Critical Assessment of Genome Interpretation 2011 Conference

描述(由申请者提供)：我们建议在2011年12月组织一次题为基因组解释的批判性评估(CAGI)的会议。这次会议将是一个社区实验的高潮，该实验旨在客观地评估预测基因组变异的表型影响的计算方法。CAGI实验是及时的，具有广泛的相关性，因为个人基因组的可获得性迅速增长，并希望将其解释为研究和临床应用。目前，该领域对各种不同预测方法的绝对和相对适用性缺乏共识。这次会议将对基因组变异解释的现状进行首次大规模评估，会议结果将公布，以确保结果的广泛传播。在CAGI实验中，以结构预测的关键评估(CASP)为模型，参与者被提供了遗传变异，并将对结果的分子、细胞或生物表型进行预测。预计数据集将包括罕见疾病、常见特征和疾病、生殖系和体细胞癌变异，重点是nsSNPs、影响剪接的SNPs、外显子和拷贝数变异。独立评估者将对照实验表征的表型对预测进行评估。CAGI会议在实验结束时举行。会议的具体目标是：(1)评估目前用于解释基因组数据的计算方法的质量，并突出创新和进展；(2)指导未来在计算基因组解释方面的研究努力，并建立一个强大的合作和互动社区；以及(3)在会议上变异表型预测社区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。这将是第一次全面的CAGI实验。2010年秋季，我们组织了初步的CAGI实验，在来自8个国家的17个小组的6个数据集上产生了108个预测。40人参加了2010年12月的讲习班，7人观看了会议实况转播。社会各界一致认为，这项实验是必要的，应该在更大范围内重新组织起来。组织者将大力鼓励妇女和少数群体参加，并鼓励受训人员和资深科学家广泛参加CAGI会议。要求提供资金，为学生和博士后研究人员颁发19项见习研究金，以支付他们参加会议费用的大约三分之二(旅费、注册费和生活费)。此外，我们寻求资金补贴CAGI实验的独立评审员和组织者参加会议的费用的一半。 与公共卫生相关：基因组变异是导致许多罕见疾病的原因，是许多常见特征和疾病的倾向，也是癌症进化的关键特征。目前，我们描述基因差异的能力远远超过了我们解释它的能力，无论是为了基础研究理解还是为了临床诊断。基因组解释的关键评估将提供对当前最先进技术的评估，并有助于促进了解基因组变异的进展。

DESCRIPTION (provided by applicant): We propose to organize a meeting titled Critical Assessment of Genome Interpretation (CAGI) in December 2011. The meeting 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 because of the burgeoning availability of individuals' genomes, and the desire to interpret them for research and clinical applications. Currently, the field lacks a consensus on the absolute and relative suitability of the panoply of different methods for prediction. This meeting will provide the first large-scale assessment of the state of the art of genome variation interpretation, and outcome of the meeting will be published to ensure wide dissemination of the results. In the CAGI experiment, modeled on the Critical Assessment of Structure Prediction (CASP), participants are provided genetic variants and will 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 nsSNPs, splice-affecting SNPs, exomes, and copy number variation. Independent assessors will evaluate the predictions against experimentally characterized phenotypes. The CAGI Conference is held at the end of the 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 broader audience via publication of results in peer-reviewed journals. This will be the first full-scale CAGI experiment. In fall 2010 we organized the preliminary CAGI experiment, which yielded 108 predictions on 6 datasets, from 17 groups in 8 countries. Forty people attended the December 2010 workshop and seven viewed the live feed of the meeting. The community was unanimous that this experiment is necessary and should be organized again on a larger scale. The organizers will strongly encourage the participation of women and 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 approximately 2/3 of their meeting participation costs (travel, registration, and subsistence). In addition, we seek funding to subsidize half of meeting participation costs of independent assessors and organizers of the CAGI experiment. PUBLIC HEALTH RELEVANCE: Genomic variation is responsible for numerous rare diseases, propensity for many common traits and diseases, 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 to understand genomic variation.