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Fetal-specific DNA methylation ratio permits noninvasive prenatal diagnosis of trisomy 21

Nature Medicine volume 17, pages 510–513 (2011)Cite this article

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Abstract

The trials performed worldwide toward noninvasive prenatal diagnosis (NIPD) of Down's syndrome (or trisomy 21) have shown the commercial and medical potential of NIPD compared to the currently used invasive prenatal diagnostic procedures. Extensive investigation of methylation differences between the mother and the fetus has led to the identification of differentially methylated regions (DMRs). In this study, we present a strategy using the methylated DNA immunoprecipitation (MeDiP) methodology in combination with real-time quantitative PCR (qPCR) to achieve fetal chromosome dosage assessment, which can be performed noninvasively through the analysis of fetal-specific DMRs. We achieved noninvasive prenatal detection of trisomy 21 by determining the methylation ratio of normal and trisomy 21 cases for each tested fetal-specific DMR present in maternal peripheral blood, followed by further statistical analysis. The application of this fetal-specific methylation ratio approach provided correct diagnosis of 14 trisomy 21 and 26 normal cases.

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Figure 1: Schematic illustration of the fetal-specific DNA methylation ratio approach.
Figure 2: DNA methylation ratio values obtained from the 12 DMRs.
Figure 3: Box plot representation of the results obtained from four DMRs.

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References

  1. Hultén, M.A., Dhanjal, S. & Pertl, B. Rapid and simple prenatal diagnosis of common chromosome disorders: advantages and disadvantages of the molecular methods FISH and QF-PCR. Reproduction 126, 279–297 (2003).

    Article  Google Scholar 

  2. Lo, Y.M. et al. Presence of fetal DNA in maternal plasma and serum. Lancet 350, 485–487 (1997).

    Article  CAS  Google Scholar 

  3. Honda, H. et al. Fetal gender determination in early pregnancy through qualitative and quantitative analysis of fetal DNA in maternal serum. Hum. Genet. 110, 75–79 (2002).

    Article  CAS  Google Scholar 

  4. Bianchi, D.W., Avent, N.D., Costa, J.M. & van der Schoot, C.E. Noninvasive prenatal diagnosis of fetal Rhesus D: ready for prime(r) time. Obstet. Gynecol. 106, 841–844 (2005).

    Article  Google Scholar 

  5. Lo, Y.M. et al. Prenatal diagnosis of fetal RhD status by molecular analysis of maternal plasma. N. Engl. J. Med. 339, 1734–1738 (1998).

    Article  CAS  Google Scholar 

  6. Lo, Y.M. et al. Quantitative analysis of fetal DNA in maternal plasma and serum: implications for noninvasive prenatal diagnosis. Am. J. Hum. Genet. 62, 768–775 (1998).

    Article  CAS  Google Scholar 

  7. Chan, K.C. et al. Size distributions of maternal and fetal DNA in maternal plasma. Clin. Chem. 50, 88–92 (2004).

    Article  CAS  Google Scholar 

  8. Poon, L.L., Leung, T.N., Lau, T.K., Chow, K.C. & Lo, Y.M. Differential DNA methylation between fetus and mother as a strategy for detecting fetal DNA in maternal plasma. Clin. Chem. 48, 35–41 (2002).

    CAS  PubMed  Google Scholar 

  9. Chim, S.S. et al. Detection of the placental epigenetic signature of the maspin gene in maternal plasma. Proc. Natl. Acad. Sci. USA 102, 14753–14758 (2005).

    Article  CAS  Google Scholar 

  10. Chiu, R.W. et al. Hypermethylation of RASSF1A in human and rhesus placentas. Am. J. Pathol. 170, 941–950 (2007).

    Article  CAS  Google Scholar 

  11. Old, R.W., Crea, F., Puszyk, W. & Hulten, M.A. Candidate epigenetic biomarkers for non-invasive prenatal diagnosis of Down syndrome. Reprod. Biomed. Online 15, 227–235 (2007).

    Article  CAS  Google Scholar 

  12. Chim, S.S. et al. Systematic search for placental DNA-methylation markers on chromosome 21: toward a maternal plasma-based epigenetic test for fetal trisomy 21. Clin. Chem. 54, 500–511 (2008).

    Article  CAS  Google Scholar 

  13. Fazzari, M.J. & Greally, J.M. Epigenomics: beyond CpG islands. Nat. Rev. Genet. 5, 446–455 (2004).

    Article  CAS  Google Scholar 

  14. Grunau, C., Clark, S.J. & Rosenthal, A. Bisulfite genomic sequencing: systematic investigation of critical experimental parameters. Nucleic Acids Res. 29, E65 (2001).

    Article  CAS  Google Scholar 

  15. Rakyan, V.K. et al. An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res. 18, 1518–1529 (2008).

    Article  CAS  Google Scholar 

  16. Papageorgiou, E.A. et al. Sites of differential DNA methylation between placenta and peripheral blood: molecular markers for noninvasive prenatal diagnosis of aneuploidies. Am. J. Pathol. 174, 1609–1618 (2009).

