Balkan Journal of Medical Genetics

ARRAY-COMPARATIVE GENOMIC HYBRIDIZATION RESULTS IN CLINICALLY AFFECTED CASES WITH APPARENTLY BALANCED CHROMOSOMAL REARRANGEMENTS
Satkin NB, Karaman B, Ergin S, Kayserili H, Kalelioglu IH, Has R, Yuksel A, Basaran S
*Corresponding Author: Nihan B. Satkin, Ph.D., Department of Medical Genetics, Istanbul University Faculty of Medicine, Millete Street, 34093, Istanbul, Turkey. Tel.: +90-536-561-0313. Fax: +90-212-414-2000. E-mail: bilgenihan@gmail.com
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MATERIALS AND METHODS

The study contains the cytogenetic and array-comparative genomic hybridization (aCGH) results of 34 affected patients (13 prenatal, 21 postnatal) carrying ABCRs and 76 of family members (including parents and siblings) investigated between the years 2001-2017. All cases were examined, counseled and laboratory work was performed at the Department of Medical Genetics, Istanbul University Faculty of Medicine, Istanbul, Turkey. Fetal ultrasonography (USG) and invasive procedures [one chorionic villus sampling (CVS), four fetal blood sampling (FSB) and eight by amniocentesis (AC)] were performed at the Perinatology Division of the Obstetrics and Gynecology Department, Istanbul University Faculty of Medicine, Istanbul, Turkey. Lymphocytes cultures of peripheral and cord blood samples, amniotic fluid and chorionic villus samples using short and long-term cell cultures were performed according to traditional techniques. Routine cytogenetic analyses were performed on metaphase chromosomes at 550-600 banding levels using Giemsa-Pancreatin-Leishman’s banding. Chromosomal Microarray Analysis. Genomic DNA was extracted using High Pure polymerase chain reaction (PCR) Template Preparation kit following the manufacturer’s protocol (Roche Diagnostics, Indianapolis, IN, USA). Chromosomal microarray testing was performed in patients using NimbleGen 3 × 1.4 M Whole-Genome Tiling Array, which has 1,400,000 copy number variations (CNV) probes across the entire genome according to the manufacturer’s instructions (Roche NimbleGen, Madison, WI, USA). The SurePrint G3+SNP (single nucleotide polymorphism) Human CGH Microarray (4 × 180 K) dual-color array containing more than 170,334 distinct biological probes with 13 kb genome-wide median probes spacing was carried out following the protocols provided by the manufacturer (Agilent Technologies Inc., Santa Clara, CA, USA) in parents to detect inheritance and for confirmation of detected CNVs that were larger than 1 Mb in index cases. Aberration calls using Nexus Copy Number (Bio- Discovery, El Segundo, CA, USA) was implemented following thresholds for copy numbers; 100 kb gains, 50 kb losses across the genome with a minimum of 25 markers to make the call. For regions of known significance, the minimal setting was 25 kb and 25 markers for gains and losses. Detected variations were classified according to the American College of Medical Genetics and Genomics (ACMG) guidelines [8,9]. Only likely pathogenic or pathogenic variations were reported and uncertain CNVs were evaluated by taking into consideration of ACMG classification scores [8,9]. This study was reviewed and approved by the Ethics Committee of the Istanbul Medical Faculty [N. 08/13]. Written informed consent was obtained from all subjects or their legal guardians included in this study.

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