The Cancer Genome Anatomy Project's Genetic Annotation I

作为美国国家癌症研究所癌症基因组解剖项目（CGAP）的一部分，遗传注释倡议（GAI）旨在扩大癌症研究中基于基因的遗传分析试剂的收集。 我们已经确定了超过30，000个高概率的候选单核苷酸多态性（SNP），通过分析公开可用的表达序列标签色谱与一套序列分析工具。这种方法也被应用于识别小鼠中超过16，000个候选SNP。使用来自92个无关个体的合并DNA和MALDI-TOF质谱，我们已经验证了7,000多个人类SNP。 为了以对人类遗传学界有用的格式呈现遗传变异，我们构建了整合的遗传/物理SNP图谱。参考标记的遗传图谱位置来自CHLC/ABI第1版连锁图谱;物理图谱位置来自GeneMap'98 Genebridge 4辐射杂交图谱。这些图的组织特异性和癌症特异性视图也可用。这些图谱允许选择具有特定表达模式的基因的SNP。 通过相关的CGAP基础设施，还可以在其他生物学相关背景下查看SNP数据。基因本体浏览器使用户能够通过生物过程、细胞成分或分子功能来识别基因。CGAP的其他工具可以使生物化学途径可视化。 我们已经将我们的SNP发现工作与其他工作者的工作相结合，以全面了解基于基因的SNP。我们提供了一个浏览器，它显示了mRNA序列中多态性的位置，并指出变异是否会导致氨基酸取代。Pfam数据库中的编码区和保守蛋白质基序也显示在浏览器中。如果SNP改变了保守蛋白质结构域中的氨基酸，我们评估氨基酸取代如何影响蛋白质与基序模型的拟合。 整合的地图，一个基于Java的工具，用于查看候选SNP的背景下，EST组件，试剂信息（包括PCR引物和延伸引物），和SNP搜索引擎可在我们的网站：http://lpgws.nci.nih.gov/GAI/。我们提供非商业用途的SNP检测软件。

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.