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

2008 ◽  
Vol 54 (3) ◽  
pp. 500-511 ◽  
Author(s):  
Stephen S C Chim ◽  
Shengnan Jin ◽  
Tracy Y H Lee ◽  
Fiona M F Lun ◽  
Wing S Lee ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Blood Cells ◽  
Trisomy 21 ◽  
Maternal Blood ◽  
Maternal Plasma ◽  
Chromosome 21 ◽  
Noninvasive Detection ◽  
Fetal Dna ◽  
Noninvasive Prenatal Diagnosis ◽  
Methylation Patterns

Abstract Background: 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. Methods: 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. Results: 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. Conclusion: 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.

scholarly journals Noninvasive Prenatal Detection of Trisomy 21 by an Epigenetic–Genetic Chromosome-Dosage Approach

2010 ◽  
Vol 56 (1) ◽  
pp. 90-98 ◽  
Author(s):  
Yu K Tong ◽  
Shengnan Jin ◽  
Rossa WK Chiu ◽  
Chunming Ding ◽  
KC Allen Chan ◽  
...  
Keyword(s):  
Prenatal Diagnosis ◽  
Genetic Markers ◽  
Blood Cells ◽  
Trisomy 21 ◽  
Maternal Blood ◽  
Maternal Plasma ◽  
Plasma Samples ◽  
Prenatal Detection ◽  
Fetal Dna ◽  
Noninvasive Prenatal Diagnosis

Abstract Background: The use of fetal DNA in maternal plasma for noninvasive prenatal diagnosis of trisomy 21 (T21) is an actively researched area. We propose a novel method of T21 detection that combines fetal-specific epigenetic and genetic markers. Methods: We used combined bisulfite restriction analysis to search for fetal DNA markers on chromosome 21 that were differentially methylated in the placenta and maternal blood cells and confirmed any target locus with bisulfite sequencing. We then used methylation-sensitive restriction endonuclease digestion followed by microfluidics digital PCR analysis to investigate the identified marker. Chromosome-dosage analysis was performed by comparing the dosage of this epigenetic marker with that of the ZFY (zinc finger protein, Y-linked) gene on chromosome Y. Results: The putative promoter of the HLCS (holocarboxylase synthetase) gene was hypermethylated in the placenta and hypomethylated in maternal blood cells. A chromosome-dosage comparison of the hypermethylated HLCS and ZFY loci could distinguish samples of T21 and euploid placental DNA. Twenty-four maternal plasma samples from euploid pregnancies and 5 maternal plasma samples from T21 pregnancies were analyzed. All but 1 of the euploid samples were correctly classified. Conclusions: The epigenetic–genetic chromosome-dosage approach is a new method for noninvasive prenatal detection of T21. The epigenetic part of the analysis can be applied to all pregnancies. Because the genetic part of the analysis uses paternally inherited, fetal-specific genetic markers that are abundant in the genome, broad population coverage should be readily achievable. This approach has the potential to become a generally usable technique for noninvasive prenatal diagnosis.

scholarly journals Maternal Plasma DNA Analysis with Massively Parallel Sequencing by Ligation for Noninvasive Prenatal Diagnosis of Trisomy 21

2010 ◽  
Vol 56 (3) ◽  
pp. 459-463 ◽  
Author(s):  
Rossa WK Chiu ◽  
Hao Sun ◽  
Ranjit Akolekar ◽  
Christopher Clouser ◽  
Clarence Lee ◽  
...  
Keyword(s):  
Prenatal Diagnosis ◽  
Trisomy 21 ◽  
Massively Parallel Sequencing ◽  
Maternal Plasma ◽  
Chromosome 21 ◽  
Massively Parallel ◽  
Plasma Dna ◽  
Parallel Sequencing ◽  
Noninvasive Prenatal Diagnosis ◽  
Sequencing By Synthesis

