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The effects of electronic medical record phenotyping details on genetic association studies: hdl-c as a case studyDumitrescu et al. BioData Mining (2015) 8:15 DOI 10.1186/s13040-015-0048-2 The effects of electronic medical recordphenotyping details on genetic associationstudies: HDL-C as a case study Logan Dumitrescu1,2, Robert Goodloe1,2, Yukiko Bradford3, Eric Farber-Eger1, Jonathan Boston1and Dana C Crawford4* * Correspondence: 4Department of Epidemiology and Background: Biorepositories linked to de-identified electronic medical records Biostatistics, Institute forComputational Biology, Case (EMRs) have the potential to complement traditional epidemiologic studies in Western Reserve University, genotype-phenotype studies of complex human diseases and traits. A major challenge Wolstein Research Building, 2103 in meeting this potential is the use of EMR-derived data to extract phenotypes and Cornell Road, Suite 2527, Cleveland,OH 44106, USA covariates for genetic association studies. Unlike traditional epidemiologic data, Full list of author information is EMR-derived data are collected for clinical care and are therefore highly variable across available at the end of the article patients. The variability of clinical data coupled with the challenges associated withsearching unstructured clinical notes requires the development of algorithms toextract phenotypes for analysis. Given the number of possible algorithms that couldbe developed for any one EMR-derived phenotype, we explored here the impactalgorithm decision logic has on genetic association study results for a singlequantitative trait, high density lipoprotein cholesterol (HDL-C).
Results: We used five different algorithms to extract HDL-C from African Americansubjects genotyped on the Illumina Metabochip (n = 11,519) as part of EpidemiologicArchitecture for Genes Linked to Environment (EAGLE). Tests of association betweenHDL-C and genetic risk scores for HDL-C associated variants suggest that the geneticeffect size does not vary substantially across the five HDL-C definitions.
Conclusions: These data collectively suggest that, at least for this quantitative trait,algorithm decision logic and phenotyping details do not appreciably impact geneticassociation study test statistics.
Keywords: Electronic medical record, Genetic risk score, HDL-C, eMERGE network,PAGE I study Biorepositories linked to de-identified electronic medical records (EMR) are an emerging resource for genetic association studies Compared with traditional epidemiologic studies, EMR-based studies offer multiple advantages including relative ease of ascertainment, rapid accrual of samples and associated data, longitudinal measures, and the potential for lengthy follow-up. Another major advantage of EMR-based or clinic-based studies is their potential for pharmaocogenomics and other applications associated with personalized medicine.
2015 Dumitrescu et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the CreativeCommons Attribution License which permits unrestricted use, distribution, andreproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedicationwaiver applies to the data made available in this article, unless otherwisestated.
Dumitrescu et al. BioData Mining (2015) 8:15 While clinic-based studies linked to EMRs offer multiple advantages, they also offer multiple challenges when accessed for research such as genetic association studies. A major challenge of the EMR is that the data are not collected for research purposes; that is, the data are collected as part of routine clinical care.
Therefore, unlike traditional epidemiologic studies, there is no "baseline" measurementor examination of all study participants, and the number of overall measurements and exams can vary widely by patient. This variability is in stark contrast to longitudinal epidemiologic studies where participants are surveyed and examined uniformly every few years.
Because of the variable and somewhat erratic nature of the EMR data, investigators accessing these data for genetic association studies must make specific decisions in de- veloping phenotype algorithms designed to extract outcomes and covariates for ana- lysis. For example, for a commonly studied measurement such as body mass index, the investigator has multiple options including the first height and weight mentioned, the last height and weight mentioned, an average of all heights and weights mentioned for all clinic visits, the height and weight mentioned closest to another clinical diagnosis (such as type 2 diabetes), and so on.
