12302 results for "cancer rna-seq"

in 100.57 milliseconds.

• Exploring the evolution of atypical fibroxanthoma to pleomorphic dermal sarcoma: a genomic and pharmacological insight

  The study includes an integrated genomic and pharmacological analysis of atypical fibroxanthoma (AFX) and its progression to pleomorphic dermal sarcoma (PDS), two rare cutaneous mesenchymal tumors with overlapping clinical and histological features but distinct prognostic profiles. The findings will shed light on the molecular mechanisms underlying this progression and provide preliminary evidence for potential therapeutic vulnerabilities, particularly in the context of targeted and immune-based approaches.

  Study EGAS50000001741

• Axes of Biological Variation in Diffuse Large B-Cell Lymphoma

  To explore the DLBCL molecular and genetic environment, we conducted genome-wide NGS sequencing on 103 DLBCL biopsy samples (named as Cornell-NCI cohort) with NGS platforms, including bulk WES, etc. The raw fastq files of the bulk WES were deposited on the EGA for user access. For additional information regarding the genomic data associated with the study, please also see the paper companion website at https://llmpp.ccr.cancer.gov/local/DLBCL_singlecell/

  Study EGAS50000001227

• PTEN homozygous deletion is a negative prognostic factor in Tumor Treating Fields-treated glioblastoma, IDH wildtype patients

  This study investigates genomic determinants of outcome in glioblastoma, IDH-wildtype patients treated with Tumor Treating Fields (TTFields) in addition to standard radiochemotherapy. Tumor tissue from primary glioblastoma at initial diagnosis was profiled using the Illumina TruSight Oncology 500 (TSO500) targeted sequencing panel to characterise somatic alterations. The overarching goal is to provide exploration of genomic determinants of survival and treatment response in TTFields-treated glioblastoma, IDH-wildtype.

  Study EGAS50000001469

• Correlative Genomic Analysis of Durvalumab plus Pazopanib Combination in Patients with Advanced Soft Tissue Sarcomas

  We conducted an open-label, phase 2 study to determine the activity of the anti-VEGF receptor tyrosine-kinase inhibitor, pazopanib, combined with the anti-PD-L1 immune checkpoint inhibitor, durvalumab, in unselected advanced sarcomas. In addition, we conducted whole exome and transcriptomic sequencing with pre-treatment tissue biopsy to correlate clinical outcomes with molecular and genomic biomarkers to identify patients who would most likely benefit from the combination treatment.

  Study EGAS50000000082

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by targeted sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by a targeted panel for somatic mutation and sCNA analysis (7 samples), subject to cell availability. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them.

  Dataset EGAD50000001898

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by targeted sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by a targeted panel for somatic mutation and sCNA analysis (7 samples), subject to cell availability. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them.

  Dataset EGAD50000001897

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by targeted sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by a targeted panel for somatic mutation and sCNA analysis (7 samples), subject to cell availability. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them.

  Dataset EGAD50000001896

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by targeted sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by a targeted panel for somatic mutation and sCNA analysis (7 samples), subject to cell availability. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them.

  Dataset EGAD50000001890

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by targeted sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by a targeted panel for somatic mutation and sCNA analysis (7 samples), subject to cell availability. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them.

  Dataset EGAD50000001888

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by targeted sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by a targeted panel for somatic mutation and sCNA analysis (7 samples), subject to cell availability. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them.

  Dataset EGAD50000001899

• Whole-exome sequencing (WES) analysis of untreated head and neck cancer patient-derived xenografts (PDXs) matched patient tumor tissue and normal mucosa tissue.

  WES analysis was performed on untreated patient tumor/normal mucosa tissue and matched patient-derived xenograft (PDX) models of primary head and neck squamous cell carcinoma (HNSCC) to investigate the preservation of tumor-specific genomic alterations in the in vivo context. 183 total samples were sequenced with paired reads on 8-10 lanes from different flowcells. They were loaded as 3538 separate files to maintain the data as it was received from BGI - each sample is therefore composed of 5 separate EGAN with 2-4 files each, adding a 0.1 - .. - 0.5 to each BioSample ID to generate sample aliases. All R1 (and R2, separately) files referring to a BioSample ID should be concatenated to obtain fastq files corresponding to single patients or PDXs.

