Evaluating phecodes, clinical classification software, and ICD-9-CM codes for phenome-wide association studies in the electronic health record.
Evaluating phecodes, clinical classification software, and ICD-9-CM codes for phenome-wide association studies in the electronic health record.
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DOI：
10.1371/journal.pone.0175508
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发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Denny JC
中科院分区：
文献类型：
--
作者：
Wei WQ;Bastarache LA;Carroll RJ;Marlo JE;Osterman TJ;Gamazon ER;Cox NJ;Roden DM;Denny JC
比较三组电子健康记录 (EHR) 计费代码代表临床有意义的表型和复制已知遗传关联的能力。三个测试的编码系统是国际疾病分类第九版临床修改 (ICD-9-CM) 代码、ICD-9-CM 医疗保健研究和质量临床分类软件 (CCS) 代码，以及旨在促进 EHR 中全表组关联研究 (PheWAS) 的手动策划的“phecodes”。我们选择了 100 种疾病表型，并比较了每个编码系统在不进行额外分组的情况下准确表示它们的能力。这 100 种表型包括之前全基因组关联研究 (GWAS) 中随机选择的 25 种临床表型，以及来自 189,289 名个体的自由文本问题列表中提到的另外 75 种常见疾病表型。然后，我们评估了每个编码系统复制 440 个 SNP 表型对的已知关联的性能。在 100 个测试的临床表型中，有 83 个 phecode 完全匹配，而 ICD-9-CM 为 53 个，CCS 为 32 个。 ICD-9-CM 代码通常过于详细（需要自定义分组），而 CCS 代码通常不够精细。在 440 个测试的已知 SNP 表型关联中，使用 phecode 复制了 153 个 SNP 表型对，而 ICD-9-CM 复制了 143 个，CCS 复制了 139 个。对于已知关联，Phecode 通常还比 ICD-9-CM 和 CCS 产生更强的比值比和更低的 p 值。最后，通过 PheWAS 对几个 SNP 进行评估，发现了新的潜在信号，其中一些信号仅在使用 phecode 方法时可见。其中PEPD中的rs7318369与消化道出血相关。我们的结果表明，phecode 分组与临床实践或基因组研究中提到的临床疾病更好地一致。 ICD-9-CM、CCS 和 phecode 分组都适用于 PheWAS 类型的研究，尽管 phecode 分组产生了更好的结果。
To compare three groupings of Electronic Health Record (EHR) billing codes for their ability to represent clinically meaningful phenotypes and to replicate known genetic associations. The three tested coding systems were the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) codes, the Agency for Healthcare Research and Quality Clinical Classification Software for ICD-9-CM (CCS), and manually curated “phecodes” designed to facilitate phenome-wide association studies (PheWAS) in EHRs. We selected 100 disease phenotypes and compared the ability of each coding system to accurately represent them without performing additional groupings. The 100 phenotypes included 25 randomly-chosen clinical phenotypes pursued in prior genome-wide association studies (GWAS) and another 75 common disease phenotypes mentioned across free-text problem lists from 189,289 individuals. We then evaluated the performance of each coding system to replicate known associations for 440 SNP-phenotype pairs. Out of the 100 tested clinical phenotypes, phecodes exactly matched 83, compared to 53 for ICD-9-CM and 32 for CCS. ICD-9-CM codes were typically too detailed (requiring custom groupings) while CCS codes were often not granular enough. Among 440 tested known SNP-phenotype associations, use of phecodes replicated 153 SNP-phenotype pairs compared to 143 for ICD-9-CM and 139 for CCS. Phecodes also generally produced stronger odds ratios and lower p-values for known associations than ICD-9-CM and CCS. Finally, evaluation of several SNPs via PheWAS identified novel potential signals, some seen in only using the phecode approach. Among them, rs7318369 in PEPD was associated with gastrointestinal hemorrhage. Our results suggest that the phecode groupings better align with clinical diseases mentioned in clinical practice or for genomic studies. ICD-9-CM, CCS, and phecode groupings all worked for PheWAS-type studies, though the phecode groupings produced superior results.
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影响因子：
4.5
作者：
Pendergrass SA;Brown-Gentry K;Dudek S;Frase A;Torstenson ES;Goodloe R;Ambite JL;Avery CL;Buyske S;Bůžková P;Deelman E;Fesinmeyer MD;Haiman CA;Heiss G;Hindorff LA;Hsu CN;Jackson RD;Kooperberg C;Le Marchand L;Lin Y;Matise TC;Monroe KR;Moreland L;Park SL;Reiner A;Wallace R;Wilkens LR;Crawford DC;Ritchie MD
通讯作者：
Ritchie MD
影响因子：
46.9
作者：
通讯作者：
--
影响因子：
14.9
作者：
Köhler S;Doelken SC;Mungall CJ;Bauer S;Firth HV;Bailleul-Forestier I;Black GC;Brown DL;Brudno M;Campbell J;FitzPatrick DR;Eppig JT;Jackson AP;Freson K;Girdea M;Helbig I;Hurst JA;Jähn J;Jackson LG;Kelly AM;Ledbetter DH;Mansour S;Martin CL;Moss C;Mumford A;Ouwehand WH;Park SM;Riggs ER;Scott RH;Sisodiya S;Van Vooren S;Wapner RJ;Wilkie AO;Wright CF;Vulto-van Silfhout AT;de Leeuw N;de Vries BB;Washingthon NL;Smith CL;Westerfield M;Schofield P;Ruef BJ;Gkoutos GV;Haendel M;Smedley D;Lewis SE;Robinson PN
通讯作者：
Robinson PN
DOI：
10.1136/amiajnl-2012-000896
发表时间：
2013-06-01
影响因子：
6.4
作者：
Newton, Katherine M.;Peissig, Peggy L.;Denny, Joshua C.
通讯作者：
Denny, Joshua C.
影响因子：
5
作者：
Hebbring, S. J.;Schrodi, S. J.;Ye, Z.;Zhou, Z.;Page, D.;Brilliant, M. H.
通讯作者：
Brilliant, M. H.