Tools for detecting biologically important sequence variation in cancer

用于检测癌症中具有重要生物学意义的序列变异的工具

• 批准号: 8113745
• 负责人: Rachel Karchin
• 金额: $ 26.97万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-16 至 2013-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8113745
• 关键词: Algorithms; Animal Model; Antineoplastic Agents; Architecture; Atlases; Binding; Biochemical; Bioinformatics; Biological; Biological Assay; Biometry; Cancer Center; Cell Line; Cell model; Cell physiology; Classification; Code; Codon Nucleotides; Collaborations; Common Data Element; Communities; DNA Resequencing; Data; Databases; Detection; Development; Diagnosis; Disease; Drug Delivery Systems; Exons; Foundations; Funding; Future; Genes; Genetic Variation; Genomics; Goals; Grant; Human; Imagery; Individual; Investigation; Knowledge; Letters; Link; Malignant Neoplasms; Maps; Medical Research; NCI Center for Cancer Research; Oncogenes; Oncogenic; Online Systems; Pathway Analysis; Pathway interactions; Pilot Projects; Point Mutation; Positioning Attribute; Predisposition; Primary Neoplasm; Property; Proteins; Publishing; Research Infrastructure; Research Personnel; Resources; Role; Sampling; Sequence Analysis; Software Engineering; Software Tools; Source; Staging; System; Technology; Testing; Time; Translations; Tumor Suppressor Proteins; Tumor-Derived; Variant; Work; biomedical informatics; cancer genome; cancer genomics; cancer type; computerized tools; cost; design; drug development; exome; experience; genome sequencing; improved; interest; novel; outcome forecast; software development; tool; tumor; tumor progression; user-friendly; web based interface

DESCRIPTION (provided by applicant): The detection of biologically important sequence variation is a major goal of modern cancer genomics. In an effort to focus resequencing investigations on high-value regions, many researchers have chosen to focus on the exome (protein-coding exons), which is expected to be enriched for functional variation. In the near future, comprehensive resequencing of an individual's exome may cost less than $1000, substantially less than whole-genome sequencing. We anticipate that these developments will yield an enormous amount of exonic sequence variation in cancer genomes that will provide leads to new cancer genes and drug targets. Most of this variation is likely to be effectively neutral, thus the cancer genomics community will have to identify and prioritize those variants that warrant further studies in assay systems, e.g. cell lines and model organisms. At this time, there are no publicly available resources that enable researchers who are not bioinformatics experts to explore the biological importance of sequence variants discovered in their investigations. There is a pressing need for tools that enable transparent, researcher-driven exploration of variation, by mapping variants onto proteins and pathways and presenting results in a way that is accessible to the average researcher. Development of such resources will allow rapid translation of genomic investigations into tangible progress in medical research. We propose here to develop a novel computational application tailored to the needs of researchers who are discovering variation in the exomes of cancers. Our work will produce a high- throughput annotation pipeline, with associated web-based analysis and visualization tools. This resource will enable users to interpret and prioritize tumor-derived sequence changes and help them think about how to design functional tests for variants of interest. We will demonstrate the utility of the application by collaborating with researchers from the Johns Hopkins Sidney Kimmel Cancer Research Center, who are sequencing the exomes of eleven cancer types during the two years for which we request funding (approximately 23 primary tumors per cancer type). The application will be used in collaboration with this team of researchers, led by Drs. Bert Vogelstein, Ken Kinzler, and Victor Velculescu to identify genes responsible for susceptibility to and progression of these cancers (Support Letter attached). This work will lay the foundation for a broader application of the tools to exomic variation data in additional cancers, such as those being studied by NCI's Cancer Genome Atlas project and TARGET. PUBLIC HEALTH RELEVANCE: We propose to develop software tools that will enable genomics researchers to analyze sequence variation in the human exome, for the purpose of improving diagnosis, prognosis and drug development targeted at cancers. In the pilot stage of the project, we will use the tools to identify variants, genes, and groups of related genes that underlie susceptibility to and progress of eleven cancer types being sequenced at Johns Hopkins' Sidney Kimmel Cancer Center.

描述（由申请人提供）：检测生物学上重要的序列变异是现代癌症基因组学的主要目标。为了将重测序研究集中在高价值区域，许多研究人员选择将重点放在外显子（蛋白质编码外显子）上，该外显子有望丰富功能变异。在不久的将来，个人外显子组的全面重测序可能花费不到1000美元，大大低于全基因组测序。我们预计这些进展将在癌症基因组中产生大量的外显子序列变异，这将为新的癌症基因和药物靶点提供线索。大多数这种变异可能是有效的中性的，因此癌症基因组学社区将不得不识别和优先考虑那些值得在分析系统中进一步研究的变异，例如细胞系和模式生物。目前，没有公开的资源使非生物信息学专家的研究人员能够探索在他们的研究中发现的序列变异的生物学重要性。目前迫切需要一种工具，通过将变异映射到蛋白质和途径上，并以普通研究人员可以访问的方式呈现结果，从而实现透明的、研究人员驱动的变异探索。这些资源的开发将使基因组研究迅速转化为医学研究的实际进展。我们在此建议开发一种新的计算应用程序，以满足正在发现癌症外显子组变异的研究人员的需求。我们的工作将产生一个高吞吐量的注释管道，与相关的基于web的分析和可视化工具。该资源将使用户能够解释和确定肿瘤衍生序列变化的优先级，并帮助他们思考如何为感兴趣的变体设计功能测试。我们将与约翰霍普金斯大学Sidney Kimmel癌症研究中心的研究人员合作，展示该应用程序的实用价值。在我们申请资助的两年中，他们正在对11种癌症类型的外显子组进行测序（每种癌症类型大约有23种原发肿瘤）。该应用程序将与该研究小组合作使用。Bert Vogelstein, Ken Kinzler，和Victor Velculescu，以确定对这些癌症的易感性和进展负责的基因（附支持信）。这项工作将为更广泛地将这些工具应用于其他癌症的外显子组变异数据奠定基础，例如NCI的癌症基因组图谱项目和TARGET正在研究的癌症。