Application of Array-based Comparative Genome Hybridization in Children with Developmental Delay or Mental Retardation

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1 Pediatr Neonatol 2008;49(6): REVIEW ARTICLE Application of Array-based Comparative Genome Hybridization in Children with Developmental Delay or Mental Retardation Jao-Shwann Liang 1,2 *, Keiko Shimojima 1,Toshiyuki Yamamoto 1 1 International Research and Educational Institute for Integrated Medical Sciences (IREIIMS), Tokyo Women s Medical University, Taiwan 2 Department of Pediatrics, Far Eastern Memorial Hospital, Taiwan Received: Jul 23, 2008 Revised: Sep 25, 2008 Accepted: Jun 25, 2008 KEY WORDS: array-based comparative genomic hybridization; cytogenic test; developmental delay; mental retardation Children with developmental delay or mental retardation (DD/MR) are commonly en countered in child neurology clinics, and establishing an etiologic diagnosis is a challenge for child neurologists. Among the etiologies, chromosomal imbalance is one of the most important causes. However, many of these chromosomal imbalances are submicroscopic and cannot be detected by conventional cytogenetic methods. Microarray-based comparative genomic hybridization (array CGH) is considered to be superior in the investigation of chromosomal deletions or duplications in children with DD/MR, and has been demonstrated to improve the diagnostic detection rate for these small chromosomal abnormalities. Here, we review the recent studies of array CGH in the evaluation of patients with idiopathic DD/MR. 1. Introduction Mental retardation (MR) is a condition of arrested or incomplete development of the brain with the onset occurring before 18 years or age, and is estimated to affect 2 3% of the population. 1,2 The term developmental delay (DD), often used in children before 5 years of age, can involve motor function, cognitive ability, language or combinations. MR may become evident during infancy or early childhood as developmental delay, but it is best diagnosed during school years. DD is a common problem in child health and a frequent reason for referral to a child neurologist. However, in a large number of these patients, the etiology is unknown. Causes of DD/MR include premature birth, genetic and heredity disorders and infections. For child neurologists, determining whether DD/MR is associated with multiple congenital anomalies and/or dysmorphic features can be helpful and guide the selection of diagnostic testing. Genetic abnormalities are the most common iden tifiable cause of DD/MR. 3 The traditional study of human chromosomes with banding techniques can discover large-scale genomic changes and has been an important diagnostic tool in identification of causes of DD/MR. However, conventional cytogenetic analysis cannot reliably detect rearrangements of genomic segments smaller than 3 5 million base pairs (Mb). 4 Fortunately, array-based comparative genomic hybridization (array CGH) analysis development allows for detection of submicroscopic deletions or duplications which cannot be detected by conventional cytogenetic methods. Detection rates *Corresponding author. Department of Pediatrics, Far Eastern Memorial Hospital, 21 Nanya South Road, Section 2, Panchiao City, Taipei 22060, Taiwan. jao59@hotmail.com 2008 Taiwan Pediatric Association

2 214 J.S. Liang et al Mb q11.22 Deletion 17.9 Mb q12.1 q Mb q13.2 q13.32 Chromosome view 20.4 Mb Gene view Figure 1 Chromosomal deletion of 22q11.2 shown by CGH analytics version 3.5 (Agilent), in the Chromosome view (left) and the Gene view (right). The deletion region of 22q11.2 is shown in Chromosome view (arrow), and expanded in Gene view. Vertical axis indicates chromosomal physical locus, and horizontal axis indicates log ratio of sample intensity. Plus and minus indicate gain and loss of genomic copy numbers, respectively. In the Gene view, dots indicate locus and the log ratio of those intensities, and alphabetic characters indicate location of genes and copy number variations. for chromosome abnormalities with array CGH range from 5 17% in individuals with normal results from prior routine cytogenetic testing. 4 Here, we review recent advances in research and diagnostic application of array CGH in the evaluation of patients with idiopathic DD/MR. 2. Array CGH Array CGH uses cloned DNA fragments as a probe during hybridization to replace the metaphase chromosomes used in conventional CGH. Metaphase CGH uses hybridization to metaphase chromosomes to screen the whole genome with an average resolution of > 2 Mb. The detection of submicroscopic imbalances has been achieved by the replacement of metaphase chromosomes with arrayed DNA fragments immobilized on glass slides. 3,5 Formerly, bacterial artificial chromosomes (BACs) or P1-derived artificial chromosome (PAC) clones ranging in size from 75 to 200 Kb were used as the probe DNA. 6 8 This method offers greater sensitivity and resolution than conventional CGH in detecting copy number changes. The level of the resolution of array CGH depends on the size of and distance between the arrayed interrogating probes. Currently, synthetic oligonucleotides, ranging in size from bp, are used for high-density array CGH. The oligo-array CGH has proven to be a powerful and promising method that is revolutionizing cytogenetic diagnosis. 9 Recently, screening large patient cohorts with DD/MR by array CGH has led to the characterization of several novel microdeletion and microduplication syndromes. These novel syndromes have been reviewed by Slavotinek. 10 An example of array CGH using oligonucleotides to detect a 22q11.2 deletion is shown in Figure Cytogenetic Evaluation in Children with DD/MR Cytogenetic evaluation is an important part of the in vestigation of causes of congenital anomalies, DD/ MR or other developmental disabilities. Based on a literature review, the mean yield of chromosome aberration is 9.5% in MR. 11 G-banding can discover numerical and large-scale chromosomal abnormalities. For clinical settings, band karyotyping should be the essential and initial diagnostic tool to evaluate children with DD/MR. However, G-banding is not always sufficient to characterize complex and subtle chromo somal abnormalities. Further analysis using high-resolution G-banding and fluorescence in-situ hybridization (FISH) should be considered consequently when particular syndromes or aberrant karyotypes are suspected. Because the ends of chromosomes lack distinctive G-bands, it is difficult to