Abstract Background: Noninvasive prenatal diagnosis of trisomy 21 (T21) has recently been shown to be achievable by massively parallel sequencing of maternal plasma on a sequencing-by-synthesis platform. The quantification of several other human chromosomes, including chromosomes 18 and 13, has been shown to be less precise, however, with quantitative biases related to the chromosomal GC content. Methods: Maternal plasma DNA from 10 euploid and 5 T21 pregnancies was sequenced with a sequencing-by-ligation approach. We calculated the genomic representations (GRs) of sequenced reads from each chromosome and their associated measurement CVs and compared the GRs of chromosome 21 (chr21) for the euploid and T21 pregnancies. Results: We obtained a median of 12 × 106 unique reads (21% of the total reads) per sample. The GRs deviated from those expected for some chromosomes but in a manner different from that previously reported for the sequencing-by-synthesis approach. Measurements of the GRs for chromosomes 18 and 13 were less precise than for chr21. z Scores of the GR of chr21 were increased in the T21 pregnancies, compared with the euploid pregnancies. Conclusions: Massively parallel sequencing-by-ligation of maternal plasma DNA was effective in identifying T21 fetuses noninvasively. The quantitative biases observed among the GRs of certain chromosomes were more likely based on analytical factors than biological factors. Further research is needed to enhance the precision for measuring for the representations of chromosomes 18 and 13.

scholarly journals DNA Methylation Alterations in Blood Cells of Toddlers with Down Syndrome

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1115
Author(s):  
Oxana Yu. Naumova ◽  
Rebecca Lipschutz ◽  
Sergey Yu. Rychkov ◽  
Olga V. Zhukova ◽  
Elena L. Grigorenko
Keyword(s):  
Dna Methylation ◽  
Down Syndrome ◽  
Blood Cells ◽  
Trisomy 21 ◽  
Developmental Stages ◽  
Published Data ◽  
Age Group ◽  
Genome Wide ◽  
Prior Literature ◽  
Methylation Patterns

Recent research has provided evidence on genome-wide alterations in DNA methylation patterns due to trisomy 21, which have been detected in various tissues of individuals with Down syndrome (DS) across different developmental stages. Here, we report new data on the systematic genome-wide DNA methylation perturbations in blood cells of individuals with DS from a previously understudied age group—young children. We show that the study findings are highly consistent with those from the prior literature. In addition, utilizing relevant published data from two other developmental stages, neonatal and adult, we track a quasi-longitudinal trend in the DS-associated DNA methylation patterns as a systematic epigenomic destabilization with age.

scholarly journals Size Distributions of Maternal and Fetal DNA in Maternal Plasma

2004 ◽  
Vol 50 (1) ◽  
pp. 88-92 ◽  
Author(s):  
K C Allen Chan ◽  
Jun Zhang ◽  
Angela B Y Hui ◽  
Nathalie Wong ◽  
Tze K Lau ◽  
...  
Keyword(s):  
Pregnant Women ◽  
Size Distribution ◽  
Maternal Plasma ◽  
Rapid Expansion ◽  
Molecular Characteristics ◽  
Dna Fragments ◽  
Dna Molecules ◽  
Plasma Dna ◽  
Fetal Dna ◽  
Noninvasive Prenatal Diagnosis

Abstract Background: The discovery of fetal DNA in maternal plasma has opened up an approach for noninvasive prenatal diagnosis. Despite the rapid expansion in clinical applications, the molecular characteristics of plasma DNA in pregnant women remain unclear. Methods: We investigated the size distribution of plasma DNA in 34 nonpregnant women and 31 pregnant women, using a panel of quantitative PCR assays with different amplicon sizes targeting the leptin gene. We also determined the size distribution of fetal DNA in maternal plasma by targeting the SRY gene. Results: The median percentages of plasma DNA with size >201 bp were 57% and 14% for pregnant and nonpregnant women, respectively (P <0.001, Mann–Whitney test). The median percentages of fetal-derived DNA with sizes >193 bp and >313 bp were 20% and 0%, respectively, in maternal plasma. Conclusion: Plasma DNA molecules are mainly short DNA fragments. The DNA fragments in the plasma of pregnant women are significantly longer than those in the plasma of nonpregnant women, and the maternal-derived DNA molecules are longer than the fetal-derived ones.

scholarly journals Microsystem for Isolation of Fetal DNA from Maternal Plasma by Preparative Size Separation

