Use of Computational Phenotypes for Predicting Genetic Subgroups of Cerebral Palsy

Emerging evidence suggests that 20%-30% of cases of cerebral palsy (CP) may have a genetic cause. Our group previously identified subsets of patients with CP or CP-masquerading conditions who warrant genetic testing, including those with regression or progressive neurological symptoms (CP masqueraders) and those without any known risk factors for CP (cryptogenic CP). Recognition of these subgroups in clinical settings remains challenging.

To address this challenge, we developed and evaluated a computational phenotyping approach using international classification of diseases (ICD)-9/ICD-10 billing codes to automatically identify patients with unexplained CP or CP-masquerading conditions who may benefit from genetic testing. We applied this computational phenotyping approach to a cohort of 250 participants from the Boston Children's Hospital CP Sequencing Study, aimed at identifying genetic causes in CP and CP-masquerading conditions.

Manual review served as the gold standard, identifying 8% as CP masqueraders, 42% as cryptogenic CP, and 50% as noncryptogenic CP. Computational phenotyping based on ICD-9/ICD-10 codes achieved a sensitivity of 95%, specificity of 72%, positive predictive value of 77%, and negative predictive value of 94% in identifying cases warranting genetic testing.

Our findings demonstrate the feasibility of using computational phenotyping to identify patients with CP or CP-masquerading conditions who warrant genetic testing. Further studies are needed to evaluate the effectiveness and real-world application of this tool in larger health care systems. Nevertheless, the computational phenotyping approach holds promise as a possible clinical decision support that could be integrated into electronic health record systems, enhancing clinical workflows and facilitating actionable genetic diagnoses.