3 Array CGH in developmental delay and mental retardation 215 Developmental delay/mental retardation and/or dysmorphism G banding Suspicious known syndrome Abnormality detection ( ) Suspicious unknown syndrome FISH Subtelomeric FISH High resolution banding Abnormality detection ( ) Array CGH Figure 2 Cytogenetic test selection used in the evaluation of children with DD/MR. see small rearrangements in these regions in routine karyotype analysis and sometimes even at higher resolution (850-band). However, it is estimated that approximately 5% of unexplained cases of MR/DD can be attributed to alterations of the subtelomeric regions. 12,13 If chromosome analysis is normal at 550-band resolution, subtelomeric FISH testing may be considered. 14 Diagnosis of DD/MR has been improved by the use of subtelomeric FISH over the past few years. In cases with no abnormality of karyotyping and fragile-x DNA analysis, array CGH is indicated. 14 Array CGH can detect subtle chromosome aberrations and has been demonstrated to improve the diagnostic detection rate of these small chromosomal abnormalities. Array CGH is superior to conventional cytogenetic analysis for the investigation of chromosomal aberrations in children with DD/MR. In the individual with nonspecific DD/MR, array CGH may be used in conjunction with routine cytogenetics to replace the locus-specific and/or subtelomeric FISH. 15 The flow chart of cytogenetic tests selected for the evaluation of DD/MR is shown in Figure 2. The estimated detection ratio of genomic abnormalities in infants and children with multiple congenital anomalies (MCA) and/or DD/MR is 3 5% by banded karyotype, another 5 6% by subtelomeric FISH, and the other 4 7% by array CGH (higher for tiling-paths than for targeted arrays), finally reaching to 12 18% by use of all analyses Array CGH Studies in DD/MR We review seven studies performing array CGH in patients with idiopathic DD/MR and summarize the results in Table Six reports used BAC arrays at approximately 1-Mb intervals and one report used an oligonucleotide array at approximately 6-kb intervals across the genome. Since microarray analysis can uncover gains and losses in regions of the genome that have unclear clinical significance, some of these may be benign copy number variants (CNVs). 23 Interpretation of copy number variations as being causative of the disabilities is complex, but a useful and widely used standard is to presume that de novo gains and losses are causative. Interpretation is difficult when parental samples are unavailable, or when gains or losses are familial. 3 We conclude from the data in Table that a causative genetic abnormality was detected in about 11.7% of cases, with a range of 6.4 to 17%. These detection rates are affected by the patient selection because patients included have varying prior diagnostic studies and a varying range of phenotypes. The detection rate of genomic rearrangements in patients with DD/MR is higher when DD/MR is combined with the malformations or dysmorphic features and severe retardation. However, an overall estimate might be that array CGH with 1-Mb resolution can detect causative changes in 10 15% of patients with idiopathic DD/MR and a normal banded karyotype. 3 These genomic abnormalities are mainly interstitial deletions and duplications. Conclusions In summary, recent studies have demonstrated that array CGH is a powerful and efficient method for diagnosis and research of DD/MR. Array CGH has a greater sensitivity than high-resolution karyotyping and can target more loci than FISH and in a costeffective manner. This technological advance in cytogenetic testing has increased the chance of a positive diagnosis for patients with DD/MR and their families. Clarification of the genetic abnormalities de tected by array CGH allows for family counseling and prenatal diagnosis. In addition, it can help

4 216 J.S. Liang et al Table 1 Reports of developmental delay/mental retardation studied by array CGH Study No. of cases Type of cases Prior studies Array Abnormal Clone Number Distribution (%) Shaw-Smith et al Idiopathic MR with Normal karyotype BACs Mb 14.0 (7/50) dysmorphism or other (41 patients had normal features subtelomere test) Menten et al MR and/or MCA Normal karyotype BACs Mb 13.6 (19/140) (31 patients had normal subtelomere test) Thuresson et al MR with MCA Normal karyotype BACs Not provided 1 Mb 10.4 (5/48) and subtelomere test Krepischi-Santos et al Syndromic MR or Normal karyotype BACs Mb 17 (16/95) other features Schoumans et al Idiopathic MR with Normal karyotype BACs Mb 9.8 (4 of 41) dysmorphism (30 patients had normal subtelomere test) Friedmann et al Idiopathic MR Normal karyotype Oligo 100 k 30 Kb 11.0 (11/100) Shevell et al Non-syndromal GDD 93 patients had BACs Mb 6.4 (6 of 94) normal karyotype MCA = multiple congenital anomalies; MR = mental retardation; GDD = global developmental delay.

