Spontaneous pregnancy loss occurs in approximately 1 in 4 pregnancies; however, diagnostic workup is mostly restricted to women with recurrent pregnancy loss. The lack of workup on first pregnancy loss is likely a result of the high de novo fetal aneuploidy rate; however, this ignores the association of euploid pregnancy loss with an increased risk of future losses. Diagnosis of ploidy is advantageous but requires collection of pregnancy tissue. Cell-free fetal DNA (cffDNA) has revolutionized prenatal screening and has shown evidence in 2 small studies of diagnostic utility in pregnancy loss. The prospective Copenhagen Pregnancy Loss (COPL) study is a large initiative with the overall aim to explore the causes of pregnancy loss.

This prospective cohort study of women from the COPL aimed to investigate the clinical utility of cffDNA-based testing in women with pregnancy loss. Adult women with a pregnancy loss before gestational age 22 weeks seen between November 2020 and May 2022 at 1 of the 3 participating COPL sites were invited to participate. Blood samples for cffDNA analysis were obtained before treatment to remove pregnancy tissue or within 24 hours of passage of pregnancy tissue. Pregnancy tissue was collected for direct sequencing and comparison to cffDNA results. Aneuploidy was assessed for all chromosomes, and discordant results were considered false-positive if the cffDNA result was aneuploid and false-negative if the cffDNA result was euploid.

A total of 1000 women were recruited and underwent cffDNA blood draws, and 32% of women either did not manage to collect pregnancy tissue or collected a sample classified as unknown tissue. The cffDNA result was inconclusive in 112 (11%) of initial cases due to a low fetal fraction or low sequencing quality and were excluded from sensitivity and specificity analysis. The association between inconclusive results and gestational age was approximately 10% from gestational age 7 weeks on, whereas results were inconclusive approximately 50% of the time at earlier gestational ages. The final cohort for analysis thus included 888 cases, 446 (50%) of which were euploid, 405 (46%) aneuploid, and 37 (4%) contained multiple aneuploidies. The sensitivity of cffDNA testing compared with direct sequencing of pregnancy tissue was 85% (95% confidence interval [CI], 79–90), specificity was 93% (CI, 88–96), and accuracy was 89% (95% CI, 85–92).

The results of this study demonstrate that cffDNA-based testing has a high sensitivity, specificity, and accuracy for the diagnosis of ploidy when compared with direct sequencing of pregnancy tissue. In addition, approximately a third of women were not able to collect true pregnancy tissue, illustrating the importance of introducing a pregnancy tissue-independent alternative for diagnostics in pregnancy loss.