7082 results for "canc*"

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• Genomic and Transcriptomic Data from Advanced Rare Cancer Patients Treated with Pembrolizumab

  This dataset comprises whole exome sequencing data and RNA-seq data of advanced rare cancer patients.

  Dataset EGAD50000002182

• MD Anderson Data Access Committee: Pembrolizumab in Advanced Rare Cancers

  Dac EGAC50000000860

• Heterogeneity of IKZF1 genomic alterations and risk of relapse in childhood B-cell precursor acute lymphoblastic leukemia

  Purpose Genomic alterations of IKZF1 are common and associated with adverse clinical features in B-ALL, but the relationship between the type of IKZF1 alteration, disease subtype and outcome are incompletely understood. Patients and Methods We used transcriptome and genomic sequencing, and SNP microarray data to determine leukemia subtype and genomic alterations for 688 pediatric patients with B-ALL enrolled into St. Jude Total Therapy 15 and 16 studies. Results IKZF1 alterations were identified in 115 (16.7%) patients, commonly in BCR::ABL1 (78%) and CRLF2-rearranged, BCR::ABL1-like B-ALL (70%), and were associated with five-year cumulative incidence of relapse (CIR) of 14.8 ± 3.3% compared to 5.0 ± 0.9% for patients without any IKZF1 alteration (P < 0.0001). IKZF1 deletions of exon 4-7 (P = 0.0002), genomic IKZF1plus with any IKZF1 deletion (P = 0.006) or with focal IKZF1 deletion (P = 0.0007), and unfavorable genomic subtypes (P < 0.005) were independently adversely prognostic. Patients with both IKZF1 exon 4-7 deletion and unfavorable genomic subtype had a significantly increased risk of relapse (HR = 58.3; 95% CI, 11.9 – 285.4, P < 0.0001) whereas IKZF1 sequence mutations were not independently predictive of outcome. Conclusions Genomic IKZF1plus with any IKZF1 deletion, IKZF1 deletion of exon 4-7, and unfavorable subtype confer increased risk of relapse. The combination of unfavorable genomic subtype and IKZF1 deletion of exon 4-7 identified patients at greatest risk of relapse despite MRD-directed therapy. The type of IKZF1 alteration together with subtype are informative for risk stratification and predict response in patients with B-ALL.

  Study EGAS50000000106

• Comprehensive genetic landscape, immune checkpoint profiling, and establishment of patient-derived xenograft (PDX) of metachronous brain tumors from constitutive mismatch repair deficiency with a biallelic variant on MSH6

  Constitutional mismatch repair deficiency (CMMRD) syndrome is a rare genetic disorder caused by biallelic pathogenic variants in mismatch repair genes (PMS2, MSH6, MLH1, or MSH2) resulting in the development of a variety of different tumors, including brain neoplasms. This study molecularly characterized a Brazilian child with CMMRD, harboring two metachronous brain tumors (medulloblastoma and high-grade glioma), and established a patient-derived xenograft (PDX) of the CMMRD-associated brain tumor. Keywords: Brazil, Constitutional mismatch repair deficiency syndrome, exome, MSH6, medulloblastoma, high-grade glioma.

  Study EGAS50000000351

• A 3D genome atlas of breast cancer progression (BRCA3D)

  In this study, we aimed to understand how the 3D genome changes during breast cancer development and progression, in situ. Towards this goal, we collected cells from patient biopsies and performed Hi-C on four types of biopsies representing different stages of disease progression: healthy mammary tissue, primary breast tumours, liver metastasis and malignant pleural effusions. We survey the changes in the 3D genomes at the level of structural variation, compartments and TADs, as well as ERα associated distal interactions.

  Study EGAS50000000444

• SickKids_Cancer Molecular Diagnostics

  Cancer Molecular Diagnostics at Hospital for Sick Children

  Dac EGAC50000000375

• NeoRhea Bulk RNA and Single nuclei RNA & ATAC

  The aim of this study is to compare baseline and surgery samples of ER+/HER2- early breast cancer patients. Patients have been treated with endocrine therapy in combination with palbociclib. Samples have been collected pre and post treatment.

