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Utility of trio-based exome sequencing in the elucidation of the genetic basis of isolated syndromic intellectual disability: illustrative cases

Authors Carneiro TNR, Krepischi ACV, Costa SS, Tojal da Silva I, Vianna-Morgante AM, Valieris R, Ezquina SAM, Bertola DR, Otto PA, Rosenberg C

Received 17 February 2018

Accepted for publication 12 April 2018

Published 22 August 2018 Volume 2018:11 Pages 93—98

DOI https://doi.org/10.2147/TACG.S165799

Checked for plagiarism Yes

Review by Single-blind

Peer reviewers approved by Dr Andrew Yee

Peer reviewer comments 2

Editor who approved publication: Prof. Dr. Martin H. Maurer


Thaise NR Carneiro,1 Ana CV Krepischi,1 Silvia S Costa,1 Israel Tojal da Silva,2 Angela M Vianna-Morgante,1 Renan Valieris,2 Suzana AM Ezquina,1 Debora R Bertola,3 Paulo A Otto,1 Carla Rosenberg1

1Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil; 2Laboratory of Computational Biology and Bioinformatics, International Research Center, A. C. Camargo Cancer Center, São Paulo, Brazil; 3Genetics Unit, Instituto da Criança, Hospital das Clínicas, Medical School, University of São Paulo, São Paulo, Brazil

Introduction: Exome sequencing is recognized as a powerful tool for identifying the genetic cause of intellectual disability (ID). It is uncertain, however, whether only the exome of the proband should be sequenced or if the sequencing of parental genomes is also required, and the resulting increase in diagnostic yield justifies the increase in costs.
Patients and methods: We sequenced the exomes of eight individuals with sporadic syndromic ID and their parents.
Results and discussion: Likely pathogenic variants were detected in eight candidate genes, namely homozygous or compound heterozygous variants in three autosomal genes (ADAMTSL2, NALCN, VPS13B), one in an X-linked gene (MID1), and de novo heterozygous variants in four autosomal genes (RYR2, GABBR2, CDK13, DDX3X). Two patients harbored rare variants in two or more candidate genes, while in three other patients no candidate was identified. In five probands (62%), the detected variants explained their clinical findings. The causative recessive variants would have led to diagnosis even without parental exome sequencing, but for the heterozygous dominant ones, the exome trio-based approach was fundamental in the identification of the de novo likely pathogenic variants.

Keywords: exome, intellectual disability, next-generation sequencing

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