Editorial For reprint orders, please contact
[email protected]
Chromosomal microarray analysis in ocular developmental anomalies Expert Review of Molecular Diagnostics Downloaded from informahealthcare.com by 206.227.136.100 on 05/20/14 For personal use only.
Expert Rev. Mol. Diagn. 12(5), 425–427 (2012)
Andrée Delahaye Author for correspondence: AP-HP, Laboratoire de Cytogénétique, Hôpital Jean Verdier, Service d’Histologie, Embryologie, et Cytogénétique, Avenue du 14 Juillet, Bondy 93140, France and Université Paris-Nord, Paris 13, UFR SMBH, Bobigny, France and INSERM, U676, Paris, France Tel.: +33 1 48 02 66 74 Fax: +33 1 48 02 67 37
[email protected]
Eva Pipiras AP-HP, Hôpital Jean Verdier, Service d’Histologie, Embryologie, et Cytogénétique, Bondy, France and Université Paris-Nord, Paris 13, UFR SMBH, Bobigny, France and INSERM, U676, Paris, France
Brigitte Benzacken AP-HP, Hôpital Jean Verdier, Service d’Histologie, Embryologie, et Cytogénétique, Bondy, France and Université Paris-Nord, Paris 13, UFR SMBH, Bobigny, France and INSERM, U676, Paris, France
“...the utility of chromosomal analysis in patients with ocular developmental anomalies was established before the advent of microarray technologies.” Ocular developmental anomalies
Ocular developmental anomalies (ODAs) are structural defects of the eye with various severities, caused by the disruption of the complex process of ocular morpho genesis. Although the reported prevalence at birth varies greatly, congenital eye malformations are rare; they are estimated to occur in four to six per 10,000 neonates in European registries [101] . ODAs include heterogeneous eye anomalies such as anophthalmia, microphthalmia, coloboma (optic fissure closure defects), congenital cataract (clouding of the lens) and anterior segment dysgenesis. These conditions can be present in uni- or bi-lateral forms. They can occur separately or in combination, and can be associated with other congenital malformations and/or with intellectual disabilities (here termed ‘syndromal ODAs’).
“...chromosomal microarray analysis should be undertaken in patients with syndromal or isolated ocular developmental anomalies.” Among the known etiologies of ODAs, environmental factors and exposure to infections or toxins during pregnancy have been involved, but the extent of their contribution to ODAs remains to be clarified [1] . Familial clustering of the conditions has implicated a significant genetic component [2] . More than 30 different loci and
several genes that are known to play a role in ocular development have been implicated in ODAs. However, each known gene is responsible for only a small percentage of cases, and causative mutations in these genes do not account for all ODA cases, suggesting that additional causative genetic factors still await identification. Chromosomal anomalies & ocular developmental anomalies
Historically, the conventional method for screening chromosomal aberrations was metaphase karyotyping. Chromosomal abnormalities were then detected in 7–10% of neonates with ODAs [3] . Complete aneuploidies, such as trisomies 9, 13 and 18, were found to be associated with microphthalmia or anophthalmia [4] . Segmental aneu ploidies were also found to be associated with ODAs, and were detected with standard karyotyping or, for smaller aberrations, by techniques restricted to only one or a few loci (such as FISH) when a specific microdeletion or microduplication syndrome was suspected. For instance, 22q duplication (cat eye syndrome, OMIM#115470), 4p16 (Wolf Hirschhorn syndrome, OMIM #194190) and 11p13 (Wilms tumor, aniridia, genitourinary anomalies, and mental retardation syndrome, OMIM#194072) were found to be commonly associated with coloboma and aniridia [5] . Therefore, the utility of chromosomal analysis in patients with ODAs was established before the advent of microarray technologies. Aside from their importance
Keywords : chromosomal microarray analysis • congenital eye malformations • copy number variant • karyotyping • microarray • ocular developmental anomalies
www.expert-reviews.com
10.1586/ERM.12.41
© 2012 Expert Reviews Ltd
ISSN 1473-7159
425
Editorial
Delahaye, Pipiras & Benzacken
for diagnosis and genetic counselling, chromosomal analyses have already had research applications in some cases. The characterization of chromosomal rearrangements found in patients with ODAs has indeed greatly contributed to the identification of genes involved in eye development, either studying breakpoints of apparently balanced translocations (e.g., for PITX2 [6] or SOX2 [7] identification) or studying recurrent deletions (e.g., for PAX6 identification [8]).
Expert Review of Molecular Diagnostics Downloaded from informahealthcare.com by 206.227.136.100 on 05/20/14 For personal use only.
