Comprehensive analysis of chromosome abnormalities by chromosome conformation based karyotyping (C-MoKa) in patients with conception failure and pregnancy loss

•C-MoKa shows the potential utility in precisely unraveling SVs, mosaic aneuploidies, CNVs, and UPD in clinical settings in a single test.•C-MoKa is able to decode intricate and cryptic chromosomal abnormalities missed by traditional karyotyping.•C-MoKa demonstrates superior fragment resolution and more precise breakpoints. Chromosome abnormalities are a leading cause of conception failure and pregnancy loss. While traditional cytogenetics technologies like karyotyping have been helpful in identifying structural variations (SVs), they face challenges in detecting complex rearrangements and cryptic structures. In this study, we developed a new method called chromosome conformation based karyotyping (C-MoKa) to comprehensively detect different types of chromosomal abnormalities in patients with conception failure and pregnancy loss. A total of 70 clinical samples exhibiting known results of SVs, mosaic aneuploidies, copy number variations （CNVs） and uniparental disomy (UPD) were included in our cohort and underwent C-MoKa analysis. The results obtained from different techniques, including karyotyping, CNV-seq, and CMA were compared and analyzed. Distinct chromosomal conformation patterns of various variations were observed and analyzed in clinical samples. Our C-MoKa method not only validated all the findings of karyotyping, CNV-seq and CMA, but also provided more detailed results. It demonstrated superior fragment resolution (100 kb). Moreover, C-MoKa showed higher sensitivity in decoding intricate rearrangements in a single test. Our results highlight the potential utility of C-MoKa in precisely unraveling SVs, mosaic aneuploidies, CNVs, and UPD in clinical settings, which can significantly impact further clinical decision-making.