Identification of genetic factors contributing to risk for classical Chiari malformation type 1 (CM1) has been challenging. Moreover CM1 patients with symptoms of connective tissue disorders (CTD+), such as Ehlers Danlos Syndrome (EDS), may have different genetic etiologies than CM1 patients without CTD symptoms (CTD-). While most genetic studies have interrogated primarily intronic genetic variation, next generation sequencing (NGS) technology captures functional variants within a gene, which may be truly causal. Aims. We utilized NGS of previously identified CM1 and EDS candidate genes to test for an excess burden of functional variants in CM1 cases versus controls, and to investigate differences among CM1 cases with and without CTD symptoms.
DNA samples were obtained from 186 female Caucasian CM1 cases ascertained through the Chiari1000 project and from a CM1 family study at Duke University. Targeted sequencing of 21 genes was performed; sequencing reads were aligned and variants called using GATK best practices. Gene-level burden analysis was used to compare the frequency of rare, functional variants detected in CM1 cases versus publically available controls from gnomAD, and between CTD+ and CTD- CM1 cases.
Six genes (COL5A2, COL6A5, COL1A2, NRP1, VEGFB, FLT1) had significantly more rare variants in CM1 cases compared to controls. Of interest, over 25% of CM1 cases had rare variants in COL6A5. Among CM1 cases, we identified four genes (COL7A1, CDX1, VEGFA, DSE) that were significantly different between CTD+ and CTD- subtypes.
We identified an enrichment of rare functional variants in CM1 and EDS candidate genes when comparing CM1 patients to controls, and when comparing CTD+ versus CTD- CM1 patients. Our findings underscore the contribution of rare genetic variants to CM1, and differences in genetic etiologies of CM1 with and without CTD symptoms. Future directions include evaluating these genes with respect to cranial morphology.