Although chromosomal instability (CIN) is a common phenomenon in cleavage-stage embryogenesis following in vitro fertilization (IVF)1,2,3, its rate in naturally conceived human embryos is unknown. CIN leads to mosaic embryos that contain a combination of genetically normal and abnormal cells, and is significantly higher in in vitro-produced preimplantation embryos as compared to in vivo-conceived preimplantation embryos4. Even though embryos with CIN-derived complex aneuploidies may arrest between the cleavage and blastocyst stages of embryogenesis5,6, a high number of embryos containing abnormal cells can pass this strong selection barrier7,8. However, neither the prevalence nor extent of CIN during prenatal development and at birth, following IVF treatment, is well understood. Here we profiled the genomic landscape of fetal and placental tissues postpartum from both IVF and naturally conceived children, to investigate the prevalence and persistence of large genetic aberrations that probably arose from IVF-related CIN. We demonstrate that CIN is not preserved at later stages of prenatal development, and that de novo numerical aberrations or large structural DNA imbalances occur at similar rates in IVF and naturally conceived live-born neonates. Our findings affirm that human IVF treatment has no detrimental effect on the chromosomal constitution of fetal and placental lineages.
This is a preview of subscription content, access via your institution
Subscribe to Nature+
Get immediate online access to Nature and 55 other Nature journal
Subscribe to Journal
Get full journal access for 1 year
only $6.58 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Get time limited or full article access on ReadCube.
All prices are NET prices.
All SNP array data generated in this study were deposited in the NCBI Gene Expression Omnibus under accession no. GSE93353.
Custom code is available from the author upon reasonable request.
Vanneste, E. et al. Chromosome instability is common in human cleavage-stage embryos. Nat. Med. 15, 577–583 (2009).
Chavez, S. L. et al. Dynamic blastomere behaviour reflects human embryo ploidy by the four-cell stage. Nat. Commun. 3, 1251 (2012).
Zamani Esteki, M. et al. Concurrent whole-genome haplotyping and copy-number profiling of single cells. Am. J. Hum. Genet. 96, 894–912 (2015).
Tsuiko, O. et al. Genome stability of bovine in vivo-conceived cleavage-stage embryos is higher compared to in vitro-produced embryos. Hum. Reprod. 32, 2348–2357 (2017).
McCoy, R. C. et al. Evidence of selection against complex mitotic-origin aneuploidy during preimplantation development. PLoS Genet. 11, e1005601 (2015).
McCoy, R. C. et al. Common variants spanning PLK4 are associated with mitotic-origin aneuploidy in human embryos. Science 348, 235–238 (2015).
Fragouli, E. et al. Cytogenetic analysis of human blastocysts with the use of FISH, CGH and aCGH: scientific data and technical evaluation. Hum. Reprod. 26, 480–490 (2011).
Popovic, M. et al. Chromosomal mosaicism in human blastocysts: the ultimate challenge of preimplantation genetic testing? Hum. Reprod. 33, 1342–1354 (2018).
Vanneste, E. et al. What next for preimplantation genetic screening? High mitotic chromosome instability rate provides the biological basis for the low success rate. Hum. Reprod. 24, 2679–2682 (2009).
van Echten-Arends, J. et al. Chromosomal mosaicism in human preimplantation embryos: a systematic review. Hum. Reprod. Update 17, 620–627 (2011).
Destouni, A. et al. Zygotes segregate entire parental genomes in distinct blastomere lineages causing cleavage-stage chimerism and mixoploidy. Genome Res. 26, 567–578 (2016).
Ledbetter, D. H. Chaos in the embryo. Nat. Med. 15, 490–491 (2009).
Kalousek, D. K. & Vekemans, M. Confined placental mosaicism. J. Med. Genet. 33, 529–533 (1996).
Biesecker, L. G. & Spinner, N. B. A genomic view of mosaicism and human disease. Nat. Rev. Genet. 14, 307–320 (2013).
Santos, M. A. et al. The fate of the mosaic embryo: chromosomal constitution and development of day 4, 5 and 8 human embryos. Hum. Reprod. 25, 1916–1926 (2010).
Greco, E., Minasi, M. G. & Fiorentino, F. Healthy babies after intrauterine transfer of mosaic aneuploid blastocysts. N. Engl. J. Med. 373, 2089–2090 (2015).
Dimitriadou, E. et al. Principles guiding embryo selection following genome-wide haplotyping of preimplantation embryos. Hum. Reprod. 32, 687–697 (2017).
