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Analytic Methods

A Pragmatic Framework for Single-site and Multisite Data Quality Assessment in Electronic Health Record-based Clinical Research

Kahn, Michael G. MD, PhD*,†; Raebel, Marsha A. PharmD‡,§; Glanz, Jason M. PhD, MS‡,∥; Riedlinger, Karen MPH, MT (ASCP); Steiner, John F. MD, MPH

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doi: 10.1097/MLR.0b013e318257dd67
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Answers to important clinical research questions increasingly require data that are aggregated across multiple sites. Some research studies require large sample sizes to detect small but important treatment benefits or harms.1 Comparative effectiveness research (CER) studies attempt to associate naturally occurring clinical practice variations with differences in clinical outcomes. In both cases, findings arising from a multisite study are more likely to be generalizable than findings from a single site. In multisite research studies, site-level differences in disease incidence, predictive variables, and health outcomes can either represent true “small area” variation in practice patterns and outcomes,2,3 or variability in data collection methods across sites. Distinguishing between true and artifactual variation that arises from problems with data quality is an essential first step in a multisite comparative effectiveness study.

Assessing data variability across sites is particularly important in studies that use data from the electronic health records (EHRs). EHR data are gathered during routine practice by individuals with a wide range of backgrounds and with different levels of commitment to data quality. As a result, EHR data are rarely subjected to the stringent data quality assessment that is routinely applied to prospective observational or interventional research.4 If data quality issues with EHR data across sites can be identified and addressed5–7 using a standardized approach, this rich data source can increase the efficiency and reduce the costs of observational CER studies and pragmatic clinical trials.

Data quality assessments (DQAs) for multisite studies are typically performed in 2 stages. In stage 1, source datasets are created at each site and evaluated using a “fit-for-use” perspective. A comprehensive approach to the initial stage of data quality assessment in an EHR-based, multisite study requires both within-site and across-site data quality assessment using consensus standards, as multisite assessment often identifies data quality issues not evident from single-site assessment alone. These assessments typically include comparisons of simple cross-tabulations and descriptive statistics such as means, medians, and histograms across sites. Once agreed-upon standards are met, smaller analytic datasets designed to test specific hypotheses are created. Data quality assessment stage 2 is then conducted on these analytic datasets, typically focusing on the independent and dependent variables directly related to the research question. When necessary, medical record review is used in stage 2 to validate outcomes, exposures, and/or covariates.

Individual researchers tend to focus only on “data cleaning” necessary to test a hypothesis of interest within an already-assembled dataset—in other words, on stage 2. Although some investigators, data analysts, and data coordinating centers develop procedures for assessing data quality during stage 1, a comprehensive conceptual framework for this initial stage is lacking. In this paper, we present a pragmatic conceptual model for stage 1 characterization of data quality using a “fit-for-use” perspective.8,9 We then describe an approach for single-site and multisite data quality assessment in large observational studies that employ EHR data. Examples from actual multisite studies illustrate data quality issues and highlight approaches to detecting and resolving these problems.


Many frameworks have been proposed in the information sciences literature to conceptualize the multiple dimensions of data quality.10–18 All approaches acknowledge that data quality is a multidimensional process that can require trade-offs between dimensions because of organizational and data-use priorities and resource constraints. None of these approaches have been directly applied to clinical or health services research studies, however.

Recent publications in information sciences have focused on achieving data quality standards that makes the data “fit-for-use by data consumers.”19 Unfortunately, competing descriptive models have resulted in the lack of a clear unified framework for measuring data quality or procedures to improve data quality.12 In a comprehensive review, Wand and Wang listed 26 data quality dimensions. Five of these dimensions (accuracy, reliability, timeliness, relevance, and completeness) appear in most published data quality frameworks.20 Wang and Strong proposed a comprehensive “fit-for-use” data quality assessment model that encompassed both a data-element and a data-system perspective.19 In its original form, the model categorized 118 data quality features into 4 high-level categories: intrinsic features, contextual features, representational features, and accessibility. These 4 categories were used to define 15 data quality dimensions. Given the absence of conceptual frameworks for data quality in clinical or health services research, we have modified and simplified this model in Table 1, and have also provided clinical examples.

A “Fit-For-Use” Data Quality Model Adapted For Clinical Research

Clinical data quality assessment must always be considered within the design and implementation of the particular study. No standardized definitions apply across all data contexts. Yet, several uniform elements should always be considered when evaluating fitness for use. These include (a) the intended data application; (b) the quality characteristics of highest importance within the application; (c) the user’s expectations of useful information; and (d) the resources available. The weighting of each element varies from situation to situation.


