Whole Genome Sequencing (WGS) on IVF Embryos and Individual Patients

Fertility Issues Clinical Trial

— EmbryoWGS  

Official title:

Study of the Effect of Paternal Age on de Novo Mutation Rate by Using Whole Genome Sequencing of IVF Embryos

Clinical Trial Details — Status: Recruiting

Administrative data

• NCT number: NCT05739890
• Other study ID #: RP-GE_02
• Status: Recruiting
• Start date: June 1, 2023
• Est. completion date: August 2024

Study information

• Verified date: September 2023
• Source: GenEmbryomics Pty. Ltd
• Contact: Santiago Munné, PhD
• Phone: +1-646-2072897
• Email: santiago.munne[@]gmail.com
• Is FDA regulated: No
• Study type: Observational [Patient Registry]

Clinical Trial Summary

This research project aims to utilise recent advances in whole genome sequencing of preimplantation genetic diagnosis embryos to investigate the impact of paternal age on de novo mutation rates in IVF embryos. Embryos that are deemed unsuitable for transfer following preimplantation genetic testing for monogenic/single gene disorders (PGT-M) due to the detection of genetic abnormalities will be utilized for this study. These embryos will undergo re-biopsy, and both the biopsied samples as well as the remaining embryo tissue will be subject to whole genome sequencing. This will allow the assessment of de novo mutation rates based on the paternal age.

Description:

This project proposes a paired non-inferiority trial utilizing the retrospective testing of research embryos to establish the optimized parameters for amplified trophectoderm biopsy and whole genome sequencing compared to traditional preimplantation genetic testing for aneuploidy (PGT-A).

The primary outcome is the de novo mutation rate, which will be compared between embryos subjected to trophectoderm biopsy and whole genome sequencing versus reanalysis with Sanger sequencing. Trio testing will be performed for each embryo using DNA from the genetic parents in addition to embryo. The study will compare cases that include couples with at least one embryo deemed unsuitable for transfer. A paired study design will be used, with embryos from each couple split into two arms - one subjected to trophectoderm biopsy and whole genome sequencing, the other to reanalysis with targeted sequencing.

Biopsied trophectoderm samples and the remaining embryo tissues from the whole genome sequencing arm will undergo sequencing. Sequencing will also be performed on DNA samples from each genetic parent.

Derivation of de novo mutation rates is a key goal, as these provide insights into effects of paternal age and other factors on germline mutations in preimplantation embryos, increasing the knowledge of the risks associated with advanced paternal age. Secondary metrics will be investigated to supplement the analysis, including clean reads and clean bases indicating the amount of high-quality data for the source templates. Mapping rate, unique rate and duplicate rate, assessing data accuracy and quality. Comparison of multiple metrics will determine the optimized parameters for performing amplified trophectoderm biopsy and whole genome sequencing. This can then inform future research and clinical studies.

The de novo mutation rate will be derived by modelling the observed mutation rate as a function of parental ages, specifically the paternal age. Whole genome sequencing of embryo samples as well as both parents will identify raw numbers of de novo mutations. The paternal age coefficient for the de novo mutation rate will be calculated using a regression model with the number of de novo mutations as the dependent variable and paternal age as the key independent variable. Covariates like maternal age and sequencing quality metrics will also be included to account for potential confounding factors. The regression model will determine the increase in de novo mutations per year of paternal age, providing the paternal age coefficient. Comparing embryos from older and younger males will reveal differences in mutation rates. The overall model will establish the quantitative relationship between paternal age and de novo mutations in preimplantation embryos based on the study's whole genome sequencing data.

Recruitment information / eligibility

• Status: Recruiting
• Enrollment: 100
• Est. completion date: August 2024
• Est. primary completion date: March 2024
• Gender: All
• Age group: 18 Years to 48 Years

Eligibility

Couples undergoing IVF with 1= embryo sample unsuitable for transfer due to genetic or chromosome abnormalities.

Cases with parental DNA available directly or consenting follow-up.

Exclusion Criteria:

• Female patients with low ovarian reserve (< 10 follicles or FSH>10, AMH <1).

Related Conditions & MeSH terms

• Fertility Issues
• Genetic Diseases, Inborn
• Infertility
• Single-Gene Defects

Intervention

Other:
• Embryo genome sequencing
This project proposes the testing of a cohort of research embryos to establish the key parameters for amplified trophectoderm biopsied embryos using minimum depth required for genome sequencing (>depth of 30x per base).The remaining embryo tissue will be whole genome sequenced to validate the results of the biopsy.
• Parents genome sequencing
Analysis will be performed using trio testing of each embryo in addition to the DNA from the genetic parent to facilitate the derivation of de novo mutation rate.

Locations

Country	Name	City	State
Turkey	Preimplantation Genetic Testing Unit ART and Reproductive Genetics Unit, Memorial Sisli Hospital	Istanbul	Okmeydani-Sisli
United States	Poma Fertility	Kirkland	Washington
United States	Neway Fertility	New York	New York
United States	ORM Fertility	Portland	Oregon

Sponsors (1)

Lead Sponsor	Collaborator
GenEmbryomics Pty. Ltd

Countries where clinical trial is conducted

United States,  Turkey, 

Outcome

Type	Measure	Description	Time frame	Safety issue
Primary	De novo mutation rates	Metrics for investigation include: clean reads, clean bases (Mp), mapping rate, unique rate, duplicate rate, mismatch rate, average sequencing depth, Ti/Tv (Transition/ Transversion) ratio, true-positive rate, false-positive rate, false-negative rate which enables the derivation of de novo mutation rates.	Month 6
Primary	Variant pathogenicity, Zygosity and mode of inheritance	Variant pathogenicity; the zygosity and mode of inheritance will be assessed and documented for validation of variant calls for heritable and non-inherited variants. There will be an examination of the sequencing data from the embryo cohort by using the parental genomes as a validation reference. Initially this will focus on single nucleotide polymorphisms (SNPs) and small insertions/deletions (Indels).	Month 6