Features Influencing Diagnostic Yield of Exome Sequencing in the DECIPHERD Study in Chile

Abstract Background Exome sequencing (ES) has become a key diagnostic tool for rare diseases (RDs). However, most evidence on ES performance comes from high-income countries and patients from European ancestry. In countries such as Chile, limited access to next generation sequencing amplifies health disparities and highlights the need to identify which patients are most likely to benefit from ES. Methods This study presents the second phase of the Chilean DECIPHERD project, in which we performed ES in a new group of patients with RDs presenting with multiple congenital anomalies (MCA), neurodevelopmental disorders (NDD), and/or suspected inborn errors of immunity. To identify clinical and demographic factors associated with an increased probability of obtaining an informative ES result, we conducted a logistic regression analysis, combining the results of the first and second phases of the project. We also objectively evaluated global ancestry measured using ADMIXTURE, as a potential factor. Results Sixty-seven patients participated in this second phase of DECIPHERD with a median age of 6 years (range: 0–27); 55.2% were female, with an average (± s.d.) proportion of Native American ancestry of 0.615 ± 0.18. Clinically, 52.2% presented with both MCA and NDD, and the rest had other phenotype combinations. An informative result, including pathogenic or likely pathogenic variants in genes consistent with the patient’s phenotype, was identified in 34.3% of the cohort; 61% of these variants had not been previously reported in databases such as ClinVar. By combining the two phases of the study, we reached a total of 167 patients, in whom the presence of NDD and/or MCA significantly increased the probability of achieving an informative ES outcome. In contrast, previous use of gene panel testing was associated with a decreased likelihood of receiving an informative result. Ancestry was not associated with diagnostic yield. Conclusions This study demonstrates the utility of ES in achieving a diagnosis in a clinically diverse cohort of Chilean patients with RDs, and characterized features associated with a higher diagnostic yield. These findings may contribute to evidence-based patient prioritization strategies in settings with limited access to NGS resources.