使用二代测序的扩展RAS和BRAF突变分析

数据集获取（Figshare）

• 源站标题：Extended <i>RAS</i> and <i>BRAF</i> Mutation Analysis Using Next-Generation Sequencing
• DOI：10.1371/journal.pone.0121891
• 发布日期：2015-05-08
• 文件数：6 个
• 文件总体积：8.29 MB
• 源站页面：https://plos.figshare.com/articles/dataset/Extended_i_RAS_i_and_i_BRAF_i_Mutation_Analysis_Using_Next_Generation_Sequencing/2667127

命令行下载

curl -L -o "S1 Fig.tif" "https://ndownloader.figshare.com/files/4329454"
curl -L -o "S2 Fig.tif" "https://ndownloader.figshare.com/files/4329457"
curl -L -o "S1 Table.xlsx" "https://ndownloader.figshare.com/files/4329466"
curl -L -o "S2 Table.xlsx" "https://ndownloader.figshare.com/files/4329472"
curl -L -o "S3 Table.xlsx" "https://ndownloader.figshare.com/files/4329475"
curl -L -o "S4 Table.xlsx" "https://ndownloader.figshare.com/files/4329481"

文件清单

• S1 Fig.tif（3.28 MB）
• S2 Fig.tif（4.97 MB）
• S1 Table.xlsx（9.95 KB）
• S2 Table.xlsx（10.88 KB）
• S3 Table.xlsx（10.38 KB）
• S4 Table.xlsx（13.11 KB）

文件总体积 8.29 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

Somatic mutations in KRAS, NRAS, and BRAF genes are related to resistance to anti-EGFR antibodies in colorectal cancer. We have established an extended RAS and BRAF mutation assay using a next-generation sequencer to analyze these mutations. Multiplexed deep sequencing was performed to detect somatic mutations within KRAS, NRAS, and BRAF, including minor mutated components. We first validated the technical performance of the multiplexed deep sequencing using 10 normal DNA and 20 formalin-fixed, paraffin-embedded (FFPE) tumor samples. To demonstrate the potential clinical utility of our assay, we profiled 100 FFPE tumor samples and 15 plasma samples obtained from colorectal cancer patients. We used a variant calling approach based on a Poisson distribution. The distribution of the mutation-positive population was hypothesized to follow a Poisson distribution, and a mutation-positive status was defined as a value greater than the significance level of the error rate (α = 2 x 10-5). The cut-off value was determined to be the average error rate plus 7 standard deviations. Mutation analysis of 100 clinical FFPE tumor specimens was performed without any invalid cases. Mutations were detected at a frequency of 59% (59/100). KRAS mutation concordance between this assay and Scorpion-ARMS was 92% (92/100). DNA obtained from 15 plasma samples was also analyzed. KRAS and BRAF mutations were identified in both the plasma and tissue samples of 6 patients. The genetic screening assay using next-generation sequencer was validated for the detection of clinically relevant RAS and BRAF mutations using FFPE and liquid samples.

许可

CC BY 4.0

引用

学术使用请引用 DOI 10.1371/journal.pone.0121891（source: https://plos.figshare.com/articles/dataset/Extended_i_RAS_i_and_i_BRAF_i_Mutation_Analysis_Using_Next_Generation_Sequencing/2667127）。