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Cell-free DNA fragmentation patterns in amniotic fluid identify genetic abnormalities and changes due to storage

Peter, Inga and Tighiouart, Hocine and Lapaire, Olav and Johnson, Kirby L. and Bianchi, Diana W. and Terrin, Norma. (2008) Cell-free DNA fragmentation patterns in amniotic fluid identify genetic abnormalities and changes due to storage. Diagnostic molecular pathology, Vol. 17, H. 3. pp. 185-190.

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Official URL: http://edoc.unibas.ch/dok/A6005780

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Abstract

Circulating cell-free DNA (cfDNA) has become a promising biomarker in prenatal diagnosis. However, despite extensive studies in different body fluids, cfDNA predictive value is uncertain owing to the confounding factors that can affect its levels, such as gestational age, maternal weight, smoking status, and medications. Residual fresh and archived amniotic fluid (AF) supernatants were obtained from gravid women (mean gestational age 17 wk) carrying euploid (N=36) and aneuploid (N=29) fetuses, to characterize cfDNA-fragmentation patterns with regard to aneuploidy and storage time (-80 degrees C). AF cfDNA was characterized by the real-time quantitative polymerase chain reaction amplification of glyceraldehyde-3-phosphate dehydrogenase, gel electrophoresis, and pattern recognition of the DNA fragmentation. The distributions of cfDNA fragment lengths were compared using 6 measures that defined the locations and slopes for the first and last peaks, after elimination of the confounding variables. This method allowed for the unique classification of euploid and aneuploid cfDNA samples in AF, which had been matched for storage time. In addition, we showed that archived euploid AF samples gradually lose long cfDNA fragments: this loss accurately distinguishes them from the fresh samples. We present preliminary data using cfDNA-fragmentation patterns, to uniquely distinguish between AF samples of pregnant women with regard to aneuploidy and storage time, independent of gestational age and initial DNA amount. In addition to potential applications in prenatal diagnosis, these data suggest that archived AF samples consist of large amounts of short cfDNA fragments, which are undetectable using standard real-time polymerase chain reaction amplification.
Faculties and Departments:03 Faculty of Medicine > Bereich Spezialfächer (Klinik) > Gynäkologie und Geburtshilfe > Gynäkologie (Heinzelmann)
03 Faculty of Medicine > Departement Klinische Forschung > Bereich Spezialfächer (Klinik) > Gynäkologie und Geburtshilfe > Gynäkologie (Heinzelmann)
UniBasel Contributors:Lapaire-Mayer, Olav Carl
Item Type:Article, refereed
Article Subtype:Research Article
Bibsysno:Link to catalogue
Publisher:Raven Press
ISSN:1052-9551
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:25 Apr 2014 08:01
Deposited On:25 Apr 2014 08:01

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