Results From Study Co-Led by Reprogenetics, Complete Genomics, BGI and New York University Fertility Center Published in Genome Research; Significant Advancement in Preimplantation Genetic Diagnosis
Reprogenetics, the largest U.S. genetics laboratory specializing in Preimplantation Genetic Diagnosis (PGD), announced today 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 containing 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 addition to Reprogenetics, researchers from Complete Genomics, a leader in accurate whole human genomic sequencing, BGI-Shenzhen ("BGI"), a leading international genomics organization based in Shenzhen, China, and the New York University (NYU) Fertility Center at the NYU Langone Medical Center collaborated on the study.
"These findings are a significant step in developing advanced whole-genome sequencing as the 'ultimate' screen to find the healthiest embryos through PGD," says Santiago Munné, Ph.D., Founder and Director of Reprogenetics and Founder of Recombine. "This new approach can detect almost all genome variation, which may eliminate the need for further genetic testing during pregnancy or after birth while ensuring selection of the healthiest embryo for transfer to the future mother."
In the study, advanced massively parallel WGS was performed on three 5-10 cell biopsies from embryos cultured for five days in the laboratory. Experimentally derived haplotypes and barcoded read data were used to detect and phase de novo single base mutations in the embryos, achieving a false positive rate of approximately one error per Giga base, that is calling erroneously a mutation in one out of one billion letters, and resulting in fewer than 10 errors per embryo. The data show an approximately 100-fold lower error rate than previously published from 10 cells, and is the first demonstration that advanced WGS can accurately identify de novo mutations despite numerous additional mutations associated with the extensive DNA amplification required for deep sequencing.
"That de novo mutations can be detected with such high sensitivity and an exceptionally low error rate using so few embryonic cells is remarkable," says Brock Peters, Ph.D., Director, Research at Complete Genomics and the study's lead investigator. "Combining massively parallel DNA sequencing with barcoded sequence analysis obtained through our long fragment read technology provides an extremely efficient and cost-effective solution for clinically accurate WGS, and we look forward to continuing our research efforts in this area."
De novo mutations, including single nucleotide and short indel mutations, may cause severe intellectual disability, autism, epileptic encephalopathies and other serious congenital diseases. Since these mutations are unique to the specific sperm and egg that create an embryo, whole genome analysis of the parents is unable to detect them.
"Up to five percent of newborns are affected by diseases caused by a genetic defect," says Alan Berkeley, M.D., Professor and Director, Department of Obstetrics and Gynecology at the New York University Fertility Center. "Our WGS approach is both comprehensive and targeted in identifying healthy embryos. This may alleviate some of the emotional and physical stress of IVF, especially for those couples at risk of transmitting a genetic disorder."