Experience analyzing >190,000 embryo trophectoderm biopsies using a novel FAST-SeqS PGT assay

ABSTRACT Research Question Is FAST-SeqS an accurate methodology for preimplantation genetic testing for whole-chromosome aneuploidy (PGT-A), what additional types of chromosomal abnormalities can be assessed, and what are the observed aneuploidy rates in a large clinical cohort? Design FAST-SeqS, a next-generation sequencing- (NGS-) based assay amplifying genome-wide LINE1 repetitive sequences, was validated using reference samples. Sensitivity and specificity were calculated. Clinically-derived trophectoderm biopsies submitted for PGT-A were assessed, and aneuploidy and mosaicism rates among biopsies were determined. Clinician-provided outcome rates were calculated. Results Sensitivity and specificity were >95% for all aneuploidy types tested in the validation. Comparison of FAST-SeqS to VeriSeq showed high concordance (98.5%). Among embryos with actionable results (n=182,827), 46.2% were aneuploid. Whole-chromosome aneuploidies were most commonly observed (72.9% without or 8.7% with a segmental aneuploidy [SA]), with rates increasing with egg age, while SA rates did not. SAs (n=20,557) were observed on all chromosomes (most commonly deletions), with frequencies roughly correlated with chromosome length. Mosaic-only abnormalities constituted 10.1% (n=3,862/38,145) of samples. Abnormal ploidy constituted 1.8% (n=2,370/128,991) of samples, triploidy being the most common (73.6%). Across 3,297 frozen embryo transfers, the mean clinical pregnancy rate was 62% (range 38-80%); the mean combined ongoing pregnancy and live birth rate was 57% (range 38-72%). Conclusion FAST-SeqS is a clinically reliable and scalable method for PGT-A, is comparable to whole genome amplification-based platforms, and detects additional information related to ploidy using SNP analysis. Clinical outcomes suggest an ongoing benefit of PGT-A using FAST-SeqS, consistent with other platforms.