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Expanded clinical validation of Haploseek for comprehensive preimplantation genetic testing

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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Fig. 1: Embryo classification within genomic regions of consanguinity using Haploseek.
Fig. 2: Embryo classification within genomic regions of consanguinity using the Haploseek “diff plot”.
Fig. 3: Clinical utility of Haploseek for preimplantation genetic testing for monogenic disease (PGT-M) using only a single grandparent of the embryo for haplotype phasing.
Fig. 4: Clinical utility of Haploseek for preimplantation genetic testing for monogenic disease (PGT-M) of X-linked disorders.

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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Correspondence to David A. Zeevi.

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Ethics Declaration

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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