Diagnostic yield of a multigene sequencing approach in children classified as idiopathic short stature

Abstract

Objective

Most children with short stature remain without an etiologic diagnosis after extensive clinical and laboratory evaluation and are classified as idiopathic short stature (ISS). This study aimed to determine the diagnostic yield of a multigene analysis in children classified as ISS.

Design and methods

We selected 102 children with ISS and performed the genetic analysis as part of the initial investigation. We developed customized targeted panel sequencing, including all genes already implicated in the isolated short-stature phenotype. Rare and deleterious single nucleotide or copy number variants were assessed by bioinformatic tools.

Results

We identified 20 heterozygous pathogenic (P) or likely pathogenic (LP) genetic variants in 17 of 102 patients (diagnostic yield = 16.7%). Three patients had more than one P/LP genetic alteration. Most of the findings were in genes associated with the growth plate differentiation: IHH ( n  = 4), SHOX ( n  = 3), FGFR3 ( n  = 2), NPR2 ( n  = 2), ACAN ( n  = 2), and COL2A1 ( n  = 1) or involved in the RAS/MAPK pathway: NF1 ( n  = 2), PTPN11 ( n  = 1), CBL ( n  = 1), and BRAF ( n  = 1). None of these patients had clinical findings to guide a candidate gene approach. The diagnostic yield was higher among children with severe short stature (35% vs 12.2% for height SDS ≤ or > −3; P = 0.034). The genetic diagnosis had an impact on clinical management for four children.

Conclusion

A multigene sequencing approach can determine the genetic etiology of short stature in up to one in six children with ISS, removing the term idiopathic from their clinical classification.