Preimplantation genetic testing for aneuploidy (PGT‐A) reduces miscarriage risk, increases the success of IVF, shortens time to pregnancy, and reduces multiple gestation rates without compromising outcomes. The progression of PGT‐A has included common application of next‐generation sequencing (NGS) from single nucleotide polymorphism microarray, quantitative real‐time PCR, and array comparative hybridization platforms of analysis. Additional putative advances in PGT‐A capability include classifying embryos as mosaic and predicting the presence of segmental imbalance. A critical component in the process of technical validation of these advancements involves evaluation of concordance between reanalysis results and initial testing results. While many independent studies have investigated the concordance of results obtained from the remaining embryo with the original PGT‐A diagnosis, compilation and systematic analysis of published data has not been performed. Here, we review results from 26 primary research articles describing concordance in 1271 human blastocysts from 2260 pairwise comparisons. Results illustrate significantly higher discordance from PGT‐A methods which utilize NGS and include prediction of mosaicism or segmental imbalance. These results suggest caution when considering new iterations PGT‐A.

Preimplantation genetic testing for polygenic disease risk (PGT-P) represents a new tool to aid in embryo selection. Previous studies demonstrated the ability to obtain necessary genotypes in the embryo with accuracy equivalent to in adults. When applied to select adult siblings with known type I diabetes status, a reduction in disease incidence of 45–72% compared to random selection was achieved. This study extends analysis to 11,883 sibling pairs to evaluate clinical utility of embryo selection with PGT-P. Results demonstrate simultaneous relative risk reduction of all diseases tested in parallel, which included diabetes, cancer, and heart disease, and indicate applicability beyond patients with a known family history of disease.

To validate the detection of abnormal ploidy in preimplantation embryos and evaluate its frequency in transferrable blastocysts. A high-throughput genome-wide single nucleotide polymorphism microarray-based preimplantation genetic testing (PGT) platform was validated using multiple positive controls, including cell lines of known haploid and triploid karyotypes and rebiopsies of embryos with initial abnormal ploidy results. This platform was then tested on all trophectoderm biopsies in a single PGT laboratory to calculate the frequency of abnormal ploidy and the parental and cell division origins of error. Preimplantation genetic testing laboratory. The embryos from in vitro fertilization patients who elected for PGT were evaluated. Any patients who provided saliva samples were further analyzed for the parental and cell division origins of abnormal ploidy. None. Evaluable positive controls showed 100% concordance with original karyotypes. The overall frequency of abnormal ploidy within a single PGT laboratory cohort was 1.43%. All cell lines showed 100% concordance with the expected karyotype. Additionally, all evaluable rebiopsies showed 100% concordance with the original abnormal ploidy karyotype. The frequency of abnormal ploidy was 1.43%, with 29% of those being haploid or uniparental isodiploid, 2.5% uniparental heterodiploid, 68% triploid, and 0.4% tetraploid. Twelve haploid embryos contained maternal deoxyribonucleic acid, and 3 contained paternal deoxyribonucleic acid. Thirty-four triploid embryos were of maternal origin, and 2 were of paternal origin. Thirty-five triploid embryos had a meiotic origin of error, and 1 was of mitotic error. Of those 35 embryos, 5 originated from meiosis I, 22 originated from meiosis II, and 8 were deemed inconclusive. On the basis of specific abnormal ploidy karyotypes, 41.2% of embryos would be falsely classified as euploid, and 22.7% would be false-positive mosaics with the use of the conventional next-generation sequencing-based PGT methods. This study demonstrates the validity of a high-throughput genome-wide single nucleotide polymorphism microarray-based PGT platform to accurately detect abnormal ploidy karyotypes and predict the parental and cell division origins of error of evaluable embryos. This unique method improves the sensitivity of detection for abnormal karyotypes, which can reduce the chances of adverse pregnancy outcomes.

Purpose: This study aimed to evaluate whether a high-throughput high-resolution PGT-A method can detect copy number variants (CNVs) that could have clinical implications for patients and their embryos. Methods: A prospective analysis of PGT-A cases was conducted using a high-resolution SNP microarray platform with over 820,000 probes. Cases where multiple embryos possessed the same segmental imbalance were identified, and preliminary PGT-A reports were issued recommending either parental microarray or conventional karyotyping to identify CNVs or translocations. Results: Analysis of 6080 sequential PGT-A cases led to identification of 41 cases in which incidental findings were observed (0.7%) and parental testing was recommended. All cases, in which parental studies were completed, confirmed the original PGT-A incidental findings. In 2 of the cases, parental studies indicated a pathogenic variant with clinical implications for the associated embryos. In one of these cases, the patient was identified as a carrier of a duplication in chromosome 15q11.2:q11.2 (SNRPN + +), which is associated with autism spectrum disorder. In the second case, the patient was heterozygous positive for an interstitial deletion of 3p26.1:p26.3, which is associated with 3p deletion syndrome and had clinical implications for the patient and associated embryos. In each case, parental studies were concordant with PGT-A findings and revealed the presence of an otherwise unknown CNV. Conclusion: High-throughput high-resolution SNP array–based PGT-A has the ability to detect previously unknown and clinically significant parental deletions, duplications, and translocations. The use of cost-effective SNP array–based PGT-A methods may improve the effectiveness of PGT by identifying and preventing previously unknown pathogenic CNVs in children born to patients seeking in vitro fertilization.

Summary paragraph: Genome editing by DNA double-strand breaks (DSB) is currently being investigated as a tool to treat or even prevent heritable diseases ¹ . However, DNA repair mechanisms in the human embryo remain poorly understood and DSBs may result in chromosome loss ^2,3 . Here we provide evidence of whole and segmental chromosome loss in over one third of chromosomes 16, 17 and X targeted by CRISPR/Cas9-induced DNA DSB, including pericentromeric and mid-arm sites. Chromosomal changes were asymmetric relative to the Cas9 cut site: segmental losses occurred on both centric as well as acentric chromosome arms, while gains were exclusively found on acentric arms, suggesting that centromeres in broken chromosomes continued to mediate sister chromatid separation. Using this pattern of chromosomal errors, we were able to define new genomic coordinates of the active centromere on chromosome 16. Asymmetry was also found in the attrition of gDNA at the break site: attrition occurred centromeric of the DSB, while telomeric to the break, chromosomal ends were protected. Thus, spindle forces at centromeres and end tethering and protection at DSBs are antagonistic forces that interfere with accurate segregation of sister chromatids. Thereby, a single DSB is sufficient to result in the loss of a chromosome from the embryo. These results highlight the risks of aneuploidy in CRISPR/Cas9 genome editing, while also providing a mechanism for mitotically acquired aneuploidy caused by DNA breaks in human embryos.