Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei, 10055, Taiwan.
Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, 10055, Taiwan.
BMC Bioinformatics. 2021 Jun 28;22(1):350. doi: 10.1186/s12859-021-04243-z.
An individual's genetics play a role in how RNA transcripts are generated from DNA and consequently in their translation into protein. Transcriptional and translational profiling of patients furnishes the information that a specific marker is present; however, it fails to provide evidence whether the marker correlates with response to a therapeutic agent. A comparative analysis of the frequency of genetic variants, such as single nucleotide polymorphisms (SNPs), in diseased and general populations can identify pathogenic variants in individual patients. This is in part because SNPs have considerable effects on protein function and gene expression when they occur in coding regions and regulatory sequences, respectively. Therefore, a tool that can help users to obtain the allele frequency for a corresponding transcript is the need of the day. Several annotation tools such as SNPnexus and VariED are publicly available; however, none of them can use transcript IDs as input and provide the corresponding genomic positions of variants.
In this study, we developed an R package, called transcript annotation tool (TransAT), that provides (i) SNP ID and genomic position for a user-provided transcript ID from patients, and (ii) allele frequencies for the SNPs from publicly available global populations. All data elements are extracted, collected, and displayed in an easily downloadable format in two simple command lines. TransAT is available on Windows/Linux/MacOS and is operative for R version 4.0.4 or later. It is available at https://github.com/ShihChingYu/TransAT and can be downloaded and installed using devtools::install_github("ShihChingYu/TransAT", force=T) on the R execution page. Thereafter, all functions can be executed by loading the package into R with library(TransAT).
TransAT is a novel tool that seamlessly provides genetic annotations for queried transcripts. Such easily obtainable information would be greatly advantageous for physicians, assisting them to make individualized decisions about specific drug treatments. Moreover, allele frequencies from user-chosen global ethnic populations will highlight the importance of ethnicity and its effect on patient pathogenicity.
个体的遗传因素在 RNA 转录本从 DNA 生成以及随后翻译成蛋白质的过程中起着重要作用。对患者进行转录和翻译分析可以提供特定标志物存在的信息；然而，它无法提供标志物是否与治疗药物反应相关的证据。对疾病人群和普通人群中遗传变异（如单核苷酸多态性[SNP]）的频率进行比较分析，可以在个体患者中识别致病性变异。这在一定程度上是因为 SNP 在编码区和调控序列中分别对蛋白质功能和基因表达有很大影响。因此，有一种能够帮助用户获得相应转录本等位基因频率的工具是当务之急。有几个注释工具，如 SNPnexus 和 VariED，是公开可用的；然而，它们都不能将转录本 ID 作为输入，并提供变异的相应基因组位置。
在这项研究中，我们开发了一个名为转录本注释工具（TransAT）的 R 包，它提供了（i）从患者提供的转录本 ID 获得的 SNP ID 和基因组位置，以及（ii）来自公开的全球人群的 SNP 的等位基因频率。所有数据元素都是通过两行简单的命令以可下载的格式提取、收集和显示。TransAT 可在 Windows/Linux/MacOS 上运行，适用于 R 版本 4.0.4 或更高版本。它可以在 https://github.com/ShihChingYu/TransAT 上找到，并可以在 R 执行页面上使用 devtools::install_github("ShihChingYu/TransAT", force=T)进行下载和安装。此后，可以通过在 R 中加载包并用 library(TransAT)来执行所有函数。
TransAT 是一种新颖的工具，可以为查询的转录本提供无缝的遗传注释。这种易于获取的信息将对医生非常有利，帮助他们针对特定药物治疗做出个体化决策。此外，来自用户选择的全球种族群体的等位基因频率将突出种族的重要性及其对患者致病性的影响。
