Non-invasive Preimplantation Genetic Testing for Aneuploidies Using Cell-free DNA in Spent Culture Media

NCT04711239 | Withdrawn

• 1 other identifier: 2010-ABU-011-SJ
• Study Type: observational
• Target: N/A
• Locations: 0 countries
• Sites: N/A

Brief Summary

Analysis of embryonic cell-free DNA (cfDNA) present in the spent culture media (SCM) is a non-invasive alternative for preimplantation genetic testing for aneuploidies (PGT-A) that avoids the technical challenges and limitations of biopsy. Initial studies investigating this non-invasive PGT-A (niPGT-A) method reported variable concordance between cfDNA in SCM and the trophectoderm sample (\~ 30%-86%) and indicated a contribution from both the inner cell mass and trophectoderm to the cfDNA in SCM. This study aims to evaluate the use of the embryo culture medium as a source of genetic material for PGT-A and validate a niPGT-A protocol using cfDNA in SCM.

Conditions

Secondary Infertility

Keywords

PGT-A; cell-free DNA; spent culture media; NGS

Outcome Measures

Primary Outcomes (5)

• General concordance between results for cfDNA in SCM and trophectoderm biopsies

  General ploidy concordance rate: number of matched (euploid-euploid or aneuploid-aneuploid) result/total number cfDNA samples with a result

  4 months

• Discordance per chromosome between results for cfDNA in SCM and trophectoderm biopsies

  Discordance per chromosome: number of misidentified chromosomal errors/24\*total number of embryos with cfDNA result

  4 months

• Concordance per chromosome between results for cfDNA in SCM and trophectoderm

  Chromosome error concordance: number of correctly identified chromosomal errors/total number of chromosomal errors detected

  4 months

• Sensitivity of niPGT-A using cfDNA in SCM

  False negative rate: 1- (true euploid result/total number of samples with a result)

  4 months

• Specificity of niPGT-A using cfDNA in SCM

  False positive rate: 1- (true aneuploid result/total number of samples with a result)

  4 months

Secondary Outcomes (6)

• Pregnancy outcome for patients having an embryo transfer - Implantation rate

  12 months

• Pregnancy outcome for patients having an embryo transfer - Biochemical pregnancy rate

  12 months

• Pregnancy outcome for patients having an embryo transfer - Clinical pregnancy rate

  12 months

• Pregnancy outcome for patients having an embryo transfer - Miscarriage rate

  12 months

• Pregnancy outcome for patients having an embryo transfer - Clinical pregnancy rate

  12 months

Study Arms (1)

Two types of samples (TE and SCM) will be collected for all blastocysts included in the study

Diagnostic Test: PGT-A / niPGT-A

Interventions

PGT-A / niPGT-A DIAGNOSTIC_TEST

PGT-A and niPGT-A will be performed using next generation sequencing (NGS) analysis