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Lossless integration of multiple electronic health records for identifying pleiotropy using summary statistics.

ABSTRACT: Increasingly, clinical phenotypes with matched genetic data from bio-bank linked electronic health records (EHRs) have been used for pleiotropy analyses. Thus far, pleiotropy analysis using individual-level EHR data has been limited to data from one site. However, it is desirable to integrate EHR data from multiple sites to improve the detection power and generalizability of the results. Due to privacy concerns, individual-level patients' data are not easily shared across institutions. As a result, we introduce Sum-Share, a method designed to efficiently integrate EHR and genetic data from multiple sites to perform pleiotropy analysis. Sum-Share requires only summary-level data and one round of communication from each site, yet it produces identical test statistics compared with that of pooled individual-level data. Consequently, Sum-Share can achieve lossless integration of multiple datasets. Using real EHR data from eMERGE, Sum-Share is able to identify 1734 potential pleiotropic SNPs for five cardiovascular diseases.

SUBMITTER: Li R

PROVIDER: S-EPMC7794298 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Lossless integration of multiple electronic health records for identifying pleiotropy using summary statistics.

Li Ruowang R Duan Rui R Zhang Xinyuan X Lumley Thomas T Pendergrass Sarah S Bauer Christopher C Hakonarson Hakon H Carrell David S DS Smoller Jordan W JW Wei Wei-Qi WQ Carroll Robert R Velez Edwards Digna R DR Wiesner Georgia G Sleiman Patrick P Denny Josh C JC Mosley Jonathan D JD Ritchie Marylyn D MD Chen Yong Y Moore Jason H JH

Nature communications 20210108 1

Increasingly, clinical phenotypes with matched genetic data from bio-bank linked electronic health records (EHRs) have been used for pleiotropy analyses. Thus far, pleiotropy analysis using individual-level EHR data has been limited to data from one site. However, it is desirable to integrate EHR data from multiple sites to improve the detection power and generalizability of the results. Due to privacy concerns, individual-level patients' data are not easily shared across institutions. As a resu ...[more]

PMID: 33420026

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Project description:ObjectivePersistent somatic symptoms (PSSs) are defined as symptoms not fully explained by well-established pathophysiological mechanisms and are prevalent in up to 10% of patients in primary care. The present study aimed to explore methods to identify patients with a recognisable risk of having PSS in routine primary care data.DesignA cross-sectional study to explore four identification methods that each cover part of the broad spectrum of PSS was performed. Cases were selected based on (1) PSS-related syndrome codes, (2) PSS-related symptom codes, (3) PSS-related terminology and (4) Four-Dimensional Symptom Questionnaire scores and all methods combined.SettingCoded electronic health record data were extracted from 76 general practices in the Netherlands.ParticipantsPatients who were registered for at least 1 year during 2014-2018, were included (n=169 138).Outcome measuresIdentification methods were explored based on (1) PSS sample sizes and demographics, (2) presence of chronic conditions and (3) healthcare utilisation (HCU) variables. Overlap between methods and practice specific differences were examined.ResultsThe percentage of cases identified varied between 0.3% and 7.0% across the methods. Over 58.1% of cases had chronic physical condition(s) and over 33.8% had chronic mental condition(s). HCU was generally higher for cases selected by any method compared with the total cohort. HCU was higher for method B compared with the other methods. In 26.7% of cases, cases were selected by multiple methods. Overlap between methods was low.ConclusionsDifferent methods yielded different patient samples which were general practice specific. Therefore, for the most comprehensive data-based selection of PSS cases, a combination of methods A, C and D would be recommended. Advanced (data-driven) methods are needed to create a more sensitive algorithm for identifying the full spectrum of PSS. For clinical purposes, method B could possibly support screening of patients who are currently missed in daily practice.

Project description:There is growing interest in testing genetic pleiotropy, which is when a single genetic variant influences multiple traits. Several methods have been proposed; however, these methods have some limitations. First, all the proposed methods are based on the use of individual-level genotype and phenotype data; in contrast, for logistical, and other, reasons, summary statistics of univariate SNP-trait associations are typically only available based on meta- or mega-analyzed large genome-wide association study (GWAS) data. Second, existing tests are based on marginal pleiotropy, which cannot distinguish between direct and indirect associations of a single genetic variant with multiple traits due to correlations among the traits. Hence, it is useful to consider conditional analysis, in which a subset of traits is adjusted for another subset of traits. For example, in spite of substantial lowering of low-density lipoprotein cholesterol (LDL) with statin therapy, some patients still maintain high residual cardiovascular risk, and, for these patients, it might be helpful to reduce their triglyceride (TG) level. For this purpose, in order to identify new therapeutic targets, it would be useful to identify genetic variants with pleiotropic effects on LDL and TG after adjusting the latter for LDL; otherwise, a pleiotropic effect of a genetic variant detected by a marginal model could simply be due to its association with LDL only, given the well-known correlation between the two types of lipids. Here, we develop a new pleiotropy testing procedure based only on GWAS summary statistics that can be applied for both marginal analysis and conditional analysis. Although the main technical development is based on published union-intersection testing methods, care is needed in specifying conditional models to avoid invalid statistical estimation and inference. In addition to the previously used likelihood ratio test, we also propose using generalized estimating equations under the working independence model for robust inference. We provide numerical examples based on both simulated and real data, including two large lipid GWAS summary association datasets based on ∼100,000 and ∼189,000 samples, respectively, to demonstrate the difference between marginal and conditional analyses, as well as the effectiveness of our new approach.

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Lossless integration of multiple electronic health records for identifying pleiotropy using summary statistics.

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Lossless integration of multiple electronic health records for identifying pleiotropy using summary statistics.

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