Electronic health record phenotypes associated with genetically regulated expression of CFTR and application to cystic fibrosis.

TitleElectronic health record phenotypes associated with genetically regulated expression of CFTR and application to cystic fibrosis.
Publication TypeJournal Article
Year of Publication2020
AuthorsZhong, X, Yin, Z, Jia, G, Zhou, D, Wei, Q, Faucon, A, Evans, P, Gamazon, ER, Li, B, Tao, R, Rzhetsky, A, Bastarache, L, Cox, NJ
JournalGenet Med
Date Published2020 Apr 16
ISSN1530-0366
Abstract

PURPOSE: The increasing use of electronic health records (EHRs) and biobanks offers unique opportunities to study Mendelian diseases. We described a novel approach to summarize clinical manifestations from patient EHRs into phenotypic evidence for cystic fibrosis (CF) with potential to alert unrecognized patients of the disease.

METHODS: We estimated genetically predicted expression (GReX) of cystic fibrosis transmembrane conductance regulator (CFTR) and tested for association with clinical diagnoses in the Vanderbilt University biobank (N = 9142 persons of European descent with 71 cases of CF). The top associated EHR phenotypes were assessed in combination as a phenotype risk score (PheRS) for discriminating CF case status in an additional 2.8 million patients from Vanderbilt University Medical Center (VUMC) and 125,305 adult patients including 25,314 CF cases from MarketScan, an independent external cohort.

RESULTS: GReX of CFTR was associated with EHR phenotypes consistent with CF. PheRS constructed using the EHR phenotypes and weights discovered by the genetic associations improved discriminative power for CF over the initially proposed PheRS in both VUMC and MarketScan.

CONCLUSION: Our study demonstrates the power of EHRs for clinical description of CF and the benefits of using a genetics-informed weighing scheme in construction of a phenotype risk score. This research may find broad applications for phenomic studies of Mendelian disease genes.

DOI10.1038/s41436-020-0786-5
Alternate JournalGenet. Med.
PubMed ID32296164
Grant ListR35 HG010718 / HG / NHGRI NIH HHS / United States
W911NF1410333 / / Defense Advanced Research Projects Agency (US) /
U01HG009086 / NH / NIH HHS / United States