J Cancer 2020; 11(1):16-24. doi:10.7150/jca.33316

Research Paper

The study on copy number alteration of clear cell renal cancer in Chinese population

Ning Zhang1*, Siteng Chen2*, Guangliang Jiang1, Yishuo Wu3, Jialiang Shao2, Wennuan Liu4, Xiang Wang2✉, Rong Na1✉, Jianfeng Xu3,4

1. Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
2. Department of Urology, Shanghai Gerneral Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
3. Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
4. Program for Personalized Cancer Care, Northshore University HealthSystem, Chicago, IL 60201, USA
*Equal contributors and co-first authors

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Citation:
Zhang N, Chen S, Jiang G, Wu Y, Shao J, Liu W, Wang X, Na R, Xu J. The study on copy number alteration of clear cell renal cancer in Chinese population. J Cancer 2020; 11(1):16-24. doi:10.7150/jca.33316. Available from http://www.jcancer.org/v11p0016.htm

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Abstract

Objectives: Copy number alteration (CNA) is one of the important genetic variations. Although there are many studies on renal cancer CNA, few studies are based on the Chinese population. In our study, our objective is to acquire the whole-genome CNA landscape in Chinese population and explore the tumor risk-associated functional genes in the CNA regions, by detecting whole-genome in the clear cell renal cancer (ccRCC) tissues.

Methods: We enrolled 35 formalin fixed paraffin embedded samples, which were processed by Oncoscan assay, and then acquired the data of whole-genome CNA. Then genes annotation and enrichment analyzing were processed. Furthermore, the gene burden and the affected bp (base pair) per Mbp (million bp) regions in whole-genome were analyzed by comparison of different T stage affected by CNA.

Results: We acquired the whole-genome CNA landscape by Oncoscan detection, and found out the high-frequency CNA regions which were not reported in previous studies, for example, 11P11, 22q11.23, 20q11.3 (PDRG1), and Xp22.33 so on. During the analyzing of genes annotation and enrichment, we found out some ccRCC functional genes in the CNA regions which might play a role in the biological process, for example, the copy number loss of DNA repair genes (TTC5、PARP2, etc.) and tumor suppressor genes (TADA3, VHL, BAP1, ERC2-IT1, etc.), the copy number gain of oncogenes (ABL2, MET, HUWE1, etc.) and Notch signal pathway genes (MDK, etc.). Besides, gene fusion (GSTTP and GSTTP2) was noticed at 22q11.23 which copy number loss occurred, and the frequency is 46%. And between the different T stage patients affected by CNA, the T2+T3 group carried more high-frequency CNA regions (P-value was 0.012).

Conclusions: In this study, the whole-genome ccRCC CNA landscape in Chinese population was acquired, a few functional genes and fusion genes were found out. However, a larger scale of samples is still needed to validate our results.

Keywords: ccRCC, copy number alteration, Oncoscan, enrichment, gene burden, Chinese