2009 ◽  
Vol 55 (12) ◽  
pp. 2144-2152 ◽  
Author(s):  
Thomas Hahn ◽  
Klaus S Drese ◽  
Ciara K O'Sullivan
Keyword(s):  
Prenatal Diagnosis ◽  
High Volume ◽  
Maternal Plasma ◽  
Chromosomal Anomalies ◽  
Size Separation ◽  
Large Samples ◽  
Fetal Dna ◽  
Noninvasive Prenatal Diagnosis ◽  
Cell Free Fetal Dna ◽  
Invasive Techniques

Abstract Background: Routine prenatal diagnosis of chromosomal anomalies is based on invasive procedures, which carry a risk of approximately 1%–2% for loss of pregnancy. An alternative to these inherently invasive techniques is to isolate fetal DNA circulating in the pregnant mother’s plasma. Free fetal DNA circulates in maternal plasma primarily as fragments of lengths <500 bp, with a majority being <300 bp. Separating these fragments by size facilitates an increase in the ratio of fetal to maternal DNA. Methods: We describe our development of a microsystem for the enrichment and isolation of cell-free fetal DNA from maternal plasma. The first step involves a high-volume extraction from large samples of maternal plasma. The resulting 80-μL eluate is introduced into a polymeric microsystem within which DNA is trapped and preconcentrated. This step is followed by a transient isotachophoresis step in which the sample stacks within a neighboring channel for subsequent size separation and is recovered via an outlet at the end of the channel. Results: Recovered fractions of fetal DNA were concentrated 4–8 times over those in preconcentration samples. With plasma samples from pregnant women, we detected the fetal SRY gene (sex determining region Y) exclusively in the fragment fraction of <500 bp, whereas a LEP gene (leptin) fragment was detected in both the shorter and longer recovery fractions. Conclusions: The microdevice we have described has the potential to open new perspectives in noninvasive prenatal diagnosis by facilitating the isolation of fetal DNA from maternal plasma in an integrated, inexpensive, and easy-to-use microsystem.

scholarly journals FISH Analysis of All Fetal Nucleated Cells in Maternal Whole Blood: Improved Specificity by the Use of Two Y-chromosome Probes

2005 ◽  
Vol 53 (3) ◽  
pp. 319-322 ◽  
Author(s):  
Susanne Mergenthaler ◽  
Tatiana Babochkina ◽  
Vivian Kiefer ◽  
Olaf Lapaire ◽  
Wolfgang Holzgreve ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Y Chromosome ◽  
Blood Cells ◽  
Maternal Blood ◽  
Fish Analysis ◽  
Blood Samples ◽  
Fetal Cells ◽  
Nucleated Red Blood Cells ◽  
Noninvasive Prenatal Diagnosis

Current cytogenetic approaches in noninvasive prenatal diagnosis focus on fetal nucleated red blood cells in maternal blood. This practice may be too restrictive because a vast proportion of other fetal cells is ignored. Recent studies have indicated that fetal cells can be directly detected, without prior enrichment, in maternal blood samples by fluorescence in situ hybridization (FISH) analysis for chromosomes X and Y (XY-FISH). In our blinded analysis of 40 maternal blood samples, we therefore examined all fetal cells without any enrichment. Initial examinations using conventional XY-FISH indicated a low specificity of 69.4%, which could be improved to 89.5% by the use of two different Y-chromosome-specific probes (YY-FISH) with only a slight concomitant decrease in sensitivity (52.4% vs 42.9%). On average, 12–20 male fetal cells/ml of maternal blood were identified by XY- and YY-FISH, respectively.

Noninvasive detection of fetal trisomy 21 by sequencing of DNA in maternal blood: a study in a clinical setting

2011 ◽  
Vol 204 (3) ◽  
pp. 205.e1-205.e11 ◽  
Author(s):  
Mathias Ehrich ◽  
Cosmin Deciu ◽  
Tricia Zwiefelhofer ◽  
John A. Tynan ◽  
Lesley Cagasan ◽  
...  
Keyword(s):  
Clinical Setting ◽  
Trisomy 21 ◽  
Maternal Blood ◽  
Noninvasive Detection

scholarly journals Measurement of Allelic-Expression Ratios in Trisomy 21 Placentas by Quencher Extension of Heterozygous Samples Identified by Partially Denaturing HPLC

