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Microduplication of chromosome Xq25 encompassing STAG2 gene in a boy with intellectual disability
European Journal of Medical Genetics xxx (2014) 1e6
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Microduplication of chromosome Xq25 encompassing STAG2 gene in a boy with intellectual disability Xie Yingjun a, b,1, Tang Wen c, *,1, Liang Yujian c, Xu Lingling c, Huang Huimin c, Fang Qun a, Chen Junhong a a
Department of Prenatal Diagnosis, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, 510080, China c Department of Pediatric Intensive Care Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China b
a r t i c l e i n f o
a b s t r a c t
Article history: Received 9 May 2014 Accepted 13 October 2014 Available online xxx
Whole-genome microarray analysis is proven to be useful in the identification of submicroscopic copy number imbalances in families with intellectual disabilities. The first case of Xq25 duplication was identified using genome-wide array comparative genomic hybridization (array-CGH) in a 24-year-old patient with a syndromic intellectual disability. We report a 4-year-old boy with a de novo 591 kb duplication at Xq25. The duplication was first detected by a CytoScan HD array platform (Affymetrix, USA) and was confirmed by real-time quantitative PCR (qPCR) of the STAG2 gene, and by fluorescence in situ hybridization (FISH). The patient had clinical features partially consistent with published cases, including an intellectual disability and speech delay. The identification of this additional patient and a detailed analysis of duplications identified in other patient cohorts and absent in normal individuals support the existence of a rare pathological microduplication at Xq25 that encompasses STAG2. Ó 2014 Elsevier Masson SAS. All rights reserved.
Keywords: Intellectual disability Microduplication XIAP STAG2 Genome-wide array analysis
1. Introduction Investigation of chromosomal rearrangements in patients with intellectual disabilities (ID) has proven particularly informative in the search for novel genes. Intellectual disability, behavioral problems and physical anomalies can be the result of microdeletions or microduplications of contiguous genes in almost every chromosome [Gillberg, 1998]. The genetic factors underlying ID are very heterogeneous. With the advent of molecular karyotyping, i.e., the number of microdeletions and microduplications associated with phenotypic features, frequently including idiopathic ID, has greatly increased. Recent studies have identified a number of
Abbreviations: CASP3, cell-death proteases, caspase-3; CASP7, caspase-7; CNVs, copy number variations; DAPI, 40,6-diamidino-2-phenylindole; DD, developmental delay; FISH, fluorescence in situ hybridization; IAPs, inhibitor of apoptosis proteins; ID, intellectual disability; IUGR, intrauterine growth restriction; STAG2, stromal antigen 2; XIAP, X-linked inhibitor of apoptosis; XLMR, X-linked mental retardation. * Corresponding author. Department of Pediatric Intensive Care Unit, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Second Road, Guangzhou 510080, China. Tel.: þ86 020 87755766x8922. E-mail address: [email protected] (T. Wen). 1 These authors contributed equally to this work, and should be considered as co-first author.
copy number variations (CNVs) involved in ID, several of which lie on the X-chromosome. However, the current understanding of the monogenic causes of ID is far from comprehensive. New high resolution genetic analysis techniques often provide an explanation or a diagnosis of abnormal conditions and help define a more precise characterization of any genotype/ phenotype correlations in childhood chromosomal anomalies. Recently, small duplications involving the Xq25 region have been reportedly associated with ID. Philippe A. et al. reported two patients with an Xq25 duplication encompassing the GRIA3 and STAG2 genes with an intellectual disability, and suggested that in addition to the role of GRIA3 gene, the duplication of STAG2 (Stromal Antigen 2) gene coding for the subunit SA1 of the cohesin complex may potentially contribute to the clinical phenotype [Philippe et al., 2013]. Di Benedetto, D. et al. also reported two unrelated families with Xq25 duplications of approximately 630 kb involved three genes: THOC2, XIAP, and STAG2, whereas the minimal duplicated region was approximately 270 kb and encompassed the XIAP and STAG2 genes [Di Benedetto et al., 2014]. We report here the clinical and molecular cytogenetic findings in a boy with a de novo 591 kb duplication of the Xq25 region encompassing the XIAP, STAG2 and SH2D1A genes who presented with a developmental delay, dysmorphic features, and
http://dx.doi.org/10.1016/j.ejmg.2014.10.002 1769-7212/Ó 2014 Elsevier Masson SAS. All rights reserved.
Please cite this article in press as: Yingjun X, et al., Microduplication of chromosome Xq25 encompassing STAG2 gene in a boy with intellectual disability, European Journal of Medical Genetics (2014), http://dx.doi.org/10.1016/j.ejmg.2014.10.002
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X. Yingjun et al. / European Journal of Medical Genetics xxx (2014) 1e6
a small ear deformity. This study was conducted to refine the clinical presentation of the Xq25 microduplication and to establish the genotypeephenotype correlation.
and tooth enamel erosions and the facial anomalies also including malar flatness, prognathism, and thick vermilion of lips (Fig. 1). 2.2. Chromosomal analysis
2. Method and material Conventional karyotyping at a resolution of 550 bands of both the proband and the parents was performed on metaphase spreads from cultured lymphocytes according to the standard protocols.
