14970 results for "cancer studies using rna-seq"

in 20.81 milliseconds.

• Whole-exome sequencing of meningiomas for integrative molecular classification.

  Exome libraries were prepared using 100ng DNA of tumor tissue or matched normal DNA. Exome capture was performed using Agilent SureSelect Human Exome Library Preparation V5 or V6 COSIMC + kits.

  Dataset EGAD00001007051

• Erythroid/megakaryocytic differentiation confers BCL-XL dependency and venetoclax resistance in acute myeloid leukemia

  Myeloid neoplasms with erythroid or megakaryocytic differentiation include pure erythroid leukemia (PEL), myelodysplastic syndrome (MDS) with erythroid features, and acute megakaryoblastic leukemia (FAB M7) and are characterized by poor prognosis and limited treatment options. Here, we investigate the drug sensitivity landscape of these rare malignancies. We show that acute myeloid leukemia (AML) cells with erythroid or megakaryocytic differentiation depend on the anti-apoptotic protein BCL-XL, rather than BCL-2, using combined ex vivo drug sensitivity testing, genetic perturbation, and transcriptomic profiling. Single-cell and bulk transcriptomics of patient samples with erythroid and megakaryoblastic leukemias identified high BCL2L1 expression compared to other subtypes of AML and other hematological malignancies, where BCL2 and MCL1 were more prominent. Our results suggest targeting BCL-XL as a potential therapy option in erythroid/megakaryoblastic leukemias and highlight an AML subgroup with potentially reduced sensitivity to venetoclax-based treatments.

  Study EGAS00001006819

• Drugging the catalytically inactive state of RET kinase in RET-rearranged tumors.

  Oncogenic fusion events have been identified in a broad range of tumors. Among them, RET rearrangements represent distinct and potentially druggable targets that are recurrently found in lung adenocarcinomas. We provide further evidence that current anti-RET drugs may not be potent enough to induce durable responses in such tumors. We report that potent inhibitors, such as AD80 or ponatinib, that stably bind in the DFG-out conformation of RET may overcome these limitations and selectively kill RET-rearranged tumors. Using chemical genomics in conjunction with phosphoproteomic analyses in RET-rearranged cells, we identify the CCDC6-RETI788N mutation and drug-induced mitogen-activated protein kinase pathway reactivation as possible mechanisms by which tumors may escape the activity of RET inhibitors. Our data provide mechanistic insight into the druggability of RET kinase fusions that may be of help for the development of effective therapies targeting such tumors.

  Study EGAS00001002335

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

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

  Study EGAS00001006408

• Whole-genome sequencing across 449 samples spanning 47 ethnolinguistic groups provides insights into genetic diversity in Nigeria

  African populations have been drastically underrepresented in genomics research and failure to capture the genetic diversity across the numerous ethnolinguistic groups (ELGs) found in the continent has hindered the equity of precision medicine initiatives globally. Here, we describe the whole-genome sequencing of 449 Nigerian individuals across 47 unique self-reported ELGs. Population structure analysis reveals genetic differentiation amongst our ELGs, consistent with previous findings. From the 36 million SNPs and indels discovered in our dataset, we provide a high-level catalog of both novel and medically-relevant variation present across the ELGs. These results emphasize the value of this resource for genomics research, with added granularity by representing multiple ELGs from Nigeria. Our results also underscore the potential of using these cohorts with larger sample sizes to improve our understanding of human ancestry and health in Africa.

  Study EGAS00001007036

• Analysis of a cohort of familial ademomatous polyposis patients bearing APC gene mutation

  large number of colorectal adenomas with high risk of evolving into colorectal tumors. Mutations of the Adenomatous polyposis coli (APC) gene is often at the origin of this disease, as well as of a high percentage of spontaneous colorectal tumors. APC is therefore considered a tumor suppressor gene. While the role of APC in intestinal epithelium homeostasis is well characterized, its importance in immune responses remains ill defined. We investigated an array of immune cell features in FAP subjects carrying APC mutations. A group of 12 FAP subjects and age and sex-matched healthy controls were studied. In particular, the expression of 579 immune response genes was analyzed in whole blood cells using the Nanostring nCounter Human Immunology kit v2. (Cuche C. et al. Frontiers in Immunology, 2023, in press)

  Study EGAS00001007237

• COIN_CRC_GWAS

  Genotype data of 1,950 individuals from the COIN and COIN-B trials of advanced/metastatic colorectal cancer. Data provided in plink format, and has been quality controlled. Control data used was from the WTCCC2 project National Blood Donors (NBS) Cohort (EGAD00000000024).

  Dataset EGAD00010002186

• Whole genome sequencing data of high-grade serous ovarian cancer samples (set 10)

  Whole genome sequencing data of 56 high-grade serous carcinoma (HGSC) patients (208 samples) sequenced with Novoseq 6000

  Dataset EGAD50000000275

• Multiple Myeloma GWAS Meta-analysis

  Meta-analysis of Multiple Myeloma genome-wide association study datasets. Included are meta-analyses with and without the UK Biobank dataset.

