The evolution of prenatal Whole Exome Sequencing: from cytogenetics to precision medicine
Abstract
Prenatal genetic diagnostics have undergone a remarkable transformation, progressing from early cytogenetic techniques such as karyotyping and fluorescence in situ hybridization (FISH) to chromosomal microarray analysis (CMA) and, most recently, whole exome sequencing (WES). WES has emerged as a groundbreaking tool, allowing for identifying single-gene mutations, small insertions and deletions, and other pathogenic variants responsible for rare and complex diseases. Unlike conventional approaches, which primarily detect large chromosomal abnormalities, WES provides a high-resolution analysis of the fetal genome, significantly improving diagnostic accuracy and enabling early intervention. This review explores the historical evolution of prenatal genetic testing, highlighting key milestones from the introduction of cytogenetics in the 1960s to the integration of WES in clinical practice over the last decade. WES has proven instrumental in diagnosing monogenic disorders, uncovering the genetic basis of fetal anomalies, and investigating cases of stillbirth and recurrent pregnancy loss (RPL). However, despite its immense clinical utility, challenges such as the interpretation of variants of uncertain significance (VUS), ethical concerns surrounding incidental findings, and the financial burden associated with sequencing continue to impact its widespread adoption. Future directions in WES include its potential integration with non-invasive prenatal testing (NIPT), advancements in artificial intelligence (AI)-driven bioinformatics, and its role in precision medicine, offering more personalized and data-driven approaches to prenatal care. As technological innovations continue to enhance the speed, accuracy, and affordability of WES, its role as a cornerstone of modern prenatal diagnostics is expected to expand, shaping the future of fetal genetic screening and clinical decision-making.
##plugins.themes.bootstrap3.article.details##
Prenatal Whole Exome Sequencing (WES), Genetic Diagnostics, Monogenic Diseases, Chromosomal Microarray Analysis (CMA), Non-Invasive Prenatal Testing (NIPT), Variants of Uncertain Significance (VUS), Artificial Intelligence (AI) in Genomics
2. Löwy I. How genetics came to the unborn: 1960–2000. Stud Hist Philos Biol Biomed Sci. 2014 Sep;47 Pt A:154–62. doi: 10.1016/j.shpsc.2014.05.015. PMID: 24968964.
3. Brock DJ, Sutcliffe RG. Alpha-fetoprotein in the antenatal diagnosis of anencephaly and spina bifida. Lancet. 1972 Jul 29;2(7770):197–9. doi: 10.1016/S0140-6736(72)91634-0. PMID: 4114207.
4. Lorber J, Stewart CR, Ward AM. Alpha-fetoprotein in antenatal diagnosis of anencephaly and spina bifida. Lancet. 1973 May 26;1(7813):1187. doi: 10.1016/S0140-6736(73)91190-2. PMID: 4123575.
5. Press N, Browner CH. Why women say yes to prenatal diagnosis. Soc Sci Med. 1997 Oct;45(7):979–89. doi: 10.1016/S0277-9536(97)00011-7. PMID: 9257391.
6. Levy B, Wapner R. Prenatal diagnosis by chromosomal microarray analysis. Fertil Steril. 2018 Feb;109(2):201–12. doi: 10.1016/j.fertnstert.2018.01.005. PMID: 29447663; PMCID: PMC5856154.
7. Hillman SC, McMullan DJ, Hall G, et al. Use of prenatal chromosomal microarray: prospective cohort study and systematic review and meta-analysis. Ultrasound Obstet Gynecol. 2013 May;41(6):610–20. doi: 10.1002/uog.12464.
8. Bilgüvar K, Oztürk AK, Louvi A, et al. Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations. Nature. 2010 Sep 9;467(7312):207–10. doi: 10.1038/nature09327.
9. Goh G, Choi M. Application of whole exome sequencing to identify disease-causing variants in inherited human diseases. Genomics Inform. 2012 Dec;10(4):214–9. doi: 10.5808/GI.2012.10.4.214. PMID: 23346032; PMCID: PMC3543920.
10. Best S, Wou K, Vora N, et al. Promises, pitfalls and practicalities of prenatal whole exome sequencing. Prenat Diagn. 2018 Jan;38(1):10–9. doi: 10.1002/pd.5102. PMID: 28654730; PMCID: PMC5745303.
