20200819_EGA_Qld_Melanoma.biomarkers - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001006374 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:The lack of prognostic biomarkers and therapeutic targets in triple-negative breast cancer (TNBC) underscores an urgent need for the identification of novel biomarkers and effective treatment targets. In this study, we collected tumor and adjacent normal samples of four TNBC and four non-TNBC patients for whole-exome sequencing (WES).Comparative WES analysis uncovered the distinct landscape of somatic mutations and driver genes in TNBC.
2025-10-07 | GSE267443 | GEO
Project description:The fallopian tube (FT) has been proposed as a potential site of origin for high-grade serous ovarian cancer (HGSOC), supporting investigation of genomic alterations across matched tissues. This dataset includes whole-genome sequencing (WGS) and DigiPico data from matched samples, including peripheral blood mononuclear cells (PBMCs), fallopian tube tissue, and tumor tissue from HGSOC patients. The data support analysis of germline and somatic variants, copy number alterations (CNAs), and neoantigen prediction across matched sample types. This submission contains the WGS data DigiPico data associated with this study.
2026-04-07 | GSE301180 | GEO
Project description:Within the frame of inherited cancer predisposition, single gene carriers of pathogenic variants (PVs) have been extensively represented in the literature, whereas the oligogenic coinheritance of heterozygous PVs in cancer-related genes is a poorly studied event. Currently, due to the increment of cancer survivors, the probability of presenting multiple primary cancers (MPC) is higher. This study included MPC patients ≤45 years without known PVs in common cancer predisposition genes. We used whole exome sequencing (WES) of germline and tumoral DNA, chromosomal microarray analysis (CMA) on germline DNA (patient 1-7, and patient 9-10), and karyotype of patient 8to detect variants associated with the disease. The ten patients included in the study presented a mean of 3 cancers per patient. CMA showed two microduplications and one microdeletion, while WES of the germline DNA identified 1-3 single nucleotide variants of potential interest to the disease in each patient and two additional copy number variants. Most of the identified variants were classified as variants of uncertain significance. The mapping of the germline variants into their pathways showed a possible additive effect of these as the cause of the cancer. Twelve somatic samples from 5 patients were available for sequencing. All the germline variants were also present in the somatic samples, while no second hits were identified in the same genes. The sequencing of patients with early cancers, family history and multiple tumors is already a standard of care. However, the growing evidence suggests that patient´s assessment should not stop at the identification of one PV in a cancer predisposition gene.
2024-08-29 | GSE271498 | GEO
Project description:This is a pre-publication study looking at proteoform complexity following agonism of GPCRs. This data set is the bottom-up dataset portion of the study.
2025-04-07 | PXD060263 | JPOST Repository
Project description:The objective of the study is the provide proof of high correlation between somatic and germline mismatch repair instability. This correlation is specifically researched in an area where patients have less access to cancer education and genetic testing for various reasons such as lack of insurance and general accessibility.
The study concentrates on early diagnosis of Lynch syndrome. Lynch syndrome is usually diagnosed from a blood test resulting in a mutation of one of the mismatch repair genes. Those are MLH1, MSH2, MSH 6, PMS2. A mutation in one of these genes creates a mismatch repair instability,hence higher incidence of cancers in specific organ groups. Amongst these organs are the Uterus, Ovaries, Upper genitourinary system, Pancreas and GI system.
The most common endometrial carcinoma which is found in Lynch syndrome is of endometrioid histology. Most patients with known germline mismatch repair instability, have the same somatic mutation. Our study is looking into correlating somatic mutation to germline mutation.
By doing so, patients diagnosed with somatic mismatch repair instability will be also diagnosed with lynch syndrome without germline genetic testing.
Screening programs will be utilized earlier and preventive procedures offered.
Due to less access to educational programs, genetic counseling and testing in underserved areas, patients are sometimes lost to follow up. Our study seeks to prove high correlation between somatic and germline mutations and by doing so, patient will be diagnosed with Lynch syndrome straight after endometrial cancer staging. As a result, increased compliance will be expected and patients will be offered the recommended preventative surgeries and screening protocols.
| 2349042 | ecrin-mdr-crc
Project description:Hepatocellular carcinoma (HCC) is a highly heterogenous disease associated with an equally dynamic tumor microenvironment (TME). We generated somatic HCC mouse models bearing clinically-relevant oncogenic driver combinations that faithfully recapitulated different human HCC subclasses. Using WES data, we explored the tumor mutation frequencies between models and compared them with human datasets.
2024-02-22 | GSE234897 | GEO
Project description:Hepatocellular carcinoma (HCC) is a highly heterogenous disease associated with an equally dynamic tumor microenvironment (TME). We generated somatic HCC mouse models bearing clinically-relevant oncogenic driver combinations that faithfully recapitulated different human HCC subclasses. Using WES data, we explored the tumor mutation frequencies between models and compared them with human datasets.
2024-04-27 | GSE216716 | GEO
Project description:Exon-Level and Gene-Level Expression analysis of Tumor and Normal Samples The effect of somatic copy number alterations at the functional level can be analyzed by looking into the expression pattern of the affected genes. The task of identifying the ‘affected’ genes is facilitated by robust algorithms that carry out sensitive and confident localization of the targets of somatic copy number alterations in cancer. We had earlier identified 144 genes by GISTIC analysis that were potential targets of SCNAs. In this study we report our findings based on exon level analysis of these genes. Only a subset of these genes was found to have significant changes in expression levels. 8/24 genes were found to have fold change value >1.5 and 3 of them were reported as novel in their association with CRC. The splice index of 29 exons corresponding to 13 genes was found to be significantly altered in tumor samples. Causal network analysis was carried out to study the difference in patterns of target genes affected by transcription factors identified by the GISTIC analysis. LIMMA analysis was carried out to find differentially expressed genes and their functional significance was studied using ingenuity pathway analysis.
2014-09-01 | GSE50421 | GEO
Project description:Exon-Level and Gene-Level Expression analysis of Tumor and Normal Samples The effect of somatic copy number alterations at the functional level can be analyzed by looking into the expression pattern of the affected genes. The task of identifying the M-bM-^@M-^XaffectedM-bM-^@M-^Y genes is facilitated by robust algorithms that carry out sensitive and confident localization of the targets of somatic copy number alterations in cancer. We had earlier identified 144 genes by GISTIC analysis that were potential targets of SCNAs. In this study we report our findings based on exon level analysis of these genes. Only a subset of these genes was found to have significant changes in expression levels. 8/24 genes were found to have fold change value >1.5 and 3 of them were reported as novel in their association with CRC. The splice index of 29 exons corresponding to 13 genes was found to be significantly altered in tumor samples. Causal network analysis was carried out to study the difference in patterns of target genes affected by transcription factors identified by the GISTIC analysis. LIMMA analysis was carried out to find differentially expressed genes and their functional significance was studied using ingenuity pathway analysis. We conducted a group-wise comparison of Tumor vs Normal samples obtained from cancer patients. Array data was processed using Expression Console and AltAnalyze
2014-09-01 | E-GEOD-50421 | biostudies-arrayexpress
Project description:The study includes 14 patients with confirmed JMML and known somatic mutations (from exome data of paired tumoral and germline DNA). Bone marrow or peripheral blood mononucleated cells were injected in immundeficient mice to recapitulate the leukemia. Whole exome sequencing was performed in xenograft samples to control the persistance of patients' known mutations and look for new mutations acquired in xenograft sample.
2018-03-15 | E-MTAB-6467 | biostudies-arrayexpress