基于NGS基因面板的多癌种拷贝数变异图谱及临床应用

数据集获取（Figshare）

• 源站标题：Copy number variants landscape of multiple cancers and clinical applications based on NGS gene panel
• DOI：10.6084/m9.figshare.24569933.v1
• 发布日期：2023-11-15
• 文件数：1 个
• 文件总体积：130.48 KB
• 源站页面：https://tandf.figshare.com/articles/dataset/Copy_number_variants_landscape_of_multiple_cancers_and_clinical_applications_based_on_NGS_gene_panel/24569933

命令行下载

curl -L -o "iann_a_2280708_sm9293.xlsx" "https://ndownloader.figshare.com/files/43157465"

文件清单

• iann_a_2280708_sm9293.xlsx（130.48 KB）

文件总体积 130.48 KB（源站 API 实测）。

数据加载示例（图像类）

from PIL import Image
import glob, os

files = (glob.glob(os.path.join(path, "**", "*.png"), recursive=True)
       + glob.glob(os.path.join(path, "**", "*.jpg"), recursive=True)
       + glob.glob(os.path.join(path, "**", "*.tif"), recursive=True))
print("图像文件数:", len(files))
img = Image.open(files[0]); print("尺寸/模式:", img.size, img.mode)

# torchvision Dataset 方式:
# from torchvision import datasets
# ds = datasets.ImageFolder(path)  # 要求 子目录=类别

目录组织与标注格式以源站说明和下载后实际文件为准。

数据说明

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.
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™). 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.
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.
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.

许可

CC BY 4.0

引用

学术使用请引用 DOI 10.6084/m9.figshare.24569933.v1（source: https://tandf.figshare.com/articles/dataset/Copy_number_variants_landscape_of_multiple_cancers_and_clinical_applications_based_on_NGS_gene_panel/24569933）。