Endoscopic liquid biopsies of gastric fluid in a large human patient cohort reveal DNA content as a candidate tumor biomarker in gastric cancer

Patient data: collected from medical records. 
DNA extraction and quantification: DNA was extracted from gastric fluids that are routinely removed to allow better examination of the mucosa. These fluids were collected in sterile plastic containers attached to the endoscope suction channel and kept on ice until pH measurement and neutralization. Samples were divided in aliquots and kept frozen at -20oC (each aliquot was thawed just once), until DNA was extracted from an equal volume of gastric fluid (800 µl) by proteinase-K digestion, followed by phenol-chloroform extraction and ethanol DNA precipitation. DNA was subsequently resuspended in 100 µl of sterile nuclease-free double-deionized water and quantified by Qubit fluorometry (Thermo Fisher).
, # Data from: Endoscopic liquid biopsies of gastric fluid in a large human patient cohort reveal DNA content as a candidate tumor biomarker in gastric cancer

Dataset DOI: [10.5061/dryad.bzkh189qz](https://doi.org/10.5061/dryad.bzkh189qz)

## Description of the data and file structure

### Files and variables

#### File: Cadona_et_al_general_data.csv

**Description:** Patient demographics, general data and relevant clinical information as well as DNA concentration values.

##### Variables

* Patient ID: alphanumeric or numeric
* Endoscopy results: Cancer, gastritis, normal and pre-neoplastic conditions.
* Further endoscopic results: used to add more information to \"endoscopic results\": other
* Code endoscopy: 1) Normal; 2) Peptic diseases; 3) Pre-neoplasia; 4) Cancer.
* Sex: biological sex, male or female.
* Age group: age at diagnosis
* BMI: body mass index
* pH: pH value of the gastric juices collected
* Use of proton-pump inhibitors: indicates current use, yes or no. 
* Tumor subtypes..., Patient data were handled using a double-coding system: each participant received a unique study code, and the key linking codes to personal identifiers was stored separately under restricted access, preventing easy identification of individual patients. Furthermore, all participants signed an informed consent form that anticipates the use of their data for scientific presentation and publication, on the condition that results are reported in a de-identified manner, without names or other direct identifiers., The dataset includes relevant information, mentioned in the paper, regarding clinical information, demographics, diagnosis and DNA concentrations (ng/µl).
Gastric cancer remains a diagnostic and therapeutic challenge worldwide. Improved prognostic biomarkers could aid treatment planning across surgical, neoadjuvant, and adjuvant settings. We evaluated a novel liquid-biopsy approach integrated with esophagogastroduodenoscopy (EGD) by analyzing gastric fluid DNA (gfDNA) from a large cohort (n=1056) to assess its diagnostic utility and prognostic value in gastric cancer. In this exploratory study, gfDNA concentration was measured in patients with normal gastric mucosa, peptic diseases, preneoplastic conditions, or cancer. Variables included sex, gastric fluid pH, proton-pump inhibitor use, tumor subtype, stage, and outcomes. gfDNA levels were significantly higher in gastric cancer than in all comparison groups (mean 26.86 ng/µL; 95% CI 20.05–33.79; p=3.61 × 10e-12) and as compared to non-m...,