Hindawi Publishing Corporation Case Reports in Pediatrics Volume 2012, Article ID 459602, 7 pages doi:10.1155/2012/459602

Case Report A Novel 2.3 Mb Microduplication of 9q34.3 Inserted into 19q13.4 in a Patient with Learning Disabilities

Shalinder Singh,1 Fern Ashton,1 Renate Marquis-Nicholson,1 Jennifer M. Love,1 Chuan-Ching Lan,1 Salim Aftimos,2 Alice M. George,1 and Donald R. Love1, 3

1 Diagnostic Genetics, LabPlus, Auckland City Hospital, P.O. Box 110031, Auckland 1148, New Zealand 2 Genetic Health Service New Zealand-Northern Hub, Auckland City Hospital, Private Bag 92024, Auckland 1142, New Zealand 3 School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand

Correspondence should be addressed to Donald R. Love, [email protected]

Received 1 July 2012; Accepted 27 September 2012

Academic Editors: L. Cvitanovic-Sojat, G. Singer, and V. C. Wong

Copyright © 2012 Shalinder Singh et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Insertional translocations in which a duplicated region of one is inserted into another chromosome are very rare. We report a 16.5-year-old girl with a terminal duplication at 9q34.3 of paternal origin inserted into 19q13.4. Chromosomal analysis revealed the karyotype 46,XX,der(19)ins(19;9)(q13.4;q34.3q34.3)pat. Cytogenetic microarray analysis (CMA) identified a ∼2.3Mb duplication of 9q34.3 → qter, which was confirmed by Fluorescence in situ hybridisation (FISH). The duplication at 9q34.3 is the smallest among the cases reported so far. The proband exhibits similar clinical features to those previously reported cases with larger duplication events.

1. Clinical Report She was reviewed at the genetics clinic at 16.5 years of age. At that time, she was continuing to make good Theprobandwasbornprematurelyat35weeksgestation academic progress although she was receiving some input with a birth weight of 2040 g. She required nasogastric tube from the learning support unit attached to her school. Her feeding during the first week of life. During infancy, she height was at the 50th centile, weight at the 25th centile, was investigated for hypotonia and associated plagiocephaly; and head circumference between the 25th and 50th centiles. a brain MRI scan showed no abnormalities. She also had Facial dolichocephaly and asymmetry were noted. The eyes difficulties swallowing solids until the age of 2 years with were mildly deep set. She had a short philtrum and mild ongoing tendency to drooling and keeping her mouth open. microganthia (Figures 1(a) and 1(b)), with a high arched She walked at 2 years and 3 months of age. Her speech began palate. There was distal tapering of the fingers with radial developing at around that time. At school, she demonstrated clinodactyly of the middle three fingers (Figure 1(c)). She age appropriate reading and writing skills, but required additional help in maths. However, the degree of her learning had long halluces, curly toes, and bilateral hallux valgus difficulty was minimal and psychometric assessment was (Figure 1(d)). A mild scoliosis was also noted. not deemed to be necessary. She was also noted to have difficulties in gross motor and particularly fine motor skills and required assistance from an occupational therapist. An 2. Chromosome Analysis ophthalmic assessment at 16 years of age demonstrated myopia, with visual acuity of 6/24 in the right eye and 6/12 in Conventional G-banded chromosome analysis was per- the left eye. Fundoscopy revealed the presence of pigmentary formed on peripheral blood samples taken from the proband changes in both posterior poles. and her parents. 2 Case Reports in Pediatrics

(a) (b)

(c) (d)

Figure 1: Clinical features of the patient at the age of 16.5 years. Frontal view (a) shows the short philtrum. Lateral view (b) shows mild micrognathia. (c) shows distal tapering of the fingers with radial clinodactyly of the middle three fingers, and (d) shows Long halluces, curly toes, and bilateral hallux valgus.

