癌症易感基因致病突变：300例全基因组测序与终生电子健康记录患者调查

数据集获取（Figshare）

• 源站标题：Pathogenic Mutations in Cancer-Predisposing Genes: A Survey of 300 Patients with Whole-Genome Sequencing and Lifetime Electronic Health Records
• DOI：10.1371/journal.pone.0167847
• 发布日期：2016-12-08
• 文件数：2 个
• 文件总体积：169.98 KB
• 源站页面：https://plos.figshare.com/articles/dataset/Pathogenic_Mutations_in_Cancer-Predisposing_Genes_A_Survey_of_300_Patients_with_Whole-Genome_Sequencing_and_Lifetime_Electronic_Health_Records/4298195

命令行下载

curl -L -o "S1 Table.xls" "https://ndownloader.figshare.com/files/7014212"
curl -L -o "S2 Table.xls" "https://ndownloader.figshare.com/files/7014221"

文件清单

• S1 Table.xls（74.24 KB）
• S2 Table.xls（95.74 KB）

文件总体积 169.98 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

Background
It is unclear whether and how whole-genome sequencing (WGS) data can be used to implement genomic medicine. Our objective is to retrospectively evaluate whether WGS can facilitate improving prevention and care for patients with susceptibility to cancer syndromes.
Methods and Findings
We analyzed genetic mutations in 60 autosomal dominant cancer-predisposition genes in 300 deceased patients with WGS data and nearly complete long-term (over 30 years) medical records. To infer biological insights from massive amounts of WGS data and comprehensive clinical data in a short period of time, we developed an in-house analysis pipeline within the SeqHBase software framework to quickly identify pathogenic or likely pathogenic variants. The clinical data of the patients who carried pathogenic and/or likely pathogenic variants were further reviewed to assess their clinical conditions using their lifetime EHRs. Among the 300 participants, 5 (1.7%) carried pathogenic or likely pathogenic variants in 5 cancer-predisposing genes: one in APC, BRCA1, BRCA2, NF1, and TP53 each. When assessing the clinical data, each of the 5 patients had one or more different types of cancers, fully consistent with their genetic profiles. Among these 5 patients, 2 died due to cancer while the others had multiple disorders later in their lifetimes; however, they may have benefited from early diagnosis and treatment for healthier lives, had the patients had genetic testing in their earlier lifetimes.
Conclusions
We demonstrated a case study where the discovery of pathogenic or likely pathogenic germline mutations from population-wide WGS correlates with clinical outcome. The use of WGS may have clinical impacts to improve healthcare delivery.

许可

CC BY 4.0

引用

学术使用请引用 DOI 10.1371/journal.pone.0167847（source: https://plos.figshare.com/articles/dataset/Pathogenic_Mutations_in_Cancer-Predisposing_Genes_A_Survey_of_300_Patients_with_Whole-Genome_Sequencing_and_Lifetime_Electronic_Health_Records/4298195）。