Clone-Array Pooled Shotgun Indexing

描述（由申请人提供）：本提案的主要目标是进一步开发基因组快速物理映射的程序。克隆阵列池霰弹枪索引（CAPSI）是一种比较bac物理映射的新方法。CAPSI通过池化排列的BAC克隆，并生成shotgun序列池来实现适当的覆盖。CAPSI利用这些信息将单个bac映射到相关生物体的同源序列上。前两步，汇集BAC克隆和鸟枪测序，利用贝勒人类基因组测序中心现有的高通量方法。最后一步，将池反卷积到特定的BAC中，通过将来自池的DNA序列与相关生物体的参考基因组或cDNA序列进行比较来完成：如果来自两个不同池的两个reads在近距离上与参考序列匹配，则它们都被分配（反卷积）到两个池交叉处的BAC上，BAC被映射到两个匹配的参考序列之间的区域。本提案的具体目标是通过CAPSI将褐家鼠（Rattus Norvegicus）的2404个排列的BACs和猕猴（恒河猴）的74752个排列的BACs （4.24 X随机覆盖，假设基因组为3Gb）映射到组装的人类基因组序列上，同时开发CAPSI方法。

DESCRIPTION (provided by applicant):The main goal of this proposal is to further develop a procedure for the rapid physical mapping of genomes. Clone-Array Pooled Shotgun Indexing ("CAPSI") is a novel method for comparative physical mapping of BACs. CAPSI is carried out by pooling arrayed BAC clones, and generating shotgun sequence pools to appropriate coverage. CAPSI uses this information to map individual BACs onto homologous sequences of a related organism. The first two steps, pooling of BAC clones and shotgun sequencing, draw on existing high throughput methodology at the Baylor Human Genome Sequencing Center. The last step, deconvolution of the pools into specific BACs, is accomplished by comparison of DNA sequence reads from pools against a reference genomic or cDNA sequence of a related organism: if two reads from two different pools match the reference sequence at a close distance, they are both assigned (deconvoluted) to the BAC at the intersection of the two pools and the BAC is mapped onto the region of the reference sequence between the two matches.A specific goal of this proposal is to map 2,404 arrayed BACs of Rattus Norvegicus and 74,752 arrayed BACs of Macaque Mulatta (Rhesus Macaque) (4.24 X random coverage assuming 3Gb genome) onto assembled Human genomic sequence via CAPSI while concurrently developing the CAPSI method.