Implementation of molecular karyotyping in clinical genetics

  • Luca Lovrecic Clinical Institute of Medical Genetics, Division of Gynaecology and Obstetrics, University Medical Centre Ljubljana
  • Borut Peterlin Clinical Institute of Medical Genetics, Division of Gynaecology and Obstetrics, University Medical Centre Ljubljana
Keywords: microarrays, array-based comparative genomic hybridization, aCGH, medical genetics

Abstract

Rapid development of technologies for the study of the human genome is an expected step after the discovery and sequencing of the entire human genome. Chromosomal microarrays, which allow us to perform tens of thousands of previously individual experiments simultaneously, are being utilized in all areas of human genetics and genomics. Initially, this was applicable only for research purposes, but in the last few years their clinical diagnostic purposes are becoming more and more relevant. Using molecular karyotyping (also chromosomal microarray, comparative genomic hybridization with microarray, aCGH), one can analyze microdeletions / microduplications in the whole human genome at once. It is a first-tier cytogenetic diagnostic test instead of G-banded karyotyping in patients with developmental delay and/or congenital anomalies. Molecular karyotyping is used as a diagnostic test in patients with unexplained developmental delay and/or idiopathic intellectual disability and/or dysmorphic features and/or multiple congenital anomalies (DD/ID/DF/MCA). In addition, the method is used in prenatal diagnostics and in some centres also in preimplantation genetic diagnosis.

The aim of this paper is to inform the professional community in the field about this new diagnostic method and its implementation in Slovenia, and to define the clinical situations where the method is appropriate.

Downloads

Download data is not yet available.

References

Vissers LE, Veltman JA, van Kessel AG, Brunner HG. Identification of disease genes by whole genome CGH arrays. Human molecular genetics. 2005; 14 Spec No. 2:R215–23.

Solinas-Toldo S, Lampel S, Stilgenbauer S, Nickolenko J, Benner A, Dohner H, et al. Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer. 1997; 20: 399–407.

Rudolf G, Peterlin B. Uporaba DNK genetskega testa v medicini. Zdrav Vestn 2009; 78: 65–71.

Ballarati L, Cereda A, Caselli R, Selicorni A, Recalcati MP, Maitz S, et al. Genotype-phenotype correlations in a new case of 8p23.1 deletion and review of the literature. European journal of medical genetics. 2011; 54: 55–9.

Motobayashi M, Nishimura-Tadaki A, Inaba Y, Kosho T, Miyatake S, Niimi T, et al. Neurodevelopmental features in 2q23.1 microdeletion syndrome: report of a new patient with intractable seizures and review of literature. American journal of medical genetics. 2012; 158A: 861–8.

IS LN, Chin WH, EC PL, Tan EC. An additional case of the recurrent 15q24.1 microdeletion syndrome and review of the literature. Twin research and human genetics : the official journal of the International Society for Twin Studies. 2011; 14: 333–9.

Mulley JC, Mefford HC. Epilepsy and the new cytogenetics. Epilepsia. 2011; 52: 423–32.

Shinawi M, Cheung SW. The array CGH and its clinical applications. Drug discovery today. 2008; 13: 760–70.

Zuffardi O, Vetro A, Brady P, Vermeesch J. Array technology in prenatal diagnosis. Seminars in fetal & neonatal medicine.2011; 16: 94–8.

Albertson DG, Pinkel D. Genomic microarrays in human genetic disease and cancer. Human molecular genetics. 2003; 12 Spec No 2:R145–52.

Stankiewicz P, Beaudet AL. Use of array CGH in the evaluation of dysmorphology, malformations, developmental delay, and idiopathic mental retardation. Current opinion in genetics & development. 2007; 17: 182–92.

Shaw-Smith C, Redon R, Rickman L, Rio M, Willatt L, Fiegler H, 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. Journal of medical genetics. 2004; 41: 241–8.

Sagoo GS, Butterworth AS, Sanderson S, Shaw--Smith C, Higgins JP, Burton H. Array CGH in patients with learning disability (mental retardation) and congenital anomalies: updated systematic review and meta-analysis of 19 studies and 13,926 subjects. Genet Med. 2009; 11: 139–46.

Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, et al. Global variation in copy number in the human genome. Nature. 2006; 444: 444–54.

Darilek S, Ward P, Pursley A, Plunkett K, Furman P, Magoulas P, et al. Pre- and postnatal genetic testing by array-comparative genomic hybridization: genetic counseling perspectives. Genet Med. 2008; 10: 13–8.

Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, et al. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. American journal of human genetics.86: 749–64.

Schoumans J, Ruivenkamp C, Holmberg E, Kyllerman M, Anderlid BM, Nordenskjold M. Detection of chromosomal imbalances in children with idiopathic mental retardation by array based comparative genomic hybridisation (array-CGH). Journal of medical genetics. 2005; 42: 699–705.

Hochstenbach R, van Binsbergen E, Engelen J, Nieuwint A, Polstra A, Poddighe P, et al. Array analysis and karyotyping: workflow consequences based on a retrospective study of 36,325 patients with idiopathic developmental delay in the Netherlands. European journal of medical genetics. 2009; 52: 161–9.

Veltman JA, de Vries BB. Diagnostic genome profiling: unbiased whole genome or targeted analysis? J Mol Diagn. 2006; 8(5): 534–7; discussion 7–9.

Evans MI, Henry GP, Miller WA, Bui TH, Snidjers RJ, Wapner RJ, et al. International, collaborative assessment of 146,000 prenatal karyotypes: expected limitations if only chromosome-specific probes and fluorescent in-situ hybridization are used. Human reproduction (Oxford, England). 1999; 14: 1213–6.

Faas BH, van der Burgt I, Kooper AJ, Pfundt R, Hehir-Kwa JY, Smits AP, et al. Identification of clinically significant, submicroscopic chromosome alterations and UPD in fetuses with ultrasound anomalies using genome-wide 250k SNP array analysis. Journal of medical genetics.47: 586–94.

Shaffer LG, Dabell MP, Fisher AJ, Coppinger J, Bandholz AM, Ellison JW, et al. Experience with microarray-based comparative genomic hybridization for prenatal diagnosis in over 5000 pregnancies. Prenatal diagnosis. 2012: 32: 967-85.

De Gregori M, Ciccone R, Magini P, Pramparo T, Gimelli S, Messa J, et al. Cryptic deletions are a common finding in „balanced“ reciprocal and complex chromosome rearrangements: a study of 59 patients. Journal of medical genetics. 2007; 44: 750–62.

Schluth-Bolard C, Delobel B, Sanlaville D, Boute O, Cuisset JM, Sukno S, et al. Cryptic genomic imbalances in de novo and inherited apparently balanced chromosomal rearrangements: array CGH study of 47 unrelated cases. European journal of medical genetics. 2009; 52: 291–6.

Van den Veyver IB, Patel A, Shaw CA, Pursley AN, Kang SH, Simovich MJ, et al. Clinical use of array comparative genomic hybridization (aCGH) for prenatal diagnosis in 300 cases. Prenatal diagnosis. 2009; 29: 29–39.

Handyside AH. Preimplantation genetic diagnosis after 20 years. Reproductive biomedicine online.2010: 21: 280–2.

Harper JC, Harton G. The use of arrays in preimplantation genetic diagnosis and screening. Fertility and sterility. 2010; 94: 1173–7.

Hellani A, Abu-Amero K, Azouri J, El-Akoum S. Successful pregnancies after application of array--comparative genomic hybridization in PGS-aneuploidy screening. Reproductive biomedicine online. 2008; 17: 41–7.

Gutierrez-Mateo C, Colls P, Sanchez-Garcia J, Escudero T, Prates R, Ketterson K, et al. Validation of microarray comparative genomic hybridization for comprehensive chromosome analysis of embryos. Fertility and sterility. 2011; 95: 953–8.

Fishel S, Gordon A, Lynch C, Dowell K, Ndukwe G, Kelada E, et al. Live birth after polar body array comparative genomic hybridization prediction of embryo ploidy-the future of IVF? Fertility and sterility. 2010; 93: 1006 e7- e10.

Sills ES, Yang Z, Walsh DJ, Salem SA. Comprehensive genetic assessment of the human embryo: can empiric application of microarray comparative genomic hybridization reduce multiple gestation rate by single fresh blastocyst transfer? Archives of gynecology and obstetrics. 2012; 286: 755–61.

How to Cite
1.
Lovrecic L, Peterlin B. Implementation of molecular karyotyping in clinical genetics. TEST ZdravVestn [Internet]. 1 [cited 16May2024];82(10). Available from: http://vestnik-dev.szd.si/index.php/ZdravVest/article/view/960
Section
Review