VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees.
VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees.
复制标题
DOI：
10.1186/1471-2105-13-s8-s5
复制
发表时间：
2012
影响因子：
3
通讯作者：
Law A
中科院分区：
文献类型：
--
作者：
Paterson T;Graham M;Kennedy J;Law A
系谱基因型数据集用于分析遗传和绘制遗传标记和性状。这些数据集由数百个相关动物的数千个遗传标记的基因型组成，并且在系谱结构和相关的个体基因型数据中总是包含多个错误。这些错误表现为谱系中明显的遗传不一致，并使整个数据集的标记继承模式分析无效。清理错误数据点的原始数据集（不正确的系谱关系、不可靠的标记分析、可疑样本、错误的基因型结果等）需要对遗传系谱背景下暴露的不一致模式进行专家探索。为了帮助这一过程，我们正在开发VIPER（可视系谱资源管理器），这是一种软件工具，它集成了继承检查算法和一种新颖的空间高效的系谱可视化，因此报告的继承不一致被覆盖在系谱结构的交互式、可导航的表示上。本文描述了对VIPER如何显示实验中出现的不同规模和类型的数据集的评估，并描述了VIPER的显示界面和功能如何满足这些数据所带来的挑战。我们研究了在真实和模拟系谱基因型数据集中发现的一系列可能的错误类型，展示了如何使用VIPER接口暴露和探索这些错误，并评估了该接口对领域专家的实用性和可用性。在领域专家（遗传学家）的协助下，评估分两个阶段进行。根据用户的要求，在系谱显示的最终功能评估之前，初始评估推动了软件原型中进一步特性的迭代实现，以探索各种错误类型、数据规模和结构。VIPER显示显示有效地揭示了在实验基因型谱系中发现的错误范围，允许用户探索报告的遗传不一致的潜在原因。该界面将为完整的数据清理工具提供基础，该工具将允许用户删除孤立的不良数据点，并可逆地测试删除可疑基因型和谱系关系的效果。
Pedigree genotype datasets are used for analysing genetic inheritance and to map genetic markers and traits. Such datasets consist of hundreds of related animals genotyped for thousands of genetic markers and invariably contain multiple errors in both the pedigree structure and in the associated individual genotype data. These errors manifest as apparent inheritance inconsistencies in the pedigree, and invalidate analyses of marker inheritance patterns across the dataset. Cleaning raw datasets of bad data points (incorrect pedigree relationships, unreliable marker assays, suspect samples, bad genotype results etc.) requires expert exploration of the patterns of exposed inconsistencies in the context of the inheritance pedigree. In order to assist this process we are developing VIPER (Visual Pedigree Explorer), a software tool that integrates an inheritance-checking algorithm with a novel space-efficient pedigree visualisation, so that reported inheritance inconsistencies are overlaid on an interactive, navigable representation of the pedigree structure. This paper describes an evaluation of how VIPER displays the different scales and types of dataset that occur experimentally, with a description of how VIPER's display interface and functionality meet the challenges presented by such data. We examine a range of possible error types found in real and simulated pedigree genotype datasets, demonstrating how these errors are exposed and explored using the VIPER interface and we evaluate the utility and usability of the interface to the domain expert. Evaluation was performed as a two stage process with the assistance of domain experts (geneticists). The initial evaluation drove the iterative implementation of further features in the software prototype, as required by the users, prior to a final functional evaluation of the pedigree display for exploring the various error types, data scales and structures. The VIPER display was shown to effectively expose the range of errors found in experimental genotyped pedigrees, allowing users to explore the underlying causes of reported inheritance inconsistencies. This interface will provide the basis for a full data cleaning tool that will allow the user to remove isolated bad data points, and reversibly test the effect of removing suspect genotypes and pedigree relationships.