2.1. Clinical description The proband was a child referred to our Clinical Genetics Service for dysmorphic features and a developmental delay. The proband was the third child of healthy unrelated parents with an uneventful family history. His two older sisters were both normal. He was born at 41 weeks of gestation after an uneventful pregnancy. Prenatal diagnosis performed due to advanced maternal age showed a normal fetal karyotype (46, XY). The patient was born by normal spontaneous delivery. No intrauterine exposure to drugs or other possibly harmful factors were reported. At birth, a large fontanelle was reported (data not provided). Birth weight was 2700 g (3rd percentile), birth length was 46 cm (<3rd percentile), the head circumference was 31 cm (<3rd percentile), and the thoracic circumference was 32 cm (<3rd percentile). APGAR scores were 9/ 10 and 10 /50 . Early motor development was only slightly delayed: he sat at 8 months, walked at 18 months and pronounced his first words at 18e20 months. He began speaking single words at 1 year and 7 months. He started walking independently around 2 years old. A developmental delay (35 months, DQ 70 at Gesell-scale) and muscle hypotonia were observed since the age of two and he was diagnosed as ASD (data of assessment for ASD not provided). He was particularly friendly to foreign people although grumpy, and presented with compromised hearing on the left side compared to the right side (by clinical hearing screening). In addition, he had a history of sinusitis with nasal gland enlargement. However, he was not performed any immunological test and did not show any significant immunological disease. His previous blood test was not available. On first examination at the Genetic Clinic, at age of 3 years and 8 months, his height was 95 cm (3rd percentile), weight was 16 kg (50th percentile) and his head circumference was 45.2 cm (<3rd percentile). He presented with brachycephalia, full cheeks, medial flaring of eyebrows, long eyelashes, epicanthic folds, strabismus, small ears with total length of 4.7 cm (50th percentile), a short nose, low and widened nasal root, a long philtrum, a full lower lip,
2.3. Chromosomal microarray analysis (CMA) Genomic DNA was extracted from peripheral blood lymphocytes using QIAamp DNA Blood Mini Kit [QIAGEN, Hilden, D] for the patient and his parents according to manufacturers’ instructions. The DNA (250 ng) was amplified, labeled and hybridized to the CytoScan HD array platform (Affymetrix, USA) according to the manufacturer’s protocol. The array was designed specifically for cytogenetic research, and it offered more than 2,700,000 markers across the whole genome, including 750,000 SNP probes and 1,950,000 probes to detect copy number variations (Cyto-arrays). CEL files obtained by scanning the CytoScan arrays were analyzed using the Chromosome Analysis Suite software (Affymetrix, USA) and the annotations of the genome version GRCH37 (hg19). Only qualified measures were included in our analysis. Gains and losses that affected a minimum of 50 markers in a 100 kb length were initially considered. 2.4. Fluorescence in situ hybridization (FISH) Cytogenetic studies of the patient and his parents were performed on metaphase chromosomes derived from cultures of PHAstimulated peripheral blood lymphocytes. Fluorescent in situ hybridization analysis (FISH) was used with a combination of CEP X probe and Single-copy DNA probes, RP1-159G19 (Xq25), cloned in BACs (Vysis, USA; BlueGnome, UK) performed according to the manufacturers’ instructions. The two types of probes were used to visualize the central region and the specific-Xq25, respectively. Slides were counterstained with 40,6-diamidino-2-phenylindole (DAPI, 200 ng/ml) and were analyzed by fluorescence microscopy using an Olympus BX61 equipped with a cooled CCD Video Camera, Photometrics. Image analysis was carried out with ASI FISH software.
Fig. 1. Frontal (A) and right (B) lateral craniofacial views of our patient.
Please cite this article in press as: Yingjun X, et al., Microduplication of chromosome Xq25 encompassing STAG2 gene in a boy with intellectual disability, European Journal of Medical Genetics (2014), http://dx.doi.org/10.1016/j.ejmg.2014.10.002
X. Yingjun et al. / European Journal of Medical Genetics xxx (2014) 1e6
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Fig. 2. A. Mapping of a chromosomal Xq25 duplication. B. SNP-Array genotyping of patients. Whole-genome array-based SNP showed a 591 kb duplication stretching from 122,899,950 to 123,490,624. C. Schematic representation of the Xq25 duplication region including the DECIPHER microduplication cases, ISCA case and Philippe et al., Di Benedetto et al., Bonnet et al. reported cases.
2.5. Real-time quantitative PCR (qPCR) Confirmation of the CMA result and analysis of the unaffected sisters and the parents were performed by quantitative real-time PCR. Primer sequences can be obtained upon request. qPCR was performed on ABI PrismÒ 9700TH Sequence Detection System. 2.6. Paternity testing Paternity testing was performed using small tandem repeat (STR) marker genotyping on the patient and his parents by DNA
fragment analysis by the 3500 Genetic Analyzer in accordance with the manufacturer’s recommendations. 3. Results 3.1. Karyotyping, CMA and FISH The couple and the proband harbored a normal karyotype. Genome-wide array analysis of the proband showed a 591 Kb duplication at Xq25, ranging from 122,899,950e123,490,624 (Fig. 2A) while the CMA results of the parents were normal, that is
Fig. 3. Metaphase fluorescence in situ hybridization study of cultured lymphocytes using CEP X green probes and RP1- 159G19 red (Xq25) probes. No duplication or translocation was detected on Xq25 in the cultured lymphocytes that originated from the father (B) or the mother (A). The duplication of an Xq25 signal in the interphase nuclei on X-chromosome revealed the duplication Xq25 in the proband (C).
Please cite this article in press as: Yingjun X, et al., Microduplication of chromosome Xq25 encompassing STAG2 gene in a boy with intellectual disability, European Journal of Medical Genetics (2014), http://dx.doi.org/10.1016/j.ejmg.2014.10.002
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X. Yingjun et al. / European Journal of Medical Genetics xxx (2014) 1e6
Table 1 The comparison of clinical features in patients with overlapping microduplications between the studied patient (Mapping used hg19). Phenotypic and genotypic comparisons between the present duplication case and other genomic disruptions at Xq25. Ages for each proband are given at the time of clinical assessment. Otherwise, ages are as reported by other authors. Seven cases from the DECIPHER database. Clinical features
Present subject
DECIPHER
nsv 532914 [Kaminsky et al., 2011]
595
253540
253551
250183
264308
270242
283869
Gender Age ASD ID Cross motor deficit Language delay Recurrent seizures Dysmorphic feature Development delay Inheritance Size (Mb) Breakpoints (bp) (GRCH37/ hg19) Contain genes Additional CNVs
M 3.7 þ þ
F 15 þ þ
F 8 þ þ þ
M 10 NA NA NA
M 11 þ þ
F 6 þ
M 4 þ þ þ
F 9 þ þ þ
M NA þ þ
þ
þ
NA
þ
þ
þ
þ
NA
þ
NA
þ
þ
þ
NA
þ
dn 0.59 122899950e 123490624
mat 0.77 122390702e 123162552
dn 0.56 122801087e 123357985
dn 0.26 123003512e 123266951
mat 0.41 123014742e 123427774
dn 0.97 12235220e 123322930
uk 0.23 123056096e 123283547
dn 0.21 123388516e 123598378
mat 0.51 122869800e 123388775
XIAP, STAG2 SH2D1A
GRIA3,STAG2, THOC2,XIAP
STAG2,THOC2, XIAP
STAG2,XIAP
STAG2,XIAP
GRIA3,STAG2, THOC2,XIAP
STAG2
STAG2, XIAP
24826107e 25542728
AH2D1A,STAG2, TEN1 e
þ: feature present; : feature absent; NA: not assessable/assessed. ASD: Autism Spectrum Disorder; dn: De novo. hg18.
