Genotator: a disease-agnostic tool for genetic annotation of disease.
Genotator: a disease-agnostic tool for genetic annotation of disease.
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DOI：
10.1186/1755-8794-3-50
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发表时间：
2010-10-29
影响因子：
2.7
通讯作者：
Tonellato PJ
中科院分区：
文献类型：
--
作者：
Wall DP;Pivovarov R;Tong M;Jung JY;Fusaro VA;DeLuca TF;Tonellato PJ
疾病特异性遗传信息一直在快速增长的结果，最近的改进和测序技术的成本大幅降低。已经出现了许多旨在捕获和组织这一不断增加的遗传数据海洋的系统，但这些资源在疾病覆盖范围和遗传深度方面存在显着差异。除了少数例外，研究人员必须手动搜索各种网站，为特定的感兴趣的疾病收集一套完整的遗传证据，这是一个既耗时又容易出错的过程。我们设计了一个实时聚合工具，为任何疾病提供全面的覆盖范围和可靠的基因-疾病排名。我们的工具，称为Genotator，自动整合来自11个外部可访问的临床遗传学资源的数据，并在一个简单的公式中使用这些数据，以疾病相关性的顺序对基因进行排名。我们测试了Genotator在三种独立疾病中的覆盖率的准确性，这些疾病存在专业策划的数据库，自闭症谱系障碍，帕金森病和阿尔茨海默病。Genotator可在http://genotator.hms.harvard.edu上免费获得。Genotator表明，11个选定的数据库中的大多数都包含有关疾病遗传组成的独特信息，其中2514个基因仅在11个数据库中的一个中发现。这些调查结果证实，这些数据库的整合提供了一个更完整的图片比任何一个数据库单独。Genotator成功地识别了我们所有三个用例中至少75%的顶级基因，其中包括与阿尔茨海默病前40名候选基因的90%一致性。作为一个元查询引擎，Genotator提供了历史遗传学研究以及特定疾病遗传学理解的最新进展的高覆盖率。因此，Genotator提供了一个实时的排名数据的聚合，仍然与疾病领域的研究步伐。Genotator的算法适当地转换查询词以匹配每个目标数据库的输入要求，并准确地解析命名的同义词，以确保完全覆盖具有官方命名法的遗传结果。Genotator生成一个excel风格的输出，该输出在疾病查询中是一致的，并且可以很容易地导入到其他应用程序中。
Disease-specific genetic information has been increasing at rapid rates as a consequence of recent improvements and massive cost reductions in sequencing technologies. Numerous systems designed to capture and organize this mounting sea of genetic data have emerged, but these resources differ dramatically in their disease coverage and genetic depth. With few exceptions, researchers must manually search a variety of sites to assemble a complete set of genetic evidence for a particular disease of interest, a process that is both time-consuming and error-prone. We designed a real-time aggregation tool that provides both comprehensive coverage and reliable gene-to-disease rankings for any disease. Our tool, called Genotator, automatically integrates data from 11 externally accessible clinical genetics resources and uses these data in a straightforward formula to rank genes in order of disease relevance. We tested the accuracy of coverage of Genotator in three separate diseases for which there exist specialty curated databases, Autism Spectrum Disorder, Parkinson's Disease, and Alzheimer Disease. Genotator is freely available at http://genotator.hms.harvard.edu. Genotator demonstrated that most of the 11 selected databases contain unique information about the genetic composition of disease, with 2514 genes found in only one of the 11 databases. These findings confirm that the integration of these databases provides a more complete picture than would be possible from any one database alone. Genotator successfully identified at least 75% of the top ranked genes for all three of our use cases, including a 90% concordance with the top 40 ranked candidates for Alzheimer Disease. As a meta-query engine, Genotator provides high coverage of both historical genetic research as well as recent advances in the genetic understanding of specific diseases. As such, Genotator provides a real-time aggregation of ranked data that remains current with the pace of research in the disease fields. Genotator's algorithm appropriately transforms query terms to match the input requirements of each targeted databases and accurately resolves named synonyms to ensure full coverage of the genetic results with official nomenclature. Genotator generates an excel-style output that is consistent across disease queries and readily importable to other applications.
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影响因子：
2.1
作者：
Feher, Agnes;Anna Juhasz;Janka, Zoltan
通讯作者：
Janka, Zoltan
影响因子：
4
作者：
Brooks J;Ding J;Simon-Sanchez J;Paisan-Ruiz C;Singleton AB;Scholz SW
通讯作者：
Scholz SW
DOI：
10.1007/978-1-60327-194-3_16
发表时间：
2010-01-01
期刊：
BIOINFORMATICS METHODS IN CLINICAL RESEARCH
影响因子：
--
作者：
Krallinger, Martin;Leitner, Florian;Valencia, Alfonso
通讯作者：
Valencia, Alfonso
DOI：
10.1016/s0764-4469(99)80021-3
发表时间：
1998-10-01
期刊：
COMPTES RENDUS DE L ACADEMIE DES SCIENCES SERIE III-SCIENCES DE LA VIE-LIFE SCIENCES
影响因子：
--
作者：
Frezal, J
通讯作者：
Frezal, J
影响因子：
--
作者：
Clark, LN;Afridi, S;Marder, K
通讯作者：
Marder, K