Bolton, H. et al. Mouse model of chromosome mosaicism reveals lineage-specific depletion of aneuploid cells and normal developmental potential. Nat. Commun. 7, 11165 (2016).
Liu, P. et al. An organismal CNV mutator phenotype restricted to early human development. Cell 168, 830–842 e837 (2017).
Voet, T. & Vermeesch, J. R. Mutational processes shaping the genome in early human embryos. Cell 168, 751–753 (2017).
Merla, G., Brunetti-Pierri, N., Micale, L. & Fusco, C. Copy number variants at Williams–Beuren syndrome 7q11.23 region. Hum. Genet. 128, 3–26 (2010).
Szafranski, P. et al. Structures and molecular mechanisms for common 15q13.3 microduplications involving CHRNA7: benign or pathological? Hum. Mutat. 31, 840–850 (2010).
van Bon, B. W. et al. Further delineation of the 15q13 microdeletion and duplication syndromes: a clinical spectrum varying from non-pathogenic to a severe outcome. J. Med. Genet. 46, 511–523 (2009).
Chow S.-C., Shao, J. & Wang, H. Sample Size Calculation in Clinical Research (Marcel Dekker, 2003).
Kasak, L., Rull, K., Vaas, P., Teesalu, P. & Laan, M. Extensive load of somatic CNVs in the human placenta. Sci. Rep. 5, 8342 (2015).
Delhanty, J. D. et al. Detection of aneuploidy and chromosomal mosaicism in human embryos during preimplantation sex determination by fluorescent in situ hybridisation (FISH). Hum. Mol. Genet. 2, 1183–1185 (1993).
Munne, S. et al. Assessment of numeric abnormalities of X, Y, 18, and 16 chromosomes in preimplantation human embryos before transfer. Am. J. Obstet. Gynecol. 172, 1191–1199 (1995), discussion 1199–1201.
Ziebe, S. et al. FISH analysis for chromosomes 13, 16, 18, 21, 22, X and Y in all blastomeres of IVF pre-embryos from 144 randomly selected donated human oocytes and impact on pre-embryo morphology. Hum. Reprod. 18, 2575–2581 (2003).
Baart, E. B. et al. Preimplantation genetic screening reveals a high incidence of aneuploidy and mosaicism in embryos from young women undergoing IVF. Hum. Reprod. 21, 223–233 (2006).
Steptoe, P. C. & Edwards, R. G. Birth after the reimplantation of a human embryo. Lancet 2, 366 (1978).
Angell, R. R., Aitken, R. J., van Look, P. F., Lumsden, M. A. & Templeton, A. A. Chromosome abnormalities in human embryos after in vitro fertilization. Nature 303, 336–338 (1983).
Harper, J. C. et al. Mosaicism of autosomes and sex chromosomes in morphologically normal, monospermic preimplantation human embryos. Prenat. Diagn. 15, 41–49 (1995).
Voet, T. et al. Single-cell paired-end genome sequencing reveals structural variation per cell cycle. Nucleic Acids Res. 41, 6119–6138 (2013).
Dimitriadou, E., Zamani Esteki, M. & Vermeesch, J. R. in Methods in Molecular Biology (ed. Kroneis, T.) 197–219 (Springer, 2015).
Destouni, A. et al. Genome-wide haplotyping embryos developing from 0PN and 1PN zygotes increases transferrable embryos in PGT-M. Hum. Reprod. 33, 2302–2311 (2018).
Wang, K. et al. PennCNV: an integrated hidden markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 17, 1665–1674 (2007).
Colella, S. et al. QuantiSNP: an objective Bayes hidden-Markov model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Res. 35, 2013–2025 (2007).
Munne, S. et al. Euploidy rates in donor egg cycles significantly differ between fertility centers. Hum. Reprod. 32, 743–749 (2017).
Munne, S. et al. Detailed investigation into the cytogenetic constitution and pregnancy outcome of replacing mosaic blastocysts detected with the use of high-resolution next-generation sequencing. Fertil. Steril. 108, 62–71 e68 (2017).
Sildver, K., Veerus, P. & Lang, K. Birth weight percentiles and factors associated with birth weight: a registry-based study in Estonia. Eesti Arst. 94, 465–470 (2015).
Sankilampi, U., Hannila, M. L., Saari, A., Gissler, M. & Dunkel, L. New population-based references for birth weight, length, and head circumference in singletons and twins from 23 to 43 gestation weeks. Ann. Med. 45, 446–454 (2013).
