Mosaicism much more common than previously thought, using more sensitive PGT-A technique

Researchers in a 2024 study used a single-cell sequencing approach and found that mosaicism was detected in 82% of blastocysts, much higher than what’s been previously reported with less sensitive techniques in PGT-A.

PGT-A is used to determine whether an embryo is euploid or not, based on the sequencing of DNA from approximately 5-10 cells of the embryo biopsy.

Embryos with both euploid and aneuploid cells are called mosaic. However, determining the true incidence of mosaicism is difficult, because the small number of cells biopsied may not be representative of the whole embryo.

Chavli et al. (2024) separated all the cells from a single embryo for DNA sequencing, using a technique called single-cell whole genome sequencing or ScKaryo-seq.

For this study, I suggest you check out my post on mosaic embryos for more background, particularly the explanation on what a low/high level mosaic is.

⚠️ Remembryo summarizes and interprets IVF research for educational purposes. Posts highlight selected findings and may simplify or omit study details, including methods, analyses, author interpretations, limitations, and protocol specifics (such as timing, dosing, or eligibility criteria). These summaries are not a substitute for the original study. Always review the full publication before treatment decisions.

🔗 Original studies are referenced in this post or within the linked Remembryo posts.

💡 Reminder: Terms underlined with a dotted black line are linked to glossary entries. Clicking these does not count toward your paywall limit.

In this study, they used 79 good quality blastocysts. The ICM and trophectoderm were separated, and these structures were disaggregated using an enzyme solution to get single cells.

Most blastocysts are mosaic

After processing, there were 55 embryos available with variable numbers of single cells collected that could be DNA sequenced. Not all the embryos had all their cells separated (on average, only 42% of cells could be analyzed per embryo).

11% had normal cells (euploid).
7% had the same abnormal chromosome (aneuploid).
82% were mosaic (45 of 55 embryos). Note that this includes embryos that were either euploid with mosaicism (32 of 45) or aneuploid with mosaicism (13 of 45).

Of the euploid-mosaic embryos, there were on average 60% euploid cells. Nearly 70% of mosaics had more than one type of mosaic error.

Proportion of aneuploid cells in ICM and trophectoderm are similar

Since they separated the ICM and trophectoderm, they were able to look for differences between these cells. Generally, aneuploid cells didn’t preferentially accumulate in the ICM or trophectoderm, although complex aneuploidies were more common in the trophectoderm, which is in line with previous studies.

They found that 54% of the mosaics had errors that were in both the ICM and trophectoderm (and 46% that didn’t).

This shows that mosaics had 54% of their abnormalities shared between the ICM and trophectoderm (TE), while the other 46% was restricted to either the ICM or TE. Chavli et al. (2024), CC by 4.0.

Mock PGT-A grossly underestimates mosaic abnormalities

In another analysis, the researchers mimicked what the results would be if standard PGT-A was done using a trophectoderm biopsy. For this, they only considered 41 mosaics that had aneuploid cells in the trophectoderm.

They wanted to see how many mosaic abnormalities would be excluded with a cutoff of 20%**. They also took into account reciprocal events cancelling out, where one cell could have made a mistake in separating a chromosome during division, such that the daughter cells have either an extra chromosome or a missing chromosome.

**Remember, with current PGT-A you can’t detect a mosaic that has <20% aneuploid cells. That’s why a mosaic with <20% aneuploid cells is considered euploid, and >80% is considered aneuploid. For more info, check this post.

In this analysis, only 20% of the mosaic abnormalities would have been detected (and 80% would have been missed).

Conclusions

This study found that 82% of good quality embryos were mosaic after single cell sequencing, which is higher than what was previously reported using standard PGT-A (~2-40%, see here).

The researchers note that the incidence of mosaicism is likely even higher than this, since they weren’t able to sequence every cell from the embryos in this study.

When they used this data in a mock PGT-A cycle, they found that 80% of mosaic abnormalities would have been missed by standard PGT-A that was detected with single cell sequencing.

It’s important to point out that we can’t use single cell sequencing to do PGT-A — it requires that DNA is extracted from each cell in the embryo, which kills all the cells in the process.

The point of this study isn’t to develop a new way to do PGT-A, but to see how common mosaicism is using a very sensitive single cell sequencing test. Right now, standard PGT-A doesn’t measure mosaics with <20% aneuploid cells. This study is showing that these mosaics exist, and implies that all embryos have mosaicism to some degree.

Our results lend strong support to the notion that mosaicism is a common feature of early human development.
Chavli et al. (2024)

This might help explain why some euploid embryos fail after transfer. It’s possible that very low levels of mosaicism aren’t detectable by standard PGT-A (among other possibilities). These cells might somehow increase in number, or position themselves where they compromise embryo/fetal development.

The implications of this study shouldn’t discourage people from PGT-A. Embryos with low levels of mosaicism are comparable to euploids by some studies, while those with higher levels have reduced outcomes. PGT-A is a useful tool for selecting embryos, particularly for older patients.

Limitations of this study include the small sample size and the fact that only good quality embryos were used.

Other research has been done that looks at single cell data for PGT-A, which also suggests that most blastocysts are mosaic. You can check out those studies below.

Related studies

There were a number of studies referenced that you might want to check out, as shown below (2 links):

Reference

Chavli EA, Klaasen SJ, Van Opstal D, Laven JS, Kops GJ, Baart EB. Single-cell DNA sequencing reveals a high incidence of chromosomal abnormalities in human blastocysts. J Clin Invest. 2024 Jan 4:e174483. doi: 10.1172/JCI174483. Epub ahead of print. PMID: 38175717.

If you liked this post and want to support what I do, please consider a paid subscription, Patreon or donate through PayPal!

About Embryoman

Embryoman (Sean Lauber) is a former embryologist and the founder of Remembryo, an IVF research and fertility education website. After working in an IVF lab in the US, he returned to Canada and now focuses on making fertility research more accessible. He holds a Master’s in Immunology and launched Remembryo in 2018 to help patients and professionals make sense of IVF research. Sean shares weekly study updates on Facebook, Instagram, and Reddit regularly. He also answers questions on Reddit or in his private Facebook group.