使用SNP微阵列进行结直肠癌细胞遗传学改变的全基因组研究：未来个性化治疗的机会

数据集获取（Figshare）

• 源站标题：A Genome-Wide Study of Cytogenetic Changes in Colorectal Cancer Using SNP Microarrays: Opportunities for Future Personalized Treatment
• DOI：10.1371/journal.pone.0031968
• 发布日期：2012-02-20
• 文件数：10 个
• 文件总体积：802.51 KB
• 源站页面：https://plos.figshare.com/articles/dataset/A_Genome_Wide_Study_of_Cytogenetic_Changes_in_Colorectal_Cancer_Using_SNP_Microarrays_Opportunities_for_Future_Personalized_Treatment/128534

命令行下载

curl -L -o "Figure_S1.tif" "https://ndownloader.figshare.com/files/346672"
curl -L -o "Table_S1.csv" "https://ndownloader.figshare.com/files/346708"
curl -L -o "Table_S2.csv" "https://ndownloader.figshare.com/files/346725"
curl -L -o "Table_S3.csv" "https://ndownloader.figshare.com/files/346756"
curl -L -o "Table_S4.csv" "https://ndownloader.figshare.com/files/346772"
curl -L -o "Table_S5.csv" "https://ndownloader.figshare.com/files/346799"
curl -L -o "Table_S6.csv" "https://ndownloader.figshare.com/files/346820"
curl -L -o "Table_S7.csv" "https://ndownloader.figshare.com/files/346855"

文件清单

• Figure_S1.tif（309.38 KB）
• Table_S1.csv（31.86 KB）
• Table_S2.csv（3.73 KB）
• Table_S3.csv（4.07 KB）
• Table_S4.csv（1.97 KB）
• Table_S5.csv（38.93 KB）
• Table_S6.csv（15.38 KB）
• Table_S7.csv（12.03 KB）
• Table_S8.csv（222.20 KB）
• Table_S9.csv（162.97 KB）

文件总体积 802.51 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

In colorectal cancer (CRC), chromosomal instability (CIN) is typically studied using comparative-genomic hybridization (CGH) arrays. We studied paired (tumor and surrounding healthy) fresh frozen tissue from 86 CRC patients using Illumina’'s Infinium-based SNP array. This method allowed us to study CIN in CRC, with simultaneous analysis of copy number (CN) and B-allele frequency (BAF) - a representation of allelic composition. These data helped us to detect mono-allelic and bi-allelic amplifications/deletion, copy neutral loss of heterozygosity, and levels of mosaicism for mixed cell populations, some of which can not be assessed with other methods that do not measure BAF. We identified associations between CN abnormalities and different CRC phenotypes (histological diagnosis, location, tumor grade, stage, MSI and presence of lymph node metastasis). We showed commonalities between regions of CN change observed in CRC and the regions reported in previous studies of other solid cancers (e.g. amplifications of 20q, 13q, 8q, 5p and deletions of 18q, 17p and 8p). From Therapeutic Target Database, we identified relevant drugs, targeted to the genes located in these regions with CN changes, approved or in trials for other cancers and common diseases. These drugs may be considered for future therapeutic trials in CRC, based on personalized cytogenetic diagnosis. We also found many regions, harboring genes, which are not currently targeted by any relevant drugs that may be considered for future drug discovery studies. Our study shows the application of high density SNP arrays for cytogenetic study in CRC and its potential utility for personalized treatment.

许可

CC BY 4.0

引用

学术使用请引用 DOI 10.1371/journal.pone.0031968（source: https://plos.figshare.com/articles/dataset/A_Genome_Wide_Study_of_Cytogenetic_Changes_in_Colorectal_Cancer_Using_SNP_Microarrays_Opportunities_for_Future_Personalized_Treatment/128534）。