Cell-free DNA in maternal plasma and serum: A comparison of quantity, quality and tissue origin using genomic and epigenomic approaches
| Autor: | K.C. Allen Chan, Rossa W.K. Chiu, Peiyong Jiang, Felix C.K. Wong, Tak Yeung Leung, Yuk Ming Dennis Lo, Yvonne Kwun Yue Cheng, Kun Sun |
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| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Pregnancy Trimester Third Clinical Biochemistry Bisulfite sequencing Biology Epigenesis Genetic 03 medical and health sciences chemistry.chemical_compound 0302 clinical medicine Pregnancy Humans Digital polymerase chain reaction Epigenomics Fetus Cell-Free System DNA Genomics General Medicine Methylation DNA Methylation Molecular biology genomic DNA 030104 developmental biology Cell-free fetal DNA chemistry 030220 oncology & carcinogenesis Female |
| Zdroj: | Clinical Biochemistry. 49:1379-1386 |
| ISSN: | 0009-9120 |
| DOI: | 10.1016/j.clinbiochem.2016.09.009 |
| Popis: | Objectives The objectives of this study were to compare the concentrations, size profiles and major tissue contributors of cell-free DNA (cfDNA) in plasma and in serum. Design and methods Thirteen pregnant women in the third trimester were recruited for this study. We collected EDTA-plasma and serum samples using various collection tubes. We determined their cfDNA concentrations and fetal cfDNA fractions using a zinc-finger X (ZFX)/zinc-finger Y (ZFY) droplet digital polymerase chain reaction (ZFX/ZFY ddPCR) assay. We used paired-end massively parallel sequencing (MPS) to measure plasma and serum cfDNA sizes at single-base resolution. We deconvoluted the genome-wide bisulfite sequencing data with reference to the methylation profiles of different tissues. Results The concentrations of cfDNA collected in Sarstedt Serum Z tubes were found to be significantly higher than those in Greiner Bio-One Vacuette® Z Serum Separator Clot Activator tubes or Vacuette® Z Serum Clot Activator tubes. The concentrations of fetal cfDNA were significantly reduced in samples collected in the Vacuette® serum collection tubes. Fetal cfDNA fractions were significantly reduced in all sera compared to plasma. MPS of serum cfDNA revealed a right shift of the size distributions compared to plasma. Methylation-based tissue mapping of serum cfDNA revealed an increase of cfDNA from neutrophils and B cells but not T cells. Conclusions The use of different serum collection tubes has a significant impact on serum cfDNA concentrations. This effect is likely mediated through the combined effect of genomic DNA release from white blood cells and DNA degradation or removal. |
| Databáze: | OpenAIRE |
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