Genome-wide copy number analysis was determined the parental origin of the derivative chromosome 19 (Fig- from genomic DNA samples using the Affymetrix Cytoge- ures 2(e) and 2(f)). The duplicated region encompasses netics Whole-Genome 2.7 M array, according to the manu- approximately 92 , which are likely to contribute to the facturer’s instructions. Regions of copy number change were proband’s phenotypic features. calculated using the Affymetrix Chromosome Analysis Suite software (ChAS) v.1.0.1 and interpreted with the aid of the 3. Discussion UCSC genome browser (http://genome.ucsc.edu/;Human Mar. 2006 (hg18) assembly). Patients with 9q duplications have overlapping features, Chromosomal analysis showed a female karyotype which include variable degrees of developmental delays, 46,XX,der(19)ins(19;9)(q13.4;q34.3q34.3) for the proband learning or intellectual deficits, facies characterised by dolic- (Figure 2(a)). The father’s karyotype was 46,XY,ins(19;9)- ocephaly, asymmetry, deep set eyes or small palpebral fis- (q13.4;q34.3q34.3) (Figure 2(d)) and the mother’s karyotype sures, high arched palate, micrognathia and digital anomalies was normal (data not shown). The array revealed a terminal including arachnodactyly, camptodactyly and clinodactyly. duplication of approximately 2.3 Mb at 9q34.3, and the Furthermore, the finding of long halluces appears to be proband’s molecular karyotype was arr 9q34.3(137,864,059- a common and distinctive feature in patients with a pure 140,171,337)x3 (Figure 3; UCSC Genome Browser-NCBI duplication, although many other reported cases carry copy Build 36, Mar. 2006 assembly). number changes other than 9q duplications [1–8]. FISH confirmed that a segment of region 9q34.3 was In this study, we report a small ∼2.3 Mb duplica- inserted into the region 19q13.4 using the -specific tion of 9q34.3 detected by CMA. Our patient displayed probe D9S325, with two signals on the dolicocephaly and facial asymmetry, mildly deep-set eyes, homologues present in the proband (Figures 2(b) and short philtrum, mild microganthia, high arched palate, clin- 2(c)). FISH using the probe specific for the 19q terminal odactyly, mild scoliosis, mild myopia, and digital anomalies. region confirmed that the subtelomeres of the derivative A comparison of phenotypic anomalies of our patient with chromosome 19 were intact. FISH findings from the father previously reported cases is summarised in Table 1. demonstrated an apparently balanced translocation: part of Recently, Gijsbers et al. [8] reported a 16-year-old girl region 9q34.3 was inserted into 19q13.4, thus confirming with a triplication and duplications in the 9q34.3 region. Case Reports in Pediatrics 3 qter → + + + + + + − 2.3 Mb ∼ 9q34.3 Present case dup ] 8 ++ ++ − −− ∗ −− − − Null Null 2.4 Mb 0.53 Mb 9q34.3 ∼ ∼ triplication duplication; dup and trip Gijsbers et al. [ q34.3 ] → 7 + + + + − −− −∗ −−− − Dels al. [ 5–5.8 Mb ∼ 15q22.31-15q23; 15q25.1-15q25.2 Papadopoulou et 15q21.2-15q21.3; dup9q34.1 q34.3 ]dup 6 → ++++ + + + + − − ∗ Null et al. [ 9q34.1 Gawlik-Kuklinska ] ]. 3 5 qter → q22.1 → ∗ ∗ ∗ ∗ ∗ −− Dup 21pter Mattina et al. [ Clinical features dup 9q34.1 ] 3 qter → dup a ] 4 [ 9q33.3 Spinner et al. [ and Youngs et al. ] 2 1: Clinical features in patients with duplication and/or triplication of the 9q34 region. q34.3 → ++ +++++ ++ dup Table 9q34.1 Allderdice et al. [ ] 1 q34.3 → ++ + +++++ +++++++ +++++ ++ + ∗ ∗ ∗ Null Null Del 12p13.33 Undetermined Undetermined 13.79 Mb Undetermined 7.26 Mb dup 9q32 Hou and Wang [ ] is an 18-year follow-up report on an infant with dup 9q34 originally reported by Spinner et al. [ 4 Not reported or observed from published photographs. Youngs et al. [ Cytogenetics Size of 9q duplication determined by molecular karyotype DolicocephalyHigharchedpalate++++ +Long halluces +Cardiac defectsDevelopmental delay/intellectual disability + + + + + Arachnodactyly/ camptodactyly Beaked nose + + + + Scoliosis Deep-set eyes/small palpebral fissures Facial asymmetry Micrognathia/ retrognathia Hypotonia + + + + + + Other chromosomal anomalies Low birth weightFailure to thrive + + + + + + a ∗ 4 Case Reports in Pediatrics

