Systematic Search for Placental DNA-Methylation Markers on Chromosome 21: Toward a Maternal Plasma-Based Epigenetic Test for Fetal Trisomy 21

• Published in: Clinical chemistry (Baltimore, Md.) Vol. 54; no. 3; pp. 500 - 511
• Main Authors: Chim, Stephen S.C, Jin, Shengnan, Lee, Tracy Y.H, Lun, Fiona M.F, Lee, Wing S, Chan, Lisa Y.S, Jin, Yongjie, Yang, Ningning, Tong, Yu K, Leung, Tak Y, Lau, Tze K, Ding, Chunming, Chiu, Rossa W.K, Lo, Y.M. Dennis
• Format: Journal Article
• Language: English
• Published: Washington, DC Am Assoc Clin Chem 01.03.2008; American Association for Clinical Chemistry; Oxford University Press
• Subjects: Analytical, structural and metabolic biochemistry; Biological and medical sciences; Biomarkers - blood; Blood; Chromosomes, Human, Pair 21 - genetics; CpG Islands; Data analysis; Deoxyribonucleic acid; DNA; DNA Methylation; Down syndrome; Down Syndrome - diagnosis; Enzymes; Epigenesis, Genetic; Female; Fetus; Fetuses; Fundamental and applied biological sciences. Psychology; Genetic Markers; Humans; Investigative techniques, diagnostic techniques (general aspects); Mass spectrometry; Medical sciences; Methods; Methylation; Placenta - metabolism; Plasma; Postpartum Period; Pregnancy; Prenatal Diagnosis - methods; Technological change; Chromosomal aberration; Trisomy; Genetic marker; Fetal membrane; Chromosome G21; Aneuploidy; Exploration; Biochemistry; Down syndrome; Accessory chromosome B; Blood plasma; Placenta; Mother; Clinical biology; Epigenetics; Fetus; Molecular biology; Methylation
• ISSN: 0009-9147; 1530-8561
• DOI: 10.1373/clinchem.2007.098731

The presence of fetal DNA in maternal plasma represents a source of fetal genetic material for noninvasive prenatal diagnosis; however, the coexisting background maternal DNA complicates the analysis of aneuploidy in such fetal DNA. Recently, the SERPINB5 gene on chromosome 18 was shown to exhibit different DNA-methylation patterns in the placenta and maternal blood cells, and the allelic ratio for placenta-derived hypomethylated SERPINB5 in maternal plasma was further shown to be useful for noninvasive detection of fetal trisomy 18. To develop a similar method for the noninvasive detection of trisomy 21, we used methylation-sensitive single nucleotide primer extension and/or bisulfite sequencing to systematically search 114 CpG islands (CGIs)-76% of the 149 CGIs on chromosome 21 identified by bioinformatic criteria-for differentially methylated DNA patterns. The methylation index (MI) of a CpG site was estimated as the proportion of molecules methylated at that site. We identified 22 CGIs which were shown to contain CpG sites that were either completely unmethylated (MI = 0.00) in maternal blood cells and methylated in the placenta (MI range, 0.22-0.65), or completely methylated (MI = 1.00) in maternal blood cells and hypomethylated in the placenta (MI range, 0.00-0.75). We detected, for the first time, placental DNA-methylation patterns on chromosome 21 in maternal plasma during pregnancy and observed their postpartum clearance. Twenty-two (19%) of the 114 studied CGIs on chromosome 21 showed epigenetic differences between samples of placenta and maternal blood cells; these CGIs may provide a rich source of markers for noninvasive prenatal diagnosis.