Preimplantation genetic testing (PGT) is an essential tool for selecting embryos free of genetic abnormalities. However, current PGT methods often require separate platforms for aneuploidy (PGT-A), monogenic disorders (PGT-M), and structural rearrangements (PGT-SR), leading to increased costs and operational complexity when multiple PGT tests are needed for a single embryo. Here, we present KaryoSeq, a low-pass whole-genome sequencing-based comprehensive PGT approach that integrates PGT-A, PGT-M, and PGT-SR into a single platform. An assistant decision-making system was constructed to pre-evaluate the required sequencing depth for specific genes or regions. Clinical validation of KaryoSeq was performed on 166 blastocyst samples from 31 families previously diagnosed by using conventional PGT methods. KaryoSeq achieved 100% concordance with traditional platforms using the Infinium Asian Screening Array in combination with low-coverage whole-genome sequencing (approximately 0.1×)
it also offered improved whole-genome coverage, reduced variability, and efficient simultaneous analysis of PGT-A, PGT-M, and PGT-SR at a whole-genome sequencing depth of approximately 2× for most genes. In addition, KaryoSeq identified triploidy, uniparental disomy, parental origin of copy number variations, and maternal cell contamination, further enhancing its clinical utility and efficiency in PGT applications.