P684: Resolving genetic architecture of complex supernumerary marker chromosomes with complementary cytogenomic methodologies

Introduction: Chromosomal aneuploidy and other forms of copy number variation are a well-known cause of early pregnancy loss.Copy number analysis of products of conception (POCs) can provide critical information in determining a genetic etiology and the associated recurrence risks.In this study, we compare the utility and results of chromosomal single nucleotide variant (SNV) microarray (CMA) and cytogenetic analyses for POCs.Methods: We retrospectively reviewed the results of CMA and cytogenetic analysis performed for POCs in our laboratory from September 2024 through October 2025.Acceptable specimens for this testing include fetal tissue, placenta, umbilical cord, or chorionic villus samples submitted in transport media at room temperature.All samples underwent direct DNA extraction and simultaneous establishment and harvesting of cultured cell lines.CMA was performed for all samples with successful DNA extraction with a turnaround time of 3-4 weeks, and follow-up cytogenetic confirmation by karyotype or FISH analysis was performed on successfully cultured cells when results would be informative for recurrence risk.The results of the CMA and cytogenetic testing, when performed, were provided in a single report.Results: Between September 1, 2024 and October 21, 2025, 60 POC samples were received by our laboratory for CMA.Two samples failed DNA extraction due to poor DNA quality and testing was canceled.CMA was completed for the remaining 58 samples.Three cases submitted to the laboratory included multiple samples from different sources, resulting in 53 total cases by medical record number (MRN).A positive result was identified by CMA in 39.6% (21/53) of cases.Freestanding trisomies of autosomal chromosomes were the most frequent finding (n=10) and involved chromosomes 9, 13, 16 (n=2), 18 (n=2), 20 (n=2), 21, and 22. Monosomy X was identified in 4 cases, including 2 cases demonstrating mosaicism and containing additional abnormalities.Triploidy was detected in 4 cases, including 1 case of triploidy in combination with tetrasomy 14.Heterozygous deletions below the detection limit of cytogenetic analysis were detected in 3 cases: a 2.22 Mb 22q11.21deletion consistent with 22q11.21deletion syndrome, a 1.32 Mb recurrent pathogenic 17p12 deletion reported as an incidental finding, and a 474 kb 6q21 deletion of uncertain significance.Maternal cell contamination ranging from 5% to 95% was detected in 5 cases.The gestational age was provided for 19 of the positive cases; 63% (12/19) were from the first trimester and 37% (7/19) were from the second trimester.Tissue culture for cytogenetic testing was set up for 60 samples, and 25% (15/60) failed to achieve growth.Follow-up cytogenetic testing was performed for 7 cases.In 2 cases, karyotype analysis confirmed the CMA result.In 1 case, the CMA result was suggestive of an additional genotype and G-banding identified an apparently normal karyotype, suggesting the genotyping pattern was consistent with high level maternal cell contamination.Two cases involved mosaic monosomy X detected on CMA that was not observed on karyotype analysis.In the remaining 2 cases, CMA performed on chorionic villi detected trisomies and XY sex chromosome complements; however, karyotype analysis detected normal 46,XX karyotypes in all or most cells, suggesting maternal cell contamination.Conclusion: CMA and cytogenetic analysis each have strengths and weaknesses for analysis of POCs.CMA uses direct tissue extraction and allows for detection of maternal cell contamination and submicroscopic copy number variants while avoiding result skewing and growth failure from culturing cells.Karyotype analysis remains beneficial as a reflex test for ruling out structural abnormalities and clarifying genotyping patterns.In conclusion, CMA analysis with follow-up cytogenetic testing is an effective strategy for POC samples.