Integrating genome and RNA sequencing to enhance diagnostic precision in cerebral palsy

Cerebral palsy (CP), a group of permanent disorders of the development of movement and posture affecting developing fetal or infant brain, shows considerable genetic diversity. Genetic diagnosis is not yet the first-tier diagnostic test for CP. This study aimed to diagnose patients with CP and explore novel diagnostic strategies. This study cohort comprised 27 children diagnosed with CP and their asymptomatic parents. Whole-Genome Sequencing and RNA sequencing were employed for genetic diagnostics in these children. The R package Gene Set Variation Analysis was employed to evaluate the pathway enrichment variations between the samples. Family-based Whole-Genome Sequencing diagnostics identified pathogenic or likely pathogenic variants in 2 children and variants of uncertain significance in 7 children. A total of 216 genes with damaging de novo variant were found, including 3 genes previously associated to CP: PROC, WDR81, and SPTBN2. Additionally, 22 genes contained two or more damaging de novo variants. RNA-seq analysis revealed 5 candidate genes with abnormal expression and 250 candidate events with abnormal alternative splicing. Notably, highly reliable alternative splicing sites were found in DNMT1 and VPS13C. Furthermore, pathway analysis identified aberrant pathways that may help determine the underlying cause. This approach uncovered 3 abnormal pathways related to neurological functions in 2 children and a deleterious de novo variant in the S1PR4 gene. These findings supported the application of genetic diagnostics in CP and suggested that a combined approach using genomics and transcriptomics is more comprehensive and reliable. Therefore, we advocated for genetic diagnostics as the first-tier diagnostic test for CP, which not only aids in understanding the etiology but also provides a basis for subsequent treatment strategies.