Third-Generation Single-Molecule Sequencing for Preimplantation Genetic Testing of Aneuploidy and Segmental Imbalances.

Autor:	Tan VJ; Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore., Liu T; Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore., Arifin Z; Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore., Pak B; Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore., Tan ASC; Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore., Wong S; Preimplantation Genetic Diagnosis Centre, Department of Obstetrics and Gynaecology, National University Hospital, Singapore., Khor CC; Division of Human Genetics, Genome Institute of Singapore, Singapore., Yang H; Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore., Lee CG; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore., Huang Z; Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore., Choolani MA; Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore., Chong SS; Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.; Preimplantation Genetic Diagnosis Centre, Department of Obstetrics and Gynaecology, National University Hospital, Singapore.; Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.; Department of Laboratory Medicine, National University Hospital, Singapore.
Jazyk:	angličtina
Zdroj:	Clinical chemistry [Clin Chem] 2023 Aug 02; Vol. 69 (8), pp. 881-889.
DOI:	10.1093/clinchem/hvad062
Abstrakt:	Background: Current strategies for preimplantation genetic testing for aneuploidy or structural rearrangements (PGT-A/SR) rely mainly on next-generation sequencing (NGS) and microarray platforms, which are robust but require expensive instrumentation. We explored the suitability of third-generation single-molecule sequencing as a PGT-A/SR screening platform for both aneuploidy and segmental imbalance. Methods: Single-cell and multicell replicates from aneuploid or segmentally unbalanced cell lines (n = 208) were SurePlex-amplified, randomized, and subjected to (a) Nanopore-based single-molecule sequencing (Oxford Nanopore Technologies) and (b) NGS using a leading commercial PGT-A solution (Illumina VeriSeq PGS). Archival SurePlex-amplified trophectoderm biopsy samples (n = 96) previously analyzed using the commercial kit were blinded and reanalyzed using Nanopore. Results: Nanopore-based PGT-A identified the specific aberration in 95.45% (84/88) and 97.78% (88/90) of single-/multicells with an aneuploidy or segmental imbalance (10-30.5 Mb), respectively. Comparison against the commercial kit's results revealed concordances of 98.86% (87/88) and 98.89% (89/90) for the aneuploid and segmentally unbalanced (10-30.5 Mb aberration) samples, respectively. Detection sensitivity for smaller segmental imbalances (5-5.8 Mb aberration, n = 30) decreased markedly on both platforms. Nanopore-based PGT-A reanalysis of trophectoderm biopsy samples was 97.92% (94/96) concordant with the commercial kit results. Conclusion: Up to 24 SurePlex-amplified single-cell, multicell, or trophectoderm samples could be sequenced in a single MinION flow-cell for subsequent preimplantation genetic testing for aneuploidy or structural rearrangements (PGT-A/SR) analysis, with results obtainable in ≤3 days and at per-sample costs that are competitive with commercial offerings. Nanopore's third-generation single-molecule sequencing represents a viable alternative to current commercial NGS-based PGT-A solutions for aneuploidy and segmental imbalance (≥10 Mb) screening of single-/multicell or trophectoderm biopsy samples. (American Association for Clinical Chemistry 2023.)
Databáze:	MEDLINE
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