gms | German Medical Science

Objectives/Interrogation: This study aimed to evaluate the genetic diagnostic yield and accuracy of exome sequencing for Chinese patients with split-hand/foot malformation (SHFM), a severe heterogeneous congenital anomaly characterized by hypodevelopment of the central ray of the hands and feet.

Methods: A cohort of 8 families and 4 sporadic patients with SHFM was investigated. Genomic DNA were prepared from peripheral blood of affected and unaffected individuals. Whole exome sequencing (WES) was performed to identify pathogenic mutations. Array-based comparative genomic hybridization (aCGH), cytoscan, qPCR, and Sanger sequencing was performed to validate the WES findings. WES data of an additional cohort of 24 patients with non-SHFM congenital hand anomalies were analyzed as a control.

Results and Conclusions: Pathogenic variants of TP63, c.G956A p.R319H and c.T602A:p.L201H, were identified in two families. In the remaining patients, copy number analysis of the WES data identified pathogenic 10q24 duplication in 5 individuals out of 3 families, which was validated by cytoscan and qPCR. Duplication in 10q24 was not detected by WES in an additional cohort of 24 individuals with non-SHFM congenital hand anomaly. Importantly, qPCR analysis of the copy number of 10q24 region showed a definite consistency with WES in all individuals. Genotype-phenotype analysis showed no unique feature that can differentiate families with TP63 mutation and 10q24 duplication. Thus, our study demonstrated that WES was an accurate and sensitive method in detection of the pathogenic 10q24 duplication. Together with TP63 mutation, a single WES testing could yield a diagnosis rate of about 40% (5/12) for SHFM patients, at least in our cohort. Since there is no clear genotype-phenotype correlation, WES could be a cost-effective method for genetic diagnosis for SHFM.