    Article  CAS  Google Scholar 

  17. Weber, M. et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet. 37, 853–862 (2005).

    Article  CAS  Google Scholar 

  18. Lo, Y.M. et al. Plasma placental RNA allelic ratio permits noninvasive prenatal chromosomal aneuploidy detection. Nat. Med. 13, 218–223 (2007).

    Article  CAS  Google Scholar 

  19. Wald, N.J., Watt, H.C. & Hackshaw, A.K. Integrated screening for Down's syndrome on the basis of tests performed during the first and second trimesters. N. Engl. J. Med. 341, 461–467 (1999).

    Article  CAS  Google Scholar 

  20. Weisz, B. & Rodeck, C.H. An update on antenatal screening for Down's syndrome and specific implications for assisted reproduction pregnancies. Hum. Reprod. Update 12, 513–518 (2006).

    Article  CAS  Google Scholar 

  21. Chiu, R.W. et al. Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc. Natl. Acad. Sci. USA 105, 20458–20463 (2008).

    Article  CAS  Google Scholar 

  22. Fan, H.C., Blumenfeld, Y.J., Chitkara, U., Hudgins, L. & Quake, S.R. Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc. Natl. Acad. Sci. USA 105, 16266–16271 (2008).

    Article  CAS  Google Scholar 

  23. Chiu, R.W. et al. Maternal plasma DNA analysis with massively parallel sequencing by ligation for noninvasive prenatal diagnosis of trisomy 21. Clin. Chem. 56, 459–463 (2010).

    Article  CAS  Google Scholar 

  24. Tsui, N.B. et al. Detection of trisomy 21 by quantitative mass spectrometric analysis of single-nucleotide polymorphisms. Clin. Chem. 51, 2358–2362 (2005).

    Article  CAS  Google Scholar 

  25. Tsui, N.B. & Lo, Y.M. A microarray approach for systematic identification of placental-derived RNA markers in maternal plasma. Methods Mol. Biol. 444, 275–289 (2008).

    Article  CAS  Google Scholar 

  26. Tong, Y.K. et al. Noninvasive prenatal detection of trisomy 21 by an epigenetic-genetic chromosome-dosage approach. Clin. Chem. 56, 90–98 (2010).

    Article  CAS  Google Scholar 

  27. Tsui, N.B. et al. Non-invasive prenatal detection of fetal trisomy 18 by RNA-SNP allelic ratio analysis using maternal plasma SERPINB2 mRNA: a feasibility study. Prenat. Diagn. 29, 1031–1037 (2009).

    Article  CAS  Google Scholar 

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Acknowledgements

E.A.P. and P.C.P. were supported by the Special Non-Invasive Advances in Fetal and Neonatal Evaluation Network of Excellence European Commission Funded 6th Framework Package Project Number: LSHB-CT-2004-503243 and the Cyprus Institute of Neurology and Genetics. A.K. was supported by the University of Cyprus. E.T. was supported by the State Scholarships Foundation of Greece. V.V. was supported by the Mitera Hospital in Athens. N.C. was supported by the Wellcome Trust. We thank C. Sismani, L. Kousoulidou and G. Koumbaris for extensive discussions, as well as M. Hulten for her encouragement to initiate this project.

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Authors and Affiliations

  1. Cytogenetics and Genomics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus

    Elisavet A Papageorgiou, Evdokia Tsaliki & Philippos C Patsalis

  2. Department of Mathematics and Statistics, University of Cyprus, Nicosia, Cyprus

    Alex Karagrigoriou

  3. Department of Cytogenetics and Molecular Biology, Mitera Hospital, Athens, Greece

    Evdokia Tsaliki & Voula Velissariou

  4. Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, Athens, Greece

    Evdokia Tsaliki

  5. Molecular Cytogenetics Department, The Wellcome Trust Sanger Institute, Cambridge, Hinxton, UK

    Nigel P Carter

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  1. Elisavet A Papageorgiou
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Contributions

E.A.P. and E.T. carried out the experiments. E.A.P. wrote the manuscript. E.A.P. and A.K. performed the statistical analysis. E.T. and V.V. collected the majority of the samples in this study. N.P.C. provided input on the selection of the DMRs. P.C.P. was the principal investigator and has supervised the project. All authors reviewed, critiqued and offered comments on the text.

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Correspondence to Philippos C Patsalis.

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Competing interests

P.C.P. and E.A.P. have filed a US provisional patent for the fetal-specific DNA methylation ratio approach (application no. 61/405,421).

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Supplementary Tables 1–6, Supplementary Data and Supplementary Methods (PDF 174 kb)

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Papageorgiou, E., Karagrigoriou, A., Tsaliki, E. et al. Fetal-specific DNA methylation ratio permits noninvasive prenatal diagnosis of trisomy 21. Nat Med 17, 510–513 (2011). https://doi.org/10.1038/nm.2312

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