American Journal of Medical Genetics Part B (Neuropsychiatric Genetics) 144B:869–876 (2007) Cytogenetic and Molecular Characterization of A2BP1/FOX1 as a Candidate Gene for Autism Christa Lese Martin, 1 * Jacqueline A. Duvall, 2 Yesim Ilkin, 3 Jason S. Simon, 4 M. Gladys Arreaza, 4 Kristin Wilkes, 2 Ana Alvarez-Retuerto, 2 Amy Whichello, 5 Cynthia M. Powell, 6 Kathleen Rao, 6 Edwin Cook, 7 and Daniel H. Geschwind 2 11 Department of Human Genetics, Emory University, Atlanta, Georgia 2 Departments of Neurology and Human Genetics, and Center for Autism Research, Semel Insitute, UCLA, Los Angeles, California 3 Department of Human Genetics, University of Chicago, Chicago, Illinois 4 Schering-Plough Research Institute, Kenilworth, New Jersey 5 Duke University School of Nursing, Durham, North Carolina 6 Division of Pediatric Genetics and Metabolism, University of North Carolina, Chapel Hill, North Carolina 7 Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois Cytogenetic imbalances are increasingly being realized as causes of autism. Here, we report a de novo translocation between the short arms of chromosomes 15 and 16 in a female with autism, epilepsy, and global developmental delay. FISH analysis identified a cryptic deletion of approxi- mately 160 kb at the boundary of the first exon and first intron of the 1.7 Mb ataxin-2 binding protein-1 (A2BP1) gene, also called FOX1. Quantitative real time PCR (Q-PCR) analysis verified a deletion of exon 1 in the 5 0 promoter region of the A2BP1 gene. Reverse transcription PCR (qRT-PCR) showed reduced mRNA expression in the individual’s lymphocytes, demonstrating the functional con- sequence of the deletion. A2BP1 codes for a brain- expressed RNA binding or splicing factor. Because of emerging evidence in the role of RNA processing and gene regulation in pervasive developmental disorders, we performed further screening of A2BP1 in additional individuals with autism from the Autism Genetics Resource Exchange (AGRE) collection. Twenty-seven SNPs were genotyped across A2BP1 in 206 parent-child trios and two regions showed association at P  0.008 level. No additional deletions or clear mutations were identified in 88 probands by re- sequencing of all exons and surrounding intronic regions or quantitative PCR (Q-PCR) of exon 1. Although only nominal association was observed, and no obvious causal mutations were identified, these results suggest that A2BP1 may affect susceptibility or cause autism in a subset of patients. Further investigations in a larger sam- ple may provide additional information regarding the involvement of this gene in the autistic phenotype. ß 2007 Wiley-Liss, Inc. KEY WORDS: cytogenetic imbalance; copy num- ber variation; association analy- sis; splicing factor; RNA binding Please cite this article as follows: Martin CL, Duvall JA, Ilkin Y, Simon JS, Arreaza MG, Wilkes K, Alvarez- Retuerto A, Whichello A, Powell CM, Rao K, Cook E, Geschwind DH. 2007. Cytogenetic and Molecular Char- acterization of A2BP1/FOX1 as a Candidate Gene for Autism. Am J Med Genet Part B 144B: 869 – 876. INTRODUCTION Autism is a neurodevelopmental disorder characterized by the clinical triad of social deficits, impaired communication and repetitive restrictive behavior patterns. The prevalence of Autism Spectrum Disorders (ASD) has been estimated to be as high as 1/166, with males being affected at least four times more frequently than females [Yeargin-Allsopp et al., 2003; Muhle et al., 2004]. Many different biological causes have been implicated in the etiology of autism, but genetic factors appear to be the most important: family studies have revealed a recurrence risk of 4% among siblings of affected probands and twin studies have shown a significant difference in the concordance rates of autism between monozygotic and dizygo- tic twins [Veenstra-VanderWeele and Cook, 2004]. The genetic mechanism underlying autism has been studied using various approaches, including linkage, candidate gene, and chromo- some analyses, however, there is still a paucity of information regarding causative genetic mechanisms of the autistic phenotype. Multiple lines of evidence support the location of an autism gene in the chromosomal region 16p13. First, several genome-wide linkage scans and association studies have obtained peaks at 16p13 [IMGSAC, 1998; Philippe et al., 1999; IMGSAC, 2001; Lucarelli et al., 2003; Barnby et al., 2005]. One region, located between D16S407 (10 Mb from pter) and D16S3075 (12 Mb from pter) has been implicated by various genome-wide linkage studies with an MLS ranging from 0.74 [Philippe et al., 1999] to 2.19 – 2.52 [IMGSAC, 2001]. In addition, an association study focusing on the 16p region also identified a marginal association between D16S502 (7.8 Mb from pter) and autism [Lucarelli et al., 2003]. Interestingly, this region on 16p is close to the 1.7 Mb ataxin- 2 binding protein-1 (A2BP1) gene which binds to the ataxin-2 protein, implicated in Spinocerebellar Ataxia type 2 (SCA2). A2BP1 has been previously characterized and shown to code for an RNA-binding protein which is expressed in muscle and brain. The gene is highly conserved in C. elegans, This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www. interscience.wiley.com/jpages/1552-4841/suppmat/index.html. Grant sponsor: National Institute of Mental Health; Grant numbers: R01-MH64547. *Correspondence to: Christa Lese Martin, Ph.D., Department of Human Genetics, Emory University, Atlanta, Georgia 30322. E-mail: clmartin@genetics.emory.edu Received 6 November 2006; Accepted 23 February 2007 DOI 10.1002/ajmg.b.30530 ß 2007 Wiley-Liss, Inc.