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Evaluation of SHOX defects in the era of next‐generation sequencing
Author(s) -
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.
Publication year - 2019
Publication title -
clinical genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.543
H-Index - 102
eISSN - 1399-0004
pISSN - 0009-9163
DOI - 10.1111/cge.13587
Subject(s) - multiplex ligation dependent probe amplification , haploinsufficiency , sanger sequencing , genetics , short stature , biology , copy number variation , massive parallel sequencing , idiopathic short stature , breakpoint , dna sequencing , phenotype , gene , exon , genome , chromosome , growth hormone , biochemistry , endocrinology , hormone
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.