GSE73002 ( miRNA )

breast cancer ( breast )

A novel combination of serum microRNAs for detecting breast cancer in the early stage

Cancer : 1280 / Control : 2686

Mean and standard deviation (SD) of the 5% trimmed signals of the negative controls were calculated. Signals of miRNAs over mean+2SD of the negative controls were subtracted with the mean of the negative controls. The undetected signal was replaced with the value that was the least signal intensity on each DNA chip minus 0.1 in log2 scale followed by quantile normalization.

Additionally, 2,836 serum samples were obtained from non-cancer controls and 514 from patients with other types of cancers or benign diseases. The samples were divided to a training cohort including non-cancer controls, other cancers and breast cancer and a test cohort including non-cancer controls and breast cancer. The training cohort was used to identify a combination of miRNAs that detect breast cancer, and the test cohort was used to validate that combination.

1280 breast cancer serums (74 in training cohort, 1206 in test cohort), 54 benign breast diseases serums in test cohort, 2836 non-cancer control serums (1493 in training cohort, 1343 in test cohort), 514 non-breast benign diseases serums in training cohort.

Shimomura A, Shiino S, Kawauchi J, Takizawa S et al. Novel combination of serum microRNA for detecting breast cancer in the early stage. Cancer Sci 2016 Mar;107(3):326-34. PMID: 26749252

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 was attached in the 3D-Gene® miRNA oligo chip kit.

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