a
without the 591 kb duplication at Xq25. The 3500 Genetic Analyzer confirmed the paternity of the patient’s parents. The qPCR and FISH analysis (Fig. 3) on the proband and his parents confirmed the rearrangement and showed that the Xq25 duplication occurred de novo and harbored three genes: XIAP, STAG2, SH2D1A. Furthermore, FISH analysis (Fig. 2A) showed a unique Xq25 signal suggesting a tandem duplication. A secondary review of the CMA results in the proband did not identify any other smaller CNVs below the usual clinical reporting thresholds (200 kb for deletion; 500 kb for duplication). 3.2. Clinical features analysis We compared the clinical phenotypes of the proband (Fig. 2C), who carried an Xq25 duplication, with other reported patients who carried other Xq25 duplications (Table 1) [Bonnet et al., 2009; Di Benedetto et al., 2014; Kaminsky et al., 2011; Philippe et al., 2013]. Among the patients, all were reported to have the ID similar to our patient. These finding implied that the Xq25 region is important in neurodevelopment. 4. Discussion Until now, approximately 4% of the more than 22,000 proteincoding genes presently listed in ENSEMBL are located on the Xchromosome, and approximately 40% of these are currently known to be expressed in the brain. Therefore, several hundred genes could be involved in X-linked mental retardation (XLMR) [Ropers, 2006]. Some ID phenotypes may be attributed to dosage decreases/increases of certain protein-coding genes. Thus, functional disomy may cause dysfunction in the brain [Tejada et al., 2011]. Recently, McNamara, G. I. and Isles, A. R. [McNamara and Isles, 2013] found that brain function is exquisitely sensitive to
both decreases and increases in the expression of imprinted genes. We report a novel clinical and molecular cytogenetic finding of a boy with an idiopathic intellectual disability. These findings are found to share a strikingly similar pattern of neurosensory (mild visual impairment), neurodevelopmental (moderate developmental and adaptive delay) and somatic congenital anomalies associated with an interstitial microduplication of the Xq25 region, cryptic upon G-banding, and identified by SNP-array. Comparison with previously described individuals with similar Xq25 microduplications (Table 1) showed that the present patient had similar facial morphological anomalies (malar flatness, thick vermilion of lips, and prognathism), and ID. The common 591 Kb duplication interval of Xq25 observed in this patient includes three known genes with a variety of functions, the X-linked inhibitor of apoptosis (XIAP, OMIM 300079), stromal antigen 2 (STAG2, OMIM 300826) and SH2D1A (before exon 2). SH2D1A encodes a protein that plays a major role in the bidirectional stimulation of T and B cells. This protein associates with the signaling lymphocyte-activation molecule. Mutations in this gene cause lymphoproliferative syndrome X-linked type 1 or Duncan disease, a rare immunodeficiency characterized by extreme susceptibility to infection with EpsteineBarr virus, with symptoms including severe mononucleosis and malignant lymphoma [Overwater et al., 2014; Wu et al., 2014]. The gene XIAP belongs to a human multigene family whose members show extensive homology to baculovirus inhibitor of apoptosis proteins (IAPs) and encode proteins that inhibit apoptosis. Deveraux et al. [Deveraux et al., 1997] showed that human X-linked IAP directly inhibits at least 2 members of the caspase family of cell-death proteases, caspase-3 (CASP3) and caspase-7 (CASP7). As the caspases are highly conserved throughout the animal kingdom and are the principal effectors of apoptosis, these findings suggest that IAPs
Please cite this article in press as: Yingjun X, et al., Microduplication of chromosome Xq25 encompassing STAG2 gene in a boy with intellectual disability, European Journal of Medical Genetics (2014), http://dx.doi.org/10.1016/j.ejmg.2014.10.002
X. Yingjun et al. / European Journal of Medical Genetics xxx (2014) 1e6
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Philippe et al. [Philippe et al., 2013]
Di Benedetto et al. [Di Benedetto et al., 2014]
1
2
Family 1 Ⅱ-2
Ⅰ-2
Ⅱ-4
Ⅱ-5
Ⅲ-2
Ⅲ-6
Ⅱ-1
Ⅰ-2
M 24 þ þ
M 4 þ þ
M 51 þ þ
F 71 þ
M 38 þ
M 37 þ
M 38 þ
M 36 þ
M 14 þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
mat 1.2 NA
mat 5.02 120957860e 125980037a
mat NA mat mat mat 0.60 122697410w122703291e123259725w 123266892a
GRIA3,STAG2, THOC2,XIAP
Bonnet et al. [Bonnet et al., 2009] Family 2
THOC2,XIAP,STAG2 e
might inhibit cell death, providing evidence for a mechanism of action for these mammalian cell-death suppressors. XIAP is present in trophoblasts throughout placental development but significantly decreases during late pregnancy [Gruslin et al., 2001]. Evidence that increased XIAP levels protect the neonatal brain against hypoxia-ischemia was found in mice [Wang et al., 2004]. Placental villous apoptosis is increased at midgestation and near term in the ovine model of intrauterine growth restriction (IUGR), and this increase is associated with a significant decrease in XIAP protein in the cotyledon of IUGR animals [Arroyo et al., 2008]. West, T. et al. [West et al., 2009] identified a critical role for XIAP in regulating neuronal apoptosis in vivo and demonstrated the enhanced vulnerability of neurons to injury in the absence of XIAP in the developing brain. These considerations suggest that XIAP duplication may contribute to the ID phenotype observed in our patient. In addition to XIAP, STAG2 is known to be associated with physical support for hematopoietic cell organization [Renault et al., 2007]. Although no pathogenic mutations were found in STAG2, its function as a core component of the ring-like cohesion complex involved in sister chromatid cohesion during mitosis makes it a candidate gene for the ID trait. Abnormalities in cohesin genes are associated with human multisystem developmental disorders such as Cornelia de Lange Syndrome (CdLS, OMIM 122470) [Liu et al., 2009]. Recent report showed that duplications of cohesin genes associated with ID and craniofacial morphological anomalies [Baquero-Montoya et al., 2014; Yan et al., 2009]. These findings suggest that STAG2 could be a candidate gene for ID based on its expression in the brain or its role in neuronal development and function [Baquero-Montoya et al., 2014; Yan et al., 2009]. Our patient shows overlapping clinical features for published Xq25 microduplications, such as a developmental delay, an intellectual disability, and facial dysmorphism (see Table 1 for comparison).
