实体肿瘤46基因面板的临床适用性与成本分析

数据集获取（Figshare）

• 源站标题：Clinical applicability and cost of a 46-gene panel for genomic analysis of solid tumours: Retrospective validation and prospective audit in the UK National Health Service
• DOI：10.1371/journal.pmed.1002230
• 发布日期：2017-02-14
• 文件数：18 个
• 文件总体积：9.13 MB
• 源站页面：https://plos.figshare.com/articles/dataset/Clinical_applicability_and_cost_of_a_46-gene_panel_for_genomic_analysis_of_solid_tumours_Retrospective_validation_and_prospective_audit_in_the_UK_National_Health_Service/4650475

命令行下载

curl -L -o "S1 SQUIRE Checklist.pdf" "https://ndownloader.figshare.com/files/7589512"
curl -L -o "S1 STARD Checklist.docx" "https://ndownloader.figshare.com/files/7589539"
curl -L -o "S1 Data.xlsx" "https://ndownloader.figshare.com/files/7589578"
curl -L -o "S2 Data.xlsx" "https://ndownloader.figshare.com/files/7589602"
curl -L -o "S1 Fig.tiff" "https://ndownloader.figshare.com/files/7589638"
curl -L -o "S2 Fig.tiff" "https://ndownloader.figshare.com/files/7589686"
curl -L -o "S3 Fig.tiff" "https://ndownloader.figshare.com/files/7589713"
curl -L -o "S4 Fig.tiff" "https://ndownloader.figshare.com/files/7589746"

文件清单

• S1 SQUIRE Checklist.pdf（372.33 KB）
• S1 STARD Checklist.docx（31.61 KB）
• S1 Data.xlsx（14.57 KB）
• S2 Data.xlsx（31.59 KB）
• S1 Fig.tiff（1.43 MB）
• S2 Fig.tiff（1.62 MB）
• S3 Fig.tiff（1.80 MB）
• S4 Fig.tiff（2.13 MB）
• S5 Fig.tiff（1.40 MB）
• S1 Table.docx（16.36 KB）
• S2 Table.docx（14.76 KB）
• S3 Table.docx（36.55 KB）
• S4 Table.docx（19.93 KB）
• S5 Table.docx（18.60 KB）
• S6 Table.docx（22.75 KB）
• S7 Table.docx（22.20 KB）
• S1 Text.docx（41.22 KB）
• S2 Text.docx（121.30 KB）

文件总体积 9.13 MB（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
Single gene tests to predict whether cancers respond to specific targeted therapies are performed increasingly often. Advances in sequencing technology, collectively referred to as next generation sequencing (NGS), mean the entire cancer genome or parts of it can now be sequenced at speed with increased depth and sensitivity. However, translation of NGS into routine cancer care has been slow. Healthcare stakeholders are unclear about the clinical utility of NGS and are concerned it could be an expensive addition to cancer diagnostics, rather than an affordable alternative to single gene testing.
Methods and findings
We validated a 46-gene hotspot cancer panel assay allowing multiple gene testing from small diagnostic biopsies. From 1 January 2013 to 31 December 2013, solid tumour samples (including non-small-cell lung carcinoma [NSCLC], colorectal carcinoma, and melanoma) were sequenced in the context of the UK National Health Service from 351 consecutively submitted prospective cases for which treating clinicians thought the patient had potential to benefit from more extensive genetic analysis. Following histological assessment, tumour-rich regions of formalin-fixed paraffin-embedded (FFPE) sections underwent macrodissection, DNA extraction, NGS, and analysis using a pipeline centred on Torrent Suite software. With a median turnaround time of seven working days, an integrated clinical report was produced indicating the variants detected, including those with potential diagnostic, prognostic, therapeutic, or clinical trial entry implications. Accompanying phenotypic data were collected, and a detailed cost analysis of the panel compared with single gene testing was undertaken to assess affordability for routine patient care.
Panel sequencing was successful for 97% (342/351) of tumour samples in the prospective cohort and showed 100% concordance with known mutations (detected using cobas assays). At least one mutation was identified in 87% (296/342) of tumours. A locally actionable mutation (i.e., available targeted treatment or clinical trial) was identified in 122/351 patients (35%). Forty patients received targeted treatment, in 22/40 (55%) cases so

许可

CC BY 4.0

引用

学术使用请引用 DOI 10.1371/journal.pmed.1002230（source: https://plos.figshare.com/articles/dataset/Clinical_applicability_and_cost_of_a_46-gene_panel_for_genomic_analysis_of_solid_tumours_Retrospective_validation_and_prospective_audit_in_the_UK_National_Health_Service/4650475）。