Conlin, L. K. et al. Mechanisms of mosaicism, chimerism and uniparental disomy identified by single nucleotide polymorphism array analysis. Hum. Mol. Genet. 19, 1263–1275 (2010).
Nilsen, G. et al. Copynumber: efficient algorithms for single- and multi-track copy number segmentation. BMC Genomics 13, 591 (2012).
Hulley, S. B, Cummings, S. R, Browner, W. S, Grady, D. G. & Newman, T. B. Designing Clinical Research (Lippincott Williams & Wilkins, 2015).
Cohen, J. Statistical Power Analysis for the Behavioral Sciences (Lawrence Erlbaum Associates, 1988).
Metsalu, T. et al. Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta. Epigenetics 9, 1397–1409 (2014).
Reimand, J. et al. g:Profiler—a web server for functional interpretation of gene lists (2016 update). Nucleic Acids Res. 44, W83–W89 (2016).
Spaepen, M., Angulo, A. F., Marynen, P. & Cassiman, J. J. Detection of bacterial and mycoplasma contamination in cell cultures by polymerase chain reaction. FEMS Microbiol. Lett. 78, 89–94 (1992).
We gratefully thank all families that participated in this study in Estonia and Finland. This research was funded by an institutional research grant from the Estonian Ministry of Education and Research (no. IUT34-16 to A.S.); Enterprise Estonia (grant no. EU48695 to A.S.); the Horizon 2020 innovation (WIDENLIFE) (grant no. EU692065 to A.K.); the European Union’s FP7 Marie Curie Industry-Academia Partnerships and Pathways (grant no. EU324509 to A.S.); the Helsinki University Hospital fund (to A.Tiitinen); the Faculty of Medicine, University of Helsinki fund (to N.K.-A.); the EVA (Erfelijkheid Voortplanting & Aanleg) specialty program fund of Maastricht University Medical Centre (MUMC+) (to M.Z.E.); the Estonian Research Council (grant nos. IUT20-60 and IUT24-6); the European Union through the European Regional Development Fund Project (nos. 2014-2020.4.01.15-0012 GENTRANSMED and 2014-2020.4.01.16-0125 to R.M.); and KU Leuven funding (no. C1/018) and FWO grant (no. G.0392.14N to J.R.V. and T.Voet). We thank B. de Greef, A. van Montfoort and N. Davarzani for statistical consultations.
M.Z.E., J.R.V. and T.Voet are co-inventors on patent application ZL913096-PCT/EP2014/068315-WO/2015/028576, ‘Haplotyping and copy-number typing using polymorphic variant allelic frequencies’.
Peer review information Brett Benedetti was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
The mosaic partial trisomies (purple arrows) on Chr6, Chr9 and Chr21 are only present in one biopsy (Biopsy I) out of all the spatially different biopsies of P172 placenta.
Extended Data Fig. 3 The full Chr 2 mosaic trisomy is persistently present across the P106 placenta.
The full Chr 2 mosaic trisomy (purple arrows) is persistently present in all the spatially different biopsies of P106 placenta.
Extended Data Fig. 5 Determining fetal and maternal compartments in placenta DNA-samples using haplarithmisis.
We performed an in silico simulation by combining genotypes of the child and the mother with different proportions (from 1%Mother : 99%Child to 99%Mother : 1%Child) and deduced haplarithm profiles for each of these combinations, representing fetal and maternal compartments in placenta DNA samples (see also Source Data).
Extended Data Fig. 6 Proof-of-concept assay for the detection of mosaic aberrations using droplet digital PCR.
We mixed up a DNA sample from a trisomy 21 (copy number, CN=3) cell line with a DNA sample derived from a normal diploid cell line (CN=2) at different ratios, creating admixture series of DNA samples with 100%, 75%, 50%, 25%, 10–15% and 0% of abnormal alleles. Mosaic DNA samples were normalized to the number of fully diploid control (i.e. 0% abnormal). Each circle and error bar indicate mean and standard deviation, respectively, of four independent measurements.
About this article
Cite this article
Zamani Esteki, M., Viltrop, T., Tšuiko, O. et al. In vitro fertilization does not increase the incidence of de novo copy number alterations in fetal and placental lineages. Nat Med 25, 1699–1705 (2019). https://doi.org/10.1038/s41591-019-0620-2
This article is cited by
Nature Cell Biology (2021)
Nature Reviews Genetics (2020)