Establishing an RNA-based diagnostic in IVF

The majority of embryos created through in vitro fertilization (IVF) do not implant. It seems plausible that rates of implantation would improve if we had a better understanding of molecular factors affecting embryo competence. Currently, the process of selecting an embryo for uterine transfer uses an ad hoc combination of morphological criteria, the kinetics of development, and genetic testing for aneuploidy. However, no single criterion can ensure selection of a viable embryo. In contrast, RNA-sequencing (RNA-seq) of embryos could yield high-dimensional data, which may provide additional insight and illuminate the discrepancies among current selection criteria. Recent advances enabling the production of RNA-seq libraries from single cells have facilitated the application of this technique to the study of transcriptional events in early human development. However, these studies have not assessed the quality of their constituent embryos relative to commonly used embryological criteria.

Harvard University researchers performed proof-of-principle advancement to embryo selection procedures by generating RNA-seq libraries from a trophectoderm biopsy as well as the remaining whole embryo. They combined state-of-the-art embryological methods with low-input RNA-seq to develop the first transcriptome-wide approach for assessing embryo competence. Specifically, the researchers show the capacity of RNA-seq as a promising tool in preimplantation screening by showing that biopsies of an embryo can capture valuable information available in the whole embryo from which they are derived. Furthermore, we show that this technique can be used to generate a RNA-based digital karyotype and to identify candidate competence-associated genes. Together, these data establish the foundation for a future RNA-based diagnostic in IVF.

Experimental overview


(A) Preimplantation human development time-course depicting our comparative analytical approach. Samples were processed from blastocyst stage embryos and assessed for morphokinetic criteria and morphology before biopsy. One trophectoderm (TE) biopsy was processed for DNA-based preimplantation genetic testing for aneuploidy (PGT-A), one was harvested for RNA-seq, and the remaining whole embryo (WE) was also processed for RNA-seq. (B) Representative image of a blastocyst. (C) Data overview table. Embryos (E1-39) for which we have morphokinetic data are shaded in green; those forwhich DNA-based PGT-A yielded a result are depicted in blue; and those for which we have RNA-seq of either WE or TE biopsy are labeled in black and gray, respectively.

Groff AF, Resetkova N, DiDomenico F, Sakkas D, Penzias A, Rinn JL, Eggan K. (2019) RNA-seq as a tool for evaluating human embryo competence. Genome Res [Epub ahead of print]. [abstract]

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