II-1
II-3
F 39 þ
M 20 þ
M 20 þ
þ
þ
þ
þ
þ
þ
þ
NA
þ
þ
þ
NA
þ
þ
þ
mat
mat NA 0.63 122805729w 122815251e 123446552w 123456830a THOC2,XIAP, STAG2, SH2D1A e
mat mat 0.27 0.26 122147464e122418009
XIAP, STAG2 GRIA3 e
Compared with female carriers of previous reports on duplications at Xq25 encompassing STAG2, male individuals appears to be more severe affected of ID, as the phenotypes of the heterozygous females appeared to be modulated by their Xinactivation pattern [Di Benedetto et al., 2014]. The phenotypes of the compared patients could also differ due to the differences in the size and gene content of the duplications. The duplication shared no common breakpoints, and the shortest region of overlap of all duplications patients contained two protein-coding genes: STAG2 and XIAP (Fig. 2B). Thus, gene content analysis of the duplicated region and a review of the literature allow us to suggest that gene dosage imbalance could be directly associated with the intellectual disability described in our patient, although we cannot exclude that the duplication might exert a positional effect on the expression of other genes. The tandem duplication identified in our propositus could potentially disrupts the genomic structure of the SH2D1A gene. However, the rearrangement does not appear to impair the functionality of SH2D1A gene, as our patient did not show any significant immunological disease. We cannot exclude the possibility that the disruption of SH2D1A might be involved in the patient’s phenotype but we suggest that STAG2 has the main role in causing the phenotypes per our finding. Although there are no known LCRs in proximity to the reported duplication breakpoints, there is a relatively high density of long and short interspersed unclear elements around the proximal breakpoint. LINE-1 elements present at both duplication breakpoints in the patients are known to predispose the region to genomic instability through NAHR, resulting in recurring deletions or duplications in this region that strongly suggest that the Xq25 region is unstable [Liu et al., 2011]. Two recently published large studies of copy number variation in ID and developmental delay (DD) [Cooper et al., 2011; Kaminsky et al., 2011] and the
Please cite this article in press as: Yingjun X, et al., Microduplication of chromosome Xq25 encompassing STAG2 gene in a boy with intellectual disability, European Journal of Medical Genetics (2014), http://dx.doi.org/10.1016/j.ejmg.2014.10.002
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DECIPHER database [Bragin et al., 2014] listed several overlapping duplications involving Xq25 with variable breakpoints, length and gene contents. This, together with the phenotypic heterogeneity usually observed in the novel microduplication syndromes, complicates any genotypeephenotype correlation. Further cases need to be described and compared to evaluate a possible common phenotype and to link the Xq25 duplication to a distinct syndrome with specific characteristics. Acknowledgments We would like to thank the staff of the genetics center for helping obtain patient data. References Arroyo JA, Anthony RV, Galan HL. Decreased placental X-linked inhibitor of apoptosis protein in an ovine model of intrauterine growth restriction. Am. J. Obstet. Gynecol. 2008;199. 80.e1e80.e8. Baquero-Montoya C, Gil-Rodriguez MC, Teresa-Rodrigo ME, Hernandez-Marcos M, Bueno-Lozano G, Bueno-Martinez I, et al. Could a patient with SMC1A duplication be classified as a human cohesinopathy? Clin. Genet. 2014;85:446e51. Bonnet C, Leheup B, Beri M, Philippe C, Gregoire MJ, Jonveaux P. Aberrant GRIA3 transcripts with multi-exon duplications in a family with X-linked mental retardation. Am. J. Med. Genet. Part A 2009;149A:1280e9. Bragin E, Chatzimichali EA, Wright CF, Hurles ME, Firth HV, Bevan AP, et al. DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation. Nucleic Acids Res. 2014;42: D993e1000. Cooper GM, Coe BP, Girirajan S, Rosenfeld JA, Vu TH, Baker C, et al. A copy number variation morbidity map of developmental delay. Nat. Genet. 2011;43:838e46. Deveraux QL, Takahashi R, Salvesen GS, Reed JC. X-linked IAP is a direct inhibitor of cell-death proteases. Nature 1997;388:300e4. Di Benedetto D, Musumeci SA, Avola E, Alberti A, Buono S, Scuderi C, et al. Definition of minimal duplicated region encompassing the XIAP and STAG2 genes in the Xq25 microduplication syndrome. Am. J. Med. Genet. Part A 2014. Gillberg C. Chromosomal disorders and autism. J. Autism Dev. Disord. 1998;28:415e25. Gruslin A, Qiu Q, Tsang BK. X-linked inhibitor of apoptosis protein expression and the regulation of apoptosis during human placental development. Biol. Reprod. 2001;64:1264e72.
Kaminsky EB, Kaul V, Paschall J, Church DM, Bunke B, Kunig D, et al. An evidencebased approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities. Genet. Med.: official journal of the American College of Medical Genetics 2011;13:777e84. Liu J, Zhang Z, Bando M, Itoh T, Deardorff MA, Clark D, et al. Transcriptional dysregulation in NIPBL and cohesin mutant human cells. PLoS Biol. 2009;7: e1000119. Liu X, Malenfant P, Reesor C, Lee A, Hudson ML, Harvard C, et al. 2p15-p16.1 microdeletion syndrome: molecular characterization and association of the OTX1 and XPO1 genes with autism spectrum disorders. Eur. J. Hum. Genet.: EJHG 2011;19:1264e70. McNamara GI, Isles AR. Dosage-sensitivity of imprinted genes expressed in the brain: 15q11-q13 and neuropsychiatric illness. Biochem. Soc. Trans. 2013;41: 721e6. Overwater E, Smulders Y, van der Burg M, Lombardi MP, Meijers-Heijboer HE, Kuijpers TW, et al. The value of DNA storage and pedigree analysis in rare diseases: a 17-year-old boy with X-linked lymphoproliferative disease (XLP) caused by a de novo SH2D1A mutation. Eur. J. Pediatr. 2014. Philippe A, Malan V, Jacquemont ML, Boddaert N, Bonnefont JP, Odent S, et al. Xq25 duplications encompassing GRIA3 and STAG2 genes in two families convey recognizable X-linked intellectual disability with distinctive facial appearance. Am. J. Med. Genet. Part A 2013;161A:1370e5. Renault NK, Dyack S, Dobson MJ, Costa T, Lam WL, Greer WL. Heritable skewed Xchromosome inactivation leads to haemophilia A expression in heterozygous females. Eur. J. Hum. Genet.: EJHG 2007;15:628e37. Ropers HH. X-linked mental retardation: many genes for a complex disorder. Curr. Opin. Genet. Dev. 2006;16:260e9. Tejada MI, Martinez-Bouzas C, Garcia-Ribes A, Larrucea S, Acquadro F, Cigudosa JC, et al. A child with mild X-linked intellectual disability and a microduplication at Xp22.12 including RPS6KA3. Pediatrics 2011;128:e1029e1033. Wang X, Zhu C, Wang X, Hagberg H, Korhonen L, Sandberg M, et al. X-linked inhibitor of apoptosis (XIAP) protein protects against caspase activation and tissue loss after neonatal hypoxia-ischemia. Neurobiol. Dis. 2004;16:179e89. West T, Stump M, Lodygensky G, Neil JJ, Deshmukh M, Holtzman DM. Lack of X-linked inhibitor of apoptosis protein leads to increased apoptosis and tissue loss following neonatal brain injury. ASN Neuro 2009;1. Wu L, Lu P, Ma W, Chu C, Xu H, Qi H. Identification of a new isoform of the murine Sh2d1a gene and its functional implications. Sci. China. Life Sci. 2014;57:81e7. Yan J, Zhang F, Brundage E, Scheuerle A, Lanpher B, Erickson RP, et al. Genomic duplication resulting in increased copy number of genes encoding the sister chromatid cohesion complex conveys clinical consequences distinct from Cornelia de Lange. J. Med. Genet. 2009;46:626e34.
