Abstract
Purpose
We previously developed Haploseek, a method for comprehensive preimplantation genetic testing (PGT). However, some key features were missing, and the method has not yet been systematically validated.
Methods
We extended Haploseek to incorporate DNA from embryo grandparents and to allow testing of variants on chromosome X or in regions where parents share common haplotypes. We then validated Haploseek on 151 embryo biopsies from 27 clinical PGT cases. We sequenced all biopsies to low coverage (0.2×), and performed single-nucleotide polymorphism (SNP) microarray genotyping on the embryos’ parents and siblings/grandparents. We used the extended Haploseek to predict chromosome copy-number variants (CNVs) and relevant variant-flanking haplotypes in each embryo. We validated haplotype predictions for each clinical sample against polymerase chain reaction (PCR)-based PGT case results, and CNV predictions against established commercial kits.
Results
For each of the 151 embryo biopsies, all Haploseek-derived haplotypes and CNVs were concordant with clinical PGT results. The cases included 17 autosomal dominant, 5 autosomal recessive, and 3 X-linked monogenic disorders. In addition, we evaluated 1 Robertsonian and 2 reciprocal translocations, and 17 cases of chromosome copy-number counting were performed.
Conclusion
Our results demonstrate that Haploseek is clinically accurate and fit for all standard clinical PGT applications.
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Data availability
De-identified source data for this study are available upon request.
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Acknowledgements
The authors thank the Shaare Zedek Mirsky intramural grant for funding this research. S.C. and D.A.Z. thank the Hebrew University of Jerusalem Center for Interdisciplinary Data Science Research (CIDR; grant number 3035000322).
Author Information
Conceptualization: D.A.Z., D.B., S.C., G.A. Data curation: D.A.Z., F.Z. Formal analysis: D.A.Z., D.B., E.H.-S., S.Z., G.A. Funding acquisition: D.A.Z., P.R., S.C., G.A. Investigation: D.A.Z., D.B., E.H.-S., F.Z., R.S., S.Z., S.S., S.C., G.A. Methodology: D.A.Z., D.B, S.C., T.M., F.Z., S.Z. Resources: P.R., R.S., T.E.-G., I.B.-A., A.B.-Y. Software: D.B., F.Z. Supervision: D.A.Z., E.H.-S., P.R., R.S., I.B.-A., S.C., G.A. Validation: D.A.Z., E.H.-S., G.A. Visualization: F.Z.; Writing—original draft: D.A.Z.; Writing—review & editing: D.A.Z., D.B., S.C., G.A.
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Ethical approval for this study was obtained from the Shaare Zedek Medical Center institutional review board. DNA, tissue culture samples, and human embryo biopsies in this study were donated to the Shaare Zedek Medical Genetics Institute for research with informed consent according to Shaare Zedek institutional review board guidelines and as set forth in the Declaration of Helsinki.
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The authors declare no competing interests.
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Zeevi, D.A., Backenroth, D., Hakam-Spector, E. et al. Expanded clinical validation of Haploseek for comprehensive preimplantation genetic testing. Genet Med (2021). https://doi.org/10.1038/s41436-021-01145-6
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