Homo sapiens
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: MSV000080374PXD013455
PROVIDER: PRJNA356046 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genome wide miRNA expression profiling was performed using Affymetric miRNA v. 3.0 Array on 48 samples which included paired FFPE colon tuomor and metastisized liver and paired normal colon, normal liver). The data set was divided into two categories and identified by tissue source and patient demographics: Tissue (Colon, Liver), Source (Colon Tumor Liver Met, Colon Normal, Liver Normal), Sex (Male, Female), Patient Pair. microRNAs (miRs) are frequently dysregulated in colorectal cancer (CRC) and subsets are correlated with advanced tumor stage and metastasis. Despite this, the development of prognostic biomarkers that predict metastatic potential remain limited. Our study was designed to identify, validate, and elucidate underlying biology imposed by a miR signature that defines and predicts metastatic disease. Genome-wide miR expression profiling was performed on fourteen patient-matched stage IV primary CRC tumors and corresponding liver metastases using microRNA array technology. Based on these results, this miR panel was then validated and evaluated in normal colon tissue (N = 5), early stage (I & II, N = 11) and late stage (Stage III & IV, N = 14) colorectal primary tumors via qRT-PCR.
2017-05-02 | GSE98406 | GEO
Project description:Differential Mutations In Matched Primary and Metastatic Colorectal Cancers
| PRJNA314365 | ENA
Project description:We performed whole exome sequencing and copy number analysis for 15 triplets, each comprising normal colorectal tissue, primary colorectal carcinoma, and its synchronous matched liver metastasis. We analyzed the similarities and differences between primary colorectal carcinoma and matched liver metastases in regards to somatic mutations and somatic copy number alterationss (SCNAs). The genomic profiling demonstrated mutations in APC(73%), KRAS (33%), ARID1A and PIK3CA (6.7%) genes between primary colorectal and metastatic liver tumors. TP53 mutation was observed in 47% of the primary samples and 67% in liver metastatic samples. The grouped pairs, in hierarchical clustering showed similar SCNA patterns, in contrast to the ungrouped pairs. Many mutations (including those of known key cancer driver genes) were shared in the grouped pairs. The ungrouped pairs exhibited distinct mutation patterns with no shared mutations in key driver genes. Four ungrouped liver metastasis samples had mutations in DNA mismatch repair genes along with hypermutations and a substantial number of copy number of alterations. Genomically, colorectal and metastatic liver tumors were very similar. However, in a subgroup of patients, there were genetic variations in liver metastases in the loss of DNA mismatch repair genes. Copy number analysis of Affymetrix CytoScanHD arrays was performed for 15 primary colorectal carcinoma and 15 samples of their matched liver metastases. 15 normal samples prepared from each of the patient was used as the reference for the study. Nexus Copy number 6.1 software was used for somatic copy number alteration analysis.
2014-03-01 | E-GEOD-53799 | biostudies-arrayexpress
Project description:Comparison of genomic alterations of primary colorectal cancers with liver metastases of the same patient Keywords: array CGH, colorectal cancer, colon cancer, liver metastasis 21 primary colorectal cancers and 21 matched liver metastases hybridized against sex-matched control pools
2010-07-07 | E-GEOD-10179 | biostudies-arrayexpress
Project description:Colorectal cancer (CRC) is a commonly occurring cancer worldwide. Metastasis and recurrence are the major causes of cancer-related death. CRC progression is a multistep process, and extensive efforts have been made to identify the genomic and transcriptomic alterations that occur during this process. However, whether primary tumors and metastatic lesions possess distinct biological features remains unclear. We established 74 patient-derived organoids (PDOs) from primary tumors and patient-matched metastatic and recurrent lesions.
2021-04-01 | GSE128213 | GEO
Project description:We performed whole exome sequencing and copy number analysis for 15 triplets, each comprising normal colorectal tissue, primary colorectal carcinoma, and its synchronous matched liver metastasis. We analyzed the similarities and differences between primary colorectal carcinoma and matched liver metastases in regards to somatic mutations and somatic copy number alterationss (SCNAs). The genomic profiling demonstrated mutations in APC(73%), KRAS (33%), ARID1A and PIK3CA (6.7%) genes between primary colorectal and metastatic liver tumors. TP53 mutation was observed in 47% of the primary samples and 67% in liver metastatic samples. The grouped pairs, in hierarchical clustering showed similar SCNA patterns, in contrast to the ungrouped pairs. Many mutations (including those of known key cancer driver genes) were shared in the grouped pairs. The ungrouped pairs exhibited distinct mutation patterns with no shared mutations in key driver genes. Four ungrouped liver metastasis samples had mutations in DNA mismatch repair genes along with hypermutations and a substantial number of copy number of alterations. Genomically, colorectal and metastatic liver tumors were very similar. However, in a subgroup of patients, there were genetic variations in liver metastases in the loss of DNA mismatch repair genes.
2014-03-01 | GSE53799 | GEO
Project description:About 50% of colorectal cancer patients develop liver metastases. Patients with metastatic colorectal cancer have 5-year survival rates below 20% despite new therapeutic regimens. Tumor heterogeneity has been linked with poor clinical outcome, but was so far mainly studied via bulk genomic analyses. In this study we performed spatial proteomics via MALDI mass spectrometry imaging on six patient matched CRC primary tumor and liver metastases to characterize interpatient, intertumor and intratumor hetereogeneity. We found several peptide features that were enriched in vital tumor areas of primary tumors and liver metastasis and tentatively derived from tumor cell specific proteins such as annexin A4 and prelamin A/C. Liver metastases of colorectal cancer showed higher heterogeneity between patients than primary tumors while within patients both entities show similar intratumor heterogeneity sometimes organized in zonal pattern. Together our findings give new insights into the spatial proteomic heterogeneity of primary CRC and patient matched liver metastases.
2023-02-17 | PXD039409 | Pride
Project description:Comparison of gene expression profiles between a primary melanoma and an early metastatic specimen from the same patient will provide essential biological insight into early metastatic processes. The DASL (cDNA mediated annealing, selection, extension and ligation) assay has been used to generate gene expression data for 502 cancer-related genes from very small formalin-fixed sentinel node biopsy (SNB) melanoma samples, this data has been further compared with gene expression of the matched formalin-fixed primary melanoma. Tissue was sampled from twenty-five SNB deposits using laser capture microdissection. The mean number of genes detected using DASL with SNB samples was lower than when using a core of primary melanoma tumor (242 versus 434 genes). A large proportion of SNB samples failed (<240 genes detected) the assay (57.7%). Area of tissue microdissected, RNA concentration and qRT-PCR quality control did not predict performance of samples on the array but age of sampled tissue negatively correlated with number of genes detected (p=0.01). For samples that performed successfully, matched primary samples were available for 10 samples. Gene expression profiles correlated between all matched tumor pairs (Spearman’s rho 0.15-0.80, p<0.01), although a number of genes were differentially expressed between nodal and primary tumors in all tumor pairs. This study demonstrates that the DASL assay can be used to generate gene expression data from small formalin-fixed samples, but not consistently. Differentially expressed genes were identified across 10 matched primary and nodal tumor pairs suggesting that the DASL assay could be used to derive essential biological information about early metastasis.
2011-08-02 | GSE31139 | GEO
Project description:Exon Array Data for Colerectal Tumor and Normal Samples
| PRJNA217483 | ENA
Project description:CytoScanHD array Data for 15 normal, 15 primary colorectal carcinomas and their 15 matched liver metastases
| PRJNA233312 | ENA