24 24 23 23 13.3 13.3 22 22 p 13.2 13.2 p 21 p 21 13.1 p 13.1 13 13 12 12 der19 12 12 11 11 11 11 19pter 9qter 11 11 19qter 11 11 12 12 9qter 12 12 13.1 13.1 9pter 13 13 q q 9qter 21.1 21.1 13.2 13.2 9qter 21.2 21.2 21.3 21.3 13.3 13.3 9pter 9qter 22.1 22.1 q 22.2 q 22.2 13.4 13.4 17cen 22.3 22.3 19q13 19pter 31 31 19 der 19 17pter 32 32 33 33 34.1 34.1 34.2 34.2 17pter 34.3 34.3 17cen 99 (a) (b) (c)

24 24 23 23 13.3 13.3 22 22 p 21 p 21 p 13.2 13.2 13.1 p 13.1 13 13 12 12 12 12 11 11 17cen 9qter 9qter 11 11 11 11 11 11 17qter 12 12 9qter 9pter 19pter 12 12 19p13 13.1 13.1 der19 13 13 q 9qter 21.1 21.1 13.2 q 13.2 21.2 21.2 17cen 21.3 21.3 13.3 13.3 q 22.1 q 22.1 17pter 22.2 22.2 13.4 13.4 22.3 22.3 31 31 19 der 19 9qter 32 32 33 33 der9 19qter 19pter 34.1 34.1 9pter 34.2 34.2 34.3 34.3 9 der 9 (d) (e) (f)

Figure 2: Cytogenetics and FISH analysis of proband and father. ((a)–(c)) and (d-f) show the analysis of the proband and father, respectively. Ideograms of 9 and 19 show that part of region 9q34.3 is inserted into region 19q13.4 in the proband (a), and the father is a carrier of a balanced insertional translocation (panel d). FISH analysis used probes for 9pter (305J7-T7), 9qter (D9S325), 19pter (129F16/SP6), 19qter (D19S238E), 19q13 (GLTSCR1/GLTSCR2/CRX), while 17cen and 17q used control probes ((b)–(c) for the proband, and panels (e)–(f) for the father). These panels confirm that the part of region 9q34.3 is inserted into region 19q13.4. The subtelomeres of chromosome 19 were intact (the probes for 19pter (129F16/SP6) and 19qter (D19S238E) were used; image not shown).

