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Non-invasive prenatal paternity testing using a standard forensic genetic massively parallel sequencing assay for amplification of human identification SNPs

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Abstract

Prenatal paternity testing often relies on invasive procedures that cause risk to both the mother and the foetus. Non-invasive, prenatal paternity testing by investigating paternally inherited single nucleotide polymorphisms (SNPs) in cell-free foetal DNA (cffDNA) in maternal plasma was performed at consecutive time points during early gestation. Plasma from 15 pregnant women was investigated at consecutive time points from gestational weeks (GWs) 4–20. The Precision ID Identity Panel and an Ion S5 Sequencer was used to analyse the cffDNA. Paternally inherited foetal SNP alleles were detected from GW7. The median foetal fractions were 0%, 3.9%, 5.1%, 5.2%, and 4.7% at GWs 4, 7, 12, 16, and 20, respectively. The corresponding median numbers of detected paternally inherited foetal autosomal SNP alleles were 0, 3, 9, 10, and 12, respectively. The typical (i.e. geometric mean) paternity indices at GW12 and GW20 were 24 (range 0.0035–8389) and 199 (range 5.1–30,137), respectively. The method is very promising. However, the method can be improved by shortening the lengths of the PCR amplicons and increasing the number of SNPs. To our knowledge, this is the first study to successfully identify paternally inherited foetal SNP alleles at consecutive time points in early gestation independently of the foetal gender.

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References

  1. Lo YM, Corbetta N, Chamberlain PF, Rai V, Sargent IL, Redman CW, Wainscoat JS (1997) Presence of fetal DNA in maternal plasma and serum. Lancet. 350(9076):485–487

    Article  CAS  PubMed  Google Scholar 

  2. Renga B (2018) Non invasive prenatal diagnosis of fetal aneuploidy using cell free fetal DNA. Eur J Obstet Gynecol Reprod Biol 225:5–8

    Article  PubMed  Google Scholar 

  3. Fan HC, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR (2008) Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc Natl Acad Sci U S A 105(42):16266–16271

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Ou X, Wang H, Qu D, Chen Y, Gao J, Sun H (2014) Epigenome-wide DNA methylation assay reveals placental epigenetic markers for noninvasive fetal single-nucleotide polymorphism genotyping in maternal plasma. Transfusion. 54(10):2523–2533

    Article  CAS  PubMed  Google Scholar 

  5. Parks M, Court S, Cleary S, Clokie S, Hewitt J, Williams D, Cole T, MacDonald F, Griffiths M, Allen S (2016) Non-invasive prenatal diagnosis of Duchenne and Becker muscular dystrophies by relative haplotype dosage. Prenat Diagn 36(4):312–320

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Parks M, Court S, Bowns B, Cleary S, Clokie S, Hewitt J, Williams D, Cole T, MacDonald F, Griffiths M, Allen S (2017) Non-invasive prenatal diagnosis of spinal muscular atrophy by relative haplotype dosage. Eur J Hum Genet 25(4):416–422

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Jakobsen TR, Clausen FB, Rode L, Dziegiel MH, Tabor A (2013) Identifying mild and severe preeclampsia in asymptomatic pregnant women by levels of cell-free fetal DNA. Transfusion. 53(9):1956–1964

    Article  CAS  PubMed  Google Scholar 

  8. Lo YM (1999) Fetal RhD genotyping from maternal plasma. Ann Med 31(5):308–312

    Article  CAS  PubMed  Google Scholar 

  9. Guo X, Bayliss P, Damewood M, Varney J, Ma E, Vallecillo B, Dhallan R (2012) A noninvasive test to determine paternity in pregnancy. N Engl J Med 366(18):1743–1745

    Article  PubMed  Google Scholar 

  10. Ryan A, Baner J, Demko Z, Hill M, Sigurjonsson S, Baird ML, Rabinowitz M (2013) Informatics-based, highly accurate, noninvasive prenatal paternity testing. Genet Med 15(6):473–477

    Article  CAS  PubMed  Google Scholar 

  11. Jiang H, Xie Y, Li X, Ge H, Deng Y, Mu H, Feng X, Yin L, Du Z, Chen F, He N (2016) Noninvasive prenatal paternity testing (NIPAT) through maternal plasma DNA sequencing: a pilot study. PLoS One 11(9):e0159385

    Article  PubMed  PubMed Central  Google Scholar 

  12. Yang D, Liang H, Gao Y, Lin S, He Z, Gao J, Sun H, Li Q, Ma X, Ou X (2017) Noninvasive fetal genotyping of paternally inherited alleles using targeted massively parallel sequencing in parentage testing cases. Transfusion. 57(6):1505–1514