Please cite this article in press as: Yingjun X, et al., Microduplication of chromosome Xq25 encompassing STAG2 gene in a boy with intellectual disability, European Journal of Medical Genetics (2014), http://dx.doi.org/10.1016/j.ejmg.2014.10.002
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Array report
Microduplication of chromosome Xq25 encompassing STAG2 gene in a boy with intellectual disability Xie Yingjun a, b,1, Tang Wen c, *,1, Liang Yujian c, Xu Lingling c, Huang Huimin c, Fang Qun a, Chen Junhong a a
Department of Prenatal Diagnosis, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, 510080, China c Department of Pediatric Intensive Care Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China b
a r t i c l e i n f o
a b s t r a c t
Article history: Received 9 May 2014 Accepted 13 October 2014 Available online xxx
Whole-genome microarray analysis is proven to be useful in the identification of submicroscopic copy number imbalances in families with intellectual disabilities. The first case of Xq25 duplication was identified using genome-wide array comparative genomic hybridization (array-CGH) in a 24-year-old patient with a syndromic intellectual disability. We report a 4-year-old boy with a de novo 591 kb duplication at Xq25. The duplication was first detected by a CytoScan HD array platform (Affymetrix, USA) and was confirmed by real-time quantitative PCR (qPCR) of the STAG2 gene, and by fluorescence in situ hybridization (FISH). The patient had clinical features partially consistent with published cases, including an intellectual disability and speech delay. The identification of this additional patient and a detailed analysis of duplications identified in other patient cohorts and absent in normal individuals support the existence of a rare pathological microduplication at Xq25 that encompasses STAG2. Ó 2014 Elsevier Masson SAS. All rights reserved.
Keywords: Intellectual disability Microduplication XIAP STAG2 Genome-wide array analysis
1. Introduction Investigation of chromosomal rearrangements in patients with intellectual disabilities (ID) has proven particularly informative in the search for novel genes. Intellectual disability, behavioral problems and physical anomalies can be the result of microdeletions or microduplications of contiguous genes in almost every chromosome [Gillberg, 1998]. The genetic factors underlying ID are very heterogeneous. With the advent of molecular karyotyping, i.e., the number of microdeletions and microduplications associated with phenotypic features, frequently including idiopathic ID, has greatly increased. Recent studies have identified a number of
Abbreviations: CASP3, cell-death proteases, caspase-3; CASP7, caspase-7; CNVs, copy number variations; DAPI, 40,6-diamidino-2-phenylindole; DD, developmental delay; FISH, fluorescence in situ hybridization; IAPs, inhibitor of apoptosis proteins; ID, intellectual disability; IUGR, intrauterine growth restriction; STAG2, stromal antigen 2; XIAP, X-linked inhibitor of apoptosis; XLMR, X-linked mental retardation. * Corresponding author. Department of Pediatric Intensive Care Unit, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Second Road, Guangzhou 510080, China. Tel.: þ86 020 87755766x8922. E-mail address: [email protected] (T. Wen). 1 These authors contributed equally to this work, and should be considered as co-first author.
copy number variations (CNVs) involved in ID, several of which lie on the X-chromosome. However, the current understanding of the monogenic causes of ID is far from comprehensive. New high resolution genetic analysis techniques often provide an explanation or a diagnosis of abnormal conditions and help define a more precise characterization of any genotype/ phenotype correlations in childhood chromosomal anomalies. Recently, small duplications involving the Xq25 region have been reportedly associated with ID. Philippe A. et al. reported two patients with an Xq25 duplication encompassing the GRIA3 and STAG2 genes with an intellectual disability, and suggested that in addition to the role of GRIA3 gene, the duplication of STAG2 (Stromal Antigen 2) gene coding for the subunit SA1 of the cohesin complex may potentially contribute to the clinical phenotype [Philippe et al., 2013]. Di Benedetto, D. et al. also reported two unrelated families with Xq25 duplications of approximately 630 kb involved three genes: THOC2, XIAP, and STAG2, whereas the minimal duplicated region was approximately 270 kb and encompassed the XIAP and STAG2 genes [Di Benedetto et al., 2014]. We report here the clinical and molecular cytogenetic findings in a boy with a de novo 591 kb duplication of the Xq25 region encompassing the XIAP, STAG2 and SH2D1A genes who presented with a developmental delay, dysmorphic features, and
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Please cite this article in press as: Yingjun X, et al., Microduplication of chromosome Xq25 encompassing STAG2 gene in a boy with intellectual disability, European Journal of Medical Genetics (2014), http://dx.doi.org/10.1016/j.ejmg.2014.10.002
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a small ear deformity. This study was conducted to refine the clinical presentation of the Xq25 microduplication and to establish the genotypeephenotype correlation.
and tooth enamel erosions and the facial anomalies also including malar flatness, prognathism, and thick vermilion of lips (Fig. 1). 2.2. Chromosomal analysis
2. Method and material Conventional karyotyping at a resolution of 550 bands of both the proband and the parents was performed on metaphase spreads from cultured lymphocytes according to the standard protocols.
