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TRIO-BASED EXOME SEQUENCING IDENTIFIES DE NOVO ARID4A VARIANTS AS A CAUSE OF NEURODEVELOPMENTAL DISORDERSNora Alexander, MS, CGC 1; Kristin Monaghan PhD, FACMG1; Ashley Wilson, MS, CGC2; Alejandro Iglesias, M.D.3; Meron Azage, MS, CGC4; Dmitriy M. Niyazov, M.D.4; Ellen Moran, MS, CGC5; John Pappas, M.D.6; Jessica Litwin, M.D.7; John M. Graham, Jr M.D., ScD.8; Jessica Hoffman, MS, CGC1; Richard Person, PhD, FACMG1; Rhonda E. Schnur, M.D., FACMG1; Ganka V. Douglas, PhD; FACMG1, Sherri J. Bale, PhD, FACMG1; Jane Juusola, PhD, FACMG1
1GeneDx, Gaithersburg, MD, USA; 2Childrens Hospital of NewYork-Presbyterian, New York, NY, USA; 3Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA; 4Ochsner Hospital for Children, New Orleans, LA, USA; 5NYU Hospital for Joint Diseases, New York, NY, USA; 6NYU School of Medicine, New York, NY, USA; 7University of California, San Francisco, San Francisco, CA, USA; 8Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
Identifying the etiology of neurodevelopmental disorders (NDD) is challenging due to genetic heterogeneity and the clinical variability of these disorders. Trio-based exome sequencing (ES), which compares data from an affected proband to both parents, has been established as an effective tool for identifying the genetic etiology in patients with NDD, particularly when due to a de novo event in the proband.
Using our analytical pipeline to evaluate a data set consisting of 10,259 probands referred for clinical exome sequencing for NDD, we identified by trio-based ES de novo ARID4A variants in five unrelated individuals. The ARID4A gene plays a role in the epigenetic regulation of genomic imprinting at the Prader-Willi/Angelman syndrome domain.1, 2 To date, no sequence variants have been published in the ARID4A gene. However, a de novo 14q23.1q23.3 deletion including ARID4A was reported in an individual with developmental delay, hypoplasia of the corpus callosum, epilepsy, and neuroblastoma,3 suggesting a haploinsufficiency mechanism.
Exome sequencing was performed on exon targets isolated by capture using the Agilent SureSelect Human All Exon V4 (50 Mb) or Clinical Research Exome kit (Agilent Technologies, Santa Clara, CA).
The sequencing methodology and variant interpretation protocol has been previously described.4
Identified sequence changes of interest were confirmed in all members of the family on whom biospecimens were available by di-deoxy DNA sequence analysis.
Five unrelated individuals were found to harbor de novo variants in ARID4A. One frameshift and four missense variants were identified, none of which were observed in large population cohorts (Table 1).
Patients range in age from 6 to 28 years. All five individuals had developmental delays, and 3/5 experienced developmental regression. Intellectual disability was reported in three individuals, and IQ was not assessed in the remaining two.
All but one individual had a diagnosis of autism. Other psychiatric concerns were also reported in this cohort, including obsessive-compulsive behavior (3/5), anxiety (2/5), and bipolar disorder (1/5).
Two out of four individuals tested by brain MRI had brain anomalies (thin corpus callosum, absent septum pellucidum, and holoprocencephaly in one, pontocerebellar atrophy in another).
Only one patient was reported to have dysmorphic features including mild hypotelorism, upslanting palpebral fissures, bulbous nasal tip, mild micrognathia, hypoplastic ear lobules, bilateral bradydactyly, and nearly complete right 1-2 toe syndactyly.
Trio-based ES is an effective tool for the discovery of novel causes of molecularly heterogeneous conditions such as neurodevelopmental disorders.
Our data suggest that de novo variants in ARID4A are associated with a unique neurodevelopmental disorder characterized by a spectrum of overlapping clinical features including developmental delay, intellectual disability, autism, and brain anomalies.
We propose a haploinsufficiency mechanism of disease, given the previous report of a microdeletion involving the ARID4A gene being associated with an NDD phenotype and the observation of a frameshift variant in our cohort. Additional research is needed to further explore the association between variants in ARID4A and any resultant neurodevelopmental phenotype.
1. Gong W, et al. The Journal Of Biological Chemistry 2012; 287 (11):8531-40.
2. Wu MY, et al. Genes & Development 2006; 20 (20):2859-70.
3. Lehalle D, et al. Am. J. Med. Genet. A 2014; 164A (5):1310-7.
4. Tanaka AJ et al. Am J Hum Genet. 2015; 97:457-64.
Table 1. Patients with ARID4A variants
Patient Age Sex Variant De novo/ InheritedDevelopmental
Regression AutismIntellectual Disability
Other Psychiatric Concerns Brain Anomalies
Additional Clinical Features
1 27yo F
De novo Yes Yes Yes UNK
Bipolar disoder, obsessive-compulsive
behavior, anxiety, hyperactivity
Normal brain MRI Hashimito's thyroiditisp.C573G
2* 17yo Mc.2051 C>G
De novo Yes Yes Yes Yes Aggressive behavior
Agenesis of the corpus callosum,
holoprosenchephaly, optic nerve hypoplasia
Dysmorphic features, central hypotonia,
3 28yo Mc.2000 G>A
De novo Yes Yes No Yes Obsessive-compulsive disorder, anxiety Pontocerebellar atrophyCerebellar ataxia, spastic hemiparesis, dysarthria,
4 6yo Fc.3716 G>A
De novo Yes UNK Yes UNK No UNK None specifiedp.G1239E
5** 13yo Mc.1602dupA
De novo Yes No Yes UNK Obsessive-compulsive disorder, depression Normal brain CTNephronopthisis,
UNK = Unknown, N/A = Not Applicable
*Also heterozygous for a maternally inherited pathogenic variant in the FGFR1 gene.
**Also is homozygous for a deletion at 2q13 involving the NPHP1 gene.