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

Qiang Zhang; Xiaohong Guo; Tian Tian; Teng Wang; Qiaoli Li; Lei Wang; Yun Liu; Qinghe Xing; Lin He; Xinzhi Zhao

doi:10.1016/j.cca.2017.03.008

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

Clin Chim Acta. 2017 May:468:174-179. doi: 10.1016/j.cca.2017.03.008. Epub 2017 Mar 8.

Authors

Qiang Zhang¹, Xiaohong Guo², Tian Tian², Teng Wang³, Qiaoli Li⁴, Lei Wang⁴, Yun Liu⁴, Qinghe Xing⁵, Lin He⁶, Xinzhi Zhao⁷

Affiliations

¹ Children Hospital of Fudan University, Shanghai, China; Shanghai Key Laboratory of Prevention and Intervention of Birth Defects, Shanghai, China; Shanghai Center for Women and Children's Health, China.
² Children Hospital of Fudan University, Shanghai, China; Shanghai Key Laboratory of Prevention and Intervention of Birth Defects, Shanghai, China.
³ Children Hospital of Fudan University, Shanghai, China; Shanghai Key Laboratory of Prevention and Intervention of Birth Defects, Shanghai, China; Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
⁴ Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
⁵ Children Hospital of Fudan University, Shanghai, China; Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
⁶ Institutes of Biomedical Sciences, Fudan University, Shanghai, China; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China.
⁷ Children Hospital of Fudan University, Shanghai, China; Shanghai Key Laboratory of Prevention and Intervention of Birth Defects, Shanghai, China. Electronic address: [email protected].

PMID: 28284085
DOI: 10.1016/j.cca.2017.03.008

Abstract

Background: Early 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.

Methods: The 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.

Results: Overall, 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.

Conclusions: XIDMSs are widely spread along the X chromosome and might be effective markers for detection of TS and other X chromosome aneuploids.

Keywords: DNA methylation; Turner syndrome; X chromosome aneuploids; X-chromosome inactivation.

MeSH terms

Adolescent
Child
Child, Preschool
CpG Islands / genetics*
DNA Methylation*
Female
High-Throughput Nucleotide Sequencing
Humans
Male
Pilot Projects
Sequence Analysis, DNA
Turner Syndrome / diagnosis*
Turner Syndrome / genetics*
X Chromosome Inactivation / genetics*