P-538 Liquid biopsy (niPOC) as a new approach to genetic studies in early pregnancy loss. First clinical experience in Spain

Abstract

Abstract Study question How accurate is the use of liquid biopsy as a new tool for aneuploidy testing in cases of pregnancy losses? Summary answer This study demonstrates that genome-wide cfDNA testing in the maternal bloodstream (niPOC) constitutes a simple, tissue-independent, straightforward and reliable complement/alternative to traditional POC analysis. What is known already Around 50-70% of clinical miscarriages are caused by aneuploidies, mostly trisomies. To date, conventional cytogenetic and advanced molecular techniques are used for the analysis of POC to identify the genetic cause of miscarriage, providing valuable information for genetic counseling. However, both approaches are based in the direct analysis of the abortive tissue, which entails several limitations due to a risk of culture failure and/or maternal cell contamination. To solve these drawbacks, maternal cell-free DNA (cfDNA) testing emerges as a promising alternative due to the accumulated evidence. Study design, size, duration Retrospective study and first clinical experience, both conducted in our facilities from January 2021 to December 2023. Before carrying out the fetal tissues collection for the POC analysis, a blood sample was drawn to evaluate possible aneuploidies by cfDNA testing. Using NGS+STR POC results as the gold standard, results derived from both studies were compared to assess the percentage of concordance and the cases of non-informativeness (fetal fraction (FF) <2%), false positives, and false negatives. Participants/materials, setting, methods Herein we present a clinical validation (n = 152) and the first clinical experience (n = 103). Maternal peripheral blood samples were extracted for aneuploidy evaluation using Illumina’s sequencing platform. Genetic testing on POCs was performed using NGS (Thermo Fisher Scientific) to detect aneuploidies, and short tandem repeats to detect cases with MCC and/or polyploidy. In both groups (niPOC and POC), the percentage of concordance and cases of non-informativeness (by fetal fraction <2%, or CCM) were evaluated. Main results and the role of chance In the validation set, no significant differences in non-informativity were observed between POC and niPOC [9.2% (14/152) vs 13.8% (21/152)]. Excluding triploids, the sensitivity of niPOC compared with the pregnancy tissue sequencing result was 90.1%, specificity of 97.1% and an accuracy of 88%. In the first clinical experience, non-informativity was similar to that found in the validation (17/103, 16.5%). The percentage of abnormal cases was 43%, very close to the 50% expected according to the scientific literature. Regarding turnaround time, reports in niPOC were released in an average of 3.8 working days. Limitations, reasons for caution Current cfDNA testing technology fails in polyploidy, uniparental disomy identification, which is a potential cause of pregnancy loss. Aneuploidy detection is only feasible if the blood collection was performed before the fetal remains evacuation. Wider implications of the findings CfDNA testing before curettage or pharmacological treatment could be an alternative to POC analysis. If optimized, cfDNA testing could be used contingently with the molecular POC analysis in cases where maternal cell contamination is present. As a result, the overall success rate in the POC program could be substantially improved. Trial registration number Not applicable