Detection of cytogenomic abnormalities by OncoScan microarray assay for products of conception from formalin-fixed paraffin-embedded and fresh fetal tissues

Abstract Background The OncoScan microarray assay (OMA) using highly multiplexed molecular inversion probes for single nucleotide polymorphism (SNP) loci enabled the detection of cytogenomic abnormalities chromosomal imbalances and pathogenic copy number variants (pCNV). small size is optimal SNP genotyping fragmented DNA from fixed tissues. This retrospective study evaluated clinical utility OMA as a uniform platform to detect pregnancy loss fresh tissues products conception (POC). Results Fresh specimens POC were routinely subjected cell culture then analyzed by karyotyping. with normal karyotype (NK) or failure (CF) formalin-fixed paraffin-embedded (FFPE) extraction OMA. abnormality rate (ADR) on 94 cases POC-NK, 38 POC-CF, 35 POC-FFPE 2% (2/94), 26% (10/38), 57% (20/35), respectively. detected aneuploidies, triploidies pCNV accounted 50%, 40% 10% in POC-CF 85%, 5% POC-FFPE, False negative result cultured maternal cells contamination each one case. two unbalanced structural chromosome further defined genomic breakpoints. Conclusion showed high diagnostic yield abnormalities. approach circumvented obstacles CF provided reliable effective detecting monitoring true fetal contamination.