The authors noted that the clinical features of their proband addition, the NOTCH signalling pathway plays a pivotal role overlapped with those in one previous report [2], which in embryo development. It is likely, given the mathematical was a “pure” 9q34.3 duplication case. The same dysmorphic modelling undertaken by Raya et al. [10], that increased features are shared with the proband reported here, but expression of NOTCH1 would have an impact on the level feeding difficulties, scoliosis, and severe mental retardation of NOTCH1-associated subcomplexes, and hence alter devel- areabsent.ThemoreseverephenotypereportedbyGijsbers opmental and physiological outcomes. That NOTCH1 over- et al. [8] may be attributed to a larger ∼2.9Mb region of expression may be the principal underlying responsible duplicated and triplicated subregions (chr9q34:137,265,834- for the phenotype of our patient remains speculative at 140,207,437) that encompasses approximately 100 genes. In this stage. It is also possible that the site of insertion on our case, approximately 92 genes are duplicated in a ∼2.3 Mb chromosome 19 may affect the expression of chromosome region (chr9q34.3 : 137,864,059-140,171,337). 19 genes, which may play a role in the phenotype reported Of the genes contained within the duplicated region here. Unfortunately, the array data does not provide any detected in our patient, eleven are present in the Online clues regarding the specific site of insertion on chromosome Mendelian Inheritance in Man (OMIM; http://www.ncbi 19. .nlm.nih.gov/omim) morbid map, and of these, all but In summary, the proband reported here is a new addition NOTCH1 are associated with autosomal recessive disease to the rare collection of dup 9q34 cases. Our patient has and homozygosity for terminating mutations (Table 2). As developed a mild form of the clinical features described a consequence, these OMIM genes do not appear to play a in other 9q34 cases, possibly due to the smaller affected role in the clinical phenotype reported here which is likely to region. Patients with shorter dup 9q34 tend to have a be caused by gene overexpression, due to the increased copy better prognosis and would benefit from special education number of the 2.3 Mb region of chromosome 9, rather than with input from their parents [2]. It is hoped that with haploinsufficiency. increased reporting of similar cases, dosage changes and In the mouse, upregulation of NOTCH activity appears breakpoints in this region can be more clearly correlated to to be associated with an increase in the number of interneu- phenotypic features to aid genetic counselling and medical ronal contacts and the cessation of neurite growth [9]. In management. Case Reports in Pediatrics 5

chr9 (q34.13-q34.3) p23

Scale 2 MB chr9: 135500000 136000000 136500000 137000000 137500000 138000000 138500000 139000000 139500000 140000000 9q34.3 9q34.2 Genetic association studies of complex diseases and disorders CEL DBH COL5A1 NOTCH1 PTGDS ABO ABCA2 SURF1 GRIN1 OMIM-associated genes 607341 602930 601541 180245 601624 608167 602777 601895 611255 601012 110300 600428 130010 611971 608129 190198 602012 608137 601012 605284 612277 601541 130000 151675 600577 608582 606946 611424 191100 231050 609012 120215 164320 262600 608594 604346 611846 604383 604455 601429 601252 173310 612860 603100 610537 610253 604890 268900 180245 605366 612903 609491 609379 138249 607001 114840 606813 610224 607212 610615 609826 601619 609312 613036 610167 602660 606074 223360 613037 605107 611180 604606 612854 609072 146110 185642 612904 610882 185641 612902 606073 185640 120930 612122 256000 612905 220110 176803 185620 606533 185630 600047 185660 602030 604134 605798 274150 612057 235400 241530 RefSeq genes TSC1 ABO DBH BRD3 RXRA FCN2 KIAA0649 UBAC1 GPSM1 SNHG7 FUT7 NOXA1 MIR602 TSC1 SURF6 VAV2 COL5A1 C9orf116 NACC2 EGFL7 C8G NRARP CACNA1B TSC1 MED22 VAV2 FCN2 C9orf116 C9orf69 EGFL7 NPDC1 ENTPD8 TUBBP5 GFI1B MED22 NCRNA00094 FCN1 MRPS2 LHX3 MIR126 ABCA2 ENTPD8 GFI1B RPL7A WDR5 OLFM1 LCN1 LHX3 AGPAT2 UAP1L1 NELF GTF3C5 C9orf7 WDR5 OLFM1 OBP2A QSOX2 AGPAT2 MAN1B1 NELF GTF3C5 C9orf7 RNU6ATAC PAEP LOC26102 FAM69B DPP7 NELF CEL SLC2A6 PAEP GPSM1 SNHG7 GRIN1 MRPL41 CELP TMEM8C LOC100130954 GPSM1 SNHG7 GRIN1 WDR85 RALGDS FAM163B LOC100130954 DNLZ LCN10 GRIN1 ARRDC1 RALGDS SARDH GLT6D1 CARD9 LCN6 GRIN1 C9orf37 GBGT1 SARDH LCN9 CARD9 LCN8 GRIN1 EHMT1 OBP2B SOHLH1 SNAPC4 LCN15 LRRC26 EHMT1 SNORD24 SOHLH1 SDCCAG3 PHPT1 SSNA1 FLJ40292 SNORD36B KCNT1 SDCCAG3 PHPT1 TPRN SNORD36A CAMSAP1 SDCCAG3 MAMDC4 NDOR1 SNORD36C PMPCA EDF1 NDOR1 SURF1 INPP5E EDF1 NDOR1 SURF2 SEC16A TRAF2 EXD3 SURF4 C9orf163 FBXW5 NELF C9orf96 NOTCH1 LCN12 NELF REXO4 SNORA43 ANAPC2 ADAMTS13 SNORA17 TMEM203 ADAMTS13 LOC100128593 NDOR1 ADAMTS13 TMEM141 RNF208 ADAMTS13 KIAA1984 TUBB2C SLC2A6 LOC100131193 FAM166A ADAMTSL2 C9orf86 COBRA1 ADAMTSL2 C9orf86 PNPLA7 C9orf86 PNPLA7 MIR4292 ZMYND19 C9orf172 PTGDS LCNL1 C9orf142 CLIC3 ABCA2 C9orf139 ENTPD2 ENTPD2 C9orf140 LOC100289341 C9orf169 LOC643596 SLC34A3 SLC34A3 SLC34A3 C9orf173 C9orf167

