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Methods• 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.

• 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 11,649 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.

Background

Results• 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). In addition, a sixth individual had a missense variant also present at low levels in his unaffected father.

• Patients range in age from 6 to 28 years. All six individuals had developmental delays, and 3/6 experienced developmental regression. Intellectual disability was reported in three individuals, and IQ was not assessed in the remaining three.

• All but two individuals had a diagnosis of autism. Other psychiatric concerns were also reported in this cohort, including obsessive-compulsive behavior (3/6), anxiety (2/6), and bipolar disorder (1/6).

• 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).

• Two patients were reported to have dysmorphic features. These patients also had a second de novo variant reported in a different gene.

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.

References

ARID4A DE NOVO VARIANTS IDENTIFIED BY EXOME SEQUENCING AMONG INDIVIDUALS WITH NEURODEVELOPMENTAL DISORDERSKristin Monaghan1; Nora Alexander1; Ashley Wilson2; Alejandro Iglesias3; Meron Azage4; Dmitriy M. Niyazov4; Ellen Moran5; John Pappas6; Jessica Litwin7; John M. Graham8; Kristin Klinard9; Muge Gucsavas-Calikoglu9; Jessica Hoffman1; Richard Person1; Rhonda E. Schnur1; Ganka V. Douglas1; Maria Guillen1; Sherri J. Bale1; Jane Juusola1

1GeneDx, Gaithersburg, MD, USA; 2Children’s 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; 9University of North Carolina, Division of Genetics and Metabolism, Department of Pediatrics, Chapel Hill, NC, USA

Table 1. Patients with ARID4A variants

Patient Age Sex Variant De novo/ Inherited

Developmental Delay

Developmental Regression Autism Intellectual

DisabilityOther Psychiatric

Concerns Brain Anomalies Additional Clinical Features Additional de novo variants reported

1 27yo Fc.1717 T>Gp.C573G

De novo Yes Yes Yes Yes

Bipolar disoder, obsessive-compulsive

behavior, anxiety, hyperactivity

Normal brain MRI Hashimito's thyroiditis COL4A2 p.P577T

2 17yo Mc.2051 C>G

p.S684CDe novo Yes Yes Yes Yes Aggressive

behavior

Agenesis of the corpus callosum,

holoprosenchephaly, optic nerve hypoplasia

Dysmorphic features, central hypotonia,

peripheral spasticityKDM4B p.Q73P

3 28yo Mc.2000 G>A

p.G667EDe novo Yes Yes No Yes

Obsessive-compulsive

disorder, anxiety

Pontocerebellar atrophy

Cerebellar ataxia, spastic hemiparesis,

dysarthria, parkinsonism

4 6yo F c.3716 G>A p.G1239E De novo Yes UNK Yes UNK No UNK None specified

5** 13yo Mc.1602dupAp.Q535TfsX5

De novo Yes No Yes UNK

Obsessive-compulsive

disorder, depression

Normal brain CT Nephronopthisis, hyperparathyroidism

6 7yo Mc.599 G>Ap.C200Y

Inherited* Yes No No UNK No UNK

dysmorphic features, absent speech, failure to thrive, contractures,

growth delay, spasticity

SLC30A5 p.D230Y de novo/mosaic

UNK = Unknown*father mosaic for ARID4A variant**Also is homozygous for a deletion at 2q13 involving the NPHP1 gene.

Conclusions• 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.