Multisite research projects are comprised of data elements collected, extracted, examined, and formatted at individual sites. Combining site-specific data into a multisite dataset is rarely a straightforward process. Within each research study, specific data quality assessment routines are selected based on local knowledge of potential data problems, previous data quality concerns, or the requirements of a central data coordinating center. The data quality assessment process then proceeds through multiple iterations of within-site and cross-site assessment, as illustrated in Figure 1. Data problems identified within a single site may result in data reextraction and quality reassessment. Problems with data accuracy and with the programming used to extract and transform the data manifest at this stage. When data are aggregated across sites, additional data quality assessments may identify new anomalies, necessitating additional data quality assessment cycles at the original sites. After correction or explanation of data anomalies at each site, the data quality assessment cycle continues until datasets exceed a preestablished quality threshold (Fig. 1).

Detailed process model for multisite data quality assessment. Multiple data quality assessment cycles occur at both the single-site and multisite level. Each decision point (diamond) requires an examination of ≥1 data quality measures against predefined acceptability criteria. Many actions require continued engagement with sites to distinguish expected from unexpected site-specific data variability. HER indicates electronic health record; N, no; Y, yes.

Table 2 illustrates the results of applying the stage 1 data quality assessment process shown in Figure 1 to an EHR-based study that originally included 4 sites. In the example, the exposure was a drug dispensing within a specified timeframe and the outcome required an ICD9-CM coded diagnosis. One site had far fewer patients with the drug exposure than would be expected given its population size. Data quality assessment revealed that the site was not capturing claims for all dispensed prescriptions. When exclusion criteria were applied, this site also lost 65% of the initial cohort, in comparison with 19%–27% at the other 3 sites. Finally, no patients at this fourth site appeared to have experienced the study outcome, whereas the other three sites had between 75 and 157 outcome events. Evaluation of this discrepancy revealed that diagnostic claims were incomplete at the outlier site. The site ultimately was dropped from the study.

Example of Data Variability in Exposures and Outcomes That was not Detected With Single-site Data Quality Assessment but was Detected During Multisite Data Quality Assessment


Single-site Data Quality Assessment

The conceptual model in Table 1 ensures that relevant data quality dimensions are considered, but does not specify approaches that researchers can use to determine data quality. Specific assessment methods must be selected and executed to determine how well a given dataset meets quality expectations. Unlike the complex statistical models used to test specific study hypotheses, data quality assessment typically relies on simple distributions, cross-tabulations, and graphical visualizations to aid in inspecting data. In Table 3 we present a comprehensive set of data quality rules and quality assessment methods, adapted from Maydanchik.18 In this approach, 5 categories of rules—attribute domain constraints, relational integrity, historical integrity, state-dependent rules, and attribute dependency rules—are operationalized through multiple assessment methods.

Data Quality Assessment Methods and Rules

Attribute domain constraints focus on individual variables, looking for anomalies in data values, distributions, units, and missingness. For example, a date of birth in the year 1390 would be identified as an invalid value (perhaps a digit transposition for the year 1930). A comparison of simple descriptive statistics for prescription claims in Table 2 identified a missing data problem at 1 site.

Relational integrity rules look for inconsistencies across multiple-related variables, seeking to detect data quality issues in comparing elements from 1 data table to related elements in another data table. These rules are often called “double-checks” and “triple-checks.” As an example, a count of 8 prescriptions in a summary table should correspond to 8 filled prescriptions in the original pharmacy table.

Historical data rules assess temporal relationships. The large number of assessment methods in this category emphasizes the complex temporal in most datasets. Historical rules examine sequences, gaps, patterns and dependencies across multiple data values, and variables. For example, an individual who died in 2008 cannot have a hospitalization in 2009.

State-dependent objects rules extend the analysis of temporal data to include logical consistency, where the sequence of temporal events conforms to knowledge about the expected or allowed evolution of a process or set of states over time. For example, a series of prenatal visits would be expected to culminate in an outcome (such as a birth), and then be followed by a postpartum checkup. Similarly, assessing the impact of changes in coding schemes or allowed values over time would be included in this class of data quality assessments.

Attribute dependency rules are the most complex because they combine real-world knowledge about how objects and processes are measured and represented in a dataset. These rules examine conditional dependencies and expected correlations across subsets of data and aggregates. For example, a postpartum checkup would be unlikely to occur 18 months after the delivery date.