Development of microarray technologies for chromosomal analysis
The progressive transition in medical diagnostic laboratories from metaphase karyotyping to chromosomal microarray analysis (CMA; also commonly known as molecular karyotyping) has been previously well reviewed [9] . We will briefly summarize several important points. Metaphase karyotyping allows the analysis of the number and the structure of chromosomes with a genomewide overview but with a weak resolution; only imbalances of more than 5 Mb are routinely detected. During the early 2000s, the application of microarray technologies to chromosomal analysis has greatly increased the level of resolution. A DNA microarray is a solid surface to which numerous microscopic DNA spots (termed probes) are attached. Microarrays containing probes corresponding to genome sequences have been developed for CMA. The genome resolution of a given array depends on the physical distance on the genome between the sequences of two probes and the size of an individual probe. CMA enables the detection of genomic imbalances, also termed copy number variants (CNVs; i.e., either deletions or duplications) without detecting balanced rearrangements. Three types of CMA are currently available: array comparative genomic hybridization using bacterial artificial chromosome probes, array comparative genomic hybridization using oligonucleotide probes, and microarray with SNP arrays, which adds SNP data to CNV detection. In genetic diagnosis, CMA has become a standard tool for investigating patients with unexplained developmental disabilities and/or birth defects. CMA has even replaced the standard metaphase karyotyping as the first-tier method in many laboratories [10,11] . Genomic imbalances detected by CMA in patients with ODAs
Few authors have specifically addressed the role of submicroscopic chromosomal imbalances in patients with ODAs using CMA. In a case series of 32 affected individuals with isolated anophthalmia, microphthalmia or coloboma, Raca et al. found only one causal deletion, concluding that CNVs were not a common cause of isolated ODAs [12] . In two oligonucleotide-based array studies, potentially pathogenic CNVs were found in 13–15% of patients with syndromal or isolated ODAs, and normal metaphase karyotyping [13,14] . This diagnostic yield is similar to those reported from oligonucleotide-based array studies in patients with unexplained intellectual disability or autism spectrum disorders and/or multiple congenital anomalies [10,11] . In 8% of patients with ODAs, a causal CNV encompassing a gene that is known to be involved in ocular development (such as OTX2, FOXC1, COH1 or PAX6) is detected by CMA [13,14] . Furthermore, CMA can also identify pathogenic 426
CNVs not classically associated with abnormal ocular morpho genesis, such as del(17)(p13.3p13.3), del(10)(p14p15.3) and del(16) (p11.2p11.2) [14] . Together, these data indicate that CMA should be undertaken in patients with syndromal or isolated ODAs. Challenge for CNV interpretation
In the previously cited studies, the clinical relevance of some CNVs detected by CMA in patients with ODAs was unclear. Determining the clinical significance of variants identified by CMA can be challenging. Several guidelines for interpreting CNVs in patients with intellectual disabilities and or multiple congenital anomalies have been published [15] . Most guidelines recommend parental and family studies. However, the rule that de novo chromosomal imbalances are most likely to be clinically significant, whereas familial CNVs are not, cannot always be applied, particularly because of variable expressivity or incomplete penetrance of some pathogenic CNVs. This provides support for the initiation of CNV case–control studies in very large cohorts to provide statistical evidence for specific risks associated to a CNV [11,16] . Such large studies will probably bring very little help for interpreting CNV in ODAs owing to the lack of a large phenotypically homogenous clinical population with ODAs and the fact that rare CNVs will not occur frequently enough to reach statistical significance. However, the evidence-based review work group established by The International Standards for Cytogenomic Arrays Consortium has developed a dynamic system to assess the potential clinical relevance of CNVs throughout the genome [17] . When these data are publicly available, it will substantially help clinical laboratories for CNV interpretation, including for patients with ODAs. Five-year view: next-generation sequencing
Today, investigating the cause of ODA for a patient requires a multidisciplinary approach including examination by experienced ophthalmologists and clinical geneticists. Thorough evaluation of family history, parental eye examination, dysmorphic features, growth, development and extra-ocular malformations in a patient may guide genetic investigations. Targeted genetic testing and/or CMA can be proposed depending on the clinical findings. For instance, anterior chamber dysgenesis is an indication for analysis of PITX2 and FOXC1, and patients meeting the criteria for CHARGE (coloboma, heart anomaly, choanal atresia, retardation, genital and ear anomalies) syndrome are investigated for CHD7. However, clinical heterogeneity of phenot ypes associated with gene alterations involved in ODAs, and genetic heterogeneity of ODAs, make gene targeting difficult. Indeed, except for aniridia, for which the current genetic testing provides a diagnosis for the majority of patients, more than 60% of the patients with ODAs remain without etiological diagnosis [18] . To increase the number of genetic diagnoses in patients with ODAs, next-generation sequencing (NGS) technologies will probably be widely used in the coming years. NGS target enrichment methods reduce the cost by selecting a few genes of interest prior to massive parallel sequencing, and have already been performed in a study on patients with ODAs [19] . However, whole-genome sequencing will become more and more Expert Rev. Mol. Diagn. 12(5), (2012)
Chromosomal microarray analysis in ocular developmental anomalies
available thanks to the rapid increase in NGS throughput and its decreased cost. Furthermore, with the improvement of bioinformatics, whole-genome or targeted-exome sequencing now enables the characterization of CNVs and balanced structural variations [20] , in addition to mutation detection. Therefore, it is highly likely that NGS methods will supersede CMA as the diagnostic tool for patients with ODAs in the future.
