The Assessment of Methods for Preimplantation Genetic Testing for Aneuploidies Using a Universal Parameter: Implications for Costs and Mosaicism Detection

Author(s): Alexander Belyaev, Maria Tofilo, Sergey Popov, Ilya Mazunin, Dmitry Fomin

Preimplantation genetic testing for aneuploidies (PGT-A) is used to increase live birth rates following in vitro fertilization. The assessment of different PGT-A methods to date has relied on non-universal parameters, e.g., sensitivity and specificity, that are individually stipulated for each study and typically performed using arbitrarily selected cell lines. Here we present an alternative approach that is based on an assessment of the median noise in a large dataset of routine clinical samples. Raw sequencing data obtained during PGT-A testing of 973 trophectoderm biopsies was used for comparison of two methods: VeriSeq PGS (Illumina) and AB-PGT (AB Vector). Three times less median noise was a feature of the AB-PGT method, thereby allowing the number of multiplexed samples per sequencing run to be increased from 24 with VeriSeq PGS to 72 with AB-PGT, thus effectively reducing the price per sample without compromising data quality. The improvement is attributed to a novel SuperDOP whole genome amplification technology combined with a simplified PGT-A protocol. We show that the median noise level associated with a large dataset of biopsies is a simple, universal metric for the assessment of PGT-A methods, which has implications for other screening methods, the detection of mosaicisms, and the improvement of fertility clinics’ practices.