1. Two novel qualitative transcriptional signatures robustly applicable to non‐research‐oriented colorectal cancer samples with low‐quality RNA
- Author
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Zheng Guo, Haiyan Huang, Xing Liu, Jun Cheng, Guoxian Guan, Lu Ao, Jun He, Yating Guo, Junling Wu, and Fengle Jiang
- Subjects
0301 basic medicine ,transcriptional signature ,Transcription, Genetic ,Colorectal cancer ,colorectal cancer ,Computational biology ,Stage ii ,Biology ,03 medical and health sciences ,0302 clinical medicine ,relative expression orderings ,Databases, Genetic ,Gene expression ,Biomarkers, Tumor ,medicine ,non‐research‐oriented clinical samples ,Humans ,Protein Interaction Maps ,Relapse risk ,low‐quality RNA ,Gene ,Base Sequence ,Gene Expression Profiling ,RNA ,Cancer ,Original Articles ,Cell Biology ,medicine.disease ,Transcriptome Sequencing ,Gene Expression Regulation, Neoplastic ,Early Diagnosis ,030104 developmental biology ,030220 oncology & carcinogenesis ,Molecular Medicine ,Original Article ,Colorectal Neoplasms ,Transcriptome - Abstract
Currently, due to the low quality of RNA caused by degradation or low abundance, the accuracy of gene expression measurements by transcriptome sequencing (RNA‐seq) is very challenging for non‐research‐oriented clinical samples, majority of which are preserved in hospitals or tissue banks worldwide with complete pathological information and follow‐up data. Molecular signatures consisting of several genes are rarely applied to such samples. To utilize these resources effectively, 45 stage II non‐research‐oriented samples which were formalin‐fixed paraffin‐embedded (FFPE) colorectal carcinoma samples (CRC) using RNA‐seq have been analysed. Our results showed that although gene expression measurements were significantly affected, most cancer features, based on the relative expression orderings (REOs) of gene pairs, were well preserved. We then developed two REO‐based signatures, which consisted of 136 gene pairs for early diagnosis of CRC, and 4500 gene pairs for predicting post‐surgery relapse risk of stage II and III CRC. The performance of our signatures, which included hundreds or thousands of gene pairs, was more robust for non‐research‐oriented clinical samples, compared to that of two published concise REO‐based signatures. In conclusion, REO‐based signatures with relatively more gene pairs could be robustly applied to non‐research‐oriented CRC samples.
- Published
- 2021