Mega 2: Manipulation Environment for Genetic Analyses

描述（由申请人提供）：Mega2，遗传分析操作环境，是一个独特的计算机程序，用于从作为遗传研究的一部分收集的数据中促进创建分析就绪数据集。Mega2透明地允许用户准确有效地处理基于家庭或病例/对照研究的遗传数据。除了数据验证检查外，Mega2还为广泛选择的常用遗传分析程序提供了分析设置功能。它在全球遗传学研究界发挥了重要作用。在此提案下，我们计划使Mega2成为一个功能强大的开源应用程序，具有高度增强的功能，同时应用软件工程中的最佳实践来满足开源项目的这些关键需求：跨操作系统平台的可移植性，随着遗传学研究的需要而发展的能力，广泛的文档，最大化代码重用，以及系统的测试，调试和维护。具体来说，我们计划显著改进Mega2的可用性、数据输入处理能力、建立目标分析的能力，以及数据统计、诊断和结果的图形表示和存储。我们还将开发一个应用程序编程接口，并改进文档和教程。Mega2已被用于加速一系列复杂人类疾病的基因发现研究。改善这一关键资源将对加速基因发现过程产生重大影响，从而减轻美国和世界范围内复杂遗传疾病造成的医疗负担。相关性：Mega2用于复杂人类疾病遗传学的许多不同研究，使研究人员能够快速更改文件格式并准备文件进行统计分析，并透明地准确有效地处理遗传数据。因此，Mega2已经并将继续显著加速绘制和鉴定复杂人类疾病的易感基因位点。

DESCRIPTION (provided by applicant): Mega2, the Manipulation Environment for Genetic Analysis, is a unique computer program for facilitating the creation of analysis-ready datasets from data gathered as part of a genetic study. Mega2 transparently allows users to process genetic data for family-based or case/control studies accurately and efficiently. In addition to data validation checks, Mega2 provides analysis setup capabilities for a broad choice of commonly-used genetic analysis programs. It has served an important role in the genetics research community worldwide. Under this proposal, we plan to make Mega2 a powerful open-source application with highly enhanced capabilities, while applying best practices in software engineering to meet these critical needs of an open-source project: portability across OS platforms, ability to evolve with the needs of genetics research, extensive documentation, maximizing code reuse, as well as systematic testing, debugging and maintenance. Specifically, we plan to significantly improve Mega2's usability, data input handling capabilities, its abilities to set up target analyses, and its graphical presentation and storage of data statistics, diagnostics, and results. We will also develop an Application Programming Interface and improved documentation and tutorials. Mega2 has been used to accelerate gene discovery studies for a large list of complex human diseases. Improving this crucial resource will have a significant impact on speeding up the gene-discovery process, which in turn will ease the healthcare burden due to complex genetic disease in the US and world-wide. Relevance: Mega2 is used in many different studies of the genetics of complex human diseases, enabling researchers to swiftly change file formats and prepare files for statistical analysis and transparently processing genetic data accurately and efficiently. As such, Mega2 has and will continue to markedly accelerate the mapping and identification of susceptibility loci for complex human diseases.