2.1. Clinical description The proband was a child referred to our Clinical Genetics Service for dysmorphic features and a developmental delay. The proband was the third child of healthy unrelated parents with an uneventful family history. His two older sisters were both normal. He was born at 41 weeks of gestation after an uneventful pregnancy. Prenatal diagnosis performed due to advanced maternal age showed a normal fetal karyotype (46, XY). The patient was born by normal spontaneous delivery. No intrauterine exposure to drugs or other possibly harmful factors were reported. At birth, a large fontanelle was reported (data not provided). Birth weight was 2700 g (3rd percentile), birth length was 46 cm (<3rd percentile), the head circumference was 31 cm (<3rd percentile), and the thoracic circumference was 32 cm (<3rd percentile). APGAR scores were 9/ 10 and 10 /50 . Early motor development was only slightly delayed: he sat at 8 months, walked at 18 months and pronounced his first words at 18e20 months. He began speaking single words at 1 year and 7 months. He started walking independently around 2 years old. A developmental delay (35 months, DQ 70 at Gesell-scale) and muscle hypotonia were observed since the age of two and he was diagnosed as ASD (data of assessment for ASD not provided). He was particularly friendly to foreign people although grumpy, and presented with compromised hearing on the left side compared to the right side (by clinical hearing screening). In addition, he had a history of sinusitis with nasal gland enlargement. However, he was not performed any immunological test and did not show any significant immunological disease. His previous blood test was not available. On first examination at the Genetic Clinic, at age of 3 years and 8 months, his height was 95 cm (3rd percentile), weight was 16 kg (50th percentile) and his head circumference was 45.2 cm (<3rd percentile). He presented with brachycephalia, full cheeks, medial flaring of eyebrows, long eyelashes, epicanthic folds, strabismus, small ears with total length of 4.7 cm (50th percentile), a short nose, low and widened nasal root, a long philtrum, a full lower lip,
2.3. Chromosomal microarray analysis (CMA) Genomic DNA was extracted from peripheral blood lymphocytes using QIAamp DNA Blood Mini Kit [QIAGEN, Hilden, D] for the patient and his parents according to manufacturers’ instructions. The DNA (250 ng) was amplified, labeled and hybridized to the CytoScan HD array platform (Affymetrix, USA) according to the manufacturer’s protocol. The array was designed specifically for cytogenetic research, and it offered more than 2,700,000 markers across the whole genome, including 750,000 SNP probes and 1,950,000 probes to detect copy number variations (Cyto-arrays). CEL files obtained by scanning the CytoScan arrays were analyzed using the Chromosome Analysis Suite software (Affymetrix, USA) and the annotations of the genome version GRCH37 (hg19). Only qualified measures were included in our analysis. Gains and losses that affected a minimum of 50 markers in a 100 kb length were initially considered. 2.4. Fluorescence in situ hybridization (FISH) Cytogenetic studies of the patient and his parents were performed on metaphase chromosomes derived from cultures of PHAstimulated peripheral blood lymphocytes. Fluorescent in situ hybridization analysis (FISH) was used with a combination of CEP X probe and Single-copy DNA probes, RP1-159G19 (Xq25), cloned in BACs (Vysis, USA; BlueGnome, UK) performed according to the manufacturers’ instructions. The two types of probes were used to visualize the central region and the specific-Xq25, respectively. Slides were counterstained with 40,6-diamidino-2-phenylindole (DAPI, 200 ng/ml) and were analyzed by fluorescence microscopy using an Olympus BX61 equipped with a cooled CCD Video Camera, Photometrics. Image analysis was carried out with ASI FISH software.
Fig. 1. Frontal (A) and right (B) lateral craniofacial views of our patient.
Please cite this article in press as: Yingjun X, et al., Microduplication of chromosome Xq25 encompassing STAG2 gene in a boy with intellectual disability, European Journal of Medical Genetics (2014), http://dx.doi.org/10.1016/j.ejmg.2014.10.002
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Fig. 2. A. Mapping of a chromosomal Xq25 duplication. B. SNP-Array genotyping of patients. Whole-genome array-based SNP showed a 591 kb duplication stretching from 122,899,950 to 123,490,624. C. Schematic representation of the Xq25 duplication region including the DECIPHER microduplication cases, ISCA case and Philippe et al., Di Benedetto et al., Bonnet et al. reported cases.
2.5. Real-time quantitative PCR (qPCR) Confirmation of the CMA result and analysis of the unaffected sisters and the parents were performed by quantitative real-time PCR. Primer sequences can be obtained upon request. qPCR was performed on ABI PrismÒ 9700TH Sequence Detection System. 2.6. Paternity testing Paternity testing was performed using small tandem repeat (STR) marker genotyping on the patient and his parents by DNA
fragment analysis by the 3500 Genetic Analyzer in accordance with the manufacturer’s recommendations. 3. Results 3.1. Karyotyping, CMA and FISH The couple and the proband harbored a normal karyotype. Genome-wide array analysis of the proband showed a 591 Kb duplication at Xq25, ranging from 122,899,950e123,490,624 (Fig. 2A) while the CMA results of the parents were normal, that is
Fig. 3. Metaphase fluorescence in situ hybridization study of cultured lymphocytes using CEP X green probes and RP1- 159G19 red (Xq25) probes. No duplication or translocation was detected on Xq25 in the cultured lymphocytes that originated from the father (B) or the mother (A). The duplication of an Xq25 signal in the interphase nuclei on X-chromosome revealed the duplication Xq25 in the proband (C).
Please cite this article in press as: Yingjun X, et al., Microduplication of chromosome Xq25 encompassing STAG2 gene in a boy with intellectual disability, European Journal of Medical Genetics (2014), http://dx.doi.org/10.1016/j.ejmg.2014.10.002
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Table 1 The comparison of clinical features in patients with overlapping microduplications between the studied patient (Mapping used hg19). Phenotypic and genotypic comparisons between the present duplication case and other genomic disruptions at Xq25. Ages for each proband are given at the time of clinical assessment. Otherwise, ages are as reported by other authors. Seven cases from the DECIPHER database. Clinical features
Present subject
DECIPHER
nsv 532914 [Kaminsky et al., 2011]
595
253540
253551
250183
264308
270242
283869
Gender Age ASD ID Cross motor deficit Language delay Recurrent seizures Dysmorphic feature Development delay Inheritance Size (Mb) Breakpoints (bp) (GRCH37/ hg19) Contain genes Additional CNVs
M 3.7 þ þ
F 15 þ þ
F 8 þ þ þ
M 10 NA NA NA
M 11 þ þ
F 6 þ
M 4 þ þ þ
F 9 þ þ þ
M NA þ þ
þ
þ
NA
þ
þ
þ
þ
NA
þ
NA
þ
þ
þ
NA
þ
dn 0.59 122899950e 123490624
mat 0.77 122390702e 123162552
dn 0.56 122801087e 123357985
dn 0.26 123003512e 123266951
mat 0.41 123014742e 123427774
dn 0.97 12235220e 123322930
uk 0.23 123056096e 123283547
dn 0.21 123388516e 123598378
mat 0.51 122869800e 123388775
XIAP, STAG2 SH2D1A
GRIA3,STAG2, THOC2,XIAP
STAG2,THOC2, XIAP
STAG2,XIAP
STAG2,XIAP
GRIA3,STAG2, THOC2,XIAP
STAG2
STAG2, XIAP
24826107e 25542728
AH2D1A,STAG2, TEN1 e
þ: feature present; : feature absent; NA: not assessable/assessed. ASD: Autism Spectrum Disorder; dn: De novo. hg18.
