用于分析的数据集

数据集获取（Figshare）

• 源站标题：Data set used for analysis.
• DOI：10.1371/journal.pone.0298128.s005
• 发布日期：2024-03-25
• 文件数：1 个
• 文件总体积：11.39 KB
• 源站页面：https://plos.figshare.com/articles/dataset/Data_set_used_for_analysis_/25473378

命令行下载

curl -L -o "pone.0298128.s005.csv" "https://ndownloader.figshare.com/files/45263952"

文件清单

• pone.0298128.s005.csv（11.39 KB）

文件总体积 11.39 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

Objective
Poly(ADP-ribose) polymerase (PARP) inhibitors are used for targeted therapy for ovarian cancer with homologous recombination deficiency (HRD). In this study, we aimed to develop a homologous recombination deficiency prediction model to predict the genomic integrity (GI) index of the SOPHiA DDM HRD Solution from the Oncomine Comprehensive Assay (OCA) Plus. We also tried to a find cut-off value of the genomic instability metric (GIM) of the OCA Plus that correlates with the GI index of the SOPHiA DDM HRD Solution.
Methods
We included 87 cases with high-grade ovarian serous carcinoma from five tertiary referral hospitals in Republic of Korea. We developed an HRD prediction model to predict the GI index of the SOPHiA DDM HRD Solution. As predictor variables in the model, we used the HRD score, which included percent loss of heterozygosity (%LOH), percent telomeric allelic imbalance (%TAI), percent large-scale state transitions (%LST), and the genomic instability metric (GIM). To build the model, we employed a penalized logistic regression technique.
Results
The final model equation is -21.77 + 0.200 × GIM + 0.102 × %LOH + 0.037 × %TAI + 0.261 × %LST. To improve the performance of the prediction model, we added a borderline result category to the GI results. The accuracy of our HRD status prediction model was 0.958 for the test set. The accuracy of HRD status using GIM with a cut-off value of 16 was 0.911.
Conclusion
The Oncomine Comprehensive Assay Plus provides a reliable biomarker for homologous recombination deficiency.

许可

CC BY 4.0

引用

学术使用请引用 DOI 10.1371/journal.pone.0298128.s005（source: https://plos.figshare.com/articles/dataset/Data_set_used_for_analysis_/25473378）。