Molecular Diagnostic Outcomes from 700 Cases
Jill R. Murrell, Addie Nesbitt, Samuel W. Baker, Kieran B. Pechter, Jorune Balciuniene, Xiaonan Zhao, Elizabeth H. Denenberg, Elizabeth T. DeChene, Chao Wu, Pushkala Jayaraman, Kajia Cao, Michael Gonzalez, Marcella Devoto, Alessandro Testori, John D Monos, Matthew C. Dulik, Laura K. Conlin, Minjie Luo, Kristin McDonald Gibson, Qiaoning Guan, Mahdi Sarmady, Elizabeth Bhoj, Ingo Helbig, Elaine H. Zackai, Emma Bedoukian, Alisha Wilkens, Jennifer Tarpinian, Kosuke Izumi, Cara Skraban, Matthew A. Deardorff, Līvija Medne, Ian D. Krantz, Bryan L. Krock, Avni Santani
Abstract
Clinical exome sequencing (CES) aids in the diagnosis of rare genetic disorders. Herein, we report the molecular diagnostic yield and spectrum of genetic alterations contributing to disease in 700 pediatric cases analyzed at the Children's Hospital of Philadelphia. The overall diagnostic yield was 23%, with three cases having more than one molecular diagnosis and 2.6% having secondary/additional findings. A candidate gene finding was reported in another 8.4% of cases. The clinical indications with the highest diagnostic yield were neurodevelopmental disorders (including seizures), whereas immune- and oncology-related indications were negatively associated with molecular diagnosis. The rapid expansion of knowledge regarding the genome's role in human disease necessitates reanalysis of CES samples. To capture these new discoveries, a subset of cases (n = 240) underwent reanalysis, with an increase in diagnostic yield. We describe our experience reporting CES results in a pediatric setting, including reporting of secondary findings, reporting newly discovered genetic conditions, and revisiting negative test results. Finally, we highlight the challenges associated with implementing critical updates to the CES workflow. Although these updates are necessary, they demand an investment of time and resources from the laboratory. In summary, these data demonstrate the clinical utility of exome sequencing and reanalysis, while highlighting the critical considerations for continuous improvement of a CES test in a clinical laboratory.