5 Array CGH in developmental delay and mental retardation 217 identify the candidate gene regions/genes underlying the DD/MR. In the future, reduction of costs for array CGH will open the way for applying this method as a firsttier test in the context of children with idiopathic DD/MR. References 1. Leonard H, Wen X. The epidemiology of mental retardation: challenges and opportunities in the new millennium. Ment Retard Dev Disabil Res Rev 2002;8: Battaglia A, Bianchini E, Carey JC. Diagnostic yield of the comprehensive assessment of developmental delay/mental retardation in an institute of child neuropsychiatry. Am J Med Genet 1999;82: Stankiewicz P, Beaudet AL. Use of array CGH in the evaluation of dysmorphology, malformations, developmental delay, and idiopathic mental retardation. Curr Opin Genet Dev 2007;17(3): Shaffer LG, Bejjani BA. Medical applications of array CGH and the transformation of clinical cytogenetics. Cytogenet Genome Res 2006;115: Pinkel D, Segraves R, Sudar D, et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998;20: Lucito R, Healy J, Alexander J, et al. Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res 2003; 13: Bejjani BA, Saleki R, Ballif BC, et al. Use of targeted arraybased CGH for the clinical diagnosis of chromosomal imbalance: is less more? Am J Med Genet A 2005;134: Snijders AM, Nowak N, Segraves R, et al. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet 2001;29: Shaikh TH. Oligonucleotide arrays for high-resolution analysis of copy number alteration in mental retardation/multiple congenital anomalies. Genet Med 2007;9(9): Slavotinek AM. Novel microdeletion syndromes detected by chromosome microarrays. Hum Genet 2008;124(1): van Karnebeek CDM, Jansweijer MC, Leenders AG, Offringa M, Hennekam RC. Diagnostic investigations in individuals with mental retardation: a systematic literature review of their usefulness. Eur J Hum Genet 2005;13: Flint J, Wilkie AO, Buckle VJ, Winter RM, et al. The detection of subtelomeric chromosomal rearrangements in idiopathic mental retardation. Nat Genet 1995;9: Knight SJ, Regan R, Nicod A, et al. Subtle chromosomal rearrangements in children with unexplained mental retardation. Lancet 1999;354: Shaffer LG. American College of Medical Genetics guideline on the cytogenetic evaluation of the individual with developmental delay or mental retardation. Genet Med 2005;7: Shaffer LG, Bejjani BA. A cytogeneticist s perspective on genomic microarrays. Hum Reprod Update 2004;10: Shaw-Smith C, Redon R, Rickman L, et al. Microarray based comparative genomic hybridisation (array-cgh) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features. J Med Genet 2004;41: Menten B, Maas N, Thienpont B, et al. Emerging patterns of cryptic chromosomal imbalance in patients with idiopathic mental retardation and multiple congenital anomalies: a new series of 140 patients and review of published reports. J Med Genet 2006;43(8): Thuresson AC, Bondeson ML, Edeby C, et al. Whole-genome array-cgh for detection of submicroscopic chromosomal imbalances in children with mental retardation. Cytogenet Genome Res 2007;118(1): Krepischi-Santos ACV, Vianna-Morgante AM, Jehee FS, et al. Whole-genome array-cgh screening in undiagnosed syndromic patients: old syndromes revisited and new alterations. Cytogenet Genome Res 2006;115: Schoumans J, Ruivenkamp C, Holmberg E, Kyllerman M, Anderlid B-M, Nordenskjöld M. Detection of chromosomal imbalances in children with idiopathic mental retardation by array based comparative genomic hybridisation (array- CGH). J Med Genet 2005;42: Friedman JM, Baross A, Delaney AD, et al. Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation. Am J Hum Genet 2006;79: Shevell MI, Bejjani BA, Srour M, Rorem EA, Hall N, Shaffer LG. Array comparative genomic hybridization in global develop mental delay. Am J Med Genet B Neuropsychiatr Genet 2008;147B(7): Shaffer LG, Bejjani BA, Torchia B, Kirkpatrick S, Coppinger J, Ballif BC. The identification of microdeletion syndromes and other chromosome abnormalities: cytogenetic methods of the past, new technologies for the future. Am J Med Genet C Semin Med Genet 2007;145C(4):