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Informatics Tools for High-throughput Analysis of Cancer Mutations

用于癌症突变高通量分析的信息学工具

基本信息

批准号：
9094143
负责人：
Rachel Karchin
金额：
$ 46.28万
依托单位：
JOHNS HOPKINS UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2016
资助国家：
美国
起止时间：
2016-04-01 至 2021-03-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9094143
关键词：
Address Africa Asia Australia Bioinformatics Cancer Prognosis Clinical Communities Computer Analysis Computer software Country Data Development Education and Outreach Ensure Environment Europe Feedback Funding Gene Frequency Genes Genetic Histocompatibility Testing Hot Spot Image Imagery Informatics Internet Literature Maintenance Malignant Neoplasms Methodology Mission Mutation Mutation Analysis North America Occupations Online Systems Pathway interactions Persons Pharmaceutical Preparations Population Positioning Attribute Process Quality Control Research Personnel Retrieval Running Services Source South America System Testing The Cancer Genome Atlas Time Training Tumor Tissue Untranslated RNA Work actionable mutation anticancer research base cancer genomics cancer therapy community building design exome flexibility gene panel genome sequencing high throughput analysis interoperability novel strategies outreach protein structure public health relevance research study response social media software development tool tumor tumor heterogeneity web interface web services whole genome working group

项目摘要

DESCRIPTION (provided by applicant): Cancer sequencing projects have identified a very large number of mutations whose cancer relevance is not yet understood. To address this need, our team has produced an application for high-throughput computational analysis of cancer mutations. The application -- CRAVAT/MuPIT -- accepts millions of mutations in a single batch upload, and it is designed to work as a funnel, so that users can narrow down a very large number of mutations discovered in a sequencing project to a tractable number of those most likely to be informative. The system enables combination of multiple metrics to generate a prioritized list. Metrics include quality control of mutation calls, mutation consequence types, bioinformatic scores to identify pathogenic and driver mutations, population allele frequencies, previous occurrence in tumor tissue types, pointers to relevant literature and interactive visualization on annotated protein structures, including customizable views of biologically important positions, mutations and mutation hot spots from 21 TCGA tumor types. The CRAVAT/MuPIT application has been available through a web interface for 21/2 years. In that time, analysis jobs have been submitted by 6,056 unique users from 88 countries on six continents (North America, South America, Europe, Asia, Australia and Africa). We have processed a total 12,051 missions, ranging from a few mutations to over 62 million. In total, the application has processed over 673 million mutations. (Source: Google Analytics). We have attracted a user community that spans both basic and clinical cancer researchers, all of whom rely on high-throughput tumor sequencing in their work. To address the needs of our community going forward, we will extend the functionality of our application to more fully support analysis o non-coding mutations, identification of associations between mutations and drug response, and pathway-based interpretation of mutation impact. We will dedicate substantial effort to ensure that our tools are interoperable with other informatics services, can be run in cloud environments and can be run in locally-installed pipelines to support protected data.