Published data: Mutations detected via whole genome sequencing for IVF

Reprogenetics, a genetics laboratory specializing in Preimplantation Genetic Diagnosis (PGD), recently announced the publication of new clinical data in the March issue of Genome Research demonstrating that de novo single base mutations can be detected in embryos after in vitro fertilization (IVF). Small biopsies contain about ten cells from the embryos showed clinically relevant sensitivity and specificity using a novel advanced whole-genome sequencing (WGS) screening process.

The study is the first to show that a large majority of single base de novo mutations, which cause a disproportionately high percentage of genetic diseases, can be detected by PGD. De novo mutations only occur in reproductive cells and in embryos after fertilization. Typically these mutations are not present in the blood of the parents and will be missed, even by a comprehensive carrier screening of the parents. Standard PGD cannot detect these mutations because the tests are not sensitive enough or only look at very specific regions of the genome.

In the study, entitled “Complete and Accurate WGS on IVF Embryos,” both parents and paternal grandparents were also analyzed to allow for accurate measurements of false positive and false negative error rates. Overall, more than 95 percent of each embryonic genome was called, starting with approximately 10 cells (as few as approximately 60pg of DNA). Data also demonstrated how small de novo deletions could be detected. These results suggest that WGS using barcoded DNA has high potential as part of the PGD process to maximize comprehensiveness in detecting disease-causing mutations and may ultimately reduce the incidence of genetic diseases detected via PGD. In addition, the data open possibilities for clinical analysis of circulating fetal cells (CFC), circulating tumor cells (CTC) and other micro-biopsies in addition to IVF embryo biopsies. This may have application in non-invasive cancer screening.

To demonstrate the potential of WGS to analyze embryo biopsies, three sequencing libraries were made from biopsies of up to 10 cells from two individual 5-day-old blastocyst stage embryos from the same couple. For the purpose of de novo mutation validation, two separate biopsies were removed and two separate libraries were made from a single embryo. As a control, three additional libraries were made from approximately 10 blood cells from unrelated anonymous donors.