NGS in Advanced Cancers
Ontology highlight
ABSTRACT: In this study, we used NGS to identify somatic events in advanced stage cancer patients to demonstrate the feasibility for using this approach to improve patient treatment.
SECONDARY ACCESSION(S): PRJNA217286PRJNA217285
REPOSITORIES: dbGaP
Similar Datasets
Project description:<p>In this study, we used NGS to identify somatic events in advanced stage cancer patients to demonstrate the feasibility for using this approach to improve patient treatment.</p>
| phs000657.v1.p1 | EGA
Project description:Prostate cancer is a unique disease from a metabolic perspective. Early stage localized prostate cancer does not typically display increased aerobic glycolysis (the Warburg effect), as seen in other malignancies. However, increasing evidence suggests that advanced prostate cancer exhibits the Warburg effect and displays high glucose uptake. We describe here that trans-gnetin H (TGH), a naturally-occurring resveratrol trimer extracted from Paeonia suffruticosa, displays significant anti-cancer effects in advanced prostate cancer cells in vitro. TGH perturbs energy metabolism by blocking the availability of glucose, inducing unfolded protein response (UPR) and C-MYC pathway downregulation in PC-3 cells. Our studies demonstrate the feasibility of targeting aerobic glucose metabolism in advanced prostate cancer and identify TGH as a potential therapeutic candidate.
2023-10-01 | GSE240103 | GEO
Project description:Ovarian cancer is a global problem, is typically diagnosed at a late stage and has no effective screening strategy. Platinum-based chemotherapy or Poly(ADP-ribose) polymerase inhibitors (PARPis) treatment are most frequently applied for ovarian cancer patients who are inoperable and in the advanced stage. The recognition of homologous recombination deficiency (HRD) as a biomarker to predict the effect of Platinum-based or PARPis treatment. WGS and WES can detect tumor HRD status but have several disadvantages which restrict their clinical application. My choice HRD CDx and Foundation Focus CDx are approved by FDA for HRD detection, however, whether they are applicable to the Chinese population or not is unknown. In this study, we created an SNP-based Tg-NGS panel to fill in gaps in Chinese patients’ HRD screening. Our results showed that the panel is cost and time-saving compared with WGS, but equivalent with SNP microarray on CNV and HRD detection. In summary, this newly developed kit is promising in clinical application to guide ovarian cancer and even other cancer types therapy.
2023-02-21 | GSE203509 | GEO
Project description:In order to evaluate the performance of CNV detection in next-generation sequencing platform in varied sample types, we employed chromosomal microarray analysis (CMA) for validation of the samples with NGS-based detection results (NCBI Sequence Read Archive with accession number SRA296708). Besides array Comparative Genomics Hybridization (aCGH, Agilent) , we used a commerical SNP-array (Illumina) including early abortus, induced termination, prenatal samples and postnatal samples. CMA results were compared with NGS-based detection results. 100% consistency was obtained between NGS-based approach and CMA in pathogenic or likely pathogenic CNVs detection.
2015-10-01 | GSE73190 | GEO
Project description:BACKGROUND: Because of the distinct clinical presentation of early and advanced stage ovarian cancer, we aim to clarify whether these disease entities are solely separated by time of diagnosis or whether they arise from distinct molecular events. METHODS: Sixteen early and sixteen advanced stage ovarian carcinomas, matched for histological subtype and differentiation grade, were included. Genomic aberrations were compared for each early and advanced stage ovarian cancer by array comparative genomic hybridization. To study how the aberrations correlate to the clinical characteristics of the tumors we clustered tumors based on the genomic aberrations. RESULTS: The genomic aberration patterns in advanced stage cancer equalled those in early stage, but were more frequent in advanced stage (p?=?0.012). Unsupervised clustering based on genomic aberrations yielded two clusters that significantly discriminated early from advanced stage (p?=?0.001), and that did differ significantly in survival (p?=?0.002). These clusters however did give a more accurate prognosis than histological subtype or differentiation grade. CONCLUSION: This study indicates that advanced stage ovarian cancer either progresses from early stage or from a common precursor lesion but that they do not arise from distinct carcinogenic molecular events. Furthermore, we show that array comparative genomic hybridization has the potential to identify clinically distinct patients. Sixteen early and sixteen advanced stage ovarian carcinomas
2012-08-22 | E-GEOD-24418 | biostudies-arrayexpress
Project description:Using NGS approach we performed the search of multiple sclerosis-related miRNAs. We used PBMC as an informative and easily accessible biological material. To exclude bias in miRNA expression levels caused by disease modifying therapies, miRNA profiling was performed in treatment-naïve RRMS patients. Taking into account hypothetic gender specificity in disease pathogenesis we compared miRNA expression in RRMS patients and HCs separately for men and women. MiRNA profiling in men identified 32 differentially expressed miRNAs, which passed threshold for multiple corrections and may be attributed to MS-related. At the same time we did not find well-defined MS-specific miRNA expression signatures in women using NGS
2019-01-11 | GSE124900 | GEO
Project description:BACKGROUND: Because of the distinct clinical presentation of early and advanced stage ovarian cancer, we aim to clarify whether these disease entities are solely separated by time of diagnosis or whether they arise from distinct molecular events. METHODS: Sixteen early and sixteen advanced stage ovarian carcinomas, matched for histological subtype and differentiation grade, were included. Genomic aberrations were compared for each early and advanced stage ovarian cancer by array comparative genomic hybridization. To study how the aberrations correlate to the clinical characteristics of the tumors we clustered tumors based on the genomic aberrations. RESULTS: The genomic aberration patterns in advanced stage cancer equalled those in early stage, but were more frequent in advanced stage (p = 0.012). Unsupervised clustering based on genomic aberrations yielded two clusters that significantly discriminated early from advanced stage (p = 0.001), and that did differ significantly in survival (p = 0.002). These clusters however did give a more accurate prognosis than histological subtype or differentiation grade. CONCLUSION: This study indicates that advanced stage ovarian cancer either progresses from early stage or from a common precursor lesion but that they do not arise from distinct carcinogenic molecular events. Furthermore, we show that array comparative genomic hybridization has the potential to identify clinically distinct patients.
2012-08-22 | GSE24418 | GEO