Identification of Extremely Rare Pathogenic CNVs by Array CGH in Saudi Children with Developmental Delay, Congenital Malformations, and Intellectual Disability.

Chromosomal imbalance is implicated in developmental delay (DD), congenital malformations (CM), and intellectual disability (ID), and, thus, precise identification of copy number variations (CNVs) is essential. We therefore aimed to investigate the genetic heterogeneity in Saudi children with DD/CM/ID. High-resolution array comparative genomic hybridization (array CGH) was used to detect disease-associated CNVs in 63 patients. Quantitative PCR was done to confirm the detected CNVs. Giemsa banding-based karyotyping was also performed. Array CGH identified chromosomal abnormalities in 24 patients; distinct pathogenic and/or variants of uncertain significance CNVs were found in 19 patients, and aneuploidy was found in 5 patients including 47,XXY (n = 2), 45,X (n = 2) and a patient with trisomy 18 who carried a balanced Robertsonian translocation. CNVs including 9p24p13, 16p13p11, 18p11 had gains/duplications and CNVs, including 3p23p14, 10q26, 11p15, 11q24q25, 13q21.1q32.1, 16p13.3p11.2, and 20q11.1q13.2, had losses/deletions only, while CNVs including 8q24, 11q12, 15q25q26, 16q21q23, and 22q11q13 were found with both gains or losses in different individuals. In contrast, standard karyotyping detected chromosomal abnormalities in ten patients. The diagnosis rate of array CGH (28%, 18/63 patients) was around two-fold higher than that of conventional karyotyping (15.87%, 10/63 patients). We herein report, for the first time, the extremely rare pathogenic CNVs in Saudi children with DD/CM/ID. The reported prevalence of CNVs in Saudi Arabia adds value to clinical cytogenetics.

An SP1-binding site polymorphism in the COLIAI gene and osteoporosis in Egyptian patients with thalassemia major.

ß-Thalassemia major is an inherited blood disorder, which mainly affects the Mediterranean region. Osteoporosis represents an important cause of morbidity in ß-thalassemia major and its pathogenesis has not been completely clarified. Genetic factors play an important role in the pathogenesis of osteoporosis and several candidate gene polymorphisms have been implicated in the regulation of this process. A G→T polymorphism in the regulatory region of the collagen type I alpha 1 (COLIAI) gene at a recognition site for transcription factor Sp1 has been strongly associated with osteoporosis. The aim of the present study was to examine the distribution of COLIAI polymorphism and its relationship with bone mineral density (BMD) at the lumbar spine and femur in patients and controls. In this study, the G→T polymorphism was detected in 31 Egyptian ß-thalassemia major patients and 20 healthy controls and its possible association with BMD was investigated. Alleles S and s were detected by the presence of a G or T nucleotide, respectively, in a regulatory site of the COLIAI gene using polymerase chain reaction (PCR). A total of 80.6% of the ß-thalassemia patients were homozygous for G/G (SS) and 19.4% were heterozygotes for G/T (Ss) polymorphism. There was no ss genotype in our patients. In the control group, 70 and 30% had SS and Ss genotypes, respectively. There was no significant difference between Z-score of patients with SS and Ss at head of femur (P = 1) or at lumbar spine (P = 0.48). Conclusion Our results raise the possibility that genotyping at the Sp1 site could be of clinical value in identifying the thalassemic patients at risk of developing osteoporosis.