  Dataset EGAD50000002325

• Cergentis FFPE-TLC sequencing of colorectal carcinoma

  In this study, formalin-fixed paraffin-embedded targeted locus capture (FFPE-TLC) sequencing is used as a novel technology for targeted detection of tumor-specific genomic structural variants (SVs) in the primary tumor of 29 colorectal cancer patients with metastatic disease. The tumor region was macrodissected and sequenced for 29 patients, and the "normal" region of the same slide was macrodissected and sequenced for 8 of these patients. SVs were found in the common fragile site (CFS)-associated genes MACROD2, PRKN, FHIT and WWOX as well as SVs caused by three LINE transposable elements. Tumor-specificity of selected SVs was independently verified by droplet digital PCR of tumor tissue DNA and their applicability as plasma circulating tumor DNA biomarkers was demonstrated. This dataset contains the hg19 reference alignment of the FFPE-TLC sequences for all 29 colorectal cancers and 8 adjacent normals.

  Dataset EGAD50000000618

• Genomic Rearrangements in Pediatric Cancer

  Dataset EGAD00001007701

• Monotherapy Breast Cancer

  These samples are from locally advanced breast cancers that have been treated with epirubicin monotherapy before surgery. We will sequence some samples from patients with good response to the therapy and some with poor response to the therapy.

  Dataset EGAD00001000349

• Development of actionable molecular targets and/or biomarkers for prognostication and patient stratification in gynecological cancer based on whole-exome sequencing and epigenomic analysis

  We collected 157 oral MPA-treatment samples from 66 cases (53 endometrial hyperplasia from 31 cases, 19 atypical polypoid adenomyoma from 14 cases, 1 normal endometrium from 1 case, and 84 endometrial carcinoma from 53 cases) and matched normal tissues/whole blood. The purpose of this study is to develop actionable molecular targets and/or biomarkers for prognostication and patient stratification.

  Study JGAS000813

• The_genomic_architecture_of_mesothelioma_

  The genome-wide landscape of somatically acquired mutations in mesothelioma has not been deeply characterised to date, but advances in DNA sequencing technology now allow this to be addressed comprehensively. Harnessing massively parallel DNA sequencing platforms, we will identify somatically acquired point mutations in all coding regions of the genome from patients with mesothelioma. In addition, using paired-end sequencing, we will map copy number changes and genomic rearrangements from the same patients.

  Study EGAS00001000353

• Mutational_Signatures_of_relapse_in_rectal_cancer_FFPE_samples_in_the_CR07_clinical_trial

  The CRO7 clinical trial recruited patients with clinically operable rectal adenocarcinoma. Patients were randomized to either pre-operative short course surgery followed by chemo-radiotherapy only in those patients at high risk of local relapse. Patients in both arms the received standard %-FU based adjuvant chemotherapy as per local policy. We intend to use FFPE derived DNA from the primary tumours to identify patterns of mutations or copy number alterations that are predictive of local or distant relapse.

  Study EGAS00001000651

• Exploration_of__mutational_processes_in_human_cancer_cell_lines__Exome

  Approximately 25 cell lines representative of 11 mutation signatures have been selected and will be grown from a single cell, referred to as parental clone, for a period of 3 months to allow accumulation of mutations. Following that period, we will obtain 2 subclones from each of the parental clone for sequencing analysis. In total we will be sequencing 2 parental clones and 4 subclones per cell line for approximately 25 cell lines.

  Study EGAS00001000790

• SOFT_study___sequencing_premenopausal_breast_cancer

  Our project will examine the role of PIK3CA mutations and their sensitivity to endocrine therapies and its role, with the addition of complete ovarian suppression. We plan to test our hypotheses using tumour samples collected from patients enrolled in the SOFT/IBCSG24-02 clinical study (Suppression of Ovarian Function Trial – (NCT00066690). SOFT is a phase III trial that randomised 3066 premenopausal women to evaluate if adding ovarian suppression to adjuvant endocrine therapy will improve clinical outcomes.

  Study EGAS00001000983

• Colorectal_Adenoma_Gene_Screen

  A pilot to establish the feasability of using a custom Agilent targeted pulldown of 110 genes implicated in colorectal tumourigensis to sequence for driver mutations in a set of 30 FFPE colorectal adenomas. If successful, we propose to sequence an additional 350 adenomas as part of a MRC research study in order to define the pattern of driver mutations across the spectrum of pathological subtypes including coventional adenomas, serrated adenomas and hyperplastic polyps

  Study EGAS00001001261

• Clonal_selection_after_gene_therapy_in_SCD___Duplex_sequencing

  This study includes the targeted duplex sequencing data relating to this study. A custom targeted panel was used including 29 AML-associated genes, and a set of mutations from driver-containing clones that were sequenced during the WGS tree-building phase of the study. Targeted sequencing is performed on each of 6 individuals included at the study at at least 3 time points per individual: one prior to gene therapy, and two post-therapy time points.