    Article  CAS  PubMed  Google Scholar 

  13. Yang D, Liang H, Lin S, Li Q, Ma X, Gao J, Sun H, Chen Q, Wu J, Ou X (2018) An SNP panel for the analysis of paternally inherited alleles in maternal plasma using ion torrent PGM. Int J Legal Med 132(2):343–352

    Article  PubMed  Google Scholar 

  14. Qu N, Xie Y, Li H, Liang H, Lin S, Huang E, Gao J, Chen F, Shi Y, Ou X (2018) Noninvasive prenatal paternity testing using targeted massively parallel sequencing. Transfusion. 58(7):1792–1799

    Article  CAS  PubMed  Google Scholar 

  15. Gysi M, Arora N, Sulzer A, Voegeli P, Kratzer A (2015) Non-invasive prenatal paternity testing with STRs: a pilot study. Forensic Sci Int Genet Suppl Ser 5:E291–E292

    Article  Google Scholar 

  16. Tang DL, Li Y, Zhou X, Li X, Zheng F (2009) Multiplex fluorescent PCR for noninvasive prenatal detection of fetal-derived paternally inherited diseases using circulatory fetal DNA in maternal plasma. Eur J Obstet Gynecol Reprod Biol 144(1):35–39

    Article  CAS  PubMed  Google Scholar 

  17. van den Oever JM, van Minderhout IJ, Harteveld CL, den Hollander NS, Bakker E, van der Stoep N, Boon EM (2015) A novel targeted approach for noninvasive detection of paternally inherited mutations in maternal plasma. J Mol Diagn 17(5):590–596

    Article  PubMed  Google Scholar 

  18. Lo YM, Tein MS, Lau TK, Haines CJ, Leung TN, Poon PM, Wainscoat JS, Johnson PJ, Chang AM, Hjelm NM (1998) Quantitative analysis of fetal DNA in maternal plasma and serum: implications for noninvasive prenatal diagnosis. Am J Hum Genet 62(4):768–775

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Zhou Y, Zhu Z, Gao Y, Yuan Y, Guo Y, Zhou L, Liao K, Wang J, Du B, Hou Y, Chen Z, Chen F, Zhang H, Yu C, Zhao L, Lau TK, Jiang F, Wang W (2015) Effects of maternal and fetal characteristics on cell-free fetal DNA fraction in maternal plasma. Reprod Sci 22(11):1429–1435

    Article  PubMed  Google Scholar 

  20. Kinnings SL, Geis JA, Almasri E, Wang H, Guan X, McCullough RM, Bombard AT, Saldivar JS, Oeth P, Deciu C (2015) Factors affecting levels of circulating cell-free fetal DNA in maternal plasma and their implications for noninvasive prenatal testing. Prenat Diagn 35(8):816–822

    Article  CAS  PubMed  Google Scholar 

  21. Lo YM, Zhang J, Leung TN, Lau TK, Chang AM, Hjelm NM (1999) Rapid clearance of fetal DNA from maternal plasma. Am J Hum Genet 64(1):218–224

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Cheng WL, Hsiao CH, Tseng HW, Lee TP (2015) Noninvasive prenatal diagnosis. Taiwan J Obstet Gynecol 54(4):343–349

    Article  PubMed  Google Scholar 

  23. Akolekar R, Beta J, Picciarelli G, Ogilvie C, D’Antonio F (2015) Procedure-related risk of miscarriage following amniocentesis and chorionic villus sampling: a systematic review and meta-analysis. Ultrasound Obstet Gynecol 45(1):16–26

    Article  CAS  PubMed  Google Scholar 

  24. Wagner J, Dzijan S, Marjanovic D, Lauc G (2009) Non-invasive prenatal paternity testing from maternal blood. Int J Legal Med 123(1):75–79

    Article  PubMed  Google Scholar 

  25. Barra GB, Santa Rita TH, Chianca CF, Velasco LF, de Sousa CF, Nery LF, Costa SS (2015) Fetal male lineage determination by analysis of Y-chromosome STR haplotype in maternal plasma. Forensic Sci Int Genet 15:105–110

    Article  CAS  PubMed  Google Scholar 

  26. Chan KC, Zhang J, Hui AB, Wong N, Lau TK, Leung TN, Lo KW, Huang DW, Lo YM (2004) Size distributions of maternal and fetal DNA in maternal plasma. Clin Chem 50(1):88–92

    Article  CAS  PubMed  Google Scholar 

  27. Tsui NB, Jiang P, Chow KC, Su X, Leung TY, Sun H, Chan KC, Chiu RW, Lo YM (2012) High resolution size analysis of fetal DNA in the urine of pregnant women by paired-end massively parallel sequencing. PLoS One 7(10):e48319