Many of the challenges associated with EMR-based phenotyping are being addressed by collaborative consortiums such as the electronic MEdical Records and GEnomics (eMERGE) network, a cooperative group of several DNA biorepositories in the United States linked to EMRs funded by the National Human Genome Research Institute A major goal of the eMERGE network is the development of portable algorithms designed to define disease outcomes for use in genetic association studies [. Algorithms developed under eMERGE have been used successfully for single study site and well as eMERGE-wide studies the latter of which demonstrate the portability of these algorithms despite possible variations in clinical practice. A portion of the eMERGE EMR-derived phenotypes have also been mapped back to PhenX variables using the PhenX Toolkit suggesting that EMR-derived phenotypes are comparable to epidemiologic collected The eMERGE network has been successful in designing and implementing EMR- based algorithms for multiple phenotypes; however, it is unclear if the decision logic underlying each algorithm for phenotypes with repeated measures impacts downstream analyses for genetic association studies. To explore this possible impact, we as the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) as part of the larger Population Architecture using Genomics and Epidemiology (PAGE) I study conducted a genetic association study for the commonly measured and studied high density lipoprotein cholesterol (HDL-C). We created five HDL-C algorithms to extract this quantitative trait from African American subjects genotyped with the Illumina Metabochip [and available in BioVU, the Vanderbilt biorepository linked to de-identified electronic medical records ]. Overall, we demonstrate that the genetic effect size estimates and levels of significance are similar across all HDL-C extraction methods attempted suggesting that commonly used decision logic for repeated measures in the EMR may not have appreciable impacts on downstream analyses conducted for genetic Dumitrescu et al. BioData Mining (2015) 8:15 All study subjects are drawn from BioVU, Vanderbilt University Medical Center'sbiorespository linked to de-identified electronic medical records. A description of BioVU, including its oversight and ethics, has been previously published In brief, DNA is extracted from discarded blood samples drawn for routine clinical care from Vanderbilt University affiliated outpatient clinics. The DNA sample is linked to the patient's de-identified EMR known as the Synthetic Derivative (SD).
The SD contains billing (ICD-9) codes, procedure codes and labs. Prescription medication, including dose, is available in the SD through MedEx , an algorithm that extracts medications and their signature mentions from free-text entries available in the EMR. The SD also contains all clinical notes.
As EAGLE, a study site of PAGE I, we genotyped mostly non-European descent DNA samples available in BioVU as of 2011 on the Illumina Metabochip (described below), hereto referred as "EAGLE BioVU" (n = 15,863) The present study is limitedto African Americans within EAGLE BioVU (n = 11,519).
HDL-C definitions HDL-C measurements were extracted from a de-identified EMR using five different methods. First, for each subject, the median HDL-C value of all documented HDL-C measurements was collected ("All HDL-C"). Next, both first and last reported HDL-Cwere mined from the subject's laboratory data ("First HDL-C" and "Last HDL-C").
Lastly, HDL-C values were extracted for subjects both prior to ("pre-medicationHDL-C") or following ("post-medication HDL-C") evidence of lipid-lowering medicationsand the median value was reported. EAGLE BioVU clinical notes were searched for evidence of lipid-lowering drugs for each subject using medication class as well as medication generic and brand names (Table For each mention of lipid-lowering drug use, we extracted the date of medication mention to compare against date of HDL-C lab to determine if that measurement of HDL-C was "pre-medication" or Table 1 Lipid-lowering medication class and list of drugs Gemfibrozil (Lopid®) Atorvastatin (Lipitor®) Questran® Light, Prevalite®,Locholest®, Locholest® Light) Fenofibrate (Antara®, Colestipol (Colestid®) Fluvastatin (Lescol®) Lofibra®, Tricor®, Triglide™) Clofibrate (Atromid-S) Colesevelam Hcl (WelChol®) Lovastatin (Mevacor® and Altoprev™) Rosuvastatin Calcium (Crestor®) Simvastatin (Zocor®) Lovastatin + niacin (Advicor®) Atorovastatin + amlodipine (Caduet®) Simvastatin + ezetimibe (Vytorin™) Four major medication classes containing lipid-lowering medications were used to search the clinical notes: fibrates,niacin, resins, selective cholesterol absorption inhibitors (Ezetimibe or Zetia®), and statins (also known an HMG CoAreductase inhibitors). For each of the medication classes included in the search, we have listed the specific drugsconsidered, including both the generic and brand names.
Dumitrescu et al. BioData Mining (2015) 8:15 "post-medication." Subjects with no evidence of lipid-lowering medication prescriptionswere considered "pre-medication HDL-C." All HDL-C values used in this analysis werecollected when the subject was 18 years or older.
Genotyping and SNP selection A total of 15,863 DNA samples from mostly non-European descent subjects were genotyped on the Illumina Metabochip, including 11,519 African Americans, by Vanderbilt University Center for Human Genetics Research DNA Resources Core. The Illumina Metabochip is a custom array of approximately 200,000 variants chosen as GWAS-identified index variants or GWAS-identified regions for fine-mapping based on data from the first iteration of the 1000 Genomes Project Quality control of the Illumina Metabochip data for EAGLE BioVU followed the quality control procedures outlined in Buyske et al. [.