  Study EGAS00001007253

• Bulk_sequencing_study_for_human_male_germline

  This study aims to understand the gene expression changes in male reproductive tissues during spermatogenesis using integrated multi-omics analysis. Different populations from testis biopsies, including spermatogonia stem cells, primary spermatocytes, secondary spermatocytes, spermatids and mature sperms, were sorted based on the DNA content. In addition to the G&T sequencing results for single cells, we sorted bulk samples for those populations for Nanoseq to detect the mutations at low error rate.

  Study EGAS00001005990

• FFPE, buffycoat and cell free DNA from N. German esophagus cancer patients - 2021

  We recruited 28 patients and sequenced samples from their FFPE tissue, full blood buffy coat and plasma cell free DNA from diagnosis and other, longitudinal time points. The cell free DNA was sequenced ultra-deeply. The IDT PanCancer panel was used for targeted enrichment. Aims: detection of primary tumor mutations in cell free DNA, overlap and difference in mutation profiles between primary tumor, metastases and cell free DNA.

  Study EGAS00001006813

• FFPE CPA Accreditation Study Part 2

  FFPE CPA accreditation of genome-scale sequencing in routinely collected formalin-fixed paraffin-embedded (FFPE) cancer specimens versus matched fresh-frozen samples using targeted pulldown capture prior to Illumina sequencing.

  Dataset EGAD00001000868

• Somatic pseudogenes acquired during cancer development – Whole Exome sequencing

  Insertion of processed pseudogenes is known to occur in the germline but has not previously been observed in somatic cells. Formation of pseudogenes could represent a new class of mutation in cancers and a new source of potential driver events.

  Dataset EGAD00001000637

• Somatic pseudogenes acquired during cancer development – Whole Genome sequencing

  Insertion of processed pseudogenes is known to occur in the germline but has not previously been observed in somatic cells. Formation of pseudogenes could represent a new class of mutation in cancers and a new source of potential driver events.

  Dataset EGAD00001000638

• Somatic pseudogenes acquired during cancer development – RNAseq

  Insertion of processed pseudogenes is known to occur in the germline but has not previously been observed in somatic cells. Formation of pseudogenes could represent a new class of mutation in cancers and a new source of potential driver events.

  Dataset EGAD00001000639

• RNAseq of patients with Ewings sarcoma

  Cancer is driven my mutations in the genome. We will uncover the mutations that give rise to Ewing's sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewing's sarcoma tumours.

  Dataset EGAD00001000444

• Matched Pair Cell Line Tumour RNAseq

  In this study we will sequence the transcriptome of Verified Matched Pair Cancer Cell line tumour samples. This will be married up to whole exome and whole genome sequencing data to establish a full catalog of the variations and mutations found.

  Dataset EGAD00001000630

• MultiOMICS study of a pair of infant monozygotic twins with concordant B-cell ALL (WGS)

  B-cell acute lymphoblastic leukemia (B-cell ALL) is the most common cancer in childhood. Studying identical twins with B-cell ALL provides a unique and tractable model for deciphering the developmental timing of pre- and post-natal mutations contributing to clonal evolution. To date, this has mainly focused on major cytogenetic subgroups of childhood B-cell ALL, including MLL fusions, ETV6-RUNX1, hyperdiploidy, and BCR-ABL1. However, formal demonstration of the prenatal origin and “backtracking” the natural history of the leukemia remains understudied in “B-other”/Normal Karyotype (NK) B-cell ALL. To characterize the genetic landscape of this particular leukemia subtype, we performed whole genome DNA- and B-cell receptor (BCR)- on a pair of 8-month-old monozygotic twins diagnosed with concordant “B-other”/NK B-cell ALL.

  Dataset EGAD00001005017

• MultiOMICS study of a pair of infant monozygotic twins with concordant B-cell ALL (WGBS)

  B-cell acute lymphoblastic leukemia (B-cell ALL) is the most common cancer in childhood. Studying identical twins with B-cell ALL provides a unique and tractable model for deciphering the developmental timing of pre- and post-natal mutations contributing to clonal evolution. To date, this has mainly focused on major cytogenetic subgroups of childhood B-cell ALL, including MLL fusions, ETV6-RUNX1, hyperdiploidy, and BCR-ABL1. However, formal demonstration of the prenatal origin and “backtracking” the natural history of the leukemia remains understudied in “B-other”/Normal Karyotype (NK) B-cell ALL. To characterize the epigenetic landscape of this particular leukemia subtype, we performed DNA bisulfite-sequencing on a pair of 8-month-old monozygotic twins diagnosed with concordant “B-other”/NK B-cell ALL.

