J Pediatr Genet 2020; 09(01): 009-018
DOI: 10.1055/s-0039-1698420
Original Article
Georg Thieme Verlag KG Stuttgart · New York

The Efficiency of SNP-Based Microarrays in the Detection of Copy-Neutral Events at 15q11.2 and 11p15.5 Loci

Berk Ozyilmaz
1  Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
,
Ozgur Kirbiyik
1  Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
,
Taha R. Ozdemir
1  Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
,
Ozge Ozer Kaya
1  Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
,
Yasar B. Kutbay
1  Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
,
Kadri M. Erdogan
1  Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
,
Merve Saka Guvenc
1  Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
,
Altug Koc
1  Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
› Author Affiliations
Funding None.
Further Information

Publication History

09 July 2019

30 August 2019

Publication Date:
16 October 2019 (online)

Abstract

Prader–Willi, Angelman, Beckwith–Wiedemann, and Russell–Silver are imprinting syndromes. In this study, we aimed to compare the efficiency of single nucleotide polymorphism (SNP) microarray analysis with methylation-specific Multiplex ligation-dependent probe amplification (MS-MLPA) in the detection of uniparental disomy in these syndromes. The patient samples with regions of loss of heterozygosity (LOH), covering 15q11.2 and 11p15.5 critical loci, were analyzed with MS-MLPA to demonstrate the efficiency of SNP microarray in the detection of uniparental disomy (UPD). In a total of seven patients, LOH covering 15q11.2 and 11p15.5 critical loci was detected. Two (28.6%) of these seven patients showed aberrant methylation (suggesting UPD) in MS-MLPA. SNP microarray is a useful tool in the detection of LOH; however, it should be used with caution, since false-positive or false-negative LOH results can be obtained. Although methylation analysis is recommended as the first tier test in the diagnosis of most of the imprinting disorders, combining methylation analysis with SNP microarray can enhance our evaluation process.

Ethics Approval

The study was not submitted to a research ethics committee. No financial or nonfinancial benefits have been received or will be received from any party related directly or indirectly to the subject of this article. All procedures followed were in accordance with the ethical standards of the responsible committee on human experimentation (institutional and national) and with the Helsinki Declaration of 1975 (in its most recently amended version). Informed consent was obtained from all patients included in the study. Additional informed consent was obtained from all patients for whom identifying information is included in this article. All institutional and national guidelines for the care and use of laboratory animals were followed. This article does not contain any studies with human or animal subjects.


Authors' Contributions

All the authors contributed to the design and implementation of the research, analysis of the results, and writing of the article.