Investigation of the Genomic Representation of Plasma DNA in Pregnant Women by Comparative Genomic Hybridization Analysis: A Feasibility Study

Prenatal diagnosis is part of the established obstetric care in most developed countries. However, current methods for obtaining fetal tissues for prenatal diagnosis, including chorionic villus sampling and amniocentesis, are invasive and carry a risk of fetal loss. Analysis of circulating cell-free DNA from pregnant women provides new possibilities for noninvasive prenatal diagnosis. Clinical applications of plasma fetal DNA analysis in maternal plasma include fetal RhD genotyping (1)(2), fetal aneuploidy detection (3)(4), and the prenatal diagnosis of several genetic diseases, including myotonic dystrophy (5), congenital adrenal hyperplasia (6), and β-thalassemia (7)(8). In addition to exploring the clinical applications of circulating DNA analysis, our group has investigated the molecular characteristics of cell-free DNA in maternal plasma and has shown that plasma DNA fragments in pregnant women are longer than those in nonpregnant women (9). More importantly, we have shown that the fragment size of fetal DNA in maternal circulation is shorter than that of the maternally derived DNA (9). This observation has allowed the enrichment of fetal DNA from maternal plasma (10).In this study, we used comparative genomic hybridization (CGH), a technique that can provide gene dosage information for the entire genome, to investigate the genomic representation of plasma DNA in pregnant women. The generation of this information is important because any potential unequal representation of any particular region would raise fundamental questions regarding the underlying mechanisms of DNA release into and degradation from the plasma. Diagnostically, a variety of genes [e.g., β-globin (11)(12) and glyceraldehyde-3-phosphate dehydrogenase (13)] have been chosen for the quantitative analysis of total plasma DNA. If unequal representation is observed, additional care must be exercised in the design and performance of DNA analyses and interpretation of quantitative data obtained from plasma.Healthy pregnant women without pregnancy-associated complications, …