Noninvasive Prenatal Diagnosis by Analysis of Fetal DNA in Maternal Plasma

  • Rossa W. K. Chiu
  • Y. M. Dennis Lo
Protocol
Part of the Methods in Molecular Biology™ book series (MIMB, volume 336)

Abstract

Prenatal diagnosis has become a standard part of obstetrics care. Genetic diagnoses are established prenatally through the sampling of fetal genetic material by invasive methods such as amniocentesis or chorionic villus sampling, which are associated with a risk of fetal loss. Hence, the recent discovery of the presence of fetal DNA in maternal plasma has led to exciting possibilities of noninvasive prenatal diagnosis. Numerous applications have since been reported for the analysis of circulating fetal DNA. The accuracy of fetal DNA assessment from maternal plasma is dependent on the appropriate preanalytical handling of maternal blood samples, an efficient fetal DNA extraction protocol, and a sensitive and specific detection method. The protocol that has been applied regularly in the laboratory of the authors for the reliable detection and quantification of circulating fetal DNA is presented in this chapter.

Key Words

Fetal DNA prenatal diagnosis noninvasive real-time quantitative PCR circulating nucleic acids 

References

  1. 1.
    Lo, Y. M. D., Corbetta, N., Chamberlain, P. F., et al. (1997) Presence of fetal DNA in maternal plasma and serum. Lancet 350, 485–487.PubMedCrossRefGoogle Scholar
  2. 2.
    Lo, Y. M. D., Tein, M. S., Lau, T. K., et al. (1998) Quantitative analysis of fetal DNA in maternal plasma and serum: implications for noninvasive prenatal diagnosis. Am. J. Hum. Genet. 62, 768–775.PubMedCrossRefGoogle Scholar
  3. 3.
    Birch, L., English, C. A., O'Donoghue, K., Barigye, O., Fisk, N. M., and Keer, J. T. (2005) Accurate and robust quantification of circulating fetal and total DNA in maternal plasma from 5 to 41 weeks of gestation. Clin. Chem. 51, 312–320.PubMedCrossRefGoogle Scholar
  4. 4.
    Gonzalez-Gonzalez, C., Garcia-Hoyos, M., Trujillo-Tiebas, M. J., et al. (2005) Application of fetal DNA detection in maternal plasma: a prenatal diagnosis unit experience. J. Histochem. Cytochem. 53, 307–314.PubMedCrossRefGoogle Scholar
  5. 5.
    Lo, Y. M. D., Zhang, J., Leung, T. N., Lau, T. K., Chang, A. M., and Hjelm, N. M. (1999) Rapid clearance of fetal DNA from maternal plasma. Am. J. Hum. Genet. 64, 218–224.PubMedCrossRefGoogle Scholar
  6. 6.
    Ariga, H., Ohto, H., Busch, M. P., et al. (2001) Kinetics of fetal cellular and cellfree DNA in the maternal circulation during and after pregnancy: implications for noninvasive prenatal diagnosis. Transfusion 41, 1524–1530.PubMedCrossRefGoogle Scholar
  7. 7.
    Smid, M., Galbiati, S., Vassallo, A., et al. (2003) No evidence of fetal DNA persistence in maternal plasma after pregnancy. Hum. Genet. 112, 617–618.PubMedGoogle Scholar
  8. 8.
    Lo, Y. M. D., Leung, T. N., Tein, M. S., et al. (1999) Quantitative abnormalities of fetal DNA in maternal serum in preeclampsia. Clin. Chem. 45, 184–188.PubMedGoogle Scholar
  9. 9.
    Farina, A., Sekizawa, A., Rizzo, N., et al. (2004) Cell-free fetal DNA (SRY locus) concentration in maternal plasma is directly correlated to the time elapsed from the onset of preeclampsia to the collection of blood. Prenat. Diagn. 24, 293–297.PubMedCrossRefGoogle Scholar
  10. 10.
    Lo, Y. M. D., Lau, T. K., Zhang, J., et al. (1999) Increased fetal DNA concentrations in the plasma of pregnant women carrying fetuses with trisomy 21. . Chem. 45, 1747–1751.Google Scholar
  11. 11.
