Concordance rates of SNP-NIPT and SNP-array products of conception analysis from a single laboratory

To analyze the concordance of single nucleotide polymorphism-based non-invasive prenatal testing (SNP-NIPT) and SNP-array based products of conception (POC) testing in cases identified to have SNP-NIPT prior to a loss sent for SNP-POC analysis. We present a retrospective review of 582 SNP-NIPT cases with SNP-POC testing performed at the same reference laboratory from May 27, 2021 - May 25, 2022. Samples not returning results on SNP-NIPT were excluded from analysis. Of 551 cases included, 146 (26.5%) received a high-risk result by SNP-NIPT for trisomy 21 (n=25), trisomy 18 (n=11), trisomy 13 (n=11), monosomy X (n=21), 22q11.2 deletion (n=1), Vanished Twins/Triploidy (n=22), fetal fraction-based risk (FFBR, n=46), or an atypical finding (AF, n=9). POC testing returned fetal results on 144/146 (98.6%) of these cases. Excluding FFBR (46/144) and AF (8/144) cases, the concordance rate for cases with a chromosomal condition detected was 95.6% (86/90). For cases at elevated risk (FFBR and AF), 57.4% (31/54) had a chromosomal anomaly by POC. The remaining 405 (73.5%) cases were low-risk by SNP-NIPT; 12 POC cases with maternal cell contamination/inconclusive results and 20 cases with abnormal POC results not screened for by SNP-NIPT, were excluded, giving a concordance rate of 99.2% (370/373). The overall concordance rate of SNP-NIPT and SNP-POC analysis was 94% (487/517). High-risk aneuploidy results on NIPT demonstrated high accuracy, with a concordance rate of 96%. For high-risk FFBR and AF NIPT cases, the concordance rate was lower at ∼57%, with ∼30% of these cases having a POC result, such as a deletion/duplication, warranting further family testing. Although low-risk NIPT cases had a very high concordance, 5% of these cases had another type of abnormality detected on POC analysis not screened for by SNP-NIPT. These findings support follow-up genetic testing on a pregnancy loss after NIPT, which can help guide medical management.