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

Author(s)

Funari, Mariana F. A. ^[1] ; de Barros, Juliana S. ^[2] ; Santana, Lucas S. ^[3] ; Lerario, Antonio M. ^{[4, 3, 1]} ; Freire, Bruna L. ^[1] ; Homma, Thais K. ^{[3, 1]} ; Vasques, Gabriela A. ^{[3, 1]} ; Mendonca, Berenice B. ^[1] ; Nishi, Mirian Y. ^[1] ; Jorge, Alexander A. L. ^{[3, 1]}

Affiliation

^[1] Univ Sao Paulo, Unidade Endocrinol Desenvolvimento, Lab Hormonios & Genet Mol LIM42, Hosp Clin, Fac Med, Sao Paulo - Brazil

^[2] Univ Sao Paulo, Inst Biociencias, Dept Genet & Biol Evolut, Sao Paulo - Brazil

^[3] Univ Sao Paulo, Fac Med, Unidade Endocrinol Genet LIM25, Sao Paulo - Brazil

^[4] Univ Michigan, Dept Internal Med, Div Metab Endocrinol & Diabet, Ann Arbor, MI 48109 - USA

• Document type: Journal article
• Source: Clinical Genetics; v. 96, n. 3 JULY 2019.
• Web of Science Citations: 0

Abstract

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. (AU)

• FAPESP's process: 13/03236-5 - New approaches and methodologies in molecular-genetic studies of growth and pubertal development disorders
• Grantee: Alexander Augusto de Lima Jorge
• Support Opportunities: Research Projects - Thematic Grants