Detection and Occurrence of Nine Recurrent Microdeletion Syndromes Using High Resolution PGT-A.

Objective: The primary objective of this study was to evaluate the accuracy, sensitivity and specificity of a PGT-A platform incorporating detection of nine del/dup disorders (based on occurrence and severity). A secondary objective was to survey the frequency of syndromic occurrence in a large cohort of preimplantation embryos. Design: A preliminary group of 300 samples with confirmed del/dup disorders was analyzed to determine SNP density and resolution and estimate sensitivity and specificity. A second cohort of 6000 de-identified preimplantation embryos was used to assess the baseline detection rate. A larger retrospective study of 10,000 preimplantation embryos will be reported. Materials and Methods: De-identified trophectoderm biopsies were processed using primary template-directed amplification, target enriched and prepared for next-generation sequencing. A bioinformatics pipeline was applied to identify del/dup region-specific CNV through allelic balance analysis. Cell lines and clinical samples with confirmed deletions and duplications were used to develop and verify the method. Results: In the control group, an initial accuracy estimate for del/dup-specific detection was 97-99% with sensitivity and specificity ranging from 82-96% and 92-99%, respectively. Occurrence rates in the limited clinical cohort varied between 1-2x the reported live birth prevalence. A larger preimplantation cohort is being re-analyzed, leveraging orthogonal multiplex ligation-dependent probe amplification (MLPA) or medium-depth whole genome sequencing to confirm the presence or absence of del/dups. Conclusions: This study confirms the utility of a high-resolution PGT-A method to accurately detect segmental del/dups that underly syndromic disorders. Results indicate an elevated preimplantation occurrence rate above that seen in live birth. Overall, PGT-A with del/dup detection could deliver more complete results to further inform embryo transfer decisions. Support: Funded provided by CooperSurgical.