Assessing the efficacy of targeted enrichment protocol in PGT-M applications: a comprehensive analysis

Abstract

PurposeThe aim of this study is to assess whether the Targeted Sequence Enrichment (TSE) protocol improves the efficiency of Preimplantation Genetic Testing for Monogenic Diseases (PGT-M) by reducing allele dropout (ADO) rates.MethodsThis retrospective data analysis included 928 patients and compared ADO rates across three different PGT-M approaches: (1) conventional targeted STR-based Single Cell Multiplex Nested PCR (PGT-M_Only), (2) Whole Genome Amplification (WGA)-based PGT-M method used in combined applications (WGA + PGT-M), and (3) WGA-bas.ed TSE method implemented for combined PGT-M applications. While the majority of cases involved single-gene disorders, some cases included testing for two, three, or four genes.MethodsThis retrospective data analysis included 928 patients and compared ADO rates across three different PGT-M approaches: (1) conventional targeted STR-based Single Cell Multiplex Nested PCR (PGT-M_Only), (2) Whole Genome Amplification (WGA)-based PGT-M method used in combined applications (WGA + PGT-M), and (3) WGA-bas.ed TSE method implemented for combined PGT-M applications. While the majority of cases involved single-gene disorders, some cases included testing for two, three, or four genes.ResultsADO rates were comparable between the TSE group and the PGT-M_Only group (1.01% and 0.80%, respectively). However, the conventional WGA-based PGT-M approach, lacking targeted enrichment, exhibited a significantly higher ADO rate of 4.76%, approximately five times greater. The complexity of the test, in terms of the number of genes analyzed per case, did not significantly influence ADO rates.ConclusionConventional WGA-based PGT-M methods using STR markers are associated with substantially higher ADO rates compared to the STR-based method with direct PCR from lysed single cells. The TSE protocol significantly reduces ADO, increases test sensitivity, and allows for simultaneous PGT-A and PGT-M analysis from a single WGA sample.