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European Journal of Human Genetics (2010) 18, 429–435 & 2010 Macmillan Publishers Limited All rights reserved 1018-4813/10 $32.00 www.nature.com/ejhg ARTICLE Identification of ANKRD11 and ZNF778 as candidate genes for autism and variable cognitive impairment in the novel 16q24.3 microdeletion syndrome Marjolein H Willemsen*,1, Bridget A Fernandez2, Carlos A Bacino3, Erica Gerkes4, Arjan PM de Brouwer1, Rolph Pfundt1, Birgit Sikkema-Raddatz4, Stephen W Scherer5, Christian R Marshall5, Lorraine Potocki3, Hans van Bokhoven1 and Tjitske Kleefstra1 The clinical use of array comparative genomic hybridization in the evaluation of patients with multiple congenital anomalies and/or mental retardation has recently led to the discovery of a number of novel microdeletion and microduplication syndromes. We present four male patients with overlapping molecularly defined de novo microdeletions of 16q24.3. The clinical features observed in these patients include facial dysmorphisms comprising prominent forehead, large ears, smooth philtrum, pointed chin and wide mouth, variable cognitive impairment, autism spectrum disorder, structural anomalies of the brain, seizures and neonatal thrombocytopenia. Although deletions vary in size, the common region of overlap is only 90 kb and comprises two known genes, Ankyrin Repeat Domain 11 (ANKRD11) (MIM 611192) and Zinc Finger 778 (ZNF778), and is located approximately 10 kb distally to Cadherin 15 (CDH15) (MIM 114019). This region is not found as a copy number variation in controls. We propose that these patients represent a novel and distinctive microdeletion syndrome, characterized by autism spectrum disorder, variable cognitive impairment, facial dysmorphisms and brain abnormalities. We suggest that haploinsufficiency of ANKRD11 and/or ZNF778 contribute to this phenotype and speculate that further investigation of non-deletion patients who have features suggestive of this 16q24.3 microdeletion syndrome might uncover other mutations in one or both of these genes. European Journal of Human Genetics (2010) 18, 429–435; doi:10.1038/ejhg.2009.192; published online 18 November 2009 Keywords: 16q24.3 microdeletion; ANKRD11; ZNF778; cognitive impairment; autism INTRODUCTION localization of several genes associated with developmental disorders Whole-genome scanning technologies such as array comparative or abnormal brain development, 8 including CHD7 (MIM 608892) in genomic hybridization (array CGH) and single-nucleotide poly- CHARGE syndrome17 and FOXG1(MIM 164874) in congenital Rett morphism oligonucleotide arrays (SNP array) have enabled the syndrome.18 Aberrations of chromosome 16q with clinical relevance detection of submicroscopic chromosomal aberrations, which pre- have rarely been reported. Before this report, interstitial deletions viously escaped detection by routine cytogenetic and molecular restricted to band 16q24.3 have not been described. There are only a cytogenetic techniques.1–3 These methods have proven invaluable in few reports in medical literature with regard to patients with larger, the elucidation of genomic regions associated with mental retardation cytogenetically visible deletions comprising this region, mostly because and/or congenital anomalies.4–8 Several clinically distinct microdele- of an unbalanced complex chromosomal rearrangement.19–29 In this tion and microduplication syndromes have been reported on the basis study, we aimed to characterize the clinical and molecular features of of data derived from these techniques, such as the 17q21.31 micro- four patients with submicroscopic interstitial 16q24.3 microdeletions deletion syndrome5 and the 1q41–1q42 microdeletion syndrome,9 as ascertained by genome-wide array analysis and to determine the well as microduplication syndromes involving 7q11.2310,11 and shortest region of overlap (SRO) to