Characterizing trends in clinical genetic testing: A single-center analysis of EHR data from 1.8 million patients over two decades.

in American journal of human genetics by Lisa Bastarache, Rory J Tinker, Bryce A Schuler, Lucas Richter, John A Phillips, William W Stead, Gillian W Hooker, Josh F Peterson, Douglas M Ruderfer

TLDR

  • The study found that genetic testing is becoming increasingly important in healthcare, with the proportion of patients receiving genetic testing rising from 1.0% in 2002 to 6.1% in 2022.
  • The study highlights the growing role of genetic testing in explaining the observed medical phenome and demonstrating its utility in providing personalized treatment plans for patients.

Abstract

A lack of structural data in electronic health records (EHRs) makes assessing the impact of genetic testing on clinical practice challenging. We extracted clinical genetic tests from the EHRs of more than 1.8 million patients seen at Vanderbilt University Medical Center from 2002 to 2022. With these data, we quantified the use of clinical genetic testing in healthcare and described how testing patterns and results changed over time. We assessed trends in types of genetic tests, tracked usage across medical specialties, and introduced a new measure, the genetically attributable fraction (GAF), to quantify the proportion of observed phenotypes attributable to a genetic diagnosis over time. We identified 104,392 tests and 19,032 molecularly confirmed diagnoses. The proportion of patients with genetic testing in their EHRs increased from 1.0% in 2002 to 6.1% in 2022, and testing became more comprehensive with the growing use of multi-gene panels. The number of unique diseases diagnosed with genetic testing increased from 51 in 2002 to 509 in 2022, and there was a rise in the number of variants of uncertain significance. The phenome-wide GAF for 6,505,620 diagnoses made in 2022 was 0.46%, and the GAF was greater than 5% for 74 phenotypes, including pancreatic insufficiency (67%), chorea (64%), atrial septal defect (24%), microcephaly (17%), paraganglioma (17%), and ovarian cancer (6.8%). Our study provides a comprehensive quantification of the increasing role of genetic testing at a major academic medical institution and demonstrates its growing utility in explaining the observed medical phenome.

Overview

  • The study aimed to assess the impact of genetic testing on clinical practice by extracting clinical genetic tests from electronic health records (EHRs) of over 1.8 million patients at Vanderbilt University Medical Center from 2002 to 2022.
  • The research quantified the use of clinical genetic testing, tracked changes in testing patterns and results over time, and introduced a new measure, genetically attributable fraction (GAF), to assess the proportion of observed phenotypes attributable to genetic diagnoses.
  • The primary objective of the study was to provide a comprehensive quantification of the increasing role of genetic testing at a major academic medical institution and demonstrate its growing utility in explaining the observed medical phenome.

Comparative Analysis & Findings

  • The proportion of patients with genetic testing in their EHRs increased from 1.0% in 2002 to 6.1% in 2022, with testing becoming more comprehensive with the growing use of multi-gene panels.
  • The number of unique diseases diagnosed with genetic testing increased from 51 in 2002 to 509 in 2022, and there was a rise in the number of variants of uncertain significance.
  • The phenome-wide GAF for 6,505,620 diagnoses made in 2022 was 0.46%, and the GAF was greater than 5% for 74 phenotypes.

Implications and Future Directions

  • The study's findings highlight the growing importance of genetic testing in healthcare and its potential to explain the observed medical phenome.
  • Future research could focus on identifying the most effective ways to integrate genetic testing into clinical practice, addressing the challenges of interpreting variants of uncertain significance, and exploring novel applications of GAF in Precision Medicine.
  • The study's results also underscore the need for standardized data collection and sharing across healthcare institutions to facilitate the broader application of genetic testing in medicine.
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