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OneGene PGT: comprehensive preimplantation genetic testing method utilizing next-generation sequencing

  • Genetics
  • Published:
Journal of Assisted Reproduction and Genetics Aims and scope Submit manuscript

Abstract

Purpose

Preimplantation genetic testing for monogenic disorders (PGT-M) allows early diagnosis in embryos conceived in vitro. PGT-M helps to prevent known genetic disorders in affected families and ensures that pathogenic variants in the male or female partner are not passed on to offspring. The trend in genetic testing of embryos is to provide a comprehensive platform that enables robust and reliable testing for the causal pathogenic variant(s), as well as chromosomal abnormalities that commonly occur in embryos. In this study, we describe PGT protocol that allows direct mutation testing, haplotyping, and aneuploidy screening.

Methods

Described PGT protocol called OneGene PGT allows direct mutation testing, haplotyping, and aneuploidy screening using next-generation sequencing (NGS). Whole genome amplification product is combined with multiplex PCR used for SNP enrichment. Dedicated bioinformatic tool enables mapping, genotype calling, and haplotyping of informative SNP markers. A commercial software was used for aneuploidy calling.

Results

OneGenePGT has been implemented for seven of the most common monogenic disorders, representing approximately 30% of all PGT-M indications at our IVF centre. The technique has been thoroughly validated, focusing on direct pathogenic variant testing, haplotype identification, and chromosome abnormality detection. Validation results show full concordance with Sanger sequencing and karyomapping, which were used as reference methods.

Conclusion

OneGene PGT is a comprehensive, robust, and cost-effective method that can be established for any gene of interest. The technique is particularly suitable for common monogenic diseases, which can be performed based on a universal laboratory protocol without the need for set-up or pre-testing.

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Abbreviations

ADO :

Allele drop-out

CNV :

Copy number analysis

MDA :

Multiple displacement amplification

PGT-M :

Preimplanation genetic testing for monogenic diseases

STR :

Short tandem repeat

SNP :

Single nucleotide polymorphism

WGA :

Whole genome amplification

MPS :

Massively parallel sequencing

NGS :

Next-generation sequencing

IVF :

in vitro Fertilisation

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Author information

Authors and Affiliations

  1. REPROMEDA, Studentska 812/6, 625 00, Brno, Czech Republic

    Miroslav Hornak, Katerina Bezdekova, David Kubicek, Rostislav Navratil, Veronika Hola, Maria Balcova, Magdalena Bohmova, Katerina Weisova & Katerina Vesela

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  1. Miroslav Hornak
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Contributions

Manuscript drafting: MH; manuscript editing: DK, KB, RN, VH; developing OneGene PGT method: MH, KB; participating in experiments, sample preparation and data collection: MH, KB, DK, RN, VH, MBa, MBo, KW; final approval of the manuscript: KV. All authors have critically reviewed the manuscript and have approved the final version submitted for publication.

Corresponding author

Correspondence to Miroslav Hornak.

Ethics declarations

Ethics approval

The study was approved by the Reproductive Medicine Ethics Committee of the Repromeda IVF centre. All DNA samples used for the method validation were collected with informed consent, allowing the laboratory to use them anonymously for research purposes.

Conflict of interest

The authors declare no competing interests.

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Supplementary Information

Below is the link to the electronic supplementary material.

10815_2023_2998_MOESM1_ESM.xlsx

Supplementary file1 (XLSX 37 KB) Supplement A. List of SNP markers used for OneGene PGT analysis. List includes rs numbers, coordinates and population allele frequency (non-Finnish Europeans from gnomAD database).

10815_2023_2998_MOESM2_ESM.xlsx

Supplementary file2 (XLSX 21 KB) Supplement B. Validation study. Results showing concordance between OneGene PGT and reference method (Sanger sequencing, karyomapping)

10815_2023_2998_MOESM3_ESM.png

Supplementary file3 (PNG 225 KB) Supplement C. Example of OneGene PGT analysis report. The example of direct mutation testing and linkage analysis results using OneGene PGT software. Informative SNP markers are shown in red/blue colour indicating paternal haplotype I or II; similarly, in yellow/green colour indicating maternal haplotype I or II.

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Hornak, M., Bezdekova, K., Kubicek, D. et al. OneGene PGT: comprehensive preimplantation genetic testing method utilizing next-generation sequencing. J Assist Reprod Genet 41, 185–192 (2024). https://doi.org/10.1007/s10815-023-02998-3

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