identify candidate genes respon- 17p11.2.12 The phenotypic characteristics of microdeletion syndromes sible for their overlapping phenotype. can be caused by haploinsufficiency of single genes, for example, TCF4 13 (MIM 602272) in Pitt–Hopkins syndrome, EHMT1 (MIM 607001) PATIENTS AND METHODS 14 in the 9q34.3 subtelomeric deletion syndrome and either CREBBP Patient 1 (MIM 600140) or EP300 (MIM 602700) in Rubinstein–Taybi Patient 1 was ascertained at the age of 22 years when SNP array was performed syndrome.15,16 The application of genome-wide array technologies because of mental retardation, autism spectrum disorder, dysmorphic features with an increasing density of probes has led to the identification and and congenital anomalies. He was born after an uncomplicated pregnancy, 1Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands; 2Disciplines of Genetics and Medicine, Memorial University of Newfoundland and Provincial Medical Genetic Program, Eastern Health, St John’s, Newfoundland and Labrador, Canada; 3Department of Molecular and Human Genetics, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX, USA; 4Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands; 5The Centre for Applied Genomics, The Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada *Correspondence: Dr MH Willemsen, 849 Department of Human Genetics, Radboud University Nijmegen Medical Centre, PO Box 9101, Nijmegen 6500 HB, The Netherlands. Tel: +31 24 3613 946; Fax: +31 24 3668 753; E-mail: [email protected] Received 30 June 2009; revised 2 September 2009; accepted 22 September 2009; published online 18 November 2009 ANKRD11 and ZNF778 in 16q24.3 microdeletions MH Willemsen et al 430 induced at 36-week gestation because of maternal preeclampsia. Growth infection was excluded and organomegaly and thrombocytopenia were parameters were appropriate for gestational age, with a birth weight between resolved. He suffered a mild intracranial hemorrhage secondary to thrombo- the 50th and 75th percentile. Head circumference was not measured at birth. cytopenia, and was diagnosed with a ventricular septal defect (VSD), patent He was diagnosed with congenital hip dysplasia, but had no other difficulties in foramen ovale (PFO), cleft mitral valve and left cryptorchidism in the newborn the neonatal period. His psychomotor development was delayed. He walked period. VSD and PFO were repaired at the age of 3 months. Routine G-banded independently at the age of 2.5 years and began using single words after the age chromosome analysis was normal. At the time of genetics consultation at the of 4 years. At the age of 3 years, he was referred to a pediatric neurologist age of 6 years and 3 months, he was admitted to hospital for an acute because of his developmental delay and epilepsy (absence and generalized parvovirus myocarditis and dilated cardiomyopathy with severely depressed epilepsy). Cerebral imaging with a computer tomography scan (CT-scan) biventricular function. Further evaluation revealed a history of developmental showed colpocephaly, hypoplasia of the corpus callosum and heterotopia. delay (he walked at the age of 3 years, and spoke his first words at 18–20 Vision and audiological evaluations were normal. Routine chromosome months), mental retardation and febrile seizures. On physical examination, he analysis showed a normal male karyotype. At the age of 22 years, he was had a height on the 5–12th percentile and a head circumference on the 10th referred for reevaluation. He was moderately mentally retarded and showed percentile. Dysmorphic features that were observed included a triangular face behavior consistent with autism spectrum disorder. A Dutch formal test for with a high forehead and frontal bossing, arched eyebrows, large ears, smooth autism spectrum disorders (AVZ-R ‘Autisme- en Verwante stoornissenschaal-Z- philtrum, wide mouth, pointed chin and high palate (Figure 1f and g). MRI of Revisie’, 1999) showed borderline results for the diagnosis of an autism the brain revealed a posterior fossa arachnoid cyst, thinned corpus callosum, spectrum disorder. His epilepsy was well under control and medical treatment periventricular heterotopias, optic nerve hypoplasia and evidence for an old left was gradually stopped. On physical examination, he exhibited dysmorphic hemorrhagic parietal infarct. The heterotopias were unilaterally localized along features, with a high forehead, bitemporal narrowing, long palpebral fissures, the lateral margin of the trigone of the right lateral ventricle extending along large ears, smooth philtrum, wide mouth and micrognathia (Figure 1c and d). the temporal horn of the right lateral ventricle. Ophthalmic examination He had kyphoscoliosis and strabismus. His height was 175 cm (3–10th revealed high myopia, intermittent exotropia, horizontal nystagmus, and percentile), weight was 64 kg (50th percentile) and head circumference was possible right amblyopia. Audiogram revealed moderate-to-severe bilateral 59.5 cm (90th percentile). Cardiac ultrasound revealed no abnormalities. Bone mixed sensorineural and conductive hearing impairment. His complete blood densitometry showed normal bone density. Genetic diagnostic evaluation with count showed mild macrocytosis (MCV 92.4 FL; normal 76–90), with normal subtelomeric multiplex ligation-dependent probe amplification (MLPA, SALSA homocysteine and folate values. The cardiomyopathy and macrocytosis MLPA Kit P036, MRC Holland, Amsterdam, The Netherlands) was normal. resolved, yet he developed complex partial seizures at the age of 7½ years, with EEG showing a seizure focus of the left
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  • (P -Value&lt;0.05, Fold Change≥1.4), 4 Vs. 0 Gy Irradiation

    (P -Value<0.05, Fold Change≥1.4), 4 Vs. 0 Gy Irradiation

    Table S1: Significant differentially expressed genes (P -Value<0.05, Fold Change≥1.4), 4 vs. 0 Gy irradiation Genbank Fold Change P -Value Gene Symbol Description Accession Q9F8M7_CARHY (Q9F8M7) DTDP-glucose 4,6-dehydratase (Fragment), partial (9%) 6.70 0.017399678 THC2699065 [THC2719287] 5.53 0.003379195 BC013657 BC013657 Homo sapiens cDNA clone IMAGE:4152983, partial cds. [BC013657] 5.10 0.024641735 THC2750781 Ciliary dynein heavy chain 5 (Axonemal beta dynein heavy chain 5) (HL1). 4.07 0.04353262 DNAH5 [Source:Uniprot/SWISSPROT;Acc:Q8TE73] [ENST00000382416] 3.81 0.002855909 NM_145263 SPATA18 Homo sapiens spermatogenesis associated 18 homolog (rat) (SPATA18), mRNA [NM_145263] AA418814 zw01a02.s1 Soares_NhHMPu_S1 Homo sapiens cDNA clone IMAGE:767978 3', 3.69 0.03203913 AA418814 AA418814 mRNA sequence [AA418814] AL356953 leucine-rich repeat-containing G protein-coupled receptor 6 {Homo sapiens} (exp=0; 3.63 0.0277936 THC2705989 wgp=1; cg=0), partial (4%) [THC2752981] AA484677 ne64a07.s1 NCI_CGAP_Alv1 Homo sapiens cDNA clone IMAGE:909012, mRNA 3.63 0.027098073 AA484677 AA484677 sequence [AA484677] oe06h09.s1 NCI_CGAP_Ov2 Homo sapiens cDNA clone IMAGE:1385153, mRNA sequence 3.48 0.04468495 AA837799 AA837799 [AA837799] Homo sapiens hypothetical protein LOC340109, mRNA (cDNA clone IMAGE:5578073), partial 3.27 0.031178378 BC039509 LOC643401 cds. [BC039509] Homo sapiens Fas (TNF receptor superfamily, member 6) (FAS), transcript variant 1, mRNA 3.24 0.022156298 NM_000043 FAS [NM_000043] 3.20 0.021043295 A_32_P125056 BF803942 CM2-CI0135-021100-477-g08 CI0135 Homo sapiens cDNA, mRNA sequence 3.04 0.043389246 BF803942 BF803942 [BF803942] 3.03 0.002430239 NM_015920 RPS27L Homo sapiens ribosomal protein S27-like (RPS27L), mRNA [NM_015920] Homo sapiens tumor necrosis factor receptor superfamily, member 10c, decoy without an 2.98 0.021202829 NM_003841 TNFRSF10C intracellular domain (TNFRSF10C), mRNA [NM_003841] 2.97 0.03243901 AB002384 C6orf32 Homo sapiens mRNA for KIAA0386 gene, partial cds.