GSE122497 ( miRNA )

Esophageal Squamous Cell Carcinoma ( esophageal )

Large-scale serum microRNA profiling for developing an esophageal squamous cell carcinoma detection model

Cancer : 566 / Control : 4965

The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetected) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

A serum miRNA combination could be a powerful classifier for the detection of esophageal squamous cell carcinoma.

Serum microRNA profiles of 5531 samples, which consist of 566 of esophageal squamous cell carcinoma and 4965 of non-cancer controls.

Sudo K, Kato K, Matsuzaki J, Boku N et al. Development and Validation of an Esophageal Squamous Cell Carcinoma Detection Model by Large-Scale MicroRNA Profiling. JAMA Netw Open 2019 May 3;2(5):e194573. PMID: 31125107

Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

total RNA

Cy5

miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol were attached in the 3D-Gene® miRNA oligo chip kit.

3D-Gene Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).