Rote application of all data quality assessment methods in Table 3 to a dataset would result in thousands of actual data quality measures. The resources in a research study are never sufficient to assess all data elements against all data quality dimensions. Thus, prioritization is critical. For a given study, the set of critical data quality assessment methods will vary on the basis of the features of the variables that drive the key scientific questions. However, in general, the DQA methods listed under the “attribute domain constraints” and “relational integrity rules” in Table 3 can be applied broadly across all data elements in a dataset or database.

As an example, the Observational Source Characteristics Analysis Report (OSCAR) tool developed by the Observational Medical Outcomes Partnership (OMOP) program generates summary statistics for all categorical and continuous variables, resulting in thousands of assessments without any prioritization.21 The related Generalized Review of OSCAR Uniform Checking (GROUCH) tool extracts only those OSCAR measures that fail to meet prespecified data quality specifications.22 These thresholds can be set for all categorical or continuous variables or for individual variables in the dataset. The OSCAR tool is comprehensive but nonselective; the GROUCH tool provides prioritization and specificity.


Local data entry processes, data quality validation checks, data storage models, and data extraction routines affect the data structure at a single site. The term syntactic variability expresses data variability caused by differences in the representation of data elements. For example, weights may be recorded and stored in different locations within an EHR, and in different formats or units. Failure to extract data from all locations and to transform into a common format would result in incomplete data. Syntactic issues tend to be detectable and resolvable using single-site data.

When data are combined from multiple sites, data that are syntactically identical (same format, same units) can show important differences if data elements that supposedly represent the same concept actually represent different concepts at each site. The term semantic variability expresses data variability caused by differences in the meaning of data elements. Differences in data collection, abstraction and extraction methods, or measurement protocols can result in semantic variability. For example, failure to distinguish between fasting and random blood glucose, finger-stick or venipuncture sampling, or serum or plasma measurements would result in glucose values that do not represent the same concept. Semantic variability is difficult to detect using single-site data alone because data semantics tend to be consistent within an institution. Only when data are combined from multiple sites can such semantic differences be detected.

The assessment methods in Table 3 were developed to assess single-site data quality. Few standardized approaches have been proposed to extend such single-site data quality assessment methods to multisite data. Two standardized approaches in clinical and health services research are: (1) The OMOP GROUCH data quality analysis tool described previously; and (2) The HMO Research Network (HMORN) Virtual Data Warehouse (VDW). The OMOP GROUCH tool implements 35 data quality rules. Eleven rules explicitly compare OSCAR-generated data quality measures from 1 site against all other sites.22 The HMORN VDW research resource maintains a standardized quality assessment battery of SAS programs that enables all HMORN sites to evaluate their VDW data tables in comparison with a standardized set of “pass/fail” metrics common across all HMORN sites and to evaluate within-site attribute domain constraints, relational integrity, and historical integrity.23

In multisite data comparisons, calculation of simple descriptive statistics such as expected event rates, frequency distributions, and time trends allows detection of typical semantic anomalies such as: wide variation in counts or event rates, differences in distributions (eg, histograms) and temporal trends, including sudden deviation from previous trends, and the degree of missing data (as exemplified in Table 2). Such differences may be quite pronounced. In Figure 2, we provide a comparison of fasting serum glucose tests completed per 1000 patients at 7 different sites over a 6-year period. The data in this figure starkly demonstrate 4 different quality anomalies.

Variability over time and across sites in number of serum fasting glucose tests performed per 1000 patients.

An observed site-level deviation in stage 1 does not necessarily indicate a data quality issue. True differences in populations, measurement processes, clinical workflows, or treatment strategies can result in significant differences across data sources. Such naturally occurring variation in clinical practice has been a source of important research for many years.3,24,25 The data quality assessment process in Figure 1 will detect these differences, but cannot always explain them. As highlighted in Figures 1 and 2, observed anomalies need to be interpreted in collaboration with the local site to determine if the differences can be explained by factors other than data quality. Site data owners have intimate knowledge about local workflows, data collection conventions, and changes in technologies (new systems, new updates, expanded implementations) that usually are not known to multisite collaborators.

In dynamic datasets that are regularly updated, information gleaned from previous data quality assessments within and between sites can identify areas that need extra evaluation during subsequent data quality assessments. For example, the HMORN VDW conducts across-site quality assessment yearly, whereas within-site assessment of previously identified data quality concerns occurs during the intervening months. By guiding resources and attention to known data quality concerns, data efficiency and consistency from each primary site improve over time.

Detailed documentation of the rationale for conducting data quality assessment and the outcomes of those assessments is essential, because every data quality assessment plan is a compromise between limited time and resources and the desire for the highest possible data quality. Investigators must be aware that, in many cases, data quality decisions are made by database managers and programmers who provide support to multiple studies that rely on the same data sources. Investigators may not be aware of crucial data quality decisions unless they are recorded and accessible.