Expert Review of Molecular Diagnostics Downloaded from informahealthcare.com by 206.227.136.100 on 05/20/14 For personal use only.
References 1
2
3
Busby A, Dolk H, Armstrong B. Eye anomalies: seasonal variation and maternal viral infections. Epidemiology 16(3), 317–322 (2005). Shah SP, Taylor AE, Sowden JC et al. Anophthalmos, microphthalmos, and typical coloboma in the United Kingdom: a prospective study of incidence and risk. Invest. Ophthalmol. Vis. Sci. 52(1), 558–564 (2011). Kallen B, Tornqvist K. The epidemiology of anophthalmia and microphthalmia in Sweden. Eur. J. Epidemiol. 20(4), 345–350 (2005).
4
Verma AS, Fitzpatrick DR. Anophthalmia and microphthalmia. Orphanet. J. Rare Dis. 2, 47 (2007).
5
Gregory-Evans CY, Williams MJ, Halford S, Gregory-Evans K. Ocular coloboma: a reassessment in the age of molecular neuroscience. J. Med. Genet. 41(12), 881–891 (2004).
6
7
8
Semina EV, Datson NA, Leysens NJ et al. Exclusion of epidermal growth factor and high-resolution physical mapping across the Rieger syndrome locus. Am. J. Hum. Genet. 59(6), 1288–1296 (1996). Fantes J, Ragge NK, Lynch SA et al. Mutations in SOX2 cause anophthalmia. Nat. Genet. 33(4), 461–463 (2003). Ton CC, Hirvonen H, Miwa H et al. Positional cloning and characterization of a paired box- and homeobox-containing gene
www.expert-reviews.com
Financial & competing interests disclosure
The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties. No writing assistance was utilized in the production of this manuscript.
from the aniridia region. Cell 67(6), 1059–1074 (1991). 9
Keren B, Le Caignec C. Oligonucleotide microarrays in constitutional genetic diagnosis. Expert Rev. Mol. Diagn. 11(5), 521–532 (2011).
10
Miller DT, Adam MP, Aradhya S et al. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am. J. Hum. Genet. 86(5), 749–764 (2010).
11
12
13
14
Editorial
Kaminsky EB, Kaul V, Paschall J et al. An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities. Genet. Med. 13(9), 777–784 (2011). Raca G, Jackson CA, Kucinskas L et al. Array comparative genomic hybridization analysis in patients with anophthalmia, microphthalmia, and coloboma. Genet. Med. 13(5), 437–442 (2011). Balikova I, De Ravel T, Ayuso C et al. High frequency of submicroscopic chromosomal deletions in patients with idiopathic congenital eye malformations. Am. J. Ophthalmol. 151(6), 1087–1094.e45 (2011). Delahaye A, Bitoun P, Drunat S et al. Genomic imbalances detected by array-CGH in patients with syndromal ocular developmental anomalies. Eur. J. Hum. Genet. 20(5), 527–533 (2012).
15
Hanemaaijer NM, Sikkema-Raddatz B, Van Der Vries G et al. Practical guidelines for interpreting copy number gains detected by high-resolution array in routine diagnostics. Eur. J. Hum. Genet. 20(2), 161–165 (2012).
16
Cooper GM, Coe BP, Girirajan S et al. A copy number variation morbidity map of developmental delay. Nat. Genet. 43(9), 838–846 (2011).
17
Riggs ER, Church DM, Hanson K et al. Towards an evidence-based process for the clinical interpretation of copy number variation. Clin. Genet. 81(5), 403–412 (2012).
18
Shah SP, Taylor AE, Sowden JC et al. Anophthalmos, microphthalmos, and coloboma in the United Kingdom: clinical features, results of investigations, and early management. Ophthalmology 119(2), 362–368 (2012).
19
Jimenez NL, Flannick J, Yahyavi M et al. Targeted ‘next-generation’ sequencing in anophthalmia and microphthalmia patients confirms SOX2, OTX2 and FOXE3 mutations. BMC Med. Genet. 12, 172 (2012).
20
Karakoc E, Alkan C, O’Roak BJ et al. Detection of structural variants and indels within exome data. Nat. Methods 9(2), 176–178 (2011).
Website 101
EUROCAT. www.eurocat-network.eu
427
