Genomic findings in bone blood paired DNA comparison of nonsyndromic craniosynostosis

OBJECTIVE: The purpose of this study is to elucidate genetic variants contributing to nonsyndromic craniosynostosis by comparing samples from abnormally fused bones, unaffected bones, and parent saliva, to those from patient peripheral whole blood (PWB). METHODS: We applied whole genome sequencing, then performed best practice genomic alignment and variant calling, trio joint genotyping for germline genomic variants, consensus somatic variant calling for PWB-bone comparisons, and variant annotation. Alternative allele frequencies, variant damaging predictions, and inheritance models were used to filter variants. RESULTS: The study included 109 DNA samples from 26 trios, in which 17 families have affected bone tissue DNA. Patients’ affected bone samples were sequenced to an average depth of 112.7X with the rest biospecimens to 35.7X. On average, 2629 somatic variants were identified in the affected bones. After filtering, we identified 40 genes with somatic pathogenic/likely pathogenic (P/LP) variants. We also detected germline P/LP variants, mostly from de novo events. We confirmed known craniosynostosis genes FGFR3 and IHH (both with germline de novo variants), and FREM1 (with a somatic variant in affected bone). From a single patient, we also discovered a germline de novo CHPF variant and a somatic CHPF variant in affected bone. CONCLUSION: We identified a novel candidate craniosynostosis gene CHPF in the same pathway as those required for bone development and digit patterning, which shows promise for further investigation.