  Dataset EGAD00001005018

• Deep targeted DNA sequencing dataset for the study "Molecular characteristics in Burkitt lymphoma over age groups"

  We performed deep targeted DNA sequencing with a panel of 134 selected cancer-related genes previously identified to be recurrently mutated in BL/B-AL. A Nextera rapid capture custom kit was designed using the Illumina DesignStudio. For every gene, all regions in which previous mutations had been described were covered. For 40 of these genes, the entire coding sequence was covered. Targeted deep sequencing was performed on a MiSeq-Sequencer using MiSeq Reagent Kit v2 (300 cycle) with 24 samples per run. There are 396 samples in this targetedDNAseq-dataset with 298 tumors (288 patients and 10 cell lines) and 98 normals. There are 132 female, 262 male, and 2 unknown gender samples in this dataset.

  Dataset EGAD00001007708

• Dataset for Ewing_sarcoma_PNET-WHOLE_GENOME

  Rare cancer sequencing data of 18 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008874

• Dataset for colorectal_cancer-WHOLE_GENOME

  Rare cancer sequencing data of 54 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008872

• Dataset for Ewing_sarcoma_PNET-EXON

  Rare cancer sequencing data of 30 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008873

• Dataset for gynecologic_cancer-EXON

  Rare cancer sequencing data of 55 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008877

• Dataset for liposarcoma-EXON

  Rare cancer sequencing data of 29 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008886

• Dataset for NSCLC-EXON

  Rare cancer sequencing data of 42 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008892

• Dataset for synovial_sarcoma-EXON

  Rare cancer sequencing data of 34 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008898

• WGS and Avenio Surveillance Panel data to previously submitted data under study number EGAS00001004276 of ALK-rearranged lung cancer

  Some data was previously submitted data under study number EGAS00001004276. In this new dataset we provide additional WGS and Avenio Surveillance Panel data. We utilized 43 ALK+ NSCLC patients receiving targeted ALK therapy to evaluate ctDNA levels based on matched panel-based targeted next generation sequencing (tNGS) and untargeted shallow whole genome sequencing (sWGS). For the Avenio panel the sequencing was done on Illumina NextSeq 550 paired end 150 bp, for WGS the sequencing was done on Illumina HiSeq 4000, partly with KAPA_Hyper_Prep_Kit. In this dataset there are 132 WGS tumor samples and 134 panel sequencing data of plasma.

  Dataset EGAD00001007818

• WGS of cell-free DNA derived from plasma of CRC patients and healthy controls, and WGS of matched tumor tissue and saliva

  This dataset contains: 1.) Whole-genome sequencing (WGS) data (~6x) of 259 cfDNA samples obtained from 50 colorectal cancer (CRC) patients and 61 healthy controls. Paired-end sequencing was performed with 2x101 bp reads on the NovaSeq 6000 system. Data is provided as mapped .bam files (aligned to GRCh38/hg38). 2.) WGS data (~1x) of 50 tumor biopsy and 45 saliva samples from CRC patients. Paired-end sequencing was performed with 2x101 bp reads on the NovaSeq 6000 system. Data is provided as mapped .bam files (aligned to GRCh38/hg38).

  Dataset EGAD00001009309

• Whole genome sequencing data of high-grade serous ovarian cancer samples (set 3)

  Whole genome sequencing data of 9 high-grade serous carcinoma (HGSC) patients (55 samples) sequenced with HiSeq X Ten.

  Dataset EGAD00001009888

• Whole genome sequencing data of high-grade serous ovarian cancer samples (set 7a)

  Whole genome sequencing data of 36 high-grade serous carcinoma (HGSC) patients (89 samples) sequenced with HiSeq X Ten.

  Dataset EGAD00001010845

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0063_000

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0063_000 for Triple negative breast cancer patient-derived xenograft SA609X3XB01584

  Dataset EGAD00001011209

• 10x Single Cell Gene Expression Library TENX068

  10x Single Cell Gene Expression library TENX068 for Triple negative breast cancer patient-derived xenograft SA609X4XB03080

  Dataset EGAD00001011210

• 10x Single Cell Gene Expression Library TENX069

  10x Single Cell Gene Expression library TENX069 for Triple negative breast cancer patient-derived xenograft SA609X4XB03083

  Dataset EGAD00001011211

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0150_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0150_001 for Triple negative breast cancer sample SA609X5XB03230

  Dataset EGAD00001011212

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0150_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0150_002 for Triple negative breast cancer sample SA609X5XB03231

  Dataset EGAD00001011213

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0146_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0146_002 for Triple negative breast cancer patient-derived xenograft SA609X5XB03223

  Dataset EGAD00001011214

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0152_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0152_001 for Triple negative breast cancer patient-derived xenograft SA609X6XB03401

  Dataset EGAD00001011215