  Study EGAS50000001403

• Distinct genomic profiles and clinical outcomes in constitutional mismatch repair deficiency-associated high-grade gliomas: insights into mutational signatures and clonal evolution

  Constitutional mismatch repair deficiency (CMMRD) is a rare cancer-predisposition syndrome, yet the mutational processes and clonal evolution of CMMRD-associated high-grade gliomas (HGGs) remain incompletely understood. In this study, mutational signatures and tumor evolution were analyzed in 25 CMMRD-associated HGGs. Germline biallelic mutations were most frequently identified in MSH6 (56.0%), followed by PMS2 (36.0%) and MLH1 (8.0%). Affected patients showed very early disease onset (mean 5.8 years) and poor clinical outcomes, with a mean progression-free survival of 16 months. Distinct genomic and clinical differences were observed between MSH6- and PMS2-associated tumors. MSH6-deficient HGGs were enriched for SBS6, whereas PMS2-deficient tumors showed predominance of SBS21, and these mutational signatures were correlated with prognosis. Clonal evolution analyses revealed early involvement of POLE/POLD1 mutations and persistence of the founding clone at recurrence. Overall, the study highlights the importance of mutational signatures and clonal evolution in shaping tumor behavior and clinical outcomes in CMMRD-associated HGGs.

  Study EGAS50000001506

• Whole-exome sequencing and RNA-seq data of paired normal-tumour samples from MMR-proficient early-onset colorectal cancer patients

  This study aims to identify novel hereditary colorectal cancer predisposition genes by performing whole-exome sequencing and RNA-seq of paired normal colonic mucosa and colorectal cancer samples from 19 patients diagnosed with MMR-proficient colorectal cancer at an age of 50 years or younger. Both whole-exome and RNA sequencing were performed on the Illumina platform.

  Study EGAS50000001296

• Whole-exome sequencing and RNA-seq of paired normal-tumour samples from MMR-proficient early-onset colorectal cancer patients

  This dataset contains fastq files obtained from paired samples of normal colonic mucosa and tumour tissue, collected from 19 patients diagnosed with MMR-proficient colorectal cancer at an age of 50 years or younger. It includes both whole-exome sequencing and RNA-seq data, generated on the Illumina HiSeq 3000 platform. Additionally, the dataset includes phenotypic information from the patients.

  Dataset EGAD50000001844

• Pan Prostate Cancer Group Data Access Control Committee

  DACC for the PanProstate Cancer Group projects

  Dac EGAC50000000602

• Early-onset Colorectal Cancer Study TOGETHER Data Access Committee

  The Early-onset Colorectal Cancer Study TOGETHER Data Access Committee (DAC) is responsible for reviewing requests to access sequencing and clinical data from the study. Access to the data is restricted to researchers with approved ethical clearance and scientifically valid research projects. Each request will be evaluated by the DAC to ensure compliance with participants’ informed consent and all applicable data protection regulations.

  Dac EGAC50000000752

• ctDNA Quantification in Blood Plasma Using Deep Learning Based Fragle Tool

  The project aims to develop an easy to use software named Fragle that can quantify ctDNA in blood plasma. This can help in cancer screening and progress monitoring from simple blood test without any need for tumor biopsy. We aim to make Fragle usable for both low pass whole genome sequencing and targeted sequencing data of cell free DNA. Fragle can work directly on the raw bam files mapped to hg19/GRCh37. We are uploading the bam files used in this study for Fragle evaluation.

  Study EGAS50000000122

• 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

• Fragmentomics analyses of urinary cfDNA for urologic cancers

  This dataset contains sequencing data of human urinary cell-free DNA. Whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) was performed after DNA extraction from the urine samples. All samples were pair-end sequencing on Illumina system and were aligned to human genome GRCh37 (hg19). WGS and WGBS reads were aligned by SOAP2 and Methyl-Pipe, respectively. The dataset includes samples from healthy subjects, haematuria (non-cancer), and patients of bladder, kidney, or prostate cancer. Pair-end FASTQ files were provided for all the samples mentioned above.

  Dataset EGAD50000002068

• Transcriptomic profiling of prostate cancer metastasis xenograft models reveals conservation of bone microenvironment signatures

  Study EGAS00001004770

• 3D chromatin analysis of clear cell renal cell carcinoma using micro-C

  To investigate the 3D structure of chromatin in ccRCC, we performed micro-C on 3 ccRCC cell lines (786-O, A498, UMRC-2), and 1 normal kidney epithelium cell line (HK-2), cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions

  Study EGAS50000001323

• Chromatin accessibility of clear cell renal cell carcinoma

  To investigate chromatin accessibility in ccRCC, we performed ATAC-seq in 3 ccRCC cell lines (786-O, A498, UMRC-2), and 1 normal kidney epithelium cell line (HK-2), cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions

  Study EGAS50000001325

• Gene expression analysis of clear cell renal cell carcinoma

  To identify genes that are differentially expressed across different conditions (cancer vs normal, normoxic vs hypoxic), we performed RNA-seq in 3 ccRCC cell lines (786-O, A498, UMRC-2), and 1 normal kidney epithelium cell line (HK-2), cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions.

