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DNA Extraction from Various Types of Prenatal Specimens

  • Odelia Nahum
  • Amanda Thomas
  • Brynn Levy
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1885)

Abstract

A prenatal noninvasive genetic screening test that yields a positive result typically warrants further direct assessment of fetal DNA following an invasive procedure. The precious nature of these invasively acquired samples, combined with the time sensitive nature with which results should be reported, demands that the methodologies used for analysis be quick, efficient, and dependable.

Prenatal diagnosis has been performed using DNA extracted from amniotic fluid and chorionic villi for several decades, and more recently methodologies have been developed to extract cell free fetal DNA from amniotic fluid. DNA extraction methodologies in these matrices should reliably and reproducibly isolate a sufficient quality and quantity of DNA for the intended downstream application, and make it possible to purify and concentrate samples that may arrive with suboptimal quality or quantity.

Phenol-Chloroform extraction followed by DNA precipitation in ethanol has historically been used for prenatal samples, but this methodology is labor intensive, time consuming, and requires use of toxic chemicals. There are now commercially available, solid phase-based kits for rapid and reproducible DNA extraction and purification, enabling simultaneous extraction of a large number of samples. Commercial kits are available for a variety of sample matrices including all prenatal specimen types, although other methodologies including organic or inorganic liquid phase extraction may also be utilized.

Here, we describe extraction using both commercially available kits for direct amniocytes and chorionic villi and cell free fetal DNA derived from amniotic fluid, as well as inorganic liquid phase extraction for tissue culture of amniocytes, CVS, and products of conception.

Key words

DNA extraction Amniotic fluid Chorionic villi Cell free amniotic fluid Cell culture DNA prep Precipitation cffDNA Inorganic liquid phase extraction DNA extraction kit 

References

  1. 1.
    Rebello MT, Hackett G, Smith J et al (1991) Extraction of DNA from amniotic fluid cells for the early prenatal diagnosis of genetic disease. Prenat Diagn 11(1):41–46CrossRefGoogle Scholar
  2. 2.
    Williamson R, Eskdale J, Coleman DV et al (1981) Direct gene analysis of chorionic villi: a possible technique for first-trimester antenatal diagnosis of haemoglobinopathies. Lancet 2(8256):1125–1127CrossRefGoogle Scholar
  3. 3.
    Old JM (2011) Prenatal diagnosis of the hemoglobinopathies. In: Milunsky AMJ (ed) Genetic disorders and the fetus: diagnosis, prevention, and treatment, 6th edn. John Wiley & Sons, Ltd, Oxford, UKGoogle Scholar
  4. 4.
    Winsor EJ, Silver MP, Theve R et al (1996) Maternal cell contamination in uncultured amniotic fluid. Prenat Diagn 16(1):49–54.  https://doi.org/10.1002/(SICI)1097-0223(199601)16:1<49::AID-PD808>3.0.CO;2-UCrossRefPubMedGoogle Scholar
  5. 5.
    Saura R, Roux D, Taine L et al (1994) Early amniocentesis versus chorionic villus sampling for fetal karyotyping. Lancet 344(8925):825–826CrossRefGoogle Scholar
  6. 6.
    Bianchi DW, LeShane ES, Cowan JM (2001) Large amounts of cell-free fetal DNA are present in amniotic fluid. Clin Chem 47(10):1867–1869PubMedGoogle Scholar
  7. 7.
    Hui L, Bianchi DW (2011) Cell-free fetal nucleic acids in amniotic fluid. Hum Reprod Update 17(3):362–371.  https://doi.org/10.1093/humupd/dmq049CrossRefPubMedGoogle Scholar
  8. 8.
    Larrabee PB, Johnson KL, Pestova E et al (2004) Microarray analysis of cell-free fetal DNA in amniotic fluid: a prenatal molecular karyotype. Am J Hum Genet 75(3):485–491.  https://doi.org/10.1086/423288CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Lapaire O, Johnson KL, Bianchi DW (2008) Method for extraction of high-quantity and -quality cell-free DNA from amniotic fluid. Methods Mol Biol 444:303–309.  https://doi.org/10.1007/978-1-59745-066-9_24CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Shaw KJ, Thain L, Docker PT et al (2009) The use of carrier RNA to enhance DNA extraction from microfluidic-based silica monoliths. Anal Chim Acta 652(1–2):231–233.  https://doi.org/10.1016/j.aca.2009.03.038CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Pathology and Cell BiologyVagelos College of Physicians and Surgeons, Columbia University Irving Medical CenterNew YorkUSA

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