Based on a previous fine-mapping study of HDL-C using Metabochip , seven of the 22 fine-mapped HDL-C loci exhibited evidence of association at p < 1x10−4 in African Americans. The seven index SNPs from these seven associated HDL-C loci were selected for use in calculating the genetic risk score (GRS, Table .
Statistical methods Both a weighted and unweighted GRS were calculated in PLINK In general, the GRS is calculated for each subject by counting the number of effect alleles (0, 1, or 2) across each SNP, multiplying that number by the known effect size (for the unweighted GRS, effect sizes were set equal to one), summing those values, and dividing by the number of non-missing SNPs, thus providing the average score per SNP. Effect estimates for the weighted GRS were based on the meta-analysis of PAGE African Americans .
Linear regression, adjusted for sex, with GRS as the independent variable and HDL-C measurement as the dependent variable was used to determine the beta coefficient.
Approximately 43% of the 11,519 African American subjects genotyped on the Illumina Metabochip as part of EAGLE had at least one HDL-C measurement available in the EMR (Table The median number of clinic visits and medical records lengths in years was three each while the median ICD-9 code mentions (for unique codes) was 54. The median value for HDL-C ranged from 48–51 across the five different HDL-Cdefinitions explored here (Table Table 2 SNPs used to calculate the genetic risk score for HDL-C in African Americans Effect on HDL-C† (mg/dl) †Beta coefficients were drawn from meta-analysis results of PAGE African Americans Dumitrescu et al. BioData Mining (2015) 8:15 Table 3 EAGLE BioVU African American demographics for HDL-C Medical record length (years) Clinic visits (N) ICD-9 codes (N)† All HDL-C (mg/dl) First HDL-C (mg/dl) Last HDL-C (mg/dl) pre-medication HDL-C (mg/dl) post-medication HDL-C (mg/dl) Number of observations (No. Obs.) as well as medians and interquartile ranges (IQR) are given for each variable. †Includesonly unique ICD-9 codes per individual.
We first calculated the unweighted GRS using seven HDL-C associated variants (Table for each African American in EAGLE BioVU with at least one HDL-C measurement. The number of HDL-C risk alleles ranged from 3 to 12, which the majority of subjects having 8 risk alleles (Figure .
We then performed tests of association for each of the five HDL-C definitions using the unweighted GRS as the independent variable. The unweighted GRS was significantly associated with each of the five HDL-C definitions, and the levels of significance ranged from 4.06 × 10−86 (post-medication HDL-C; n = 2,085) to 3.73 × 10−197 (first HDL-C; n = 4,910). Because level of significance is influenced by sample size, we then plotted each resulting beta and 95% confidence intervals to compare the effect sizes of the unweighted GRS across the five different HDL-C definitions (Figure ).
The unweighted GRS effect size was similar across the five different HDL-C definitions (Figure . Results from the weighted GRS do not appreciably differ from the unweighted results (data not shown).
We demonstrate here that for HDL-C, a commonly studied quantitative trait for cardiovascular disease risk, algorithm decision logic and phenotyping details applied to repeated measures available in the EMR do not appreciably affect downstream Figure 1 Distribution of HDL-C risk alleles in EAGLE BioVU African Americans.
Dumitrescu et al. BioData Mining (2015) 8:15 Figure 2 Additive effects of HDL-C risk alleles on various HDL-C measurements. Effect sizes (betas) from thelinear regression analysis with the unweighted GRS, adjusted for sex, are shown as expected HDL-C levels(in mg/dl; black diamonds), along with their 95% confidence intervals.
genetic association test statistics or overall study conclusions. These data, along with on-going algorithm development within the eMERGE network suggest that phenotypes derived from EMR-based repositories are robust to the underlying variability inherent in clinical collections. Although not explicitly tested here, the similarities of genetic effect sizes observed here for the five HDL-C definitions in the same sample suggest that any one of these EMR-derived test statistics robust to algorithm decision logic can be included in meta-analyses with traditional epidemiologic While our data suggest that EMR-derived phenotypes may be robust to certain aspects of the algorithm decision logic and phenotyping details, these data do not imply that genetic association studies are not impacted by poor phenotyping. Substantial literature has documented the need for rigorous case/control phenotyping as misclassification of either can lead to loss of power [Careful phenotyping can also lead to insights into biological mechanisms or disease processes ]. Finally, careful phenotyping is also essential for creative study design and genetic discovery ].
