Performance of an electronic health record-based phenotype algorithm to identify community associated methicillin-resistant Staphylococcus aureus cases and controls for genetic association studies.
Performance of an electronic health record-based phenotype algorithm to identify community associated methicillin-resistant Staphylococcus aureus cases and controls for genetic association studies.
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DOI：
10.1186/s12879-016-2020-2
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发表时间：
2016-11-17
影响因子：
3.7
通讯作者：
Kho AN
中科院分区：
文献类型：
--
作者：
Jackson KL;Mbagwu M;Pacheco JA;Baldridge AS;Viox DJ;Linneman JG;Shukla SK;Peissig PL;Borthwick KM;Carrell DA;Bielinski SJ;Kirby JC;Denny JC;Mentch FD;Vazquez LM;Rasmussen-Torvik LJ;Kho AN
社区相关耐甲氧西林金黄色葡萄球菌（CA-MRSA）是美国皮肤和软组织感染的最常见原因之一，各种遗传宿主因素被怀疑是复发感染的危险因素。基于CDC的定义，我们开发并验证了一种基于电子健康记录（EHR）的CA-MRSA表型算法，该算法利用了结构化和非结构化数据。该算法在三个eMERGE联盟网站进行了验证，并计算了阳性预测值，阴性预测值和灵敏度。然后运行该算法，并在总共七个站点收集数据。所得数据用于GWAS分析。在7个研究中心，CA-MRSA表型算法在基因分型的欧洲和非洲裔美国人生物库人群中共识别出349例病例和7761例对照。病例的PPV范围为68 - 100%，对照为96 - 100%;病例的灵敏度范围为94 - 100%，对照为75 - 100%。不同地点人群中的病例频率差异很大。没有合理的GWAS显著性（p < 5 E −8）结果。EHR数据表示和筛查模式的差异可能影响了病例和对照的识别，并导致了不同站点之间的频率差异。有必要在今后开展工作，确定这些模式。本文的在线版本（doi：10.1186/s12879-016-2020-2）包含补充材料，可供授权用户使用。
Community associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is one of the most common causes of skin and soft tissue infections in the United States, and a variety of genetic host factors are suspected to be risk factors for recurrent infection. Based on the CDC definition, we have developed and validated an electronic health record (EHR) based CA-MRSA phenotype algorithm utilizing both structured and unstructured data. The algorithm was validated at three eMERGE consortium sites, and positive predictive value, negative predictive value and sensitivity, were calculated. The algorithm was then run and data collected across seven total sites. The resulting data was used in GWAS analysis. Across seven sites, the CA-MRSA phenotype algorithm identified a total of 349 cases and 7761 controls among the genotyped European and African American biobank populations. PPV ranged from 68 to 100% for cases and 96 to 100% for controls; sensitivity ranged from 94 to 100% for cases and 75 to 100% for controls. Frequency of cases in the populations varied widely by site. There were no plausible GWAS-significant (p < 5 E −8) findings. Differences in EHR data representation and screening patterns across sites may have affected identification of cases and controls and accounted for varying frequencies across sites. Future work identifying these patterns is necessary. The online version of this article (doi:10.1186/s12879-016-2020-2) contains supplementary material, which is available to authorized users.
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影响因子：
4.2
作者：
Casey, J. A.;Cosgrove, S. E.;Stewart, W. F.;Pollak, J.;Schwartz, B. S.
通讯作者：
Schwartz, B. S.
影响因子：
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2.4
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Kho, Abel N.;Doebbeling, Bradley N.;Overhage, J. Marc
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