High throughput sequencing analysis of miRNAs expression in fresh gastric cancer tissues and paraffin embedded tissues / 重庆医学

ABSTRACT

Objective To analyze formalin-fixed and paraffin-embedded(FFPE) sample by next generation sequencing(NGS) technology for high throughput DNA sequencing and related bioinformatics analysis,and to explore the reliability and clinic significance of miRNAs in the detection of sample from FFPE gastric cancer tissue.Methods FFPE and fresh frozen samples of the same tissue were excised from 2 cases of gastric cancer in 2015 and 2016.RNA was extracted from the samples and the small RNA library was isolated and constructed,and high throughput DNA sequencing was conducted with Illumina sequencing platform.The DNA sequencing results were analyzed by quantifying the expression of known miRNAs families sequence,and the expression profiling of known miRNAs was constructed.Spearman correlation analysis was performed on the miRNAs of the samples to assess the difference in the expression of miRNAs.Results The total RNA extracted from the fresh frozen sample had higher quality and complete RNA coverage,and the results showed that the 28S was 1.3-1.4 times of 18S.The RNA extracted from the FFPE sample showed different degrees of degradation,and the peaks of 28S and 18S were not significant.The spearman correlation of miRNAs expression profiling in frozen and FFPE samples was 0.90 and 0.86 respectively,and the expression levels of miRNAs in two samples were consistent and had significant correlation.Conclusion miRNAs in FFPE sample can retain certain level of integrity and can be used in tumor test by NGS.