Exome sequencing early in outpatient evaluation in NCGENES 2: Changing the course of the diagnostic odyssey?

The impact of clinical exome and genome sequencing (ES/GS) depends on the clinical setting. In the sequencing arm of a multifactor randomized clinical trial to evaluate broadening access, we assessed the diagnostic and inconclusive findings of ES as a "first-tier" test in 101 pediatric participants in whom suspicion of a genetic condition by primary care providers had prompted initial outpatient consultation in a pediatric genetics or neurology clinic. This implementation focused on the early stages of the diagnostic odyssey, capturing a clinically less-selected population with lower pre-test probability than traditional specialist cohorts. Variants were prioritized using phenotype-driven gene lists. After returning the results to participants, the clinical teams performed familial variant testing or additional phenotyping at their discretion, based on potential diagnostic benefit. We then implemented a multidisciplinary case conference in which the laboratory and clinical teams assessed additional clinical information. Initially, 57% of participants had non-negative reports: 5% had one or more variant findings considered explanatory for the presenting phenotype, with 52% having results initially classified as inconclusive. After family testing and/or phenotypic characterization, a total of 9% were considered positive/diagnostic, 10% were reclassified from inconclusive to negative, and 38% remained inconclusive. While ES, as a first-tier genetic test, can expedite some diagnoses, these results demonstrate challenges in early implementation. In this population, initial testing can leave substantial residual uncertainty, shifting the diagnostic odyssey rather than concluding it and necessitating factors such as parental testing, ongoing phenotyping, and reassessment of variants over time to resolve inconclusive results.