2008 ◽  
Vol 54 (2) ◽  
pp. 437-440 ◽  
Author(s):  
Attie T J I Go ◽  
Allerdien Visser ◽  
Ofir T Betsalel ◽  
John M G van Vugt ◽  
Marinus A Blankenstein ◽  
...  
Keyword(s):  
Real Time ◽  
Trisomy 21 ◽  
First Trimester ◽  
Maternal Plasma ◽  
Rapid Identification ◽  
Chromosome 21 ◽  
Wave System ◽  
Exon 2 ◽  
Reading Frame ◽  
Time Required

Abstract Background: Measuring the allelic ratios of placental transcripts in maternal plasma permits noninvasive prenatal detection of chromosomal aneuploidy. Current methods, however, require highly specialized equipment (MALDI-TOF), limiting the widespread implementation of this powerful RNA single-nucleotide polymorphism (SNP) strategy in routine diagnostic settings. We adapted and applied the Transgenomic WAVE System and quencher extension (QEXT) for this purpose. Methods: The expressed SNP (rs2187247) in exon 2 of the placentally expressed C21orf105 gene (chromosome 21 open reading frame 105) on chromosome 21 was tested in a trisomy 21 model system in which we obtained RNA selectively released from syncytiotrophoblasts of normal and trisomy 21 placentas during first trimester. Results: In identifying heterozygous samples, we observed an exact correspondence between sequencing results and results obtained with the WAVE System. With respect to the analysis time required, the WAVE System was superior. In addition, the real-time QEXT assay (as optimized and validated with calibration standards consisting of 262-bp C21orf105 cDNA amplicons) accurately measured allele ratios after we optimized fragment purification, concentrations of input DNA and quencher label, and calculations of reporter signals. Finally, the optimized and validated QEXT assay correctly distinguished normal placentas from trisomy 21 placentas in tests of the following clinically relevant combinations: diploid homozygous (CC), diploid heterozygous (AC), triploid homozygous (AAA), and triploid heterozygous (AAC or ACC). Conclusion: The QEXT method, which is directly adaptable to current real-time PCR equipment, along with rapid identification of informative samples with the WAVE System, may facilitate routine implementation of the RNA-SNP assay for noninvasive aneuploidy diagnostics.

scholarly journals Whole-genome fetal and maternal DNA methylation analysis using MeDIP-NGS for the identification of differentially methylated regions

2016 ◽  
Vol 98 ◽  
Author(s):  
ANNA KERAVNOU ◽  
MARIOS IOANNIDES ◽  
KYRIAKOS TSANGARAS ◽  
CHARALAMBOS LOIZIDES ◽  
MICHAEL D. HADJIDANIEL ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Chorionic Villus ◽  
Maternal Blood ◽  
Maternal Plasma ◽  
Chorionic Villus Sampling ◽  
Whole Genome ◽  
Differentially Methylated Regions ◽  
Epigenetic Marker ◽  
Novel Approach ◽  
Targeted Enrichment

SummaryDNA methylation is an epigenetic marker that has been shown to vary significantly across different tissues. Taking advantage of the methylation differences between placenta-derived cell-free DNA and maternal blood, several groups employed different approaches for the discovery of fetal-specific biomarkers. The aim of this study was to analyse whole-genome fetal and maternal methylomes in order to identify and confirm the presence of differentially methylated regions (DMRs). We have initially utilized methylated DNA immunoprecipitation (MeDIP) and next-generation sequencing (NGS) to identify genome-wide DMRs between chorionic villus sampling (CVS) and female non-pregnant plasma (PL) and peripheral blood (WBF) samples. Next, using specific criteria, 331 fetal-specific DMRs were selected and confirmed in eight CVS, eight WBF and eight PL samples by combining MeDIP and in-solution targeted enrichment followed by NGS. Results showed higher enrichment in CVS samples as compared to both WBF and PL samples, confirming the distinct methylation levels between fetal and maternal DNA for the selected DMRs. We have successfully implemented a novel approach for the discovery and confirmation of a significant number of fetal-specific DMRs by combining for the first time MeDIP and in-solution targeted enrichment followed by NGS. The implementation of this double-enrichment approach is highly efficient and enables the detailed analysis of multiple DMRs by targeted NGS. Also, this is, to our knowledge, the first reported application of MeDIP on plasma samples, which leverages the implementation of our enrichment methodology in the detection of fetal abnormalities in maternal plasma.

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