ORIGINAL RESEARCH ARTICLE ©American College of Medical Genetics and Genomics Novel 9q34.11 gene deletions encompassing combinations of four Mendelian disease genes: STXBP1, SPTAN1, ENG, and TOR1A Ian M. Campbell, BS1, Svetlana A. Yatsenko, MD1,14, Patricia Hixson, PhD1, Tyler Reimschisel, MD2, Matthew Thomas, MS3, William Wilson, MD3, Usha Dayal, MD4, James W. Wheless, MD5, Amy Crunk, MS6, Cynthia Curry, MD7, Nicole Parkinson, MS8, Leona Fishman, MD8, James J. Riviello, MD9, Malgorzata J.M. Nowaczyk, MD10, Susan Zeesman, MS10, Jill A. Rosenfeld, MS11, Bassem A. Bejjani, MD11, Lisa G. Shaffer, PhD11, Sau Wai Cheung, PhD1, James R. Lupski, MD, PhD1,12,13, Pawel Stankiewicz, MD, PhD1 and Fernando Scaglia, MD1,13 Purpose: A number of genes in the 9q34.11 region may be haplo­ of which molecular defects lead to early­onset primary dystonia. insufficient. However, studies analyzing genotype–phenotype corre­ Ninety­four other RefSeq genes also map to the genomic intervals lations of deletions encompassing multiple dosage­sensitive genes in investigated. the region are lacking. Conclusion: STXBP1 haploinsufficiency results in progressive Methods: We mapped breakpoints of 10 patients with 9q34.11 dele­ encephalopathy characterized by intellectual disability and may tions using high­resolution 9q34­specific array comparative genomic be accompanied by epilepsy, movement disorders, and autism. We hybridization (CGH) to determine deletion size and gene content. propose that 9q34.11 genomic deletions involving ENG, TOR1A, Results: The 9q34.11 deletions range in size from 67 kb to 2.8 STXBP1, and SPTAN1 are responsible for multisystemic vascular Mb. Six patients exhibit intellectual disability and share a common dysplasia, early­onset primary dystonia, epilepsy, and intellectual deleted region including STXBP1; four manifest variable epilepsy. disability, therefore revealing cis­genetic effects leading to complex In five subjects, deletions include SPTAN1, previously associated phenotypes. with early infantile epileptic encephalopathy, infantile spasms, intel­ Genet Med 2012:14(10):868–876 lectual disability, and hypomyelination. In four patients, the dele­ tion includes endoglin (ENG), causative of hereditary hemorrhagic Key Words: cis­genetics, dystonia, early infantile epileptic encephal­ telangiectasia. Finally, in four patients, deletions involve TOR1A, opathy, hereditary hemorrhagic telangiectasia, intellectual disability INTRODUCTION natural course consists of progressive neurological dysfunction Neonatal or early infantile epileptic encephalopathies represent manifesting with concomitant cognitive and motor impairment a class of severe epileptic disorders that can be caused by abnor­ leading to severe developmental delay (DD) or intellectual dis­ mal brain development as a result of congenital brain malfor­ ability (ID). EIEE belongs to a broader class of disorders known mations or, less frequently, by inborn errors of metabolism.1 as age­dependent epileptic encephalopathies, with evolving Early infantile epileptic encephalopathy (EIEE) with a burst­ clinical phenotype and electroencephalogram characteristics as suppression pattern, also known by the eponym of Ohtahara the brain matures.3 The majority of patients with EIEE subse­ syndrome, is a rare and severe form of epileptic encephalopa­ quently develop infantile spasms (IS), or West syndrome, later thy characterized by early­onset of intractable seizures, with in childhood. In some children, the epileptic phenotype may mostly tonic spasms or, more rarely, partial seizures and a later evolve to Lennox–Gastaut syndrome by 6 years of age.4 specific pattern on electroencephalogram known as suppres­ The etiology of EIEE is heterogeneous; structural abnormali­ sion burst.2 EIEE has a neonatal or early infantile onset and the ties of the brain such as Aicardi syndrome, cortical dysgenesis, The first two authors contributed equally to this work. B.A.B. is currently unaffiliated with Signature Genomic Laboratories. 1Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; 2Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA; 3Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, Virginia, USA; 4Carolina Neurological Clinic, Charlotte, North Carolina, USA; 5Department of Pediatric Neurology, University of Tennessee Health Science Center, Memphis, Tennessee, USA; 6Shodair Hospital, Helena, Montana, USA; 7Genetic Medicine of Central California, University of California San Francisco, Fresno, California, USA; 8Department of Pediatrics, Hospital for Sick Children, Toronto, Ontario, Canada; 9Department of Neurology, New York University Langone Medical Center, New York, New York, USA; 10Department of Pathology and Molecular Medicine and Pediatrics, McMaster University, Hamilton, Ontario, Canada; 11Signature Genomic Laboratories, PerkinElmer Inc., Spokane, Washington, USA; 12Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA; 13Texas Children’s Hospital, Houston, Texas, USA. 14Present address: Obstetrics and Gynecology and Reproductive Sciences, Magee Women’s Hospital, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA. Correspondence: Fernando Scaglia ([email protected]) Submitted 3 January 2012; accepted 9 May 2012; advance online publication 21 June 2012. doi:10.1038/gim.2012.65 868 Volume 14 | Number 10 | October 2012 | GENETICS in MEDICINE Novel 9q34.11 deletions | CAMPBELL et al ORIGINAL RESEARCH ARTICLE porencenphaly, and hemimegalencephaly may be accompanied Signature Genomic Laboratories (P1, P2, and P7–P10) for a by EIEE, whereas inborn errors of metabolism such as glycine diverse range of clinical indications. Four patients (P1, P2, encephalopathy and Leigh syndrome have been associated with P7, and P8) were identified by SignatureChipOS v1.1 105K other cases.2,4 More recently, studies have ascertained that EIEE oligo whole­genome array (Agilent Technologies, Santa with a burst­suppression pattern is genetically heterogeneous Clara, CA) and two patients (P9 and P10) were identified as well, with causative mutations identified in at least 12 genes by SignatureChipOS v2.0 135K oligo whole­genome array (Supplementary Table S1, online).1,5–8 In addition to the 12 (Roche NimbleGen, Madison, WI). P4 was identified by known genes, one individual with EIEE and a de novo balanced BCM CMA v7.1 105 K oligo whole­genome array (Agilent translocation disrupting the SRGAP2 gene has recently been Technologies). P6 was identified by BCM CMA v7.4 105K reported.9 oligo exon­targeted array (Agilent Technologies). P3 and Of note, two of the genes previously implicated in the etiol­ P5 were identified by BCM CMA v8.1 180K oligo exon­ ogy of EIEE, STXBP1, and SPTAN1, are both located within the targeted array (Agilent Technologies). Informed consent for same 9q34.11 genomic region. To date, only three patients with the research use of genetic material and clinical information microdeletions encompassing both STXBP1 and SPTAN1 have was obtained from the parent or guardian of each patient. been described.8,10,11 Two subjects presented with the character­ Peripheral blood samples were obtained from individuals and istic clinical features of EIEE.8,11 Although the authors of the sec­ available family members. All subjects had apparently nor­ ond study do not specifically mention SPTAN1, it and STXBP1 mal G­banded chromosome analyses. Clinical details appear are likely deleted from the chromosome of their patient pre­ in Supplementary Materials and Methods, online. senting with IS.10 De novo missense, nonsense, frameshift, and splice­site mutations, as well as genomic deletions of STXBP1 Array-CGH studies have been found in association with EIEE, suggesting STXBP1 Patients’ genomic DNA was extracted from peripheral blood haploinsufficiency as a cause of this epileptic phenotype.8,11–14 samples according to the manufacturers’ protocols. Two sepa­ However, a 4­bp deletion within STXBP1 exon 4, resulting in a rate custom, high­resolution 9q34 arrays were designed using premature stop 41 codons downstream in the sixth of 20 exons, a 60K array format (Agilent Technologies, Santa Clara, CA) has been identified in one child of Japanese ancestry who pre­ and were used on the basis of availability at time of patient sented with IS but did not exhibit the classical features consis­ ascertainment. Version 1 of the custom array had an average tent with EIEE.12 Furthermore, other publications reporting the probe spacing of ~1,250 bp per probe; version 2 had an aver­ clinical cases of patients of diverse ethnic backgrounds affected age spacing of ~250 bp per probe. Sex­matched DNA samples with epilepsy and carrying STXBP1 mutations sometimes failed from either a normal male or female individual were used as a to identify the burst­suppression pattern on electroencephalo­ hybridization reference control. DNA digestion, labeling, and gram characteristic of EIEE.10,15,16 Finally, a de novo truncating hybridization were performed according to the manufacturer’s STXBP1 mutation has been found in a 21­year­old patient with instructions (Agilent Technologies). Data were analyzed using ID and no evidence of epilepsy, expanding the clinical spectrum Agilent Genomic Workbench Software (Agilent Technologies) associated with molecular defects of STXBP1.17 and plotted using the R Statistical Computing Package (R Core Therefore, the complete range of phenotypic features caused Development