Studies of post-partum placentas provide insights into the origin of structural chromosomal aberrations

Can comprehensive cytogenetic follow-up of the placenta post-partum uncover possible explanations for discrepancies between non-invasive prenatal testing (NIPT) showing structural chromosomal aberrations and foetal follow-up showing normal results or other chromosomal aberrations?

In 18/31 (58%) cases of structural chromosomal aberrations detected with NIPT, where foetal and maternal follow-up was normal or the foetus had another chromosomal aberration, genome-wide examination of term placental chorionic villi confirmed the discrepancy and in 7/18 (39%) confirmed cases complex foeto-placental mosaicism was found.

Complex chromosomal rearrangements are often seen in single-cell studies of preimplantation embryos, but it is unknown if these persist into the mature placenta. Confined placental mosaicism explains most discordant NIPTs involving a trisomy, but little is known about structural chromosome aberrations.

We performed a retrospective diagnostic test study of cytogenetic follow-up data from post-partum placentas. We included data from pregnancies where (i) NIPT showed a structural aberration, (ii) follow-up of foetus (amniotic fluid and/or cord blood) and mother (genomic DNA and/or cfDNA after birth) was normal or the foetus showed another chromosomal aberration, (iii) follow-up was performed in the Erasmus MC, (iv) more than one sample from the post-partum placenta was analysed, and (v) samples were of good quality (not in formaldehyde, sufficient material).In the period from January 2014 to March 2022, 115 231 NIPTs were performed in the Erasmus MC; 217 of these showed structural chromosomal aberrations and 123 were followed up in the Erasmus MC (inclusion criteria 3). After exclusion of the foetal (same aberration as with NIPT) and maternal structural chromosome aberrations, 48 placentas were requested to elucidate the discrepancies seen between NIPT (abnormal) and foetal karyotype (normal or differently abnormal; inclusion criteria 1-2). Of these, 31 met criteria 4 and 5 and were included in this study.

In a diagnostic setting, we performed a cytogenetic analysis of postpartum placentas in order to confirm confined placental mosaicism in 31 cases in which NIPT showed a structural chromosome aberration. Two to four chorionic villus biopsies were taken per placenta, and separated enzymatically into cytotrophoblast (CTB) and mesenchymal core (MC) and analysed using SNP arrays. In our analysis, cases were assessed for copy number variants ≥0.5 Mb and regions of homozygosity ≥3 Mb.

In 18/31 cases (58%), we could confirm the structural chromosome aberration detected with NIPT in one or more placental biopsies. In 13/31 cases (42%), the structural chromosomal aberration detected with NIPT was not confirmed, but in one case an apparently unrelated aberration was found in the CTB of two biopsies. In 11/18 confirmed cases, the same aberration as detected with NIPT, was confirmed in the placenta. All these cases concerned chromosomally normal foetuses with a chromosome aberration confined to the placenta. In one case, an extra, apparently unrelated, aberration was found in one placental biopsy. In 7/18 confirmed cases, the aberration detected with NIPT was confirmed in the placenta and showed to be involved in complex mosaicism involving different abnormal cell lines. In four of these seven cases, the foetus was affected with a pathogenic chromosome aberration that was different from the NIPT aberration. In three cases, a related but benign chromosome aberration was present in the foetus.

As conventional karyotyping, FISH or whole genome sequencing were not performed, we can only hypothesize on the mechanisms behind the origin of the complex foeto-placental mosaicism we see in seven cases, although there is more strong evidence in the literature as well.

Our results have several implications. First, a genome-wide rather than a targeted approach in foetal follow-up examinations after NIPT showing a structural chromosomal aberration is warranted, as other aberrations may be overlooked in the foetus. Second, counselling of pregnant couples after NIPT showing a structural chromosomal aberration should focus not only on the specific aberration detected by NIPT but also on the possibility that the foetus may harbour another, possibly related, structural aberration. Additionally, a structural chromosomal aberration of apparently uncertain significance may unmask truly pathogenic aberrations in the foetus itself, so all potential foetal cases of structural chromosome aberrations should be followed up. Third, we show how comprehensive examinations of the placenta, specifically the separation of CTB and MC, provides crucial insights into the embryonic origins and mechanisms behind structural chromosomal aberrations. Lastly, our results show that complex chromosomal rearrangements as often seen in single-cell studies of pre-implantation embryos, are not artefacts but a biological phenomenon that can actually persist into the mature placenta and foetus.

Simon H. Thomsen was funded by a private research donation and the Department of Clinical Medicine, Aarhus University. All authors declare no conflict of interest.

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