The present study focuses on examining the impact algorithm decision logic has on genetic associations related to a single quantitative trait, HDL-C. As such, the conclusions offered here may be limited to HDL-C or to quantitative traits defined from repeated measures available in the EMR. Further study is needed to more fully explore the limitations and impact algorithm decision logic may have on genetic association studies for binary clinical outcomes such as myocardial infarction or pharmacogenomic studies for traits such as warfarin dosing. For the HDL-C data included here, additional limitations of the present study include limitations associated with extracting HDL-C from the EMR. For example, we searched clinic notes for mentions of lipid-lowering medication classes and drugs (genetic and brand names), but we did not include any common misspellings of these search terms. It is possible, therefore, that the"pre-medication" HDL-C definition contains HDL-C measurements while the subject wason lipid-lowering medication. Another limitation of the EMR is that, unlike most epidemiologic studies, fasting status or time to last meal is not available as a structured field. Here, we assumed that the HDL-C measured in EAGLE BioVU was measured for subjects who fasted for at least eight hours. This assumption is most likely incorrect, but its violation is unlikely to impact HDL-C levels substantially.
Dumitrescu et al. BioData Mining (2015) 8:15 Another limitation of the present study is related to sample size and power. We present here tests of association between various HDL-C derived variables and an unweighted GRS. The unweighted GRS, by design, is calculated by the number of risk alleles at loci known to be significantly associated with HDL-C levels. Therefore, with only a few thousand samples, we were able to statistically replicate the expected association between the unweighted GRS and the various HDL-C variables to further examine the genetic effect sizes estimated from these tests of associations. While the sample size of the present study was large enough for replicating known associations such as the loci represented in the unweighted GRS, the sample size is not large enough to perform discovery studies with the entire Metabochip dataset, even when limited to common variation (minor allele frequency >5%). Indeed, tests of association between the various HDL-C variables and common variants on the Metabochip failed to identify a statistically significant association after correction for multiple testing (data not shown). Furthermore, neither significance rankings nor genetic effect sizes could be reliably compared across HDL-C variables given the chance findings of non-significant tests of associations. Larger sample sizes are needed to make comprehensive comparisons of genetic effect sizes and significance rankings for EMR-derived phenotypes susceptible to algorithm decision logic and pheno- typing details.
Despite the limitations, this study had multiple strengths including the depth of the clinical data and the diversity of EAGLE BioVU. EMR-derived datasets such as EAGLE BioVU coupled with genotype and sequence data promise to enrich existing and complimentary datasets for future genetic association studies for complex human diseases These data collectively suggest that, at least for HDL-C, algorithm decision logic and phenotyping details do not appreciably impact genetics association study tests statistics.
Competing interestsThe authors declare that they have no competing interests.
Authors' contributionsDCC and LD designed the experiment. RG, YB, EF-E, and JB performed the data extraction, performed the genotypingquality control, and assisted in the analysis. LD performed the main analyses and drafted the manuscript. DCC securedthe major funding for the project. All authors read and approved the final manuscript.
AcknowledgementsThe dataset(s) used for the analyses described were obtained from Vanderbilt University Medical Center's BioVU whichis supported by institutional funding and by the Vanderbilt CTSA grant UL1 TR000445 from NCATS/NIH. This work issupported in part by NIH U01 HG004798 and its ARRA supplements, NIH U01 HG006378, NIH U01 HG004603, and NIHU01 HG006385. The Vanderbilt University Center for Human Genetics Research, Computational Genomics Coreprovided computational and/or analytical support for this work.
Author details1Center for Human Genetics Research, Vanderbilt University, 2215 Garland Avenue, 519 Light Hall, Nashville, TN 37232,USA. 2Department of Molecular Physiology and Biophysics, Vanderbilt University, 2215 Garland Avenue, 519 Light Hall,Nashville, TN 37232, USA. 3Center for Systems Genomics, Department of Biochemistry and Molecular Biology, ThePennsylvania State University, 512 Wartik Laboratory, University Park, PA 16802, USA. 4Department of Epidemiology andBiostatistics, Institute for Computational Biology, Case Western Reserve University, Wolstein Research Building, 2103Cornell Road, Suite 2527, Cleveland, OH 44106, USA.
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