Systematic identification of pharmacogenomics information from clinical trials.
Systematic identification of pharmacogenomics information from clinical trials.
复制标题
DOI：
10.1016/j.jbi.2012.04.005
复制
发表时间：
2012-10
影响因子：
4.5
通讯作者：
Lu, Zhiyong
中科院分区：
文献类型：
--
作者：
Li, Jiao;Lu, Zhiyong
高通量基因组学技术的最新进展使药物基因组学研究从候选基因药物基因组学转向临床药物基因组学(PGx)。许多与临床相关的问题可能会被问到，比如‘携带突变等位基因的患者应该开什么药？’通常，这些问题的答案可以在提到感兴趣的基因-药物-疾病关系的出版物中找到。在这项工作中，我们假设ClinicalTrials.gov是一个丰富的PGx相关信息的可比来源。在这方面，我们开发了一种系统的方法，从ClinicalTrials.gov上的试验记录中自动识别基因、药物和疾病之间的PGx关系。在我们的评估中，我们发现我们提取的关系与PGx数据库中的文献中精选的事实知识显著重叠，并且大多数关系在临床试验中比相应的出版物中平均提前5年出现，这表明临床试验可能对于验证已知的已知信息和更及时地捕获新的PGx相关信息都是有价值的。此外，两位人工审查者对计算机生成的关系的一部分进行了判断，发现我们的文本挖掘方法的总体准确率为74%。这项工作对丰富我们关于PGx基因-药物-疾病关系的现有知识以及建议ClinicalTrials.gov和其他PGx知识库之间的交叉链接具有实际意义。
Recent progress in high-throughput genomic technologies has shifted pharmacogenomic research from candidate gene pharmacogenetics to clinical pharmacogenomics (PGx). Many clinical related questions may be asked such as ‘what drug should be prescribed for a patient with mutant alleles?’ Typically, answers to such questions can be found in publications mentioning the relationships of the gene–drug–disease of interest. In this work, we hypothesize that ClinicalTrials.gov is a comparable source rich in PGx related information. In this regard, we developed a systematic approach to automatically identify PGx relationships between genes, drugs and diseases from trial records in ClinicalTrials.gov. In our evaluation, we found that our extracted relationships overlap significantly with the curated factual knowledge through the literature in a PGx database and that most relationships appear on average 5 years earlier in clinical trials than in their corresponding publications, suggesting that clinical trials may be valuable for both validating known and capturing new PGx related information in a more timely manner. Furthermore, two human reviewers judged a portion of computer-generated relationships and found an overall accuracy of 74% for our text-mining approach. This work has practical implications in enriching our existing knowledge on PGx gene–drug–disease relationships as well as suggesting crosslinks between ClinicalTrials.gov and other PGx knowledge bases.
登录
查看更多内容
影响因子：
5.8
作者：
Chang, JT;Schütze, H;Altman, RB
通讯作者：
Altman, RB
DOI：
10.1197/jamia.m2233
发表时间：
2007-05-01
影响因子：
6.4
作者：
Ide, Nicholas C.;Loane, Russell F.;Demner-Fushman, Dina
通讯作者：
Demner-Fushman, Dina
影响因子：
3
作者：
Garten Y;Altman RB
通讯作者：
Altman RB
影响因子：
120.1
作者：
Orloff, John;Douglas, Frank;Golub, Howard
通讯作者：
Golub, Howard
DOI：
10.2165/00129785-200505010-00005
发表时间：
2005-01-01
期刊：
AMERICAN JOURNAL OF PHARMACOGENOMICS
影响因子：
--
作者：
Penny, MA;McHale, D
通讯作者：
McHale, D