a
without the 591 kb duplication at Xq25. The 3500 Genetic Analyzer confirmed the paternity of the patient’s parents. The qPCR and FISH analysis (Fig. 3) on the proband and his parents confirmed the rearrangement and showed that the Xq25 duplication occurred de novo and harbored three genes: XIAP, STAG2, SH2D1A. Furthermore, FISH analysis (Fig. 2A) showed a unique Xq25 signal suggesting a tandem duplication. A secondary review of the CMA results in the proband did not identify any other smaller CNVs below the usual clinical reporting thresholds (200 kb for deletion; 500 kb for duplication). 3.2. Clinical features analysis We compared the clinical phenotypes of the proband (Fig. 2C), who carried an Xq25 duplication, with other reported patients who carried other Xq25 duplications (Table 1) [Bonnet et al., 2009; Di Benedetto et al., 2014; Kaminsky et al., 2011; Philippe et al., 2013]. Among the patients, all were reported to have the ID similar to our patient. These finding implied that the Xq25 region is important in neurodevelopment. 4. Discussion Until now, approximately 4% of the more than 22,000 proteincoding genes presently listed in ENSEMBL are located on the Xchromosome, and approximately 40% of these are currently known to be expressed in the brain. Therefore, several hundred genes could be involved in X-linked mental retardation (XLMR) [Ropers, 2006]. Some ID phenotypes may be attributed to dosage decreases/increases of certain protein-coding genes. Thus, functional disomy may cause dysfunction in the brain [Tejada et al., 2011]. Recently, McNamara, G. I. and Isles, A. R. [McNamara and Isles, 2013] found that brain function is exquisitely sensitive to
both decreases and increases in the expression of imprinted genes. We report a novel clinical and molecular cytogenetic finding of a boy with an idiopathic intellectual disability. These findings are found to share a strikingly similar pattern of neurosensory (mild visual impairment), neurodevelopmental (moderate developmental and adaptive delay) and somatic congenital anomalies associated with an interstitial microduplication of the Xq25 region, cryptic upon G-banding, and identified by SNP-array. Comparison with previously described individuals with similar Xq25 microduplications (Table 1) showed that the present patient had similar facial morphological anomalies (malar flatness, thick vermilion of lips, and prognathism), and ID. The common 591 Kb duplication interval of Xq25 observed in this patient includes three known genes with a variety of functions, the X-linked inhibitor of apoptosis (XIAP, OMIM 300079), stromal antigen 2 (STAG2, OMIM 300826) and SH2D1A (before exon 2). SH2D1A encodes a protein that plays a major role in the bidirectional stimulation of T and B cells. This protein associates with the signaling lymphocyte-activation molecule. Mutations in this gene cause lymphoproliferative syndrome X-linked type 1 or Duncan disease, a rare immunodeficiency characterized by extreme susceptibility to infection with EpsteineBarr virus, with symptoms including severe mononucleosis and malignant lymphoma [Overwater et al., 2014; Wu et al., 2014]. The gene XIAP belongs to a human multigene family whose members show extensive homology to baculovirus inhibitor of apoptosis proteins (IAPs) and encode proteins that inhibit apoptosis. Deveraux et al. [Deveraux et al., 1997] showed that human X-linked IAP directly inhibits at least 2 members of the caspase family of cell-death proteases, caspase-3 (CASP3) and caspase-7 (CASP7). As the caspases are highly conserved throughout the animal kingdom and are the principal effectors of apoptosis, these findings suggest that IAPs
Please cite this article in press as: Yingjun X, et al., Microduplication of chromosome Xq25 encompassing STAG2 gene in a boy with intellectual disability, European Journal of Medical Genetics (2014), http://dx.doi.org/10.1016/j.ejmg.2014.10.002
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Philippe et al. [Philippe et al., 2013]
Di Benedetto et al. [Di Benedetto et al., 2014]
1
2
Family 1 Ⅱ-2
Ⅰ-2
Ⅱ-4
Ⅱ-5
Ⅲ-2
Ⅲ-6
Ⅱ-1
Ⅰ-2
M 24 þ þ
M 4 þ þ
M 51 þ þ
F 71 þ
M 38 þ
M 37 þ
M 38 þ
M 36 þ
M 14 þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
þ
mat 1.2 NA
mat 5.02 120957860e 125980037a
mat NA mat mat mat 0.60 122697410w122703291e123259725w 123266892a
GRIA3,STAG2, THOC2,XIAP
Bonnet et al. [Bonnet et al., 2009] Family 2
THOC2,XIAP,STAG2 e
might inhibit cell death, providing evidence for a mechanism of action for these mammalian cell-death suppressors. XIAP is present in trophoblasts throughout placental development but significantly decreases during late pregnancy [Gruslin et al., 2001]. Evidence that increased XIAP levels protect the neonatal brain against hypoxia-ischemia was found in mice [Wang et al., 2004]. Placental villous apoptosis is increased at midgestation and near term in the ovine model of intrauterine growth restriction (IUGR), and this increase is associated with a significant decrease in XIAP protein in the cotyledon of IUGR animals [Arroyo et al., 2008]. West, T. et al. [West et al., 2009] identified a critical role for XIAP in regulating neuronal apoptosis in vivo and demonstrated the enhanced vulnerability of neurons to injury in the absence of XIAP in the developing brain. These considerations suggest that XIAP duplication may contribute to the ID phenotype observed in our patient. In addition to XIAP, STAG2 is known to be associated with physical support for hematopoietic cell organization [Renault et al., 2007]. Although no pathogenic mutations were found in STAG2, its function as a core component of the ring-like cohesion complex involved in sister chromatid cohesion during mitosis makes it a candidate gene for the ID trait. Abnormalities in cohesin genes are associated with human multisystem developmental disorders such as Cornelia de Lange Syndrome (CdLS, OMIM 122470) [Liu et al., 2009]. Recent report showed that duplications of cohesin genes associated with ID and craniofacial morphological anomalies [Baquero-Montoya et al., 2014; Yan et al., 2009]. These findings suggest that STAG2 could be a candidate gene for ID based on its expression in the brain or its role in neuronal development and function [Baquero-Montoya et al., 2014; Yan et al., 2009]. Our patient shows overlapping clinical features for published Xq25 microduplications, such as a developmental delay, an intellectual disability, and facial dysmorphism (see Table 1 for comparison).