Papadopoulou et al. [7]

Gijsbers et al. [8]

Present case

Figure 3: Location and extent of 9q34 duplications. UCSC Genome Browser (March 2006 (hg18) assembly) view of the chromosomal region 9q34.13-q34.3 (chr9:134,776,210-140,171,337) is shown, together with Refseq, OMIM, and GAD genes. The bottom panel shows the location and extent of the 9q34.3-qter region of the patient described here, and of other cases reported in the literature. Note: the region highlighted in yellow is the ∼2.3 Mb region duplicated in our case, and the thicker green block represents the triplicated region reported by Gijsbers et al. [8]. 6 Case Reports in Pediatrics

Table 2: Duplicated region and OMIM genes.

OMIM Gene Disorder Molecular genetics Combined pituitary Homozygosity for intragenic 600577 LIM/homeodomain protein LHX3 LHX3 hormone deficiency-3 deletion/nonsense mutation Homozygosity for mutations in the 613037 Inositol polyphosphate-5-phosphatase INPP5E Joubert syndrome 1 INPP5E gene that lead to decreased phosphatase activity Mental retardation, truncal Homozygous nonsense mutation detected obesity, retinal dystrophy, in the INPP5E gene and micropenis Autosomal recessive form Caspase recruitment domain-containing Homozygous nonsense mutation in the 607212 CARD9 of familial chronic protein 9 CARD9 gene mucocutaneous candidiasis Notch, Drosophila, homolog of, 1, Heterozygosity for nonsense/frameshift 190198 translocation associated Notch homolog; NOTCH1 Aortic valve disease mutations NOTCH1 Leukemia, T-cell acute lymphoblastic 1-Acylglycerol-3-phosphate Lipodystrophy, congenital Homozygous or compound heterozygous 603100 AGPAT2 O-acyltransferase 2 generalised, type 1; CGL1 mutations Autosomal recessive 613354 Taperin TPRN Homozygous truncating mutations nonsyndromic deafness-79 Mental retardation, 604346 Mannosidase, alpha, class 1B member 1 MAN1B1 Homozygous mutations autosomal recessive 15 Glutamate receptor, ionotropic, Mental retardation, Missense mutation; in-frame duplication 138249 GRIN1 N-methyl D-aspartate 1 autosomal dominant 8 of codon 560 Solute carrier family 34 Hypophosphatemic rickets 609826 (sodium/phosphate cotransporter), SLC34A3 Homozygous single-nucleotide deletion with hypercalciuria member 3 Nasal embryonic luteinizing Hypogonadotropic 608137 NELF A thr480-to-ala mutation in the NELF gene hormone-releasing hormone factor hypogonadism Heterozygous nonsense/frameshift mutation, in the EHMT1 gene; terminal 607001 Euchromatic histone methyltransferase 1 EHMT1 Kleefstra syndrome deletions, interstitial deletions, derivative chromosomes, and complex rearrangements The entries in this table were taken from the OMIM database (http://www.ncbi.nlm.nih.gov/omim).

