Whole exome sequencing should be the first genetic-molecular approach for children with syndromic short stature without clinical diagnosis

Author(s)

Bruna Lucheze Freire

• Document type: Doctoral Thesis
• Press: São Paulo.
• Institution: Universidade de São Paulo (USP). Faculdade de Medicina (FM/SBD)
• Defense date: 2021-10-26

Examining board members

Alexander Augusto de Lima Jorge; Chong Ae Kim; Adriana Aparecida Siviero Miachon

• Advisor: Alexander Augusto de Lima Jorge

Abstract

Diseases that compromise human growth have a strong genetic influence. The main aim of the current project was to evaluate the usefulness of complete exome sequencing as the first molecular-genetic approach in the investigation of the etiology of syndromic short stature in patients without a recognized clinical diagnosis. Therefore, patients with syndromic characteristics underwent extensive clinical evaluation in our clinic and, in selected cases, complete exome sequencing was used to establish the genetic etiology responsible for the growth disorder. Thus, 86 patients with short stature (Z-score for height less than or equal to -2) or short stature in relation to their family pattern (Z-score of patient height minus Z-score of target height -2) associated with dysmorphisms, major congenital malformations, neuropsychomotor development disorders or intellectual deficit were prospectively selected for WES. The selected patients do not have a clinical diagnosis or the initial clinical suspicion was ruled out by a previous molecular study based on a candidate gene. These were subjected to exome sequencing with capture of target regions by SureSelect (Agilent) or xGen Exome Research Panel v2 (IDT) technology. In 61 cases only the proband was initially analyzed and in 25 there was a joint analysis with other family members (trios). The analysis of the samples generated an average coverage of 152 times with more than 98.15% of the target region with coverage > 10 reads. In these samples, 47 deleterious variants were identified in 41 patients. In 22 patients the variants were considered pathogenic and in 19 probably pathogenic. Among the variants considered pathogenic or probably pathogenic, there was great heterogeneity between the genes, with variants being identified in ACTB, AFF4, ANKRD11, BCL11B(x2), BRCA1, CHD7, COL2A1(x3), DPH1, DYRK1A, FBN1, FOXP1, GINS1 genes. , HDAC8. IGF1R, INPP5K, KIF11, KDM5C, KMT2A, KIF11, KRAS, MVK, PCNT, PDHA1, POC1A, POLG1, PUF60, RPL5, RPS6KA3, SCN1A, SCUBE3, SETD5, SMARCA4, SRCAP(x2), STAT5B, and 3 duplications and one deletion found by CNV analysis. We can conclude that the massive parallel sequencing technique of the exome was efficient in establishing the molecular diagnosis of syndromic short stature, and it was possible to identify the genetic etiology in 47,7% of the studied cohort (AU)

• FAPESP's process: 18/10893-6 - Prospective evaluation of exome sequencing in the etiological investigation of syndromic short stature patients without clinical diagnosis
• Grantee: Bruna Lucheze Freire
• Support Opportunities: Scholarships in Brazil - Doctorate