  Study EGAS50000000292

• Nanopore whole-genome sequencing of human sarcomas

  We performed single and multi-region nanopore whole-genome sequencing on human sarcoma samples from adult and paediatric patients.

  Study EGAS50000000651

• Shallow dataset

  Associated with Molecular biomarkers in progression from refractory celiac disease to the lethal cancer variety enteropathy associated T cell lymphoma (EATL) Study. shallow Whole Genome Sequencing (sWGS) of 63 samples. sWGS was done to analyze copy number aberration.

  Dataset EGAD50000001165

• DNA sequencing of sgRNAs enriched from the CRISPR-Cas9 screened HCC organoids

  Project aims to find enriched or depleted sgRNAs to identify functional genes in HCC progression and lenvatinib resistance

  Study EGAS50000000848

• Single-cell Transcriptome Profiling of Treatment-naïve and Post-treatment Colorectal Cancer: Insights into Putative Mechanisms of Chemoresistance

  These terms and conditions govern access to the managed access datasets to which the User Institution has requested access. The User Institution agrees to be bound by these terms and conditions.

  Dac EGAC50000000482

• Whole genome sequencing of osteosarcoma from patients seen at UT MD Anderson Cancer Center.

  Whole genome sequencing of 35 osteosarcoma patients (primary, relapsed, and metastatic) with matched normals. Tumors were sequenced at target 60X and matched normals at target 30X.

  Dataset EGAD00001005389

• Lowpass whole genome sequencing of single circulating tumor cells (CTCs) in ALK-rearranged non-small-cell lung cancer resistant to ALK inhibitors

  Lowpass whole genome sequencing of 43 single CTCs and one tumor biopsy

  Dataset EGAD00001007700

• RNAseq - Colorectal organoids and tumoroids (2015-08-05)

  Transcriptome sequencing of tumour tissue, adjacent normal tissue and derived organoids/tumoroids from colorectal cancer. This dataset contains all the data available for this study on 2015-08-05.

  Dataset EGAD00001001459

• EPITREAT extended cohort

  Data set of 22 tumor/normal pairs of non-small cell lung cancer (NSCLC) patients. All tissue pairs were screened with MeDIP methylation enrichment sequencing and validations were performed with targeted bisulfite re-sequencing.

  Dataset EGAD00001003944

• Targeted and shallow whole genome sequencing identifies therapeutic opportunities in p53abn endometrial cancers

  Targeted panel sequencing of 188 formalin-fixed paraffin-embedded p53abn endometrial cancer samples.

  Dataset EGAD00001015349

• Clinical data

  Clinical data from this cohort of patients, including hormone sensitive or castration resistant prostate cancer, overall survival, NMF subtypes, tumor TMB, prior treatment status, PD-L1 IC and TC scores from SP142 and SP263 as well as percentage of CD8 IHC at tumor center.

  Dataset EGAD00001008761

• 10x Genomics Single Cell Gene Expression for SA535X4XB05462

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA535 passage 4

  Dataset EGAD00001009115

• 10x Genomics Single Cell Gene Expression for SA535X6XB03099

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA535 passage 6

  Dataset EGAD00001009116

• 10x Genomics Single Cell Gene Expression for SA535X6XB03101

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA535 passage 6

  Dataset EGAD00001009149

• 10x Genomics Single Cell Gene Expression for SA535X5XB02891

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA535 passage 5

  Dataset EGAD00001009155

• 10x Genomics Single Cell Gene Expression for SA535X5XB02895

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA535 passage 5

  Dataset EGAD00001009156

• 10x Genomics Single Cell Gene Expression for SA604X9XB02425

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA604 passage 9

  Dataset EGAD00001009159

• 10x Genomics Single Cell Gene Expression for SA1035X6XB03216

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA1035 passage 6

  Dataset EGAD00001009154

• 10x Genomics Single Cell Gene Expression for SA535X4XB02498

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA535 passage 4

  Dataset EGAD00001009152

• WGS of a Li-Fraumeni patient's HSPCs

  WGS data of clonally expanded HSPCs from a Li-Fraumeni patient at the time of second cancer (Burkitt lymphoma and <5% t-MN) after primary osteosarcoma diagnosis and a reference MSC bulk.

  Dataset EGAD00001011257

• Genome and transcriptome sequence data from a pre-B all (2nd relapse in CNS) tumor patient

  Genome and transcriptome sequence data from a pre-B all (2nd relapse in CNS) patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015291

• 10x Genomics Single Cell Gene Expression for SA604X6XB01979

  10x Genomics Single Cell Gene Expression for Triple negative breast cancer patient-derived xenograft SA604 passage 6

  Dataset EGAD00001009117