Evidence of spread of X Chromosome inactivation on Chromosome 15 in a girl with an Unbalanced t(X;15) Translocation

Abstract

We report on a baby girl with multiple congenital defects including cleft palate, intrauterine growth restriction and double outlet right ventricle (DORV) with ventricular septal defect. G-banding revealed that the proband had a de novo karyotype of 46,XX,der(15)t(X;15) (q10;q10) in all the cells analysed in peripheral blood lymphocytes, resulting in trisomy for the long arm of chromosome X and monosomy for the short arm of chromosome 15. Array-comparative genomic hybridisation showed that a 84Mb copy gain of Xq13.1- Xq28 containing the X inactivation center, whereas there was no copy gain or loss involving genes in chromosome 15. The phenotype of triple X syndrome is usually mild; spread of X inactivation into chromosome 15 leading to partial functional monosomy 15 was suspected which could result in a more severe phenotype. Therefore we study the spreading of X inactivation in terms of DNA methylation changes using the Illumina HumanMethylation450 BeadChip, which is a whole genome DNA methylation microarray which includes a total of 15259 probes in chromosome 15. Results showed there was gain in DNA methylation of more than 20% in 586 CpG sites spanning the long arm of chromosome 15. Since it is known that genes subjected to X chromosome inactivation will have an increase in DNA methylation level in the CpG-island containing promoter, we further examined the hypermethylated CpG sites located in this region only. A total of 75 probes representing 24 genes were hypermethylated. Nearly all of these probes are located in region proximal to the breakpoint, from 15q11.2 to 15q21.3 (35Mb), suggesting that X inactivation was spread to the proximal region of 15q and could potentially worsen the phenotype of our patient. We concluded that DNA methylation microarray can be used to study the spreading of X inactivation in X translocated autosome.