The application of the molecular work-up based on the stepwise use of QF-PCR and SNP array in pregnancy losses

Abstract

Objective: The evaluation of Quantitative Fluorescence PCR (QF-PCR) and single nucleotide polymorphism array (SNP array) analysis for the identification of chromosomal abnormalities in the products of conception (POC).

Material and Methods: A total of 1094 POC samples were processed at Gennet between 2018 and 2020. Chromosomal aneuploidies were tested by QF-PCR using Multibor set (STR markers 13, 18, 21, X a Y), SAB-I set (STR markers 2, 7, 15, 16, 22), SAB-II set (from November 2019, STR markers 4, 6, 14) followed by SNP array analysis (Illumina) on samples with negative QF-PCR result. All POC samples were tested for maternal contamination.

Results: After exclusion of maternal contamination (30.6% samples) the total number of 742 POC samples were tested by QF-PCR. Chromosomal aneuploidies were found in 273 POC samples (36.8%). 469 QF-PCR negative POC samples were tested by SNP array analysis. Normal female/male profile was confirmed in 402 samples (85,7%) and chromosomal aneuploidies and chromosomal aberrations (deletion/duplication > 10 Mb) in 51 samples (10.9 %). Microdeletion/microduplication was found in 16 POC samples (3.4%), two were classified as pathogenic variants and 14 as variants of unknown significance. In a group of women >35years statistically significant increase of chromosomal abnormalities was confirmed. No statistically significant difference between the IVF group and the group of spontaneous conception was found.

Conclusion: The application of the molecular workup based on the stepwise use of QF-PCR and SNP array clarifies the cause of the abortion in 43% POC samples. The overall detection rate in I. trimester was 50.4%.