Software for genomic and methylation-specific MLPA probe design

用于基因组和甲基化特异性 MLPA 探针设计的软件

• 批准号: 7706242
• 负责人: Jizu Zhi
• 金额: $ 3.9万
• 依托单位: STATE UNIVERSITY NEW YORK STONY BROOK
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-17 至 2010-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7706242
• 关键词: Aberrant DNA Methylation; Acids; Area; Biological Assay; Clinical Research; Computer software; Copy Number Polymorphism; DNA Methylation; Detection; Generations; Genomics; Goals; Human; Ligation; Methods; Methylation; Mus; Nucleotides; Online Systems; Process; Publishing; Rattus; Reaction; Research; Techniques; Time; computerized tools; design; human disease; public health relevance; software development; tool

DESCRIPTION (provided by applicant): MLPA (multiplex ligation-dependent probe amplification) and MS-MLPA (methylation- specific MLPA) have rapidly evolved as promising methods for copy number variation and DNA methylation studies. The goal of this proposal is to continue the development of software for genomic and methylation-specific MLPA probe design. We have developed H-MAPD, a web based probe design tool that automates the generation and selection of probes for human genomic MLPA. We propose to expand the software in two ways: 1) To extend H-MAPD to support mouse and rat genomic MLPA probe design. 2) To develop a separate tool to handle MS-MLPA probe design. One major obstacle for MLPA and MS-MLPA is the difficulty in probe design. By automating the tedious probe design process, our software will become a valuable tool in the implementation of MLPA and MS-MLPA. PUBLIC HEALTH RELEVANCE: An increasing number of human diseases are now known to be associated with copy number variation and/or aberrant DNA methylation. The proposed software provides a computational tool that will facilitate research in these two areas.

描述(申请人提供)：MLPA(多重连接依赖的探针扩增)和MS-MLPA(甲基化特异的MLPA)已迅速发展成为拷贝数变异和DNA甲基化研究的有前途的方法。这项提议的目标是继续开发用于基因组和甲基化特异性MLPA探针设计的软件。我们已经开发了H-MAPD，这是一个基于网络的探针设计工具，可以自动生成和选择人类基因组MLPA的探针。我们建议从两个方面对软件进行扩展：1)扩展H-MAPD以支持小鼠和大鼠基因组MLPA探针的设计。2)开发单独的工具来处理MS-MLPA探针设计。MLPA和MS-MLPA的一个主要障碍是探针设计的困难。通过自动化繁琐的探头设计过程，我们的软件将成为实施MLPA和MS-MLPA的有价值的工具。 公共卫生相关性：现在已知，越来越多的人类疾病与拷贝数变异和/或异常的DNA甲基化有关。拟议的软件提供了一个计算工具，将促进这两个领域的研究。

项目成果

2-(2-Meth-oxy-phen-oxy)pyrazine.

2-（2-氧化氧基 - 氧基）吡嗪。

• DOI: 10.1107/s1600536811044321
• 发表时间: 2011-11
• 期刊: Acta crystallographica. Section E, Structure reports online
• 作者: Nasir SB;Fairuz ZA;Abdullah Z;Ng SW;Tiekink ER
• 通讯作者: Tiekink ER

MAPD: a probe design suite for multiplex ligation-dependent probe amplification assays.

MAPD：用于多重连接依赖性探针扩增测定的探针设计套件。

• DOI: 10.1186/1756-0500-3-137
• 发表时间: 2010
• 期刊: BMC research notes
• 影响因子: 1.8
• 作者: Zhi,Jizu