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Lo YM, Chan KC, Sun H, Chen EZ, Jiang P, Lun FM, Zheng YW, Leung TY, Lau TK, Cantor CR, Chiu RW (2010) Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus. Sci Transl Med 2(61):61ra91

    Article  CAS  PubMed  Google Scholar 

  29. Fan HC, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR (2010) Analysis of the size distributions of fetal and maternal cell-free DNA by paired-end sequencing. Clin Chem 56(8):1279–1286

    Article  CAS  PubMed  Google Scholar 

  30. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature. 389(6648):251–260

    Article  CAS  PubMed  Google Scholar 

  31. Børsting C, Pereira V, Andersen JD, Morling N (2014) Single nucleotide polymorphism. In: Jamieson A, Moenssens AA (eds) Wiley encyclopedia of forensic science. John Wiley & Sons, Chichester, UK, pp 1–18

    Google Scholar 

  32. Sanchez JJ, Phillips C, Borsting C, Balogh K, Bogus M, Fondevila M, Harrison CD, Musgrave-Brown E, Salas A, Syndercombe-Court D, Schneider PM, Carracedo A, Morling N (2006) A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis. 27(9):1713–1724

    Article  CAS  PubMed  Google Scholar 

  33. Borsting C, Rockenbauer E, Morling N (2009) Validation of a single nucleotide polymorphism (SNP) typing assay with 49 SNPs for forensic genetic testing in a laboratory accredited according to the ISO 17025 standard. Forensic Sci Int Genet 4(1):34–42

    Article  PubMed  Google Scholar 

  34. Pakstis AJ, Speed WC, Fang R, Hyland FC, Furtado MR, Kidd JR, Kidd KK (2010) SNPs for a universal individual identification panel. Hum Genet 127(3):315–324

    Article  PubMed  Google Scholar 

  35. Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF (2008) New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res 18(5):830–838

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Buchard A, Kampmann ML, Poulsen L, Borsting C, Morling N (2016) ISO 17025 validation of a next-generation sequencing assay for relationship testing. Electrophoresis. 37(21):2822–2831

    Article  CAS  PubMed  Google Scholar 

  37. Nachman MW, Crowell SL (2000) Estimate of the mutation rate per nucleotide in humans. Genetics. 156(1):297–304

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Morling N, Allen RW, Carracedo A, Geada H, Guidet F, Hallenberg C, Martin W, Mayr WR, Olaisen B, Pascali VL, Schneider PM (2002) and Paternity Testing Commission of the International Society of Forensic G. Paternity Testing Commission of the International Society of Forensic Genetics: recommendations on genetic investigations in paternity cases. Forensic Sci Int 129(3):148–157

    Article  PubMed  Google Scholar 

  39. Ashoor G, Syngelaki A, Poon LC, Rezende JC, Nicolaides KH (2013) Fetal fraction in maternal plasma cell-free DNA at 11-13 weeks’ gestation: relation to maternal and fetal characteristics. Ultrasound Obstet Gynecol 41(1):26–32

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

The authors thank Nadia Vilgerte Jochumsen and Maryam Sharafi Farzad for outstanding technical assistance and all of Herlev Fertility Clinic for assistance and guidance during this project. We also thank Jeppe Dyrberg Andersen for statistical assistance and Brian Stidsen for bioinformatics help.

Funding

This work was supported by Ellen and Aage Andersen’s Foundation.

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Authors and Affiliations

  1. Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

    Sofie Lindgren Christiansen, Britt Jakobsen, Claus Børsting, Anders Buchard, Marie-Louise Kampmann & Niels Morling

  2. Fertility Clinic, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark

    Hanne Udengaard & Marie Louise Grøndahl

Authors
  1. Sofie Lindgren Christiansen
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  2. Britt Jakobsen
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  3. Claus Børsting
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  4. Hanne Udengaard
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  5. Anders Buchard
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  6. Marie-Louise Kampmann
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  7. Marie Louise Grøndahl
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  8. Niels Morling
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Corresponding author

Correspondence to Sofie Lindgren Christiansen.

Ethics declarations

The project was approved by the Committee on Health Research Ethics in the Capital Region of Denmark (H-3-2014-131) and all procedures were performed in accordance with the Helsinki declaration. The research biobank was approved by the Danish Data Protection Agency (2011-54-1262). Informed consent was obtained from all individuals participating in the project.

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The authors declare that they have no conflict of interest.

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Christiansen, S.L., Jakobsen, B., Børsting, C. et al. Non-invasive prenatal paternity testing using a standard forensic genetic massively parallel sequencing assay for amplification of human identification SNPs. Int J Legal Med 133, 1361–1368 (2019). https://doi.org/10.1007/s00414-019-02106-0

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  • DOI: https://doi.org/10.1007/s00414-019-02106-0

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