11. Talkowski ME, Rehm HL. Introduction of genomics into prenatal diagnostics. Lancet. 2019 Feb 23;393(10173):719–21. doi: 10.1016/S0140-6736(19)30193-X. PMID: 30712881.
12. Qiao Y, Wen J, Tang F, et al. Whole exome sequencing in recurrent early pregnancy loss. Mol Hum Reprod. 2016 May;22(5):364–72. doi: 10.1093/molehr/gaw008. PMID: 26826164; PMCID: PMC4847612.
13. Carss KJ, Hillman SC, Parthiban V, et al. Exome sequencing improves genetic diagnosis of structural fetal abnormalities revealed by ultrasound. Hum Mol Genet. 2014 Jun 15;23(12):3269–77. doi: 10.1093/hmg/ddu038.
14. Pereira R, Oliveira J, Sousa M. Bioinformatics and computational tools for next-generation sequencing analysis in clinical genetics. J Clin Med. 2020 Jan 3;9(1):132. doi: 10.3390/jcm9010132. PMID: 31947757; PMCID: PMC7019349.
15. Wang Y, Yin F, Chai Y, et al. Prenatal diagnosis of fetuses with ultrasound anomalies by whole-exome sequencing in Luoyang city, China. Front Genet. 2024 Jan 22;14:1301439. doi: 10.3389/fgene.2023.1301439. PMID: 38318287; PMCID: PMC10838985.
16. Qin Y, Yao Y, Liu N, et al. Prenatal whole-exome sequencing for fetal structural anomalies: a retrospective analysis of 145 Chinese cases. BMC Med Genomics. 2023 Oct 25;16(1):262. doi: 10.1186/s12920-023-01697-3. PMID: 37880672; PMCID: PMC10601195.
17. Lei L, Zhou L, Xiong JJ. Whole-exome sequencing increases the diagnostic rate for prenatal fetal structural anomalies. Eur J Med Genet. 2021 Sep;64(9):104288. doi: 10.1016/j.ejmg.2021.104288.
18. Stanley KE, Giordano J, Thorsten V, et al. Causal genetic variants in stillbirth. N Engl J Med. 2020 Sep 17;383(12):1107–16. doi: 10.1056/NEJMoa1908753. PMID: 32786180; PMCID: PMC7604888.
19. Diderich KEM, Klapwijk JE, van der Schoot V, et al. Challenges and pragmatic solutions in pre-test and post-test genetic counseling for prenatal exome sequencing. Appl Clin Genet. 2023 May 15;16:89–97. doi: 10.2147/TACG.S411185. PMID: 37216148; PMCID: PMC10198275.
20. Van Der Merwe N, Ramesar R, De Vries J. Whole exome sequencing in South Africa: stakeholder views on return of individual research results and incidental findings. Front Genet. 2022 Jun 8;13:864822. doi: 10.3389/fgene.2022.864822. PMID: 35754817; PMCID: PMC9216214.
21. Liu S, Yang F, Chang Q, et al. Positive predictive value estimates for noninvasive prenatal testing from data of a prenatal diagnosis laboratory and literature review. Mol Cytogenet. 2022 Jul 6;15(1):29. doi: 10.1186/s13039-022-00607-z. PMID: 35794576; PMCID: PMC9261060.
22. Radoi VE, Bohiltea CL, Bohiltea RE, et al. Cell free fetal DNA testing in maternal blood of Romanian pregnant women. Iran J Reprod Med. 2015 Oct;13(10):623–6. PMID: 26644790; PMCID: PMC4668349.
23. Drury S, Hill M, Chitty LS. Cell-free fetal DNA testing for prenatal diagnosis. Adv Clin Chem. 2016;76:1–35. doi: 10.1016/bs.acc.2016.05.004.
24. Brand H, Whelan CW, Duyzend M, et al. High-resolution and noninvasive fetal exome screening. N Engl J Med. 2023 Nov 23;389(21):2014–6. doi: 10.1056/NEJMc2216144. PMID: 37991862; PMCID: PMC10711678.
25. Setty ST, Scott-Boyer MP, Cuppens T, et al. New developments and possibilities in reanalysis and reinterpretation of whole exome sequencing datasets for unsolved rare diseases using machine learning approaches. Int J Mol Sci. 2022 Jun 18;23(12):6792. doi: 10.3390/ijms23126792. PMID: 35743235; PMCID: PMC9224427.
