Array CGH and Partial Genome Sequencing for Rapidly Karyotyping IVF Blastocysts Before Single Transfer

The relatively high levels of aneuploidy identified in IVF embryos recently have raised the opportunity to improve pregnancy rates and liveborn outcomes with IVF by identifying and transferring only one chromosomally balanced embryo. With the increased use of CGH, it has been observed that any of the chromosomes can be involved in aneuploidy and even de novo segmental aneuploidies may contribute to implantation failure and miscarriage in a typical IVF cycle. The previous limitations in FISH complexity had meant that the full benefits of aneuploidy screening were not initially realised. The impact of reliable whole chromosome amplification methods and the availability of quality controlled commercial microarrays has seen strong uptake of total chromosome screening by many clinics around the world with substantial changes in implantation rates for the selected embryos reported in most cases. In spite of these benefits, the cost of the aCGH process appears to have limited the availability for a significant number of patients. The price of arrays has reduced in the last few years, but this remains a substantial cost burden in many situations. An alternative approach that can still meet the criteria of total chromosome screening but is potentially more cost-effective could bring the benefits of total chromosome screening to an even wider patient group. Partial genome sequencing (PGS) or low-pass sequencing is one alternative that can be used to rapidly karyotype whole-genome-amplified samples from human blastocysts. We compared these with array-based comparative genomic hybridization (aCGH) karyotypes. Readily available open-source software was customised and then used to map the individual Next Generation Sequencing (NGS) reads to chromosomes providing considerable flexibility for resolving both total chromosomes as well as segmental variations. Qualitatively, there was complete diagnostic agreement between the two approaches. Quantitatively, the sequencing approach also offered simple implementation of objective measures of levels of mosaicism within the multi-cell trophectoderm biopsy piece aiding final decision-making regarding suitability for transfer of the nominated (single) embryo. Depending on individual laboratory capabilities, either technique can have shortened protocols that enable next day transfer of one euploid embryo. Standard protocols for aCGH or PGS can fit timing wise with cleavage stage biopsy. Embryos biopsied on day 5 of cycle will only be transferrable the next day, while slower developing embryos biopsied on day 6 may need to be frozen and transferred at a later time. While reports of day 3 blastomere biopsy show improved pregnancy rates after screening, the final outcomes do not appear to be as good as blastocyst stage biopsy, thus not realising the full potential of screening. Applied correctly, simplified, cost-effective routine aneuploidy analysis via aCGH or NGS promises high live birth rates per single transferred embryo.