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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE253260 | GEO | 2024/01/18

REPOSITORIES: GEO

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

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

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The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers

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2008-09-09 | GSE12072 | GEO

The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers

2008-09-09 | E-GEOD-12072 | biostudies-arrayexpress

Human B cell response to influenza vaccination

Project description:We used ultrasound-guided fine needle aspiration of the draining axillary lymph nodes to interrogate influenza vaccine-induced GC responses in humans.

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Comparative transcriptomic characterisation of canine prostate fine-needle-aspiration and tissue samples - from sampling to sequencing

Project description:Ultrasound-guided fine-needle aspiration (US-FNA) biopsy is a widely used minimally invasive sampling procedure for cytological diagnosis. This study investigates the feasibility of using US-FNA samples for both cytological diagnosis and whole transcriptome RNA-sequencing analysis (RNA-Seq), with the ultimate aim of improving canine prostate cancer management. The feasibility of the US-FNA procedure was evaluated intra vitam on 43 dogs. Additionally, aspirates from 31 euthanised dogs were collected for standardising the procedure. Each aspirate was separated into two subsamples: for cytology and RNA extraction. Additional prostate tissue samples served as control for RNA quantity and quality evaluation, and differential expression analysis. The US-FNA sampling procedure was feasible in 95% of dogs. RNA isolation of US-FNA samples was successfully performed using phenol-chloroform extraction. The extracted RNA of 56% of a subset of US-FNA samples met the quality requirements for RNA-seq. Expression analysis revealed that only 153 genes were exclusively differentially expressed between non-malignant US-FNAs and tissues. Moreover, only 36 differentially expressed genes were associated with the US-FNA sampling technique and unrelated to the diagnosis. Furthermore, the gene expression profiles clearly distinguished between non-malignant and malignant samples. This proves US-FNA to be useful for molecular profiling.

2019-10-08 | GSE122916 | GEO

High-quality endoscopic ultrasound-guided fine needle aspiration tissue acquisition.

Project description:Endoscopic ultrasound-guided fine needle aspiration is a multistep procedure that involves proper clinical indication, correct selection of needles, adapting evidence-based techniques such as the fanning maneuver and not routinely using suction or the stylet for tissue sampling, and establishing reliable cytopathology support. Integrating cytopathology in the training curriculum and developing a more flexible platform of needles and echoendoscopes are likely to further advance the field of endosonography. This review aims to summarize the technical issues that are key to performing high-quality endoscopic ultrasound-guided fine needle aspiration.

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Germinal centre-driven maturation of B cell response to SARS-CoV-2 mRNA vaccination

Project description:We used ultrasound-guided fine needle aspiration of the draining ipsilateral axillary lymph nodes to interrogate SARS-CoV-2 mRNA vaccine-induced GC responses in humans.

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Harmonic contrast-enhanced endoscopic ultrasound fine-needle aspiration: Fact or fiction?

Project description:The negative predictive value of endoscopic ultrasonography fine-needle aspiration is relatively low. To achieve the improvement of the diagnostic yield, the following were proposed: a higher number of passes, the presence of the rapid on-site cytopathologist evaluation, the fanning technique, or the repetition of the fine needle biopsy. Harmonic contrast-enhanced endosonography may better identify the targeted area in the lesions by avoiding the inside necrosis and the vessels of fibrosis, so it can guide the fine-needle aspiration. Both techniques are complementary, not competitive, and they can be done in the same session. The combined technique is simple, safe, and requires only a few minutes with minimal extra costs compared to standard fine-needle aspiration. It minimally increases the diagnostic rate, and it permits the decrease of the number of passes. However, we will know its real clinical impact only in the future and whether it will be incorporated into the lesion assessment process.

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2011-10-31 | GSE32518 | GEO

Factors affecting cytological results of endoscopic ultrasound guided-fine needle aspiration during learning.

Project description:BACKGROUND:Endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) is a standard procedure used to obtain tissue samples for diagnosis of solid retroperitoneal tumours. However, this procedure demands high technical expertise and requires a strong learning curve. Our aim was to identify factors associated with false-negative EUS-FNA results during the learning for endoscopists. METHODS:Our retrospective analysis was based on the EUS-FNA specimens collected by two novice endoscopists in 200 patients with retroperitoneal lesions who had confirmed image- or tissue-based diagnoses of malignancy or benign lesions. RESULTS:In the first 40 performances endoscopists, the false-negative diagnostic rate of EUS-FNA was higher among patients with chronic pancreatitis than in patients without chronic pancreatitis. Patients who underwent FNA through the trans-duodenal puncture route also had lower success cytological diagnosis rate than through the trans-gastric puncture route. The rate of successful cytological diagnoses with EUS-FNA improved after 40 procedures and was not influenced by chronic pancreatitis presentation or difference puncture route. CONCLUSION:Regarding the learning curve, more than 40 procedures were required to achieve a stable success rate of EUS-FNA. Chronic pancreatitis and trans-duodenal puncture route are the predictive factors for a false-negative FNA cytological result during learning. TRIAL REGISTRATION:This was a retrospective study.

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