Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profiles of paired endoscopic tumor biopsy (initial diagnostic assessment) and subsequent surgically resected specimens.

ABSTRACT: Gene expression profiles of paired endoscopic tumor biopsy (initial diagnostic assessment) and subsequent surgically resected specimens.

PROVIDER: PRJNA667753 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12782400.fastq.gz	Fastqsanger.gz
	SRR12782500.fastq.gz	Fastqsanger.gz
	SRR12782600.fastq.gz	Fastqsanger.gz
	SRR12782401.fastq.gz	Fastqsanger.gz
	SRR12782501.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 216

Similar Datasets

Gene expression profiles of paired endoscopic tumor biopsy (initial diagnostic assessment) and subsequent surgically resected specimens.

Project description:Ongoing immunomodulatory strategies in tumors characterized by an overall hot immune phenotype may improve prognosis of head and neck squamous cell carcinomas (HNSCC). Our objective was to develop a reliable and stable scoring system for the identification of immunologically hot HNSCC and to evaluate its association with response to immunotherapies. A Hot Oral Tumor (HOT) score was developed using data from The Cancer Genome Atlas. HOT score was then computed in 27 patients with HNSCC in paired perendoscopic tumor biopsy (initial diagnostic assessment) and subsequent surgically resected specimen. None of the patients was treated with neoadjuvant therapy. Concordance and correlation of the HOT score was high in paired samples.

2022-07-07 | GSE159141 | GEO

Concordance between PIK3CA mutations in endoscopic biopsy and surgically resected specimens of esophageal squamous cell carcinoma.

Project description:BackgroundPIK3CA mutations are expected to be potential therapeutic targets for esophageal squamous cell carcinoma (ESCC). We aimed to clarify the concordance between PIK3CA mutations detected in endoscopic biopsy specimens and corresponding surgically resected specimens.MethodsWe examined five hotspot mutations in the PIK3CA gene (E542K, E545K, E546K, H1047R, and H1047L) in formalin-fixed and paraffin-embedded tissue sections of paired endoscopic biopsy and surgically resected specimens from 181 patients undergoing curative resection for ESCC between 2000 and 2011 using a Luminex technology-based multiplex gene mutation detection kit.ResultsMutation analyses were successfully performed for both endoscopic biopsy and surgically resected specimens in all the cases. A PIK3CA mutation was detected in either type of specimen in 13 cases (7.2%, 95% confidence interval: 3.9-12.0). The overall concordance rate, positive predictive value, and negative predictive value were 98.3% (178/181), 90.9% (10/11), and 98.8% (168/170), respectively. Among patients with a PIK3CA mutation detected in both types of specimens, the concordance between PIK3CA mutation genotypes was 100%. There were three cases with a discordant mutation status between the types of specimens (PIK3CA mutation in surgically resected specimen and wild-type in biopsy specimen in two cases, and the opposite pattern in one case), suggesting possible intratumoral heterogeneity in the PIK3CA mutation status.ConclusionsThe PIK3CA mutation status was highly concordant between endoscopic biopsy and surgically resected specimens from the same patient, suggesting that endoscopic biopsy specimens can be clinically used to detect PIK3CA mutations in patients with ESCC.

| S-EPMC5220610 | biostudies-literature

TRANSCRIPTOMIC ANALYSIS ON ENDOSCOPIC ULTRASOUND FINE NEEDLE ASPIRATION MATERIALS FROM PRIMARY PANCREATIC ADENOCARCINOMA

Project description:The study aimed to compare the molecular profiles of metastatic, locally advanced, and resected primary pancreatic adenocarcinoma at the genomic and transcriptomic levels. DNA and mRNA were extracted from endoscopic ultrasound-guided fine needle aspiration-biopsy material of primary tumors from 397 patients, and they were subsequently analyzed by targeted deep sequencing and RNAseq.

2024-01-18 | GSE253260 | GEO

Photoacoustic imaging of fresh human surgically and endoscopically resected gastrointestinal specimens.

Project description:ObjectivePhotoacoustic (PA) imaging is a novel noninvasive technique that offers high-contrast tomographic imaging with ultrasound-like resolution at depths of centimeters, enabling visualization of deep small vessels. The aim of this pilot study was to survey the characteristics of deep vessel networks in the mucosa of neoplastic gastrointestinal (GI) lesions using PA imaging.MethodsSpecimens of patients who had undergone surgical and endoscopic resection for GI lesions were included in this study. The PA/ultrasound imaging system for clinical research is characterized by a technology that can superimpose a PA image over an ultrasound image. Three-dimensional PA images were acquired for the resected specimen before fixation. The stomach and colon of live pigs were incised, and the walls were scanned from the mucosa.ResultsA total of 32 specimens (nine esophageal, 12 gastric, 11 colorectal) were scanned. The pathological diagnoses were adenomas (n = 2), intramucosal cancers (n = 14), and invasive cancers (n = 16). The deep vessel networks of all lesions could be visualized. In the intramucosal lesions, the deep vessel network was similar to that of a normal tissue. In invasive cancers, the thick and prominent vessel network was visible in the surface layer of esophageal cancers, infiltrated area of gastric cancers, and surface layer and infiltrated area of colorectal cancers. In the images of living pigs, visualizing the vascular network deeper than the submucosa in both the stomach and large intestine was possible.ConclusionOur study confirmed that the deep vessel networks of neoplastic GI lesions were visible by PA imaging.

