1c7fd278-9637-4dbc-9473-4adb93cddc92 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001006855 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:NABUCCO cohort 1 sequencing data. The dataset includes:
* Whole exome DNAseq pre-treatment on tumor samples (n=24) matched with blood samples (n=24)
* RNAseq pre-treatment on tumor samples (n=18)
* RNAseq post-treatment on tumor samples (n=18). Not all pre-treatment samples are linked with pre-treatment samples
* High coverage Whole exome DNAseq on pre-treatment tumor samples (n=3) matched with post-treatment metastasized lymph nodes isolated with laser microdissection (n=3)
* All samples are labelled with the response phenotype (Complete Responder or Non-Complete Responder)
| EGAD00001006250 | EGA
Project description:Data from NABUCCO cohort 1 (NCT03387761). This dataset includes High coverage Whole exome DNA sequencing on pre-treatment bladder tumor samples (n=3) matched with post-treatment metastasised adjacent lymph nodes isolated with laser microdissection (n=3) for 3 unique patients
| EGAD00001006852 | EGA
Project description:Data from NABUCCO cohort 2 (NCT03387761). This dataset includes Whole exome DNA sequencing
on bladder tumor samples matched with blood samples for patients from NABUCCO Cohort 2 (Cohort 2A and Cohort 2B). The data is pre-treatment
| EGAD00001009864 | EGA
Project description:Data from NABUCCO cohort 1 (NCT03387761). This dataset includes Whole exome DNA sequencing
on bladder tumor samples (n=24) matched with blood samples (n=24). The data is pre-treatment.
| EGAD00001006850 | EGA
Project description:Data from NABUCCO cohort 1 (NCT03387761). This dataset includes the Transcript read counts derived from the RNA sequencing data. The samples are pre-treatment (n=18) and post-treatment (n=18), and not all samples are paired.
The data processing pipeline can be found on the Methods section from the Nature Medicine paper (https://doi.org/10.1038/s41591-020-1085-z)
| EGAD00001006854 | EGA
Project description:Data from NABUCCO cohort 1 (NCT03387761). This dataset includes Tumor mutational burden (TMB) calculated on bladder tumor pre-treatment DNA sequencing data (n=24).
Details about the Tumor Mutational Burden calculation can be found on the Methods section from the Nature Medicine paper (https://doi.org/10.1038/s41591-020-1085-z)
| EGAD00001006851 | EGA
Project description:Unique sub-clones within rectal tumors may harbor mutations which contribute to inter-patient variation in response to neoadjuvant chemoradiotherapy (nCRT). Analysis of the influence of nCRT on the extent and nature of intra-tumoral genetic heterogeneity in rectal cancer may provide insights into mechanisms of resistance. Ten locally advanced rectal cancer patients underwent pre-treatment biopsies. At the time of surgery, tissue from the treated tumor was obtained and analyzed. Pre- and post-treatment specimens were subjected to whole exome and confirmatory deep sequencing for somatic mutations. Copy number variation was assessed using OncoScan SNP arrays. In total, data from 32 pre/post-treatment samples are provided. The provided data include the pre/post tumor samples and the Affymetrix OncoScan SNP arrays.
2019-09-05 | GSE136872 | GEO
Project description:The diversity and heterogeneity within high-grade serous ovarian cancer (HGSC) is not well understood. Comprehensive molecular analyses were performed including high-pass whole-genome sequencing, targeted deep DNA sequencing, RNA sequencing, reverse-phase protein arrays, mass spectrometry-based proteomics and phosphoproteomics, and immune profiling on primary and metastatic sites from highly clinically annotated HGSC samples. Samples were obtained pre-treatment based on a laparoscopic triage algorithm from patients who underwent R0 tumor debulking or received neoadjuvant chemotherapy (NACT) with excellent or poor response.
2020-05-27 | PXD014980 | Pride
Project description:We report a 29-gene diagnostic signature, which distinguishes individuals with NSCLC from controls with non-malignant lung disease with 91% Sensitivity, 79% Specificity and a ROC AUC of 92%. Accuracy on an independent set of 18 NSCLC samples from the same location was 79%. Samples from an independent location including 12 stage 1 NSCLC and 15 controls, achieved an accuracy of 74%. A study of 18 paired samples taken pre and post surgery shows that the PBMC associated “cancer” signature is significantly reduced after tumor removal, supporting the hypothesis that the signature detected in pre-surgery samples is a response to the presence of the tumor.
2009-12-01 | GSE13255 | GEO
Project description:Although the intravesical instillation of Bacillus Calmette-Guerin (BCG) is widely used as adjuvant treatment for nonmuscle-invasive bladder cancers, the clinical benefit is variable across patients, and the molecular mechanisms underlying the sensitivity to BCG administration and disease progression are poorly understood. To establish the molecular signatures that predict the responsiveness and disease progression of bladder cancers treated with BCG, we performed transcriptome sequencing (RNA-seq) for 13 treatment-naïve and 22 post-treatment specimens obtained from 14 bladder cancer patients. To overcome disease heterogeneity, we used non-negative matrix factorization to identify the latent molecular features associated with drug responsiveness and disease progression. At least 12 molecular features were present, among which the immune-related feature was associated with drug responsiveness, indicating that pre-treatment anti-cancer immunity might dictate BCG responsiveness. We also identified disease progression-associated molecular features indicative of elevated cellular proliferation in post-treatment specimens. The progression-associated molecular features were validated in an extended cohort of BCG-treated bladder cancers. Our study advances understanding of the molecular mechanisms of BCG activity in bladder cancers and provides clinically relevant gene markers for evaluating and monitoring patients.
2023-12-25 | GSE244895 | GEO