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a Laboratory for Prenatal Medicine, Department of Research/University Women's Hospital, University of Basel, Switzerland b Centre for Research in Biomedicine, University of the West of England, Bristol, UK
Key Words: limit of detection • real-time quantitative PCR • DYS14 • SRY
Present address for correspondence: Bernhard G Zimmermann, Ph.D., University of California, Los Angeles, Dental Research Institute, 73-017 Center for Health Sciences, 10833 Le Conte Avenue, Los Angeles, CA 90095-1668. Voice: 310-206-1138; fax: 310-825-7609. e-mail: bgz{at}ucla.edu
DNA of fetal origin is present in the plasma of pregnant women. The quantitative measurement of circulatory fetal DNA (cfDNA) by real-time quantitative PCR (qPCR) has been applied to investigate a possible correlation between increased levels and pregnancy-related disorders. However, as the levels of cfDNA are close to the detection limit (LOD) of the method used, the measurements may not be reliable. This is also problematic for the evaluation of preanalytical steps, such as DNA extraction and cfDNA enrichment by size separation. We optimized a protocol for the qPCR analysis of the multi-copy sequence DYS14 on the Y chromosome. This was compared with an established assay for the single-copy SRY gene. Probit regression analysis showed that the limit of detection (LOD) of the DYS14 assay, (0.4 genome equivalents (GE)) and limit of quantification (LOQ) were 10-fold lower in comparison to SRY (4 GE). The levels of cfDNA obtained from the first trimester of pregnancy could be quantified with high precision by the DYS14 assay (CV below 25%) as opposed to the SRY measurements (26–140%). Additionally, fetal sex was correctly determined in all instances. The low copy numbers of fetal DNA in plasma of women in the first trimester of pregnancy can be measured reliably, targeting the DYS14 that is present in multiple copies per Y chromosome.
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