A method for determining potential parental contamination: linkage disequilibrium-based log-likelihood ratio analysis for IVF-PGT.
Conventional in vitro fertilization (cIVF)
IVF-PGTA assay
Linkage disequilibrium (LD)
Log-likelihood ratio (LLR) analysis
Potential parental contamination
Journal
Reproductive biology and endocrinology : RB&E
ISSN: 1477-7827
Titre abrégé: Reprod Biol Endocrinol
Pays: England
ID NLM: 101153627
Informations de publication
Date de publication:
21 Oct 2024
21 Oct 2024
Historique:
received:
21
10
2023
accepted:
09
10
2024
medline:
22
10
2024
pubmed:
22
10
2024
entrez:
21
10
2024
Statut:
epublish
Résumé
At present, embryologists are attempting to use conventional in vitro fertilization (cIVF) as an alternative to intracytoplasmic sperm injection (ICSI) for preimplantation genetic testing (PGT). However, the potential parental contamination origin of sperm cells and cumulus cells is considered the main limiting factor in the inability of cIVF embryos to undergo PGT. In this study, we established an IVF-PGTA assay for parental contamination tests with a contamination prediction model based on allele frequencies and linkage disequilibrium (LD) to compute the log-likelihood ratio (LLR) under competing ploidy hypotheses, and then verified its sensitivity and accuracy. Finally, comparisons of the effectiveness of SNP-based analysis and LLR-based IVF-PGTA among 40 cIVF embryos was performed, based on both statistical analysis of the parental contamination rate and chromosomal ploidy concordance rate between TE biopsy and ICM isolations. With IVF-PGTA assay, biopsies with 10% maternal contamination could be detected accurately, and contamination caused by sperm cells could be eliminated completely. Utilizing LLR-based or single Nucleotide Polymorphism (SNP) -based analyses, our comprehensive examination of 40 clinically discarded fresh cIVF embryos revealed an absence of paternal contamination. Strikingly, the LLR-based analysis uniquely revealed a mere instance of 24% maternal contamination within the trophectoderm cell (TE) biopsy of 5* embryo. Furthermore, it was solely through this analysis that embryo (9-F) was identified as a triploid of paternal origin. In this study, we developed a new bioinformatics analysis method for identifying parental contamination during IVF-PGT, especially for couples with nonmale factor infertility.
Sections du résumé
BACKGROUND
BACKGROUND
At present, embryologists are attempting to use conventional in vitro fertilization (cIVF) as an alternative to intracytoplasmic sperm injection (ICSI) for preimplantation genetic testing (PGT). However, the potential parental contamination origin of sperm cells and cumulus cells is considered the main limiting factor in the inability of cIVF embryos to undergo PGT.
METHODS
METHODS
In this study, we established an IVF-PGTA assay for parental contamination tests with a contamination prediction model based on allele frequencies and linkage disequilibrium (LD) to compute the log-likelihood ratio (LLR) under competing ploidy hypotheses, and then verified its sensitivity and accuracy. Finally, comparisons of the effectiveness of SNP-based analysis and LLR-based IVF-PGTA among 40 cIVF embryos was performed, based on both statistical analysis of the parental contamination rate and chromosomal ploidy concordance rate between TE biopsy and ICM isolations.
RESULTS
RESULTS
With IVF-PGTA assay, biopsies with 10% maternal contamination could be detected accurately, and contamination caused by sperm cells could be eliminated completely. Utilizing LLR-based or single Nucleotide Polymorphism (SNP) -based analyses, our comprehensive examination of 40 clinically discarded fresh cIVF embryos revealed an absence of paternal contamination. Strikingly, the LLR-based analysis uniquely revealed a mere instance of 24% maternal contamination within the trophectoderm cell (TE) biopsy of 5* embryo. Furthermore, it was solely through this analysis that embryo (9-F) was identified as a triploid of paternal origin.
CONCLUSIONS
CONCLUSIONS
In this study, we developed a new bioinformatics analysis method for identifying parental contamination during IVF-PGT, especially for couples with nonmale factor infertility.
Identifiants
pubmed: 39434113
doi: 10.1186/s12958-024-01300-z
pii: 10.1186/s12958-024-01300-z
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
129Subventions
Organisme : Natural Science Foundation
ID : BXQN202232
Organisme : National Key Research and Development Program of China
ID : 2022YFC2703200
Organisme : National Key Research and Development Program of China
ID : 2022YFC2703200
Organisme : Jiangsu Key Discipline of Human Assisted Reproduction Medicine Foundation
ID : FXK202149
Organisme : Jiangsu Key Discipline of Medicine Foundation of Commission of Health
ID : ZDB2020007
Organisme : Suzhou Major Project Research
ID : 20220901
Informations de copyright
© 2024. The Author(s).
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