Research Article: Integrative Variation Analysis Reveals that a Complex Genotype May Specify Phenotype in Siblings with Syndromic Autism Spectrum Disorder

Date Published: January 24, 2017

Publisher: Public Library of Science

Author(s): Viviane Neri de Souza Reis, João Paulo Kitajima, Ana Carolina Tahira, Ana Cecília Feio-dos-Santos, Rodrigo Ambrósio Fock, Bianca Cristina Garcia Lisboa, Sérgio Nery Simões, Ana C. V. Krepischi, Carla Rosenberg, Naila Cristina Lourenço, Maria Rita Passos-Bueno, Helena Brentani, Deyou Zheng.


It has been proposed that copy number variations (CNVs) are associated with increased risk of autism spectrum disorder (ASD) and, in conjunction with other genetic changes, contribute to the heterogeneity of ASD phenotypes. Array comparative genomic hybridization (aCGH) and exome sequencing, together with systems genetics and network analyses, are being used as tools for the study of complex disorders of unknown etiology, especially those characterized by significant genetic and phenotypic heterogeneity. Therefore, to characterize the complex genotype-phenotype relationship, we performed aCGH and sequenced the exomes of two affected siblings with ASD symptoms, dysmorphic features, and intellectual disability, searching for de novo CNVs, as well as for de novo and rare inherited point variations—single nucleotide variants (SNVs) or small insertions and deletions (indels)—with probable functional impacts. With aCGH, we identified, in both siblings, a duplication in the 4p16.3 region and a deletion at 8p23.3, inherited by a paternal balanced translocation, t(4, 8) (p16; p23). Exome variant analysis found a total of 316 variants, of which 102 were shared by both siblings, 128 were in the male sibling exome data, and 86 were in the female exome data. Our integrative network analysis showed that the siblings’ shared translocation could explain their similar syndromic phenotype, including overgrowth, macrocephaly, and intellectual disability. However, exome data aggregate genes to those already connected from their translocation, which are important to the robustness of the network and contribute to the understanding of the broader spectrum of psychiatric symptoms. This study shows the importance of using an integrative approach to explore genotype-phenotype variability.

Partial Text

Autism spectrum disorder (ASD) is a neurodevelopmental disorder [1] characterized by early-onset social and communication impairment, as well as restrictive stereotypic movements and behaviors [2]. Approximately 70% of ASD patients have at least one clinical or psychiatric comorbidity, whereas 48% have two or more [3]. In addition to presenting a heterogeneous phenotype, ASD is multifactorial disorder with a complex genetic architecture [4–7]. Various reviews have provided in-depth analyses of the degree of genetic and phenotypic association between ASD and genetic syndromes [8–12]. Miles et al. [13] defined complex ASD as that observed in a subset of individuals with evidence of abnormality occurring at the beginning of morphogenesis, manifesting as dysmorphic abnormalities but not associated with a known genetic syndrome. Therefore, syndromic ASD is represented by complex cases with or without an association with a known genetic syndrome.

Our major goal in this paper was to assess genetic findings in siblings that shared syndromic features and ID, a secondary goal being to explain the differences in the presentation of their psychiatric symptoms. According to Miles et al. [13,68], the male sibling could be classified as having complex autism (autism with ID and syndromic features). Both siblings presented irritability, agitation, and aggressive behavior, symptoms that are present in cases of ASD, as well as in those of ID only. Even among individuals with ASD, these symptoms are more common in those with ID [69].The male sibling had an attachment to repetitive behaviors, did not make eye contact, showed no capacity for joint attention, had no social interests, and had no communicative ability, all of which were symptoms that were not present in the female sibling. Their social impairments and alterations in social skills differed, and the female sibling had been described as presenting periods of inappropriate, hypersocial behavior and periods during which she could not stop talking and had sleep difficulties.

One of the limitations of the current study is the sample size, which was small for an integrative analysis, given that we accessed only the exome data of the two affected siblings. Therefore, we chose to leave the inherited CNV out of the analysis and focus on the variations that were the most likely to have deleterious effects, such as de novo CNVs, as well as de novo and rare inherited nonsynonymous SNVs. Nevertheless, with this analysis of only one family, we were able to show the importance of exploring the genotype-phenotype variability beyond the effect of one SNV or CNV.




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