Application of Whole-Genome Technologies to Assisted Reproductive Treatment

Preimplantation genetic testing (PGT) allows the detection of genetic abnormalities in biopsies that comprise 1–10 cells from preimplantation embryos and is performed to avoid the transmission of inherited and de novo genetic abnormalities to the offspring (Figure 2.1) (see Chapter 13). The minute amount of genomic DNA in a single cell represented a challenge for whole-genome profiling of embryo biopsies on development of PGT in the 1990s because whole-genome analysis technologies required micrograms of input DNA. Before the adaptation of these technologies to single-cell input by whole-genome amplification (WGA) methods, PGT was performed using targeted approaches according to the couple’s indication [1] (Table 2.1). For instance, fluorescence in situ hybridization (FISH) was used to detect unbalanced karyotypes in the embryos from balanced translocation carriers or from couples with recurrent miscarriage or implantation failure. In case of Mendelian disorders, embryo biopsies were subjected to multiplex polymerase chain reaction (PCR) of the risk allele(s) together with several cosegregating polymorphic markers. These targeted approaches were developed for each family specifically, rendering them labor-intensive, costly, and time-consuming. Moreover, some mutations (e.g. a priori unknown small deletions and duplications or complex chromosomal rearrangements) were practically impossible to diagnose using these strategies. The development of WGA technologies in the early 2000s, their application in genomic array technologies thereafter, and the decrease in cost of next generation sequencing (NGS) helped to overcome these limitations and enabled whole-genome profiling of single cells. Furthermore, the improvements in embryo culture made trophectoderm (TE) biopsy possible at the blastocyst stage, enabling 5–10 cells to be biopsied and tested. Besides increasing the diagnostic accuracy, this allowed for the detection of the mosaic status of genetic variants genome-wide [1]. In parallel, the advancement of embryo cryopreservation techniques expanded the time frame required for embryo diagnosis and therefore also contributed to the development and application of new PGT technologies and data analysis.