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Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform
Published on: August 17, 2022
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Genome-wide equine preimplantation genetic testing enabled by simultaneous haplotyping and copy number detection
T De Coster1,2, Y Zhao3, O Tšuiko3
1Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Merelbeke, Belgium. tine.decoster@ugent.be.
Scientific Reports
|January 23, 2024
Summary
This study introduces a new method for equine preimplantation genetic testing (PGT) to simultaneously detect aneuploidies and monogenic traits. This genetic testing allows for the selection of healthy equine embryos, improving breeding outcomes.
Area of Science:
- Reproductive Biology
- Genetics
- Animal Science
Background:
- Embryonic aneuploidies and genome-wide errors cause developmental failure in many species.
- The increasing production of equine embryos offers opportunities for genetic selection before transfer.
- Current methods lack comprehensive genetic screening for both chromosomal and monogenic conditions in horses.
Purpose of the Study:
- To explore a universal, genome-wide preimplantation genetic testing (PGT) strategy for horses.
- To concurrently test for aneuploidies (PGT-A) and monogenic traits/diseases (PGT-M).
- To assess the incidence and spectrum of chromosomal and genome-wide errors in in vitro-produced equine embryos.
Main Methods:
- Genotyping over 70,000 single nucleotide polymorphism (SNP) positions in equine trophectoderm biopsies and blastocysts.
- Performing concurrent genome-wide copy number detection and haplotyping using haplarithmisis.
- Comparing genetic profiles of biopsy-blastocyst combinations for aneuploidies and specific gene variants (GBE1, PLOD1, B3GALNT2, MUTYH, STX17).
Main Results:
- The biopsy samples accurately predicted the euploid/aneuploid state and parental haplotypes in 9 out of 9 biopsy-blastocyst combinations.
- Two biopsies revealed chromosomal losses (maternal chromosomes 28 and 31) confirmed in corresponding blastocysts.
- Five of six arrested embryos showed significant chromosomal and/or genome-wide errors, contributing to in vitro arrest.
Conclusions:
- A genome-wide PGT strategy can effectively identify genetic errors and specific gene variants in equine embryos.
- This approach enables the selection of embryos free from genetic defects and with desired traits.
- The proposed PGT method has the potential to significantly improve foaling rates and overall horse quality in breeding programs.
