Ontology highlight
ABSTRACT:
PROVIDER: PRJNA614006 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Somatic point mutation calling in low cellularity tumors
| PRJNA209118 | ENA
Project description:Illumina 1M Omni Quad arrays were used to test mutation calling accuracy of qSNP tool (a mutation caller) Ilumina array genotypes with GenCal (GC score)>0.70 were used in the comparison of genotype calls using next generation sequencing data and qSNP (mutation caller)
2014-06-13 | GSE47904 | GEO
Project description:We have benchmarked the performance of cancer CNV calling by six most recent software tools on their detection accuracy, sensitivity, and reproducibility. We also explored the consistency of CNV calling across different orthogonal technologies, including optical mapping and microarrays. Using consensus results from six CNV callers and confirmation from three orthogonal methods, we established a high-confidence CNV call set for the reference sample.
2023-08-25 | GSE212051 | GEO
Project description:Illumina 1M Omni Quad arrays were used to test mutation calling accuracy of qSNP tool (a mutation caller) Ilumina array genotypes with GenCal (GC score)>0.70 were used in the comparison of genotype calls using next generation sequencing data and qSNP (mutation caller) 2 samples (control cell line and Melanoma cell line). This is the data for a validation step. contributor: Australian Pancreatic Cancer Genome Initiative
2014-06-13 | E-GEOD-47904 | biostudies-arrayexpress
Project description:ICGC-TCGA DREAM Somatic Mutation Calling Challenge
| PRJNA248553 | ENA
Project description:The dataset contains the somatic point mutation data from the exome-targeted region of 36 exome or whole genome sequenced microsatellite unstable colorectal cancers and the somatic point mutation data from 93 additional MiSeq sequenced microsatellite unstable colorectal cancers.
| EGAD00001004281 | EGA
Project description:Sporadic venous malformations (VM) and angiomatosis of soft tissue (AST) are benign, congenital slow-flow vascular anomalies that have no available targeted therapies. Depending on the size and location of the lesion, symptoms vary from motility disturbances to pain and disfigurement. By analyzing tissue samples from 36 patients with VM or AST, we uncover that the majority of the samples carry a somatic mutation in either TEK or PIK3CA gene. In the current data set, we study the role of PIK3CA point mutation p.H1047R on the transcriptional profile of human umbilical vein endothelial cells (HUVEC-s).
2023-06-10 | GSE196311 | GEO
Project description:The introduction of microarray techniques to cancer research brought great expectations for finding biomarkers that would improve patients’ treatment; however, the results of such studies are poorly reproducible and critical analyses of these methods are rare. In this study, we examined global gene expression in 97 ovarian cancer samples. Also, validation of results by quantitative RT-PCR was performed on 30 additional ovarian cancer samples. We carried out a number of systematic analyses in relation to several defined clinicopathological features. The main goal of our study was to delineate the molecular background of ovarian cancer chemoresistance and find biomarkers suitable for prediction of patients’ prognosis. We found that histological tumor type was the major source of variability in genes expression, except for serous and undifferentiated tumors that showed nearly identical profiles. Analysis of clinical endpoints [tumor response to chemotherapy, overall survival, disease-free survival (DFS)] brought results that were not confirmed by validation either on the same group or on the independent group of patients. CLASP1 was the only gene that was found to be important for DFS in the independent group, whereas in the preceding experiments it showed associations with other clinical endpoints and with BRCA1 gene mutation; thus, it may be worthy of further testing. Our results confirm that histological tumor type may be a strong confounding factor and we conclude that gene expression studies of ovarian carcinomas should be performed on histologically homogeneous groups. Among the reasons of poor reproducibility of statistical results may be the fact that despite relatively large patients’ group, in some analyses one has to compare small and unequal classes of samples. In addition, arbitrarily performed division of samples into classes compared may not always reflect their true biological diversity. And finally, we think that clinical endpoints of the tumor probably depend on subtle changes in many and, possibly, alternative molecular pathways, and such changes may be difficult to demonstrate. Here, we provide gene expression data from 101 ovarian cancer surgical samples: 73 serous, 12 endometrioid, 9 clear cell and 7 undifferentiated. The majority of patients (98 out of 101) were tested for BRCA1 gene mutation: 27 patients had germline BRCA1 gene mutation, one had somatic mutation, 70 had no BRCA1 mutation detected. We also checked for somatic TP53 gene mutation: 75 tumors had somatic mutation in TP53, 15 had no mutation detected, 11 were not analyzed (NA). The p53 protein accumulation in the cancer cells was analyzed by immunohistochemistry: 54 tumors had protein accumulation, 42 had no accumulation, 5 - NA. For 75 samples we provide extensive pathological and clinical data: tumor grade, histological type, FIGO stage, disease free survival time (DFS), overall survival (OS), residual tumor size (R), clinical status post first-line chemotherapy and at last follow-up, platinum sensitivity. The tumors were graded in a four-grade scale, according to the criteria given in [1]. The results of data analyses were published in [2]. [1] HRK Barber, SC Sommers, R Snyder, TH Kivon; Histologic and nuclear grading and stromal reaction as indices for prognosis in ovarian cancer. Am. J. Obstet. Gynecol, 121 (1975), p. 795-807 [2] K. Lisowska, M. Olbryt, V. Dudaladava, J. Pamuła-Piłat, K. Kujawa, E. Grzybowska, M. Jarząb, S. Student, I. K. Rzepecka, B. Jarząb J. Kupryjańczyk (2014) Gene expression analysis in ovarian cancer – faults and hints from DNA microarray study.
2014-12-06 | E-GEOD-63885 | biostudies-arrayexpress
Project description:Several DNA sequencing studies of chronic lymphocytic leukemia (CLL) revealed that the splicing factor SF3B1 accumulated somatic point mutations in about 10 percent of the patients. In most cases the mutations were located in the genomic regions coding for the C-terminal HEAT-repeat domain and in many cases, the mutations gave rise to specific amino acid substitutions. Here, we aimed to investigate differential usage of exons associated with the mutation K700E of SF3B1 in CLL tumuor cells. We generated RNA-Seq transcriptome data from two patients with mutations in SF3B1, two patient without mutations in SF3B1 and from healthy donors. We report interesting examples and possible consequences of the alternative exon usage in these genes. This dataset contains only the files resulting from the processing the RNA sequencing raw data. This avoids potential patient identifiability, but ensures the full reproducibility of the results described in the publication.
2013-12-27 | E-MTAB-2025 | biostudies-arrayexpress