SNP discovery

单核苷酸多态性（snp）是通过关联分析检测易感基因的有力遗传标记。snp频繁出现，在基因组序列中平均每1000个碱基对出现一次。这使得它们特别有用，因为有几个会出现在任何给定的基因内或非常接近，而关联分析在短距离内最有效。公共数据库中大量的序列数据将极大地促进snp的高效检测。我们将利用几种创新的方法来发现SNP并在复杂疾病中使用。首先，我们将开发和应用集成基因注释系统来跟踪基因注释和SNP信息。我们将首先使用基因序列或ESTs从公共数据库中恢复相应的基因组序列。这些序列将被注释，以帮助识别区域，以寻找snp。一些snp将通过查询NCBI的ddSNP数据库直接识别。其他潜在的snp将通过对已在公共领域的冗余EST序列进行比对来确定。可疑的snp将通过自然高效液相色谱（HPLC）和序列分析进行确认。对于少于10个序列的候选基因，我们将使用现有的序列信息来设计引物，用于从个体池中扩增多个PCR产物。这些池将以这样一种方式构建，即等位基因频率低至1-3%的snp将被识别。变性高效液相色谱将用于检测可能的snp，然后将通过序列分析确认。在五年内，这些方法将使我们能够在500个候选基因中或其附近平均发现10个snp。

Single Nucleotide Polymorphisms (SNPs) are powerful genetic markers for the detection of susceptibility genes through association analysis. SNPs occur frequently, on average once every 1000 base pairs in genomic sequence. This makes them especially useful because several will be present within or very near any given gene, and association analysis is most powerful over short distances. The large amount of sequence data available in public databases will greatly facilitate the efficient detection of SNPs. We will utilize several innovative methods for SNP discovery and use in complex disease. First, we will develop and apply the Ensemble gene annotation system to track gene annotation and SNP information.. We will first use sequences from genes or ESTs to recover the corresponding genomic sequence from public databases. These sequences will be annotated to assist in the identification of regions to search for SNPs. Some SNPs will be identified directly by querying NCBI's ddSNP database. Other potential SNPs will be identified by alignment of redundant EST sequences already in the public domain. Suspected SNPs will be confirmed by naturing High Performance Liquid Chromatograph (HPLC) and sequence analysis. For candidate genes represented by fewer than 10 sequences, we will use the available sequence information to design primers for amplification of multiple PCR products from pools of individuals. These pools will be constructed in such a way that SNPs with allele frequencies as low as 1-3% will be identified. Denaturing HPLC will be used to detect possible SNPs, which will then be confirmed by sequence analysis. In five years, these methods will enable us to discover an average of 10 SNPs within or near each of 500 candidate genes.