Critical Assessment of Genome Interpretation Conference

基因组解释会议的批判性评估

• 批准号: 8459354
• 负责人: Steven E Brenner
• 金额: $ 2.5万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-01 至 2014-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8459354
• 关键词: Affect; Area; Award; Basic Science; Characteristics; Collaborations; Communities; Computing Methodologies; Consensus; Copy Number Polymorphism; Country; Data; Data Set; Discipline; Disease; Ensure; Environment; Evaluation; Event; Evolution; Fellowship; Funding; Future; Genetic; Genome; Genomics; Goals; Individual; Journals; Malignant Neoplasms; Methods; Modeling; Molecular; Outcome; Participant; Peer Review; Pharmaceutical Preparations; Pharmacogenomics; Phenotype; Process; Provider; Publications; Publishing; RNA Splicing; Rare Diseases; Relative (related person); Reporting; Research; Research Personnel; Resources; Rewards; San Francisco; Scientist; Senior Scientist; Structure; Students; Travel; Underrepresented Minority; Variant; Woman; Work; base; clinical Diagnosis; clinical application; cost; exome; experience; genetic variant; innovation; meetings; member; planetary Atmosphere; research study; response; success; symposium; trait; transcriptomics

DESCRIPTION (provided by applicant): We propose to organize two further Critical Assessment of Genome Interpretation (CAGI) meetings, in December 2012 and December 2013. As in 2010 and 2011, the meetings will be the culmination of a community experiment to objectively assess computational methods for predicting the phenotypic impacts of genomic variation. The CAGI experiment is timely and of wide relevance due to the burgeoning availability of individuals' genomes, and the desire to interpret these for research and clinical applications. Currently, the field lacks a consensus on the absolute and relative suitability of th panoply of different methods for prediction. These meetings will provide the first large-scale assessment of the state of the art of genome variation interpretation. The outcome of the meetings will be published to ensure wide dissemination of results. In the CAGI experiments, modeled on the Critical Assessment of Structure Prediction (CASP), participants are provided genetic variants and make predictions of resulting molecular, cellular, or organismal phenotype. Datasets are expected to include rare disease, common traits and diseases, germline and somatic cancer variation, with a focus on genomes and exomes, nsSNPs, splice-affecting SNPs, and copy number variation along with other data such as transcriptomics. Independent assessors will evaluate the predictions against experimentally characterized phenotypes. A CAGI Conference is held at the end of each experiment. The specific goals of the meeting are: (1) to assess the quality of current computational methods for interpreting genomic data, and highlight innovations & progress; (2) to guide future research efforts in computational genome interpretation and build a strong community for collaboration and interaction; and (3) to disseminate results both amongst key members of the variant-phenotype prediction community at the meeting and to a broader audience via publication of results in peer-reviewed journals. The new CAGI experiments will continue the process started with the CAGI pilot in 2010, and the first full-scale CAGI experiment in 2011. The 2011 experiment yielded a total of 117 predictions on 11 datasets, from 21 groups from 18 countries. 55 people attended the December 2011 meeting, and we are disseminating results via open access publications and conference presentations. The participating community was overwhelmingly of the opinion that this experiment is necessary and should be organized again on an ongoing basis. The organizers will strongly encourage the participation of women and underrepresented minorities, and broad participation of trainees and senior scientists at the CAGI meeting. Funding is requested for awarding 19 trainee fellowships for students and postdoctoral researchers to cover registration and approximately 2/3 of their other meeting participation costs (travel and subsistence). In addition, we seek funding to subsidize registration and approximately half of meeting participation costs of the independent assessors, some data providers and scientific council members, and the organizers of the CAGI experiments. PUBLIC HEALTH RELEVANCE: Genomic variation is responsible for numerous rare diseases, propensity for many common traits and diseases, drug response, and is a key characteristic of cancer evolution. At present, our ability to characterize genetic differences far exceeds our capacity to interpret it either for basic research understanding or for clinical diagnosis. The Critical Assessment of Genome Interpretation will provide an evaluation of the current state-of-the-art and help promote progress in understanding genomic variation.

描述（由申请人提供）：我们建议在2012年12月和2013年12月再组织两次基因组解读关键评估（CAGI）会议。与2010年和2011年一样，这些会议将是一项社区实验的高潮，该实验旨在客观评估预测基因组变异表型影响的计算方法。CAGI实验是及时和广泛的相关性，由于个人的基因组的迅速发展的可用性，并希望解释这些研究和临床应用。目前，该领域缺乏一个共识的绝对和相对适用性的各种不同的预测方法。这些会议将首次对基因组变异解释的最新技术水平进行大规模评估。会议结果将予以公布，以确保广泛传播这些结果。在CAGI实验中，以结构预测的关键评估（CASP）为模型，参与者被提供遗传变异，并对产生的分子，细胞或生物表型进行预测。预计数据集将包括罕见疾病、常见性状和疾病、生殖系和体细胞癌症变异，重点关注基因组和外显子组、nsSNP、影响剪接的SNP和拷贝数变异沿着转录组学等其他数据。独立评估员将根据实验表征的表型评估预测。CAGI会议在每次实验结束时举行。会议的具体目标是：（1）评估当前用于解释基因组数据的计算方法的质量，并强调创新和进展;（2）指导未来的计算基因组解释研究工作，并建立一个强大的合作和互动社区。以及（3）在会议上在变异-表型预测界的主要成员中传播结果，并通过在同行评议的期刊上发表结果向更广泛的受众传播结果。新的CAGI实验将继续2010年CAGI试点和2011年第一次全面CAGI实验开始的进程。2011年的实验在11个数据集上产生了117个预测，来自18个国家的21个团体。55人参加了2011年12月的会议，我们正在通过开放获取出版物和会议演示文稿传播结果。与会者一致认为，这一试验是必要的，应在持续不断的基础上再次组织。组织者将大力鼓励妇女和代表性不足的少数群体的参与，以及学员和资深科学家广泛参与CAGI会议。要求提供资金，为学生和博士后研究人员颁发19个实习研究金，以支付注册费和约三分之二的其他会议参加费用（旅费和生活津贴）。此外，我们还寻求资金来补贴注册和独立评估员、一些数据提供者和科学理事会成员以及CAGI实验组织者参加会议的大约一半费用。 公共卫生相关性：基因组变异是许多罕见疾病、许多常见性状和疾病的倾向、药物反应的原因，并且是癌症演变的关键特征。目前，我们描述遗传差异的能力远远超过了我们对基础研究理解或临床诊断的解释能力。对基因组解释的批判性评估将提供对当前最先进技术的评估，并有助于促进对基因组变异的理解。