Copy Number Variations Are More Frequent on Chromosome 14 as Compared to X Chromosome in Suspected Turner Syndrome Girls - A Chromosomal Microarray Analysis

Abstract

Introduction: Turner syndrome(TS) is defined by complete/partial monosomy of X chromosome in association with classic clinical manifestations. Conventional karyotyping is the gold standard test for diagnosis of TS. However it is labour intensive and inaccurate for detecting mosaicism, marker chromosomes and sub-microscopic deletions/duplications. TS is characterized by heterogeneous phenotypes despite identical karyotypes and precise genotype-phenotype correlations have not yet been deciphered. Presence of TS specific features in absence of X chromosome abnormality, evokes the hypothesis of possible autosomal involvement. Here, we report detailed Chromosomal microarray (CMA) analysis of 47 girls with clinically suspected TS, using Affymetrix CytoScan 750K array. Materials and Methods: The clinical diagnosis of TS was based on recommendations by clinical practice guidelines from 2016 Cincinnati International TS meeting. Peripheral venous sample was collected in EDTA tubes and DNA was extracted using Qiagen-DNAeasy Blood and Tissue kit (Cat No. 69504). DNA samples were then hybridized to the Affymetrix CytoScan 750K array as per manufacturer’s instructions. The data obtained was analysed using Chromosomal Analysis suite software and public genomic databases- ISCA, OMIM, DGV, DECIPHER. For bioinformatic analysis, all the genes (172) implicated in TS were retrieved from DisGeNET database. A TS-interactome of 4033 genes was then constructed from these genes and their first-degree neighbours from complete human interactome. Thereafter compilation was done based on CMA results and a protein-protein interaction network of 316 nodes was constructed. Results: Mean age of study cohort was 15.8 ± 3.64 years with short stature being the most common presenting phenotype (91.4%). CMA analysis detected copy number variations (CNVs) on chromosome 14 in 42 (89.3%) of 47 cases while X chromosome CNVs were present in only 28 (59.5%) cases, with all patients clinically qualifying as TS. Total 445 CNVs were discovered on X chromosome and 64 CNVs were found on Chromosome 14 exhibiting either CNV gain at 14q32.33 or CNV loss at 14q11.2 or both. The 30 cell karyotype was available for 27 patients and was found to be false negative in 7 (14.8%) patients. Also, 6 out of 47 cases had Y chromosome translocation detected on CMA that failed detection by karyotype. On enrichment analysis, thirty KEGG pathways were found to be enriched by the overlapping genes between TS-interactome and the interactome constructed by genes located within 14q11.2, and 14q32.33 67% of genes (212) in this network overlap with TS-interactome. Conclusions: CMA is a superior diagnostic modality for TS than karyotyping. Functional interactomes between Chromosome X and Chromosome 14 on enrichment analysis reveal novel pathways underlying phenotypic manifestations.