  Study EGAS50000001324

• TONIC-Trial-cfDNA-Project

  Cell-free DNA (cfDNA) is an emerging technology to predict and monitor response to cancer treatment, including immune checkpoint blockade (ICB). However, data on cfDNA dynamics during ICB in metastatic triple negative breast cancer (mTNBC) are limited. While most applications of cfDNA involve assays that focus on mutation detection, mTNBC and multiple other cancer types are driven by copy number alterations (CNAs). We evaluate cfDNA-based copy number profile abnormality (CPA) score as a potential biomarker for monitoring ICB response in mTNBC, analyzing data from 87 patients enrolled in stage 1 and stage 2 of the TONIC-trial. We find significant concordance between cfDNA-based and tissue-based CNA profiles. Additionally, responders show a decrease in CPA scores upon ICB at week 6 (3 cycles of nivolumab). These findings underscore the potential of cfDNA-based CNA dynamics as a non-invasive biomarker for ICB early response assessment in patients with mTNBC.

  Study EGAS50000001308

• Oropharynx cancers sequencing study (RNA-seq from FFPE)

  This is a study of transcriptomics in HPV-associated oropharynx tumors. The goals of this study were to characterize HPV+ oropharynx tumor subtypes and to examine HPV integration events and their downstream effects. HPV-host fusion transcripts and recurrent HPV integration genes were identified. Various alternative isoforms and splicing events of HPV genes were also studied. Multiple potential biomarkers of prognosis were associated with clinical outcomes.

  Study EGAS50000000893

• Non-small cell lung cancer molecular subtypes and vulnerability to immunotherapy treatment combinations

  The phase 3 IMpower150 trial in treatment-naïve patients with metastatic non-small-cell lung cancer (NSCLC) demonstrated significantly longer progression-free (PFS) and overall survival (OS) with first-line atezolizumab (anti-PD-L1)-bevacizumab (anti-VEGF)-carboplatin-paclitaxel (ABCP) than with bevacizumab-carboplatin-paclitaxel (BCP). We characterised four molecular NSCLC subtypes identified by unsupervised clustering of transcriptomes of 564 pre-treatment primary tumour samples from IMpower150 using non-negative matrix factorization (NMF1-4). Each subtype had distinct tumour PD-L1 expression levels, epithelial characteristics, immune composition, and treatment outcomes. Both NMF2 (enriched in tumour proliferation signal, macrophages, and monocytes) and NMF4 (enriched in B-cells and T cells) had elevated tumour PD-L1 expression. Of these two, only NMF4 demonstrated PFS and OS benefits with ABCP versus either BCP or atezolizumab-carboplatin-paclitaxel (ACP). Patients with NMF1 (enriched in basal and squamous-like cells) had improved outcomes on ABCP compared with ACP or BCP; those with NMF3 (enriched in adenocarcinoma signatures) showed similar outcomes among treatments. These insights could help inform individualised first-line treatment for metastatic NSCLC.

  Study EGAS50000001272

• Clinical validity of post-surgery circulating tumor DNA (ctDNA) in stage III colon cancer patients treated with adjuvant chemotherapy: the PROVENC3 study

  The PROVENC3 study aimed to determine the clinical validity of post-surgery ctDNA testing in patients with stage III colon cancer treated with adjuvant chemotherapy (ACT). Blood was collected pre-surgery, post-surgery and post-adjuvant chemotherapy. Tumor-informed plasma ctDNA detection was performed through integrated whole genome sequencing (WGS) analyses of formalin-fixed paraffin-embedded tumor tissue DNA (80x), white blood cell germline DNA (40x) and plasma cell-free DNA (30x). These raw WGS data for 209 patients are shared in .cram format in this EGA submission.

  Study EGAS50000000804

• BCAC TIIC Data

  Data on spatially-resolved tissue infiltrating immune cells (TIICs) from 17,265 breast cancer patients of European descent, from studies participating in the Breast Cancer Association Consortium, together with linked clinical data.

  Study EGAS50000001477

• BCAC TIIC data

  TIIC dataset generated by BCAST project in BCAC from tumor cores from 12,285 breast cancer patients. Includes automated scores (multiply imputed) for CD8, CD20, CD163 and FOXP3 in all tissue, stromal and tumour tissue separately. Linked clinical patient data.

  Dataset EGAD50000002125