Impact of selection bias on polygenic risk score estimates in healthcare settings

Abstract

Background Hospital-based biobanks are being increasingly considered as a resource for translating polygenic risk scores (PRS) into clinical practice. However, since these biobanks originate from patient populations, there is a possibility of bias in polygenic risk estimation due to overrepresentation of patients with higher frequency of healthcare interactions. Methods PRS for schizophrenia, bipolar disorder, and depression were calculated using summary statistics from the largest available genomic studies for a sample of 24 153 European ancestry participants in the Mass General Brigham (MGB) Biobank. To correct for selection bias, we fitted logistic regression models with inverse probability (IP) weights, which were estimated using 1839 sociodemographic, clinical, and healthcare utilization features extracted from electronic health records of 1 546 440 non-Hispanic White patients eligible to participate in the Biobank study at their first visit to the MGB-affiliated hospitals. Results Case prevalence of bipolar disorder among participants in the top decile of bipolar disorder PRS was 10.0% (95% CI 8.8–11.2%) in the unweighted analysis but only 6.2% (5.0–7.5%) when selection bias was accounted for using IP weights. Similarly, case prevalence of depression among those in the top decile of depression PRS was reduced from 33.5% (31.7–35.4%) to 28.9% (25.8–31.9%) after IP weighting. Conclusions Non-random selection of participants into volunteer biobanks may induce clinically relevant selection bias that could impact implementation of PRS in research and clinical settings. As efforts to integrate PRS in medical practice expand, recognition and mitigation of these biases should be considered and may need to be optimized in a context-specific manner.

Decoding Genetics, Ancestry, and Geospatial Context for Precision Health

“…First, most of our enrollment occurred in tertiary hospitals. While this enabled us to include patients with rare and more severe conditions, the prevalence may not reflect the general population due to inclusion bias as previously described 63 .…”

“…First, most of our enrollment occurred in tertiary hospitals. While this enabled us to include patients with rare and more severe conditions, the prevalence may not reflect the general population due to inclusion bias as previously described 63 . Second, MGBB participants are centralized in the greater Boston area of Massachusetts, which reflects the geographic location of the two main hospitals of the MGB health system.…”