Whole Genome Sequencing (WGS) on IVF Embryos and Individual Patients
NCT ID: NCT05739890
Last Updated: 2023-09-25
Study Results
The study team has not published outcome measurements, participant flow, or safety data for this trial yet. Check back later for updates.
Basic Information
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UNKNOWN
100 participants
OBSERVATIONAL
2023-06-01
2024-08-31
Brief Summary
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Detailed Description
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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.
Conditions
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Study Design
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COHORT
OTHER
Study Groups
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Age >18yrs
The study will compare embryos from \>50 couples and their embryo samples flagged not suitable for transfer from deidentified couples with date of birth required.
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.
Interventions
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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.
Eligibility Criteria
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Exclusion Criteria
18 Years
48 Years
ALL
No
Sponsors
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GenEmbryomics Pty. Ltd
INDUSTRY
Responsible Party
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Principal Investigators
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Nicholas Murphy, PhD
Role: PRINCIPAL_INVESTIGATOR
GenEmbryomics Pty. Ltd
Locations
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Neway Fertility
New York, New York, United States
ORM Fertility
Portland, Oregon, United States
Poma Fertility
Kirkland, Washington, United States
Preimplantation Genetic Testing Unit ART and Reproductive Genetics Unit, Memorial Sisli Hospital
Istanbul, Okmeydani-Sisli, Turkey (Türkiye)
Countries
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Central Contacts
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Facility Contacts
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Semra Kahraman, M.D.
Role: primary
Other Identifiers
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RP-GE_02
Identifier Type: -
Identifier Source: org_study_id
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