II-1
II-3
F 39 þ
M 20 þ
M 20 þ
þ
þ
þ
þ
þ
þ
þ
NA
þ
þ
þ
NA
þ
þ
þ
mat
mat NA 0.63 122805729w 122815251e 123446552w 123456830a THOC2,XIAP, STAG2, SH2D1A e
mat mat 0.27 0.26 122147464e122418009
XIAP, STAG2 GRIA3 e
Compared with female carriers of previous reports on duplications at Xq25 encompassing STAG2, male individuals appears to be more severe affected of ID, as the phenotypes of the heterozygous females appeared to be modulated by their Xinactivation pattern [Di Benedetto et al., 2014]. The phenotypes of the compared patients could also differ due to the differences in the size and gene content of the duplications. The duplication shared no common breakpoints, and the shortest region of overlap of all duplications patients contained two protein-coding genes: STAG2 and XIAP (Fig. 2B). Thus, gene content analysis of the duplicated region and a review of the literature allow us to suggest that gene dosage imbalance could be directly associated with the intellectual disability described in our patient, although we cannot exclude that the duplication might exert a positional effect on the expression of other genes. The tandem duplication identified in our propositus could potentially disrupts the genomic structure of the SH2D1A gene. However, the rearrangement does not appear to impair the functionality of SH2D1A gene, as our patient did not show any significant immunological disease. We cannot exclude the possibility that the disruption of SH2D1A might be involved in the patient’s phenotype but we suggest that STAG2 has the main role in causing the phenotypes per our finding. Although there are no known LCRs in proximity to the reported duplication breakpoints, there is a relatively high density of long and short interspersed unclear elements around the proximal breakpoint. LINE-1 elements present at both duplication breakpoints in the patients are known to predispose the region to genomic instability through NAHR, resulting in recurring deletions or duplications in this region that strongly suggest that the Xq25 region is unstable [Liu et al., 2011]. Two recently published large studies of copy number variation in ID and developmental delay (DD) [Cooper et al., 2011; Kaminsky et al., 2011] and the
Please cite this article in press as: Yingjun X, et al., Microduplication of chromosome Xq25 encompassing STAG2 gene in a boy with intellectual disability, European Journal of Medical Genetics (2014), http://dx.doi.org/10.1016/j.ejmg.2014.10.002
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DECIPHER database [Bragin et al., 2014] listed several overlapping duplications involving Xq25 with variable breakpoints, length and gene contents. This, together with the phenotypic heterogeneity usually observed in the novel microduplication syndromes, complicates any genotypeephenotype correlation. Further cases need to be described and compared to evaluate a possible common phenotype and to link the Xq25 duplication to a distinct syndrome with specific characteristics. Acknowledgments We would like to thank the staff of the genetics center for helping obtain patient data. References Arroyo JA, Anthony RV, Galan HL. Decreased placental X-linked inhibitor of apoptosis protein in an ovine model of intrauterine growth restriction. Am. J. Obstet. Gynecol. 2008;199. 80.e1e80.e8. Baquero-Montoya C, Gil-Rodriguez MC, Teresa-Rodrigo ME, Hernandez-Marcos M, Bueno-Lozano G, Bueno-Martinez I, et al. Could a patient with SMC1A duplication be classified as a human cohesinopathy? Clin. Genet. 2014;85:446e51. Bonnet C, Leheup B, Beri M, Philippe C, Gregoire MJ, Jonveaux P. Aberrant GRIA3 transcripts with multi-exon duplications in a family with X-linked mental retardation. Am. J. Med. Genet. Part A 2009;149A:1280e9. Bragin E, Chatzimichali EA, Wright CF, Hurles ME, Firth HV, Bevan AP, et al. DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation. Nucleic Acids Res. 2014;42: D993e1000. Cooper GM, Coe BP, Girirajan S, Rosenfeld JA, Vu TH, Baker C, et al. A copy number variation morbidity map of developmental delay. Nat. Genet. 2011;43:838e46. Deveraux QL, Takahashi R, Salvesen GS, Reed JC. X-linked IAP is a direct inhibitor of cell-death proteases. Nature 1997;388:300e4. Di Benedetto D, Musumeci SA, Avola E, Alberti A, Buono S, Scuderi C, et al. Definition of minimal duplicated region encompassing the XIAP and STAG2 genes in the Xq25 microduplication syndrome. Am. J. Med. Genet. Part A 2014. Gillberg C. Chromosomal disorders and autism. J. Autism Dev. Disord. 1998;28:415e25. Gruslin A, Qiu Q, Tsang BK. X-linked inhibitor of apoptosis protein expression and the regulation of apoptosis during human placental development. Biol. Reprod. 2001;64:1264e72.
Kaminsky EB, Kaul V, Paschall J, Church DM, Bunke B, Kunig D, et al. An evidencebased approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities. Genet. Med.: official journal of the American College of Medical Genetics 2011;13:777e84. Liu J, Zhang Z, Bando M, Itoh T, Deardorff MA, Clark D, et al. Transcriptional dysregulation in NIPBL and cohesin mutant human cells. PLoS Biol. 2009;7: e1000119. Liu X, Malenfant P, Reesor C, Lee A, Hudson ML, Harvard C, et al. 2p15-p16.1 microdeletion syndrome: molecular characterization and association of the OTX1 and XPO1 genes with autism spectrum disorders. Eur. J. Hum. Genet.: EJHG 2011;19:1264e70. McNamara GI, Isles AR. Dosage-sensitivity of imprinted genes expressed in the brain: 15q11-q13 and neuropsychiatric illness. Biochem. Soc. Trans. 2013;41: 721e6. Overwater E, Smulders Y, van der Burg M, Lombardi MP, Meijers-Heijboer HE, Kuijpers TW, et al. The value of DNA storage and pedigree analysis in rare diseases: a 17-year-old boy with X-linked lymphoproliferative disease (XLP) caused by a de novo SH2D1A mutation. Eur. J. Pediatr. 2014. Philippe A, Malan V, Jacquemont ML, Boddaert N, Bonnefont JP, Odent S, et al. Xq25 duplications encompassing GRIA3 and STAG2 genes in two families convey recognizable X-linked intellectual disability with distinctive facial appearance. Am. J. Med. Genet. Part A 2013;161A:1370e5. Renault NK, Dyack S, Dobson MJ, Costa T, Lam WL, Greer WL. Heritable skewed Xchromosome inactivation leads to haemophilia A expression in heterozygous females. Eur. J. Hum. Genet.: EJHG 2007;15:628e37. Ropers HH. X-linked mental retardation: many genes for a complex disorder. Curr. Opin. Genet. Dev. 2006;16:260e9. Tejada MI, Martinez-Bouzas C, Garcia-Ribes A, Larrucea S, Acquadro F, Cigudosa JC, et al. A child with mild X-linked intellectual disability and a microduplication at Xp22.12 including RPS6KA3. Pediatrics 2011;128:e1029e1033. Wang X, Zhu C, Wang X, Hagberg H, Korhonen L, Sandberg M, et al. X-linked inhibitor of apoptosis (XIAP) protein protects against caspase activation and tissue loss after neonatal hypoxia-ischemia. Neurobiol. Dis. 2004;16:179e89. West T, Stump M, Lodygensky G, Neil JJ, Deshmukh M, Holtzman DM. Lack of X-linked inhibitor of apoptosis protein leads to increased apoptosis and tissue loss following neonatal brain injury. ASN Neuro 2009;1. Wu L, Lu P, Ma W, Chu C, Xu H, Qi H. Identification of a new isoform of the murine Sh2d1a gene and its functional implications. Sci. China. Life Sci. 2014;57:81e7. Yan J, Zhang F, Brundage E, Scheuerle A, Lanpher B, Erickson RP, et al. Genomic duplication resulting in increased copy number of genes encoding the sister chromatid cohesion complex conveys clinical consequences distinct from Cornelia de Lange. J. Med. Genet. 2009;46:626e34.
Please cite this article in press as: Yingjun X, et al., Microduplication of chromosome Xq25 encompassing STAG2 gene in a boy with intellectual disability, European Journal of Medical Genetics (2014), http://dx.doi.org/10.1016/j.ejmg.2014.10.002