Apollo: Collaborative, Interactive Analytics and Annotation of Genome Variants

描述（由申请人提供）：我们的目标是通过提供交互式探索性可视化工具来推进基因组分析，使研究人员能够改进，纠正和增加初始自动化结果。在过去十年中，基因组测序的成本已经大幅降低了几个数量级，自然的结果是越来越多的研究人员正在对越来越多的新基因组进行测序，无论是在种群内还是在每个物种之间。每一个新的外显子组或基因组测序都需要可视化，因为计算基因组分析仍然是一门不完美的艺术，但有了有效的可视化，基因组解释可以利用人类的感知能力来整合信息。Web Apollo将提供一个易于使用的基于Web的环境，为多个分布式用户提供交互式基因组数据探索的高性能可视化，以及为下游分析提供最大信息量的高精度注释所需的工具。这个项目将使迅速发展的基因组社区的每一个成员都能充分调动分子研究数据，无论是由个人研究人员收集的，还是从公共聚集站点提供的，以有利于遗传学和人类疾病的调查。该项目将使研究人员能够(i)注释基因组变异和单倍型使用：汇总跟踪包括背景人口频率和质量分数；将变异体投射到蛋白质显示器上，以观察与蛋白质特征（如活性位点和二级结构）的交集，以评估生物影响；以及个性化的单倍型轨迹，以注释独特的疾病相关转录本；（ii）通过在集成多序列比对（MSA）视图中直接比较相关蛋白质，提高蛋白质编码转录本的外显子-内含子准确性；（iii）用GO术语注释生物学功能（iv）利用关键位点的书签进行快速导航探索基因组，并使用新颖的圆柱形视图同时检查多个单倍型的大规模染色体重排；(v)交互式分析数据，使用图阈值法定义离散特征，对数据轨迹及其内容进行动态视觉过滤，并对基因组进行视觉折叠，以将具有相似或共享表型等共同属性的基因及其内的变体带入同一视野；（vi）通过互联网与选定的团队成员进行实时安全协作，使用混合云处理私人数据，使用免费托管的服务器处理公共数据。

DESCRIPTION (provided by applicant): Our aim is to advance genome analysis by providing interactive exploratory visualization tools enabling researchers to refine, correct and augment initial automated results. The cost of sequencing a genome has been dramatically reduced by several orders of magnitude in the last decade, and the natural consequence is that more and more researchers are sequencing more and more new genomes, both within populations and across every species. Each new exome or genome sequenced requires visualization because computational genome analysis remains an imperfect art, but with effective visualization, genome interpretation can take advantage of human perceptual capabilities to integrate information. Web Apollo will provide an easy to use, web-based environment offering multiple, distributed users high-performance visualization for interactive exploration of genome data, and the tools needed for producing highly accurate annotations that are maximally informative for downstream analysis. This project will enable every member of the burgeoning genomic community to fully mobilize molecular research data, whether collected by individual researchers or made available from public aggregation sites to benefit investigations into genetics and human diseases. This project will enable researchers to (i) Annotate genomic variants and haplotypes using: summarization tracks including background population frequencies and quality scores; projections of variants onto protein displays to see intersection with protein features such as active sites and secondary structure to assess biological impact; and individualized haplotype tracks to annotate unique disease associated transcripts; (ii) Improve exon-intron accuracy for protein coding transcripts via direct comparison to related proteins in an integrated multiple sequence alignment (MSA) view; (iii) Annotate biological function with GO terms (iv) Explore the genome using bookmarking of key sites for rapid navigation, and a novel cylindrical view to examine large-scale chromosomal rearrangements across multiple haplotypes simultaneously; (v) Analyze the data interactively using graph thresholding to define discrete features, dynamic visual filtering of data tracks and their contents, and visual folding of the genome to bring genes with shared attributes such as paralogy or shared phenotypes and the variants within them in the same visual field; (vi) Collaborate securely in real-time with selected team members over the Internet using hybrid clouds for private data and freely-hosted servers for public data.