Abstract
Objectives
This study aims to develop a novel library preparation method, plasma to library express technology (PLET), to construct next-generation sequencing (NGS) libraries directly from plasma without cell-free DNA (cfDNA) isolation.
Methods
Peripheral blood samples (600) were obtained from a retrospective cohort of 300 pregnant women prior to invasive diagnostic testing. The samples were subsequently distributed between library preparation methodologies, with 300 samples prepared by PLET and 300 by conventional methods for non-invasive prenatal testing (NIPT) to screen for common trisomies using low-pass whole genome next generation sequencing.
Results
NIPT conducted on PLET libraries demonstrated comparable metrics to libraries prepared using conventional methods, including 100% sensitivity and specificity.
Conclusions
Our study demonstrates the potential utility of PLET in the clinical setting and highlights its significant advantages, including dramatically reduced process complexity and markedly decreased turnaround time.
Funding source: Beijing Natural Science Foundation
Award Identifier / Grant number: No. 7222240
Acknowledgments
We thank all patients for consenting to participate. We also thank Catherine Perfect, MA (Cantab), from Liwen Bianji (Edanz) (www.liwenbianji.cn), for editing the English text of a draft of this manuscript.
-
Research funding: This research was supported by Beijing Natural Science Foundation (No. 7222240).
-
Author contributions: All authors have accepted responsibility for the entire content of this manuscript and approved its submission.
-
Competing interests: The authors declare that there is no known competing financial interests.
-
Informed consent: Informed consent was obtained from all individuals included in this study.
-
Ethical approval: The local Institutional Review Board deemed the study exempt from review.
References
1. The Chinese Ministry of Health. National stocktaking report on birth defect prevention. Beijing, China: Chinese Ministry of Health; 2012.Search in Google Scholar
2. Vanneste, E, Voet, T, Le Caignec, C, Ampe, M, Konings, P, Melotte, C, et al.. Chromosome instability is common in human cleavage-stage embryos. Nat Med 2009;15:577–83. https://doi.org/10.1038/nm.1924.Search in Google Scholar PubMed
3. Chen, Y, Bartanus, J, Liang, D, Zhu, H, Breman, AM, Smith, JL, et al.. Characterization of chromosomal abnormalities in pregnancy losses reveals critical genes and loci for human early development. Hum Mutat 2017;38:669–77. https://doi.org/10.1002/humu.23207.Search in Google Scholar PubMed PubMed Central
4. Wapner, RJ, Martin, CL, Levy, B, Ballif, BC, Eng, CM, Zachary, JM, et al.. Chromosomal microarray versus karyotyping for prenatal diagnosis. N Engl J Med 2012;367:2175–84. https://doi.org/10.1056/nejmoa1203382.Search in Google Scholar PubMed PubMed Central
5. Mandel, P. Les acides nucleiques du plasma sanguin chez 1 homme. C R Seances Soc Biol Fil 1948;142:241–3.Search in Google Scholar
6. Lo, YD, Corbetta, N, Chamberlain, PF, Rai, V, Sargent, IL, Redman, CW, et al.. Presence of fetal DNA in maternal plasma and serum. Lancet 1997;350:485–7. https://doi.org/10.1016/s0140-6736(97)02174-0.Search in Google Scholar PubMed
7. Chen, S, Zhang, L, Gao, J, Li, S, Chang, C, Chen, Y, et al.. Expanding the scope of non-invasive prenatal testing to detect fetal chromosomal copy number variations. Front Mol Biosci 2021;8:350. https://doi.org/10.3389/fmolb.2021.649169.Search in Google Scholar PubMed PubMed Central
8. Lo, YD, Han, DS, Jiang, P, Chiu, RW. Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies. Science 2021;372:eaaw3616. https://doi.org/10.1126/science.aaw3616.Search in Google Scholar PubMed
9. Aucamp, J, Bronkhorst, AJ, Badenhorst, CP, Pretorius, PJ. The diverse origins of circulating cell-free DNA in the human body: a critical re-evaluation of the literature. Biol Rev 2018;93:1649–83. https://doi.org/10.1111/brv.12413.Search in Google Scholar PubMed
10. Kilani, RT, Mackova, M, Davidge, ST, Winkler-Lowen, B, Demianczuk, N, Guilbert, LJ. Endogenous tumor necrosis factor α mediates enhanced apoptosis of cultured villous trophoblasts from intrauterine growth-restricted placentae. Reproduction 2007;133:257–64. https://doi.org/10.1530/rep-06-0080.Search in Google Scholar
11. Jahr, S, Hentze, H, Englisch, S, Hardt, D, Fackelmayer, FO, Hesch, RD, et al.. DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells. Cancer Res 2001;61:1659–65.Search in Google Scholar
