Core C: Bioinformatics

项目总结/ABSTACT 生物信息学核心将提供对孢子中许多项目至关重要的服务 前列腺癌，包括统计和计算技术的应用和发展 处理来自各种应用程序的下一代测序数据。核心可以应用标准 处理算法和流水线要处理大量的样本。此外，该核心的人员 拥有根据孢子的需要创建和部署定制方法和应用程序的专业知识 研究人员。核心成员可以利用他们在处理大量基因组方面的经验 数据在纪念斯隆·凯特琳癌症中心(MSKCC)为孢子项目提供最先进的- 应用程序，只需很少的开发时间或工作量；因此，大大减少了 单个项目开发自己的分析管道。生物信息学核心的具体目标是： 目标1.开发和提供最先进的基因组分析管道，用于： ·靶向DNA分析中变异的检测，MSK-IMPACT(综合突变分析 可操作的癌症靶点)和完整外显子序列(WES)。这条管道将同时检测两个 体细胞和生殖系变异叫声的核苷酸变化和小插入缺失 场景。 ·DNA拷贝数分析，可测量总拷贝数变化和特定等位基因 拷贝数，包括杂合性丢失(LOH)。 目标2：促进共享孢子研究项目产生的数据，并使 通过MSKCC cBioPortal收集、格式化和导入由以下各项生成的数据进行集成分析 将研究项目添加到cBio门户网站。

PROJECT SUMMARY/ABSTACT The Bioinformatics Core will provide services that are vital to many of the projects with in the SPORE in Prostate Cancer, including the application and development of statistical and computational techniques to process next-generation sequencing data from a variety of applications. The Core can apply standard processing algorithms and pipelines to a large number of samples. Additionally, the personnel of this Core have the expertise to create and deploy custom methods and applications as needed by the SPORE researchers. Members of the Core can leverage their experience in processing the large amount of genomic data at Memorial Sloan Kettering Cancer Center (MSKCC) to provide SPORE projects with state-of-the-art- applications with very little development time or effort; thus, greatly reducing the time and cost required for individual projects to develop their own analysis pipelines. The specific aims of the Bioinformatics Core are: Aim 1. To develop and provide state-of-the-art genomic analysis pipelines for: • the detection of variants in targeted-DNA assays, MSK-IMPACT (Integrated Mutation Profiling of Actionable Cancer Targets) and whole exome sequence (WES). This pipeline will detect both single nucleotide changes and small insertion deletions for both somatic- and germline-variant calling scenarios. • DNA copy number analysis, which can measure both total copy number changes and allele-specific copy number, including loss of heterozygosity (LOH). Aim 2: To facilitate the sharing of data generated in the SPORE research projects and enable collaboration of integrative analysis via the MSKCC cBioPortal by collecting, formatting, and importing data generated by these research projects into the cBioPortal.