The Cancer Genome Anatomy Project's Genetic Annotation I

癌症基因组解剖计划的基因注释 I

• 批准号: 6755580
• 负责人: Kenneth H Buetow
• 金额: --
• 依托单位: DIVISION OF CANCER EPIDEMIOLOGY AND GENETICS
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/6755580
• 关键词: analytical method; animal genetic material tag; biotechnology; cancer information system; clinical research; computer data analysis; computer human interaction; computer program /software; computer system design /evaluation; functional /structural genomics; gene expression; gene interaction; genetic mapping; genetic polymorphism; genetic susceptibility; genetic techniques; human genetic material tag; human tissue; laboratory mouse; matrix assisted laser desorption ionization; molecular biology information system; neoplasm /cancer epidemiology; neoplasm /cancer genetics; nucleic acid sequence; polymerase chain reaction; technology /technique development

As part of the National Cancer Institute's Cancer Genome Anatomy Project (CGAP), the Genetic Annotation Initiative (GAI) seeks to expand the collection of gene-based genetic analysis reagents for cancer research. We have identified more than 30,000 high-probability candidate single nucleotide polymorphisms (SNPs) by analyzing publicly available expressed sequence tag chromatograms with a set of sequence analysis tools. This approach has also been applied to identify more than 16,000 candidate SNPs in the mouse. Using pooled DNA from 92 unrelated individuals and MALDI-TOF mass spectrometry, we have validated more than 7,000 human SNPs. To present the genetic variants in a format useful for the human genetics community we have constructed an integrated genetic/physical SNP map. Genetic map positions of reference markers are from the the CHLC/ABI version 1 linkage map; physical map positions are from the GeneMap'98 Genebridge4 radiation hybrid map. Tissue-specific and cancer-specific views of these maps are also available. These maps permit the selection of SNPs for genes with specific expression patterns. Through related CGAP infrastructure it is also possible to view the SNP data in other biologically relevant contexts. The Gene Ontology browser enables users to identify genes by biological process, cellular component or molecular function. Other CGAP tools allow the visualization of biochemical pathways. We have integrated our SNP discovery efforts with those from other workers to give a comprehensive view of gene-based SNPs. We provide a browser that shows the location of polymorphisms in mRNA sequences and indicates whether variants cause amino acid substitutions. Coding regions and conserved protein motifs from the Pfam database are also displayed in the browser. If a SNP alters an amino acid in a conserved protein domain, we assess how the amino acid substitution affects the fit of the protein to the motif model. The integrated maps, a Java-based tool for viewing candidate SNPs in the context of EST assemblies, reagent information (including PCR primers and extension primers), and a SNP search engine are available at our website: http://lpgws.nci.nih.gov/GAI/. We provide access to our SNP detection software for non-commercial use.

作为国家癌症研究所癌症基因组解剖项目（CGAP）的一部分，遗传注释计划（GAI）旨在扩大基于基因的遗传分析试剂的癌症研究。 我们通过使用一组序列分析工具来分析公开表达的序列TAG色谱图，确定了30,000多个高概率候选单核苷酸多态性（SNP）。该方法还应用于识别鼠标中的16,000多个候选SNP。使用来自92个无关个体和MALDI-TOF质谱的合并DNA，我们已经验证了7,000多个人类SNP。 为了以一种对人类遗传学社区有用的格式呈现遗传变异，我们构建了综合的遗传/物理SNP图。参考标记的遗传图位置来自CHLC/ABI版本1链接图；物理图位置来自Genemap'98 Genebridge4辐射杂交图。这些地图的组织特异性和癌症特异性观点也可用。这些地图允许选择具有特定表达模式的基因的SNP。 通过相关的CGAP基础架构，也可以在其他与生物学相关的上下文中查看SNP数据。基因本体论浏览器使用户能够通过生物学过程，细胞成分或分子功能识别基因。其他CGAP工具允许可视化生化途径。 我们已经将SNP的发现工作与其他工人的人集成在一起，以全面了解基于基因的SNP。我们提供了一个浏览器，该浏览器显示了mRNA序列中多态性的位置，并指示了变体是否引起氨基酸取代。浏览器中还显示了来自PFAM数据库的编码区域和保守的蛋白质基序。如果SNP在保守的蛋白质结构域中改变氨基酸，我们评估氨基酸取代如何影响蛋白质对基序模型的拟合。 Integrated Maps是一种基于JAVA的工具，用于在EST组件的背景下查看候选SNP，试剂信息（包括PCR引物和扩展引物）和SNP搜索引擎，请访问我们的网站：http://lpgws.nci.nih.nih.gov/gai/。我们为非商业使用提供了对SNP检测软件的访问权限。