Evaluation of SHOX defects in the era of next‐generation sequencing

• Published in: Clinical genetics Vol. 96; no. 3; pp. 261 - 265
• Main Authors: Funari, Mariana F.A., Barros, Juliana S., Santana, Lucas S., Lerario, Antonio M., Freire, Bruna L., Homma, Thais K., Vasques, Gabriela A., Mendonca, Berenice B., Nishi, Mirian Y., Jorge, Alexander A.L.
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01.09.2019
• Subjects: Breakpoints; Copy number; copy number variants; Defects; Enhancers; growth disorder; Haploinsufficiency; Homeobox; Mutation; next‐generation sequencing; short stature; SHOX gene; targeted panel sequencing; SHOX gene; short stature; copy number variants; targeted panel sequencing; next-generation sequencing; growth disorder
• ISSN: 0009-9163; 1399-0004
• DOI: 10.1111/cge.13587

Short stature homeobox (SHOX) haploinsufficiency is a frequent cause of short stature. Despite advances in sequencing technologies, the identification of SHOX mutations continues to be performed using standard methods, including multiplex ligation‐dependent probe amplification (MLPA) followed by Sanger sequencing. We designed a targeted panel of genes associated with growth impairment, including SHOX genomic and enhancer regions, to improve the resolution of next‐generation sequencing for SHOX analysis. We used two software packages, CONTRA and Nexus Copy Number, in addition to visual analysis to investigate the presence of copy number variants (CNVs). We evaluated 15 patients with previously known SHOX defects, including point mutations, deletions and a duplication, and 77 patients with idiopathic short stature (ISS). The panel was able to confirm all known defects in the validation analysis. During the prospective evaluation, we identified two new partial SHOX deletions (one detected only by visual analysis), including an intragenic deletion not detected by MLPA. Additionally, we were able to determine the breakpoints in four cases. Our results show that the designed panel can be used for the molecular investigation of patients with ISS, and it may even detect CNVs in SHOX and its enhancers, which may be present in a significant fraction of patients. Copy number variants analyses and Sanger sequencing of breakpoint regions in Case 11, which has a heterozygous deletions involving exons 4, 5, and 6a of short stature homeobox (SHOX).