A more standardized and comprehensive approach to stage 1 data quality assessment is likely to improve the validity of multisite, EHR-based comparative effectiveness research. When data variability across multiple sites reflects true differences in clinical practice, researchers gain the opportunity to measure medication comparative safety and effectiveness, procedures and tests utilization in an observational setting. Once variability is identified and data quality problems are eliminated, traditional stage 2 data quality approaches such as manual chart review (ideally using the EHR, but at times requiring manual record review) can be used to assure the validity of critical exposure and outcome variables. Numerous studies using manual record review as the “gold standard” have demonstrated that automated clinical data from managed-care organizations can inaccurately measure disease incidence, with positive predictive values as low as 20%.26–30 These inaccuracies can be independent or dependent of treatment status, thus leading to differential or nondifferential misclassification bias that can result in both false-positive and false-negative study findings.31 Although manual medical record review can provide a “gold standard” for validating automated clinical data, it is expensive and time consuming, and thus cannot be used routinely in stage 1 data quality assessments. Developing automated stage 1 methods to identify and resolve data anomalies across multiple sites is therefore essential to both the efficiency and the validity of CER studies that rely on cross-site comparisons.

In recent years, decentralized data models for multisite research (distributed research networks, or DRNs) have been developed that bypass the need to transfer data containing protected health information to a central data warehouse.32–40 In a DRN, a centralized data coordinating center may still be responsible for data quality assessment. But as the data are not pooled, the data coordinating center must devote more attention to planning and conducting quality assessment. In a DRN, the data coordinating center distributes programming code to all participating sites. A programmer then reviews and runs the code on local data, and sends the results back to the data coordinating center for evaluation. Such a process can potentially be less efficient than a traditional centralized model initially. However, the preparatory work required in DRN assessment may lead to progressive improvements in data quality over time, as programmers have to anticipate data issues and write their code to reduce inefficiencies.

In 2010, the President’s Council of Advisors on Science and Technology (PCAST) report recommended the use of mandatory “metadata” tags attached to every data element.41 These tags provide additional information about the data element, such as where the data was created (data provenance) and privacy permissions and restrictions. These metadata tags could be expanded to include the data quality measures as listed in Table 3, either as a single summary data quality statistic or as individual values for specific data quality measures that were applied to the data before release. An example of data quality metadata tags for continuous variables would be tags that include the attribute’s mean, median, SD, interquartile range, and percentage missing across the original dataset. The simple distribution measures created by the OMOP OSCAR tool could be a useful initial set of data quality metadata tags consistent with the PCAST recommendation.

Data quality metadata tags are analogous to other metadata documentation that is required to support effective data sharing across institutions. Because data sharing is a National Institutes of Health priority,42 appropriate resources should be included in the study budget directed explicitly to metadata documentation, including documenting data quality assessment results. In the future, new informatics tools could be developed that could perform data quality and automatically attach the appropriate DQA metadata tags and assessment results directly to the dataset.


Few publications have described the use of data quality models in health care data.43–46 One case study in a large national intensive care unit registry examined the causes of error that influenced data accuracy and completeness at local sites and at a central coordinating center.44 This paper categorized data errors into 3 categories (setup and organization, data collection, and quality improvement), described error-promoting processes at data collection sites and at the central coordinating center, and proposed a comprehensive framework for improving data quality. This paper did not address most elements of the conceptual model in Table 2, and did not describe in detail the approaches used to identify and correct those data quality issues.

Because the literature is sparse, and because systematic approaches to stage 1 data quality assessment have not been proposed for both single-site and multisite projects, a conceptual framework is useful for addressing data variability in a logical and comprehensive manner. This framework can be translated into a rigorously applied strategy for data quality assessment, which defines data quality dimensions and assessment methods to assess the variability in a multisite dataset. To execute this strategy in a multisite study, a strong collaborative relationship between members of the data coordinating center and the individual sites is essential because identifying and correcting data errors is of necessity iterative. If well-designed, this strategy assures that data quality issues discovered at individual sites can be used to improve data quality for subsequent studies.

If the variability in populations, treatment exposures, and clinical outcomes is due to true “small area variations” in clinical practice or health plan benefit design, CER studies can provide critical information about medical treatment effectiveness and safety or innovations in care delivery across broad populations. However, apparent data variability because of unrecognized data quality problems has the potential to invalidate study findings. Careful differentiation between real and spurious data variability at both the single-site and multisite level is essential if the promise of CER is to be achieved.


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data quality; data quality assessment; single-site studies; multisite studies

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