Experience analysing over 190, 000 embryo trophectoderm biopsies using a novel FAST-SeqS preimplantation genetic testing assay. Issue 2 (February 2022)

• Record Type: Journal Article
• Authors: Walters-Sen, Lauren; Neitzel, Dana; Bristow, Sara L.; Mitchell, Asia; Alouf, Charlene A.; Aradhya, Swaroop; Faulkner, Nicole
• Is Part Of: Reproductive biomedicine online. Volume 44:Issue 2(2022)
• Page Start: 228
• Page End: 238
• Publication Date: 2022-02
• Subjects: Aneuploidy -- Mosaicism -- PGT-A -- Ploidy -- Validation; Human reproductive technology -- Periodicals; Human embryo -- Periodicals; Reproduction -- Periodicals; 616.692
• DOI: 10.1016/j.rbmo.2021.06.022
• Languages: English
• ISSNs: 1472-6483

Abstract

HIGHLIGHTS: FAST-SeqS is an extensively validated, accurate, automated, and scalable PGT-A assay Observed aneuploidy rates in >190, 000 clinical samples are similar to other platforms FAST-SeqS combines the benefits of WGS-NGS and SNP-based PGT-A methods 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? 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 over 95% for all aneuploidy types tested in the validation. Comparison of FAST-SeqS with VeriSeq showed high concordance (98.5%). Among embryos with actionable results ( n = 182, 827), 46.2% were aneuploid. Whole-chromosome aneuploidies were most observed (72.9% without or 8.7% with a segmental aneuploidy), with rates increasing with egg age; segmental aneuploidy rates did not. Segmental aneuploidy ( n = 20, 557) was observed on all chromosomes (most commonly deletions), with frequencies associated with chromosome length. Mosaic-only abnormalities constituted 10.1% ( n = 3862/38145) of samples. Abnormal ploidy constituted 1.8% ( n = 2370/128, 991) of samples, triploidy being the most common (73.6%). Across 3297 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. Results suggest ongoing benefit of PGT-A using FAST-SeqS, consistent with other platforms.