26. Ji X, Li Q, Qi Y, et al. When NIPT meets WES, prenatal diagnosticians face the dilemma: genetic etiological analysis of 2,328 cases of NT thickening and follow-up of pregnancy outcomes. Front Genet. 2023 Aug 2;14:1227724. doi: 10.3389/fgene.2023.1227724. PMID: 37600658; PMCID: PMC10433188.
27. Qi Q, Jiang Y, Zhou X, et al. Simultaneous detection of CNVs and SNVs improves the diagnostic yield of fetuses with ultrasound anomalies and normal karyotypes. Genes (Basel). 2020 Nov 25;11(12):1397. doi: 10.3390/genes11121397.
28. Dempsey E, Haworth A, Ive L, et al. A report on the impact of rapid prenatal exome sequencing on the clinical management of 52 ongoing pregnancies: a retrospective review. BJOG. 2021 May;128(6):1012–9. doi: 10.1111/1471-0528.16528.
29. Chen M, Chen J, Wang C, et al. Clinical application of medical exome sequencing for prenatal diagnosis of fetal structural anomalies. Eur J Obstet Gynecol Reprod Biol. 2020 Mar;251:119–24. doi: 10.1016/j.ejogrb.2020.05.003.
30. Becher N, Andreasen L, Sandager P, et al. Implementation of exome sequencing in fetal diagnostics: data and experiences from a tertiary center in Denmark. Acta Obstet Gynecol Scand. 2020 Jul;99(6):783–90. doi: 10.1111/aogs.13871.
31. Petrovski S, Aggarwal V, Giordano JL, et al. Whole-exome sequencing in the evaluation of fetal structural anomalies: a prospective cohort study. Lancet. 2019 Feb 23;393(10173):758–67. doi: 10.1016/S0140-6736(18)31940-8.
32. Lord J, McMullan DJ, Eberhardt RY, et al. Prenatal exome sequencing analysis in fetal structural anomalies detected by ultrasonography (PAGE): a cohort study. Lancet. 2019 Feb 23;393(10173):747–57. doi: 10.1016/S0140-6736(18)31940-8.
33. Smith EJ, Hill M, Peter M, et al. Implementation of a national prenatal exome sequencing service in England: cost-effectiveness analysis. BJOG. 2025 Mar;132(4):483–91. doi: 10.1111/1471-0528.18020. PMID: 39572407; PMCID: PMC11794059.
34. Deden C, Neveling K, Zafeiropopoulou D, et al. Rapid whole exome sequencing in pregnancies to identify the underlying genetic cause in fetuses with congenital anomalies detected by ultrasound imaging. Prenat Diagn. 2020 Jul;40(8):972–83. doi: 10.1002/pd.5717. PMID: 32333414; PMCID: PMC7497059.
35. PFMG 2025 – Plan France Médecine Génomique. Accessed online at: https://pfmg2025.fr/ (accessed 14.05.2025).

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
Archive of Clinical Cases is protected by copyright and may be used in accordance with copyright and other applicable laws. Content available at www.clinicalcases.eu and our digital applications is intended for personal noncommercial use.
Authors who submit a manuscript for publication in Archive of Clinical Cases agree to the following terms: a. Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal. b. Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal. c. Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) only after the final version of the manuscript was accepted and published, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access). d. It is compulsory that before submission authors ensure that their work was not published in any other medical journals or pending acceptance for publication and that "Archives of Clinical Cases" is the only beneficiary at that moment if their work/case will be accepted by us.
Guidelines for linking to www.clinicalcases.eu a. The main purpose of the site linking to the Archive of Clinical Casess site should be educational. b. Links should be made to the Archive of Clinical Casess home page (www.clinicalcases.eu) or to the articles abstract. c. It is forbidden to use the Archive of Clinical Casess cover by outside organizations unless permission has been granted in advance, notifying our Secretary. d. Material owned by the Archive of Clinical Cases (including the name, logo, cover, and text) may not be used in any manner that may induce the idea or suggest that the Archive of Clinical Cases is in some way recommending a specific company, product or service. e. You must not use or allow others to access or use, all or any part of our Site or the contents and/or applications on it for commercial purposes without our permission. To seek permission to do anything prohibited by or not contained in these TERMS, or which requires our prior consent or agreement, you can contact us.