    Wataganara, T., LeShane, E. S., Farina, A., et al. (2003) Maternal serum cell-free fetal DNA levels are increased in cases of trisomy 13 but not trisomy 18. Hum. Genet. 112, 204–208.PubMedGoogle Scholar
  12. 12.
    Leung, T. N., Zhang, J., Lau, T. K., Hjelm, N. M., and Lo, Y. M. D. (1998) Maternal plasma fetal DNA as a marker for preterm labour. Lancet 352, 1904–1905.PubMedCrossRefGoogle Scholar
  13. 13.
    Lau, T. K., Lo, K. W., Chan, L. Y. S., Leung, T. Y., and Lo, Y. M. D. (2000) Cellfree fetal deoxyribonucleic acid in maternal circulation as a marker of fetalmaternal hemorrhage in patients undergoing external cephalic version near term. Am J. Obstet. Gynecol. 183, 712–716.PubMedCrossRefGoogle Scholar
  14. 14.
    Sekizawa, A., Jimbo, M., Saito, H., et al. (2002) Increased cell-free fetal DNA in plasma of two women with invasive placenta. Clin. Chem. 48, 353–354.PubMedGoogle Scholar
  15. 15.
    Jimbo, M., Sekizawa, A., Sugito, Y., et al. (2003) Placenta increta: Postpartum monitoring of plasma cell-free fetal DNA. Clin. Chem. 49, 1540–1541.PubMedCrossRefGoogle Scholar
  16. 16.
    Sugito, Y., Sekizawa, A., Farina, A., et al. (2003) Relationship between severity of hyperemesis gravidarum and fetal DNA concentration in maternal plasma. Clin. Chem. 49, 1667–1669.PubMedCrossRefGoogle Scholar
  17. 17.
    Zhong, X. Y., Holzgreve, W., Li, J. C. Aydinli, K., and Hahn, S. (2000) High levels of fetal erythroblasts and fetal extracellular DNA in the peripheral blood of a pregnant woman with idiopathic polyhydramnios: case report. Prenat. Diagn. 20, 838–841.PubMedCrossRefGoogle Scholar
  18. 18.
    Lo, Y. M. D., Hjelm, N. M., Fidler, C., et al. (1998) Prenatal diagnosis of fetal RhD status by molecular analysis of maternal plasma. N. Engl. J. Med. 339, 1734–1738.PubMedCrossRefGoogle Scholar
  19. 19.
    Hromadnikova, I., Vechetova, L., Vesela, K., Benesova, B., Doucha, J., and Vik, R. (2005) Non-invasive fetal RHD and RHCE genotyping using real-time PCR testing of maternal plasma in RhD-negative pregnancies. J. Histochem. Cytochem. 53, 301–305.PubMedCrossRefGoogle Scholar
  20. 20.
    Chiu, R. W. K., Lau, T. K., Leung, T. N., et al. (2002) Prenatal exclusion of beta thalassaemia major by examination of maternal plasma. Lancet 360, 998–1000.PubMedCrossRefGoogle Scholar
  21. 21.
    Li, Y., Di Naro, E., Vitucci, A., Zimmermann, B., Holzgreve, W., and Hahn, S. (2005) Detection of paternally inherited fetal point mutations for beta-thalassemia using size-fractionated cell-free DNA in maternal plasma. JAMA 293, 843–849.PubMedCrossRefGoogle Scholar
  22. 22.
    Chiu, R. W. K., Lau, T. K., Cheung, P. T., Gong, Z. Q., Leung, T. N., and Lo, Y. M. D. (2002) Noninvasive prenatal exclusion of congenital adrenal hyperplasia by maternal plasma analysis: a feasibility study. Clin. Chem. 48, 778–780.PubMedGoogle Scholar
  23. 23.
    Li, Y., Holzgreve, W., Page-Christiaens, G. C., Gille, J. J., and Hahn, S. (2004) Improved prenatal detection of a fetal point mutation for achondroplasia by the use of size-fractionated circulatory DNA in maternal plasma. Prenat. Diagn. 24, 896–898.PubMedCrossRefGoogle Scholar
  24. 24.
    Chiu, R. W. K. and Lo, Y. M. D. (2004) The biology and diagnostic applications of fetal DNA and RNA in maternal plasma. Curr. Top. Dev. Biol. 61, 81–111.PubMedCrossRefGoogle Scholar
  25. 25.
    Chiu, R. W. K., Poon, L. L. M., Lau, T. K., Leung, T. N., Wong, E. M. C., and Lo, Y. M. D. (2001) Effects of blood-processing protocols on fetal and total DNA quantification in maternal plasma. Clin. Chem. 47, 1607–1613.PubMedGoogle Scholar
