Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping
Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping
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DOI：
10.1186/1471-2105-7-383
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发表时间：
2006-08-17
影响因子：
3
通讯作者：
Hoisington, David A.
中科院分区：
文献类型：
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作者：
Jayashree, B.;Reddy, Praveen T.;Hoisington, David A.
背景：随着DNA测序技术的进步，自动化基因分型过程的几个步骤已经成为可能，从而提高了通量。为了有效地处理产生的大量基因型数据并帮助进行质量控制，强烈需要一个软件系统来帮助跟踪样本，并在过程的不同步骤中捕获和管理数据。这样的系统，在服务于精确管理工作流程的同时，也通过标准化的协议，记录和注释工作流程每一步的数据，鼓励良好的实验室实践。结果：国际半干旱热带作物研究所（ICRISAT）设计并实施了一个实验室信息管理系统（LIMS），该系统满足中等高通量分子基因分型设施的要求。该应用程序被设计成模块，易于学习和使用。该应用程序引导用户完成从开始实验到存储从基因型检测步骤输出数据的过程的每个步骤，并自动启动等位基因；从而确保每个DNA样本都以相同的方式处理，并捕获所有必要的数据。该应用程序跟踪DNA样本和生成的数据。数据输入系统是通过使用表格进行文件上传。LIMS提供的功能可以追溯到电泳凝胶文件或样品来源的任何基因型数据和重复实验。LIMS目前用于获取半干旱热带地区重要的豆类（鹰嘴豆、花生和鸽豆）和谷物（高粱和小米）作物的高通量SSR（简单序列重复）基因分型数据。结论：实验室信息管理系统可用于中等高通量基因分型实验室的微卫星基因分型数据管理。该应用程序的源代码对学术用户免费提供，可以从http:// www.icrisat.org/gt-bt/lims/lims.asp下载。
Background: With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow.Results: A laboratory information management system (LIMS) has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat) genotyping data from the legume (chickpea, groundnut and pigeonpea) and cereal (sorghum and millets) crops of importance in the semi-arid tropics.Conclusion: A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping laboratory. The application with source code is freely available for academic users and can be downloaded from http:// www.icrisat.org/gt-bt/lims/lims.asp.