser-capture microscopy (LCM) to sample individual clones from breast tissue to identify whether cancer-associated mutations appear in this normal tissue, assess the mutational burden present, and identify the mutational processes causing these mutations. We will sample from a wide age range of individuals (&lt;20 to &gt;70 years old) to determine whether these processes differ in pre- and post-menopausal women. We will also be comparing the tissue from healthy individuals (samples from breast reduction surgery) to those at elevated risk of breast cancer (mastectomy from BRCA1/2 patients) and those who have breast cancer (adjacent normal, distal normal, and tumour tissue from mastectomy). This will allow us to determine how these processes are different between these groups of individuals, and gain insight into the earliest stages of tumour development. . This dataset contains all the data available for this study on 2023-03-09.

  Dataset EGAD00001010123

• CAGE analysis for endometrial carcinoma

  For endometrial cancer patients, lymphadenectomy is recommended to exclude rarely metastasized cancer cells. This procedure is performed even in patients with low risk of recurrence despite the risk of complications such as lymphedema. A method to accurately identify cases with no lymph node metastases (LN-) before lymphadenectomy is therefore highly required. We approached this clinical problem by examining primary lesions of endometrial cancers with CAGE (Cap Analysis Gene Expression), which quantifies promoter-level expression across the genome. Fourteen profiles delineated distinct transcriptional networks between LN?+?and LN- cases, within those classified as having the low or intermediate risk of recurrence.

  Study JGAS000124

• Oncogene activated human breast luminal progenitors contribute basally located myoepithelial cells

  Basal-like breast cancer originates in luminal progenitors, frequently with an altered PI3K pathway, and focally in close association with genetically altered myoepithelial cells at the site of tumor initiation. The exact trajectory behind this bi-lineage phenomenon remains poorly understood. Here we used a breast cancer relevant transduction protocol including hTERT, shp16, shp53, and PIK3CA(H1047R) to immortalize FACS isolated luminal cells, and we identified a candidate multipotent progenitor. We found that the apparent luminal phenotype of these oncogene transduced progenitors was metastable giving rise to basal-like cells dependent on culture conditions.

  Study EGAS50000000505

• ET_Exome

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 50 Essential Thrombocythemia Myeloproliferative Disease samples and matched normal DNA from the same patients. Samples will be multiplexed in one lane of Illumina HiSeq. Sequencing to a coverage of at least 30x will be performed and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Study EGAS00001000102

• Mixed_Leukemia_Rearrangement_Screen

  Genomic libraries will be generated from total genomic DNA derived from Mixed Leukemia and MPD samples and subjected to total of eight lanes of 37 bp, paired end sequencing on the illumina GA. 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 EGAS00001000180

• Test_of_PCR_library_method_on_whole_genmoe_samples

  We will sequence 2 whole genome pairs which have had the libraries prepared with a PCR step. The resulting sequence will be compared to teh same samples which have had sequence obtain using a no_PCR library method. the sequence obtained in this experiment may or may not be used in conjunction with the other sequence obtain for these samples in the search for novel cancer mutations.

  Study EGAS00001000214

• Familial_Thrombocytosis_germline_exome_sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 3 relatives from a family with multiple affected familial thrombocytosis (FT) patients. Germline DNA from 2-4 patients affected with FT will be used to prepare libraries and sequenced in one lane of HiSeq sequencing, mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Study EGAS00001000088

• Expression-Based Subtypes Define Pathologic Response to Neoadjuvant Immune-Checkpoint Inhibitors in Muscle-Invasive Bladder Cancer

  Checkpoint immunotherapy (CPI) has increased survival for some patients with advanced stage bladder cancer (BCa). However, most patients do not respond. Here, we characterized the tumor and immune microenvironment in pre- and post-treatment tumors from the PURE01 neoadjuvant pembrolizumab immunotherapy trial, using a consolidative approach that combined transcriptional and genetic profiling with digital spatial profiling.

  Study EGAS00001005549

• Genomic Evolution of Breast Cancer Metastasis and Relapse

  Recurrent breast cancer is almost universally fatal. We characterize 170 patients locally relapsed or distant metastatic cancers using massively parallel sequencing. We identify that the relapse-seeding clone disseminates late from the primary tumor. TP53 and AKT1 appear to be enriched in ER-positive cancers predisposed to relapse. Mutation acquisition continues at relapse as the same mutation signatures continue to operate and new signatures, such as that caused by radiotherapy appear de novo. In 49% of cases we identify drivers mutations private to the relapse and these are sampled from a wider range of cancer genes, including SWI-SNF complex and JAK-STAT signaling.

  Dataset EGAD00001002698

• A prospective pilot study of genome-wide exome and transcriptome profiling in patients with small cell lung cancer progressing after first-line therapy

  In this prospective study, custom genome-wide exome and whole transcriptome sequencing (NGS) was used to identify genomic events and associated expression changes in advanced Small Cell Lung Cancer (SCLC) and attempt to prescribe systemic therapy based on the results. Tumor/normal pairs were sequenced from 12 patients with advanced SCLC for this study.

  Study phs001366

• Rearrangements of the MAST Kinase and Notch Gene Families in Breast Cancer

  Paired-end transcriptome sequencing was performed on a panel of breast cancer cell lines and tissues and a set of benign cell line and tissue controls. Analyses of the paired end sequences were performed and chimeric transcripts derived from gene rearrangement events were identified. Sequencing was performed on Illumina GAII and HiSeq 2000 platforms with read lengths from 40 to 100 bases.

  Study phs000513

• A Randomized Multi-Institutional Phase II Trial of Everolimus as Adjuvant Therapy in Patients with Locally Advanced Squamous Cell Cancer of the Head and Neck

  This genomic study was an analysis of DNA samples from subjects enrolled in a randomized, interventional, parallel assignment trial of everolimus versus placebo in advanced Head and Neck Cancer. Next Generation Sequencing was performed on samples obtained from primary tumors before treatment. The purpose was to evaluate potential associations between intervention, mutations and outcomes.

  Study phs002986