High-frequency detection of deletions and variable rearrangements at the ornithine transcarbamylase (OTC) locus by oligonucleotide array CGH Oleg A. Shchelochkov a , Fang-Yuan Li a , Michael T. Geraghty b , Renata C. Gallagher c , Johan L. Van Hove c , Uta Lichter-Konecki d , Paul M. Fernhoff e , Sara Copeland f , Tyler Reimschisel g , Stephen Cederbaum h , Brendan Lee a,i , A. Craig Chinault a , Lee-Jun Wong a, * a Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, NAB 2015, Houston, TX 77030, USA b Department of Genetics, Children’s Hospital Eastern Ontario, Canada c Department of Pediatrics, University of Colorado Denver, Aurora, CO, USA d Children’s National Medical Center, Washington, DC, USA e Department of Human Genetics, Emory University, Decatur, GA, USA f Division of Medical Genetics, Department of Pediatrics, University of Iowa, Iowa City, IA, USA g Division of Developmental Medicine and Cognition, Department of Pediatrics, Vanderbilt University School of Pediatrics, TN, USA h Departments of Psychiatry, Pediatrics and Human Genetics UCLA School of Medicine, Los Angeles, CA, USA i Howard Hughes Medical Institute, USA article info Article history: Received 1 October 2008 Received in revised form 23 November 2008 Accepted 25 November 2008 Available online 12 January 2009 Keywords: Array comparative genomic hybridization aCGH Ornithine transcarbamylase OTC Ornithine transcarbamylase deficiency OTC deletion abstract Ornithine transcarbamylase (OTC) deficiency is an X-linked inborn error of metabolism characterized by impaired synthesis of citrulline from carbamylphosphate and ornithine. Previously reported data suggest that only approximately 80% of OTC deficiency (OTCD) patients have a mutation identified by OTC gene sequencing. To elucidate the molecular etiology in patients with clinical signs of OTCD and negative OTC sequencing, we subjected their DNA to array comparative genomic hybridization (aCGH) using a custom-designed targeted 44 k oligonucleotide array. Whenever possible, parental DNA was analyzed to determine the inheritance or to rule out copy number variants in the OTC locus. DNA samples from a total of 70 OTCD patients were analyzed. Forty-three patients (43/70 or 61.5%) were found to have disease-causing point mutations in the OTC gene. The remaining 27 patients (27/ 70 or 38.5%) showed normal sequencing results or failure to amplify all or part of the OTC gene. Among those patients, eleven (11/70 or 15.7%) were found to have deletions ranging from 4.5 kb to 10.6 Mb, all involving the OTC gene. Sixteen OTCD patients (16/70 or 22.8%) had normal sequencing and oligoarray results. Analysis of the deletions did not reveal shared breakpoints, suggesting that non-homologous end joining or a replication-based mechanism might be responsible for the formation of the observed rearrangements. In summary, we demonstrate that approximately half of the patients with negative OTC sequencing may have OTC gene deletions readily identifiable by the targeted oligonucleotide-based aCGH. Thus, the test should be considered in OTC sequencing-negative patients with classic symptoms of the disease. Ó 2008 Elsevier Inc. All rights reserved. Ornithine transcarbamylase (OTC, EC 2.1.3.3) deficiency is an X-linked inborn error of metabolism caused by impaired synthesis of citrulline from carbamylphosphate and ornithine. The estimated prevalence of OTC deficiency (OTCD) is 1:14,000, making it the most common urea cycle condition [1]. A total of 341 disease-caus- ing mutations in OTC gene have been reported [1]. Despite ad- vances in our understanding of the genetic and molecular etiology of OTC deficiency, only about 80% of OTCD patients have an identifiable point mutation by sequencing [1]. It has been hypothesized that the remaining 20% of OTC deficiencies may be caused by mutations in the promoter region or introns of the OTC gene, locus heterogeneity or copy number variants, such as mic- rodeletions [1]. X chromosome deletions encompassing the OTC gene with or without the involvement of neighboring genes are a relatively common cytogenetic finding in patients with OTCD. Francke (1984) published the first report of a female with partial OTC defi- ciency, caused by de novo interstitial deletion of band Xp21. X chromosome inactivation studies showed a random pattern of X inactivation. The metabolic workup revealed a positive allopurinol test and an elevation of glutamine after protein load [2]. Following 1096-7192/$ - see front matter Ó 2008 Elsevier Inc. All rights reserved. doi:10.1016/j.ymgme.2008.11.167 * Corresponding author. Fax: +1 713 798 8937. E-mail address: ljwong@bcm.edu (L.-J. Wong). Molecular Genetics and Metabolism 96 (2009) 97–105 Contents lists available at ScienceDirect Molecular Genetics and Metabolism journal homepage: www.elsevier.com/locate/ymgme