DxFit: An ensemble method for identifying EHR diagnoses consistent with a molecular finding

Abstract

As population DNA sequencing becomes more common, genomic-first approaches are increasingly used to identify individuals with possible rare genetic disorders. To accurately estimate prevalence and penetrance, these studies often confirm manifestation of the disorder using electronic health records (EHRs). Multiple strategies exist to search the EHR for diagnoses of rare disorders, however, each has its limitations. We have developed a portable, ensemble tool, DxFit, that mines EHR data (ICD codes and structured diagnosis descriptions from billing code and problem list tables) for a diagnosis consistent with a given rare genetic disorder. DxFit combines evidence across four strategies: (1) gene name searches in diagnosis descriptions and notes, (2) ICD conversion to Mondo rare disorder ontology to find exact and nearby matches, (3) word embedding similarity searches, and (4) Jaccard similarity matches. DxFit prioritizes the match type and outputs the most confident match for each participant-disorder pair. On a cohort of 350 participants with a known positive result from diagnostic genetic testing for developmental disorders, DxFit had a sensitivity of 88.7% and specificity of 86.2% using default parameters. Adjusting the linguistic scoring thresholds from 0.8 to 0.7 and allowing for synonymous matches yielded a sensitivity of 92.7% and specificity of 84.5%. Partitioning EHR evidence into windows before and after genetic testing demonstrates, as expected, that the overall DxFit rates increase after testing and the match types become more confident. DxFit is available to the public and has extensive customization options to support a wide range of uses. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=187 HEIGHT=200 SRC="FIGDIR/small/720629v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@d71d00org.highwire.dtl.DTLVardef@b11a9eorg.highwire.dtl.DTLVardef@14a9304org.highwire.dtl.DTLVardef@fa23aa_HPS_FORMAT_FIGEXP M_FIG C_FIG