Investigating DNA contamination affecting embryo biopsy specimens taken for PGT-A: Incidence and impact on the accuracy of chromosomal analysis

What is the prevalence of DNA contamination in embryo biopsy samples taken for preimplantation genetic testing for aneuploidy (PGT-A) and how often might it lead to incorrect interpretation of results? A retrospective study of 57,292 clinical PGT-A samples from 32 IVF clinics was carried out to determine the frequency of DNA contamination affecting trophectoderm biopsy specimens. Testing employed a highly validated and widely used PGT-A method, which includes genotyping of >4000 single nucleotide polymorphisms. Validation experiments confirmed the ability of the method to reliably detect DNA contamination. Overall, contamination was detected in 0.45% (256/57,292) trophectoderm biopsy specimens, but rates at individual clinics varied significantly (P<0.0001, Chi-squared test). 155 embryos with a contaminated biopsy specimen had a result from a second (uncontaminated) sample. Comparison of the two biopsies revealed that errors in classification of chromosomal status could have occurred in 44.5% (69/155) of these embryos if contamination had not been detected. DNA contamination affected 1 in 222 samples. However, frequencies below 1 in 1000 were achieved in some clinics, while others have an incidence more than 10 times higher. Contamination was associated with a substantial risk of diagnostic error, potentially leading to the discard of viable embryos, or the transfer to the uterus of aneuploid embryos. We conclude that the use of validated PGT-A methods, capable of detecting DNA contamination, should be used and that the incidence of contamination should be considered a key performance indicator for clinics offering PGT-A.