Detection of Turner syndrome using X-chromosome inactivation specific differentially methylated CpG sites: A pilot study

•XIDMSs are differentially methylated in active/inactive X chromosomes.•A group of candidate XIDMSs were screened and validated.•Quantifying X chromosome dosage using methylation level of multiple XIDMSs.•Detection Turner syndrome and other X chromosome aneuploids using XIDMSs.

BackgroundEarly diagnosis of Turner syndrome (TS) may improve preventive measures and treatment. X-chromosome inactivation specific differentially methylated CpG sites (XIDMSs) that are high methylated in inactive X chromosomes (Xi) and unmethylated in active X chromosomes (Xa) may be potential makers for TS detection.MethodsThe candidate XIDMSs were screened from 9 male and 12 female DNA samples with normal karyotypes using the Illumina 450k array and validated by bisulfite sequencing PCR and pyrosequencing assay. X chromosome dosage was calculated according to the methylation level of multiple XIDMSs.ResultsOverall, 108 candidate XIDMSs were screened by the 450k array. Validations indicated that XIDMSs gathered and formed the X-chromosome inactivation specific differentially methylated regions (XIDMRs). Using 3 XIDMRs at SAT1, UXT and UTP14A loci, 36 TS, 22 normal female and 6 male samples were analyzed. Methylation levels of the 20 XIDMSs in the XIDMRs could distinguish between TS and normal female DNA samples, the X chromosome dosage was consistent with karyotyping data. Analyzing samples of 2 triple X syndrome and 3 Klinefelter syndrome patients suggested that this method could be used to detect X chromosome aneuploids other than TS.ConclusionsXIDMSs are widely spread along the X chromosome and might be effective markers for detection of TS and other X chromosome aneuploids.