Acknowledgment [4] E. L. Youngs, T. McCord, J. A. Hellings, N. B. Spinner, A. Schneider, and M. G. Butler, “An 18-year follow-up report ThedetailsofthiscasehavebeendepositedinDeci- on an infant with a duplication of 9q34,” American Journal of pher (https://decipher.sanger.ac.uk); ID 254186. The authors Medical Genetics A, vol. 152, no. 1, pp. 230–233, 2010. wish to state that there is no conflict of interests with [5] T. Mattina, M. Pierluigi, D. Mazzone, S. Scardilli, C. Perfumo, any organization regarding the material presented in this and F. Mollica, “Double partial trisomy 9q34.1 → qter and paper. 21pter → q22.11: FISH and clinical findings,” Journal of Medi- cal Genetics, vol. 34, no. 11, pp. 945–948, 1997. [6] K. Gawlik-Kuklinska, M. Iliszko, A. Wozniak et al., “A girl References with duplication 9q34 syndrome,” American Journal of Medical Genetics, Part A, vol. 143, no. 17, pp. 2019–2023, 2007. [1] J. W. Hou and T. R. Wang, “Molecular cytogenetic studies [7] E. Papadopoulou, C. Sismani, C. Christodoulou, M. Ioan- of duplication 9q32 → q34.3 inserted into 9q13,” Clinical nides, M. Kalmanti, and P. Patsalis, “Phenotype-genotype Genetics, vol. 48, no. 3, pp. 148–150, 1995. correlation of a patient with a “balanced” translocation [2] P. W. Allderdice, B. Eales, H. Onyett et al., “Duplication 9q34 9;15 and cryptic 9q34 duplication and 15q21q25 deletion,” syndrome,” American Journal of Human Genetics, vol. 35, no. American Journal of Medical Genetics A, vol. 152, no. 6, pp. 5, pp. 1005–1019, 1983. 1515–1522, 2010. [3] N. B. Spinner, J. N. Lucas, M. Poggensee, M. Jacquette, [8] A. C. J. Gijsbers, E. K. Bijlsma, M. M. Weiss et al., “A 400 kb and A. Schneider, “Duplication 9q34 → qter identified by duplication, 2.4 Mb triplication and 130 kb duplication of chromosome painting,” American Journal of Medical Genetics, 9q34.3 in a patient with severe mental retardation,” European vol. 45, no. 5, pp. 609–613, 1993. Journal of Medical Genetics, vol. 51, no. 5, pp. 479–487, 2008. Case Reports in Pediatrics 7

[9] N. Sestan,ˇ S. Artavanis-Tsakonas, and P. Rakic, “Contact- dependent inhibition of cortical neurite growth mediated by Notch signaling,” Science, vol. 286, no. 5440, pp. 741–746, 1999. [10] A.Raya,Y.Kawakami,C.Rodr´ ´ıguez-Esteban et al., “Notch activity acts as a sensor for extracellular calcium during vertebrate left-right determination,” Nature, vol. 427, no. 6970, pp. 121–128, 2004. Copyright of Case Reports in Pediatrics is the property of Hindawi Publishing Corporation and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use.