| S-EPMC8828192 | biostudies-literature

Gauze extension method for specimens resected by endoscopic submucosal dissection.

Project description:Video 1The gauze extension method for resected specimens.

| S-EPMC9347180 | biostudies-literature

Longitudinal epigenome analysis of IDH-wildtype glioblastomas from initial and recurrent surgical specimens

Project description:Genome-wide DNA methylation profiling of 226 longitudinally collected IDH-wildtype glioblastoma tumor specimens from 106 patients, consisting of 99 initial treatment-naive resection specimens prior to any radiation or chemotherapy and 127 recurrent post-treatment resection specimens at time of recurrence/progression usually following radiation and/or chemotherapy. These 127 recurrent post-treatment resection specimens were composed of 106 first surgically-treated recurrent specimens, 19 second surgically-treated recurrent specimens, and 2 third surgically-treated recurrent specimens. The Illumina Infinium EPIC 850k version 1.0 Human DNA Methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpG sites of genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissue of the 226 IDH-wildtype glioblastomas.

2024-11-19 | GSE279073 | GEO

Simultaneous pathological findings in biopsy specimens of patients with surgically resected lung carcinoids and their role in survival.

Project description:Pulmonary carcinoid tumors are rare, low-grade malignant tumors that constitute 1-2% of all lung tumors. The present study aimed to describe the simultaneous pathological findings in biopsy specimens of patients with surgically resected lung carcinoids and determine their association with survival rates. For this purpose, 108 patients with resected carcinoid lung tumors were followed-up for 96 months and analyzed for simultaneous pathological findings in biopsy specimens. Among these, simultaneous pathological findings were found in 82 patients. The association between these findings and patient survival rates was evaluated. Atelectasis was a simultaneous finding in 52.4% of the patients, desquamative interstitial pneumonia (DIP) in 13.4%, emphysema in 24.4% and bronchiectasis in 9.8%. The survival rate was 100% for the patients with atelectasis, 81.8% for the patients with DIP, 90% for the patients with emphysema and 75% for the patients with bronchiectasis (P<0.05). According to the univariate analysis, the type of carcinoid was associated with patient survival with better survival rates for patients with typical carcinoids, while age, sex, stage and simultaneous pathological findings were not associated with patient survival. On the whole, there was a statistically significant difference in the survival rates of patients with resected lung carcinoids with different simultaneous pathological findings. However, further studies are warranted to assess the role of these findings in the survival of these patients.

| S-EPMC9353869 | biostudies-literature

CCN3 administration after surgically induced myocardial infarction

Project description:CCN3 administration after surgically induced myocardial infarction

2023-02-27 | GSE217925 | GEO

DNA methylation profiling of TNBC primary tumors

Project description:DNA methylation profiling of TNBC primary tumors (surgically resected) to validate DNA methylation epitypes. Illumina EPIC V1 set DNA methylation profiling of TNBC primary tumors (surgically resected) to validate DNA methylation epitypes. Illumina EPIC V2 set (GSM8826913-GSM8826971).

2025-03-03 | GSE290981 | GEO

RNA sequencing for endoscopic biopsy tissue samples from controls and Crohn's disease patients, and organoids derived from these specimens.

Project description:RNA sequencing for endoscopic biopsy tissue samples from controls (jejunum [S170], n=1; ileum [SN2], n=1) and patients with Crohn's disease (jejunum [non-inflamed area, A2/L2+L4/B2, infliximab maintenance therapy, S93], n=1; ileum, [non-inflamed area, A2/L2/B2, infliximab maintenance therapy, S95], n=1). Organoid culture was performed using intestinal crypts derived from these specimens, as described previously (Sato et al. Nature 2009; 459: 262–265]. Organoids were sub-cultured at least 6 passages. RNA sequencing was conducted for organoids on day 3, day 6, and day 9 [S170 and S93], and organoids treated with TNFɑ 30 ng/ml on day 3, day 6, and day 9 [S170 and S93]. RNA sequencing was conducted for organoids on day 6 and day 9 [N2 and S95], and organoids treated with TNFɑ 30 ng/ml on day 6 and day 9.

2021-04-27 | GSE173294 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data