O-210 Detection of small copy number variations as incidental findings in PGT-A: clinical utility from a multisite experience including 12,157 patients

Abstract Study question What is the technical accuracy and clinical utility of reporting small copy number variants (CNVs below 3Mb) detected by a targeted next-generation sequencing-based PGT-A platform? Summary answer Some pathogenic or likely CNVs <3Mb can be accurately this assay, increasing for subset IVF patients. known already are linked to wide range phenotypes, spanning from syndromes that include reduced penetrance variable expressivity more severe phenotypes. Prenatally, prevalence approximately 1.5%. Most platforms rely on whole genome amplification shallow sequencing have resolution limit 5-10 Mb, preventing detection smaller CNVs. Here, we report an innovative assay interrogates thousands sites in provide robust analysis allowing identification some (incidental findings, IF), outside primary scope detecting whole-chromosome aneuploidies PGT-A. design, size, duration Retrospective observational study performed between 2020-2022, involving 12,157 patients who underwent targeted-NGS (PGTseq-A) chromosome large segmental aneuploidies. If IF < 3 Mb was multiple embryos, couple advised undergo follow-up chromosomal microarray (CMA) confirm parental origin CNV, define its breakpoints determine whether it classified as benign-likely benign (B/LB), variant uncertain significance (VUS) pathogenic-likely (P/LP). Participants/materials, setting, methods The PGTseq-A employed amplifies 5,000 amplicons across evaluate number. Validation using 5-cell samples cell lines with CNVs, trophectoderm biopsies embryos structural rearrangements. An reported when gain/loss at least three consecutive appeared two same cycle. Transfer data reviewed which were transferred. This received IRB approval. Main results role chance In 77 out (0.63%;95%CI:0.5-0.8%), met criteria identified. To size pathogenicity, CMA follow up requested 67 couples. all cases, one partners confirmed CNV identified (100.0%: N 67/67 95%CI:94.6-100). maternal 36 cases (53.7%) paternal 31 (46.2%). A strong correlation PGT-A-predicted genomic coordinates defined DNA (r = 0.86). All intervals predicted included region. Twenty-seven (40.2%) B/LB, (46.2%) VUS, 9 (13.4%) P/LP. Six nine P/LP (66.6%) involved imbalances 16p. remaining deletions X, 15q 18p11.32. From review transfer data, typically transferred negative IFs first option regardless morphology pathogenicity classification CNV-positive sibling embryos. Specifically, 8 cycles where B, LB prioritized despite their poorer morphology. Limitations, reasons caution De novo not considered design because had present cohort. Furthermore, uniform predictive value non-targeted regions null. Wider implications findings detects without prior knowledge inheritance, enhancing Additionally, VUS B/LB may impact couples’ decision-making concerning embryo selection, reinforcing scientific rigor necessity evaluating capabilities Trial registration applicable