  26. 26.
    Lee, T., LeShane, E. S., Messerlian, G. M., et al. (2002) Down syndrome and cell-free fetal DNA in archived maternal serum. Am. J. Obstet. Gynecol. 187, 1217–1221.PubMedCrossRefGoogle Scholar
  27. 27.
    Lui, Y. Y. N., Chik, K. W., Chiu, R. W. K., Ho, C. Y., Lam, C. W., and Lo, Y. M. D. (2002) Predominant hematopoietic origin of cell-free DNA in plasma and serum after sex-mismatched bone marrow transplantation. Clin. Chem. 48, 421–427.PubMedGoogle Scholar
  28. 28.
    Thijssen, M. A., Swinkels, D. W., Ruers, T. J., and de Kok, J. B. (2002) Difference between free circulating plasma and serum DNA in patients with colorectal liver metastases. Anticancer Res. 22, 421–425.PubMedGoogle Scholar
  29. 29.
    Jung, M., Klotzek, S., Lewandowski, M., Fleischhacker, M., and Jung, K. (2003) Changes in concentration of DNA in serum and plasma during storage of blood samples. Clin. Chem. 49, 1028–1029.PubMedCrossRefGoogle Scholar
  30. 30.
    Angert, R. M., LeShane, E. S., Lo, Y. M. D., Chan, L. Y. S., Delli-Bovi, L. C., and Bianchi, D. W. (2003) Fetal cell-free plasma DNA concentrations in maternal blood are stable 24 hours after collection: analysis of first-and third-trimester samples. Clin. Chem. 49, 195–198.PubMedCrossRefGoogle Scholar
  31. 31.
    Chiu, R. W. K. and Lo, Y. M. D. (2002) Preanalytical issues for circulating DNA analysis: technical aspects, semantics and need for standardization, in Molecular Testing in Laboratory Medicine: Selections From Clinical Chemistry 1998-2001 (Bruns D. E., Lo Y. M. D., and Wittwer C. T., eds.). AACC, Washington: pp. 309–310.Google Scholar
  32. 32.
    Lambert, N. C., Lo, Y. M. D., Erickson, T. D., et al. (2002) Male microchimerism in healthy women and women with scleroderma: cells or circulating DNA? A quantitative answer. Blood 100, 2845–2851.PubMedCrossRefGoogle Scholar
  33. 33.
    Invernizzi, P., Biondi, M. L., Battezzati, P. M., et al. (2002) Presence of fetal DNA in maternal plasma decades after pregnancy. Hum. Genet. 110, 587–591.PubMedCrossRefGoogle Scholar
  34. 34.
    Ng, E. K. O., Tsui, N. B. Y., Lam, N. Y., et al. (2002) Presence of filterable and nonfilterable mRNA in the plasma of cancer patients and healthy individuals. Clin. Chem. 48, 1212–1217.PubMedGoogle Scholar
  35. 35.
    Chiu, R. W. K., Chan, L. Y. S., Lam, N. Y. L., et al. (2003) Quantitative analysis of circulating mitochondrial DNA in plasma. Clin. Chem. 49, 719–726.PubMedCrossRefGoogle Scholar
  36. 36.
    Ding, C., Chiu, R. W., Lau, T. K., et al. (2004) MS analysis of single-nucleotide differences in circulating nucleic acids: application to noninvasive prenatal diagnosis. Proc. Natl. Acad. Sci. USA 101, 10,762–10,767.PubMedCrossRefGoogle Scholar
  37. 37.
    Farina, A., Caramelli, E., Concu, M., et al. (2002) Testing normality of fetal DNA concentration in maternal plasma at 10-12 completed weeks' gestation: a preliminary approach to a new marker for genetic screening. Prenat. Diagn. 22, 148–152.PubMedCrossRefGoogle Scholar
  38. 38.
    Hromadnikova, I., Houbova, B., Hridelova, D., et al. (2003) Replicate real-time PCR testing of DNA in maternal plasma increases the sensitivity of non-invasive fetal sex determination. Prenat. Diagn. 23, 235–238.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press Inc. 2006

Authors and Affiliations

  • Rossa W. K. Chiu
  • Y. M. Dennis Lo

There are no affiliations available

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