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BMC Bioinformatics, 2019. 20(Suppl 10), 245-253, DOI: https://doi.org/10.1186/s12859-019-2809-2
Conventionally used reference genes are not outstanding for normalization of gene expression in human cancer research
Jihoon Jo, Sunkyung Choi
Background: The selection of reference genes is essential for quantifying gene expression. Theoretically they shouldbe expressed stably and not regulated by experimental or pathological conditions. However, identification andvalidation of reference genes for human cancer research are still being regarded as a critical point, because canceroustissues often represent genetic instability and heterogeneity. Recent pan-cancer studies have demonstrated theimportance of the appropriate selection of reference genes for use as internal controls for the normalization of geneexpression; however, no stably expressed, consensus reference genes valid for a range of different human cancers haveyet been identified.
Results: In the present study, we used large-scale cancer gene expression datasets from The Cancer Genome Atlas(TCGA) database, which contains 10,028 (9,364 cancerous and 664 normal) samples from 32 different cancer types, toconfirm that the expression of the most commonly used reference genes is not consistent across a range of cancertypes. Furthermore, we identified 38 novel candidate reference genes for the normalization of gene expression,independent of cancer type. These genes were found to be highly expressed and highly connected to relevant genenetworks, and to be enriched in tranion-translation regulation processes. The expression stability of the newlyidentified reference genes across 29 cancerous and matched normal tissues were validated via quantitative reversetranion PCR (RT-qPCR).
Conclusions: We reveal that most commonly used reference genes in current cancer studies cannot be appropriate toserve as representative control genes for quantifying cancer-related gene expression levels, and propose in this studythree potential reference genes (HNRNPL, PCBP1, and RER1) to be the most stably expressed across various cancerousand normal human tissues.
- DOI: https://doi.org/10.1186/s12859-019-2809-2
- ISBN or ISSN: 1471-2105
- 본 연구는 질병관리본부 연구개발과제연구비를 지원받아 수행되었습니다.
- This research was supported by a fund by Research of Korea Centers for Disease Control and Prevention.