Copy number variants landscape of multiple cancers and clinical applications based on NGS gene panel

Yan, Kangpeng1; Niu, Li2; Wu, Boyu3; He, Chongwu4; Deng, Lei5; Chen, Chuan6; Lan, Zhangzhang7; Lin, Chao1; Kuang, Weihua1; Lin, Huihong8; Zou, Jun1; Zhang, Wenyong7; Luo, Zhiqiang9

2023-12-12

10.1080/07853890.2023.2280708

ANNALS OF MEDICINE   影响因子和分区

0785-3890

1365-2060

Background The rapid adoption of next-generation sequencing in clinical oncology has enabled detection of molecular biomarkers which are shared between multiple tumour types. Intra-tumour heterogeneity is a mechanism of therapeutic resistance and therefore an important clinical challenge. However, the tumour-related copy number variants (CNVs), as key regulators of cancer origination, development, and progression, across various types of cancers are poorly understood.Methods We performed pan-cancer CNV analysis of cancer-related genes in 15 types of cancers including 1438 cancerous patients by next-generation sequencing using a commercially available pan-cancer panel (Onco PanScan (TM)). Downstream bioinformatics analysis was performed in order to detect CNVs, cluster analysis of the found CNVs, and comparison of the frequency of gained CNVs between different types of cancers. LASSO analysis was used for identification of the most important CNVs.Results We also identified 523 CNVs among which 16 CNVs were common while 22 CNVs were caner-specific CNVs. Meanwhile, FAM58A was most commonly found in all studied cancers in this study and significant differences were found in FAM58A between female and male patients (p = .001). Common CNVs, such as FOXA1, NFKBIA, HEY1, MECOM, CHD7, AGO2, were mutated in 6.79%, 8.45%, 7.51%, 6.43%, 7.59%, 8.16% of tumours, while most of these mutations have proven roles in positive regulation of transcription from RNA polymerase II promoter. 11 features including sex, DIS3, EPHB1, ERBB2, FLT1, HCK, KEAP1, MYD88, PARP3, TBX3, and TOP2A were found as the key features for classification of cancers using CNVs.Conclusion The 16 common CNVs between cancers can be used to identify the target of pan-cancer drug design and targeted therapies. Additionally, 22 caner-specific CNVs can be used as unique diagnostic markers for each cancer type.

Pan-cancer copy number variants GO and KEGG analysis cluster analysis

SCI

英语

通讯

General & Internal Medicine

Medicine, General & Internal

WOS:001102695900001

TAYLOR & FRANCIS LTD

CLINICAL MEDICINE

Web of Science

1.Jiangxi Canc Hosp, Dept Abdominal Surg, Nanchang, Peoples R China
2.Peking Univ, CheerLand Clin Lab Co Ltd, Med Ind Pk,Zhongguancun Life Sci Pk, Beijing, Peoples R China
3.Shangrao Municipal Hosp, Dept Gen Surg, Shangrao, Peoples R China
4.Jiangxi Canc Hosp, Dept Breast Surg, Nanchang, Peoples R China
5.Jiangxi Canc Hosp, Dept Med Oncol, Nanchang, Peoples R China
6.Shenzhen Cheerland Biotechnol Co Ltd, Shenzhen, Peoples R China
7.Southern Univ Sci & Technol, Sch Med, 1088 Xueyuan Rd, Shenzhen 518055, Guangdong, Peoples R China
8.Jiangxi Canc Hosp, Operating Room, Nanchang, Peoples R China
9.Jiangxi Canc Hosp, Chest Radiotherapy Dept 1, 519 Beijing East Rd, Nanchang 330029, Peoples R China

Yan, Kangpeng,Niu, Li,Wu, Boyu,et al. Copy number variants landscape of multiple cancers and clinical applications based on NGS gene panel[J]. ANNALS OF MEDICINE,2023,55(2).

Yan, Kangpeng.,Niu, Li.,Wu, Boyu.,He, Chongwu.,Deng, Lei.,...&Luo, Zhiqiang.(2023).Copy number variants landscape of multiple cancers and clinical applications based on NGS gene panel.ANNALS OF MEDICINE,55(2).

Yan, Kangpeng,et al."Copy number variants landscape of multiple cancers and clinical applications based on NGS gene panel".ANNALS OF MEDICINE 55.2(2023).