12. Schwarzenbach, H, Hoon, DS, Pantel, K. Cell-free nucleic acids as biomarkers in cancer patients. Nat Rev Cancer 2011;11:426–37. https://doi.org/10.1038/nrc3066.Search in Google Scholar PubMed
13. Heitzer, E, Auinger, L, Speicher, MR. Cell-free DNA and apoptosis: how dead cells inform about the living. Trends Mol Med 2020;26:519–28. https://doi.org/10.1016/j.molmed.2020.01.012.Search in Google Scholar PubMed
14. Sekizawa, A, Jimbo, M, Saito, H, Iwasaki, M, Matsuoka, R, Okai, T, et al.. Cell-free fetal DNA in the plasma of pregnant women with severe fetal growth restriction. Am J Obstet Gynecol 2003;188:480–4. https://doi.org/10.1067/mob.2003.27.Search in Google Scholar PubMed
15. Mackie, FL, Hemming, K, Allen, S, Morris, RK, Kilby, MD. The accuracy of cell-free fetal DNA-based non-invasive prenatal testing in singleton pregnancies: a systematic review and bivariate meta-analysis. BJOG An Int J Obstet Gynaecol 2017;124:32–46. https://doi.org/10.1111/1471-0528.14050.Search in Google Scholar PubMed
16. Xu, H, Wang, S, Ma, LL, Huang, S, Liang, L, Liu, Q, et al.. Informative priors on fetal fraction increase power of the noninvasive prenatal screen. Genet Med 2018;20:817–24. https://doi.org/10.1038/gim.2017.186.Search in Google Scholar PubMed
17. Dang, M, Xu, H, Zhang, J, Wang, W, Bai, L, Fang, N, et al.. Inferring fetal fractions from read heterozygosity empowers the noninvasive prenatal screening. Genet Med 2020;22:301–8. https://doi.org/10.1038/s41436-019-0636-5.Search in Google Scholar PubMed PubMed Central
18. Liang, D, Cram, DS, Tan, HU, Linpeng, S, Liu, Y, Sun, H, et al.. Clinical utility of noninvasive prenatal screening for expanded chromosome disease syndromes. Genet Med 2019;21:1998–2006. https://doi.org/10.1038/s41436-019-0467-4.Search in Google Scholar PubMed
19. Han, DS, Lo, YD. The nexus of cfDNA and nuclease biology. Trends Genet 2021;37:758–70. https://doi.org/10.1016/j.tig.2021.04.005.Search in Google Scholar PubMed
20. Taneja, PA, Snyder, HL, de Feo, E, Kruglyak, KM, Halks-Miller, M, Curnow, KJ, et al.. Noninvasive prenatal testing in the general obstetric population: clinical performance and counseling considerations in over 85 000 cases. Prenat Diagn 2016;36:237–43. https://doi.org/10.1002/pd.4766.Search in Google Scholar PubMed PubMed Central
21. Curnow, KJ, Gross, SJ, Hall, MP, Stosic, M, Demko, Z, Zimmermann, B, et al.. Clinical experience and follow-up with large scale single-nucleotide polymorphism–based noninvasive prenatal aneuploidy testing. Am J Obstet Gynecol 2014;211:527-e1. https://doi.org/10.1016/j.ajog.2014.08.006.Search in Google Scholar PubMed
22. Norton, ME, Brar, H, Weiss, J, Karimi, A, Laurent, LC, Caughey, AB, et al.. Non-Invasive Chromosomal Evaluation (NICE) Study: results of a multicenter prospective cohort study for detection of fetal trisomy 21 and trisomy 18. Am J Obstet Gynecol 2012;207:137-e1. https://doi.org/10.1016/j.ajog.2012.05.021.Search in Google Scholar PubMed
23. Palomaki, GE, Deciu, C, Kloza, EM, Lambert-Messerlian, GM, Haddow, JE, Neveux, LM, et al.. DNA sequencing of maternal plasma reliably identifies trisomy 18 and trisomy 13 as well as Down syndrome: an international collaborative study. Genet Med 2012;14:296–305. https://doi.org/10.1038/gim.2011.73.Search in Google Scholar PubMed PubMed Central
24. Swanson, A, Sehnert, AJ, Bhatt, S. Non-invasive prenatal testing: technologies, clinical assays and implementation strategies for women’s healthcare practitioners. Curr Genetic Med Rep 2013;1:113–21. https://doi.org/10.1007/s40142-013-0010-x.Search in Google Scholar PubMed PubMed Central
25. Chen, Y, Yu, Q, Mao, X, Lei, W, He, M, Lu, W. Noninvasive prenatal testing for chromosome aneuploidies and subchromosomal microdeletions/microduplications in a cohort of 42,910 single pregnancies with different clinical features. Hum Genom 2019;13:1–8. https://doi.org/10.1186/s40246-019-0250-2.Search in Google Scholar PubMed PubMed Central
26. Xu, C, Cai, X, Chen, S, Luo, Q, Xi, H, Zhang, D, et al.. Comprehensive non-invasive prenatal screening for pregnancies with elevated risks of genetic disorders: protocol for a prospective, multicentre study. BMJ Open 2021;11:e053617. https://doi.org/10.1136/bmjopen-2021-053617.Search in Google Scholar PubMed PubMed Central
Supplementary Material
This article contains supplementary material (https://doi.org/10.1515/cclm-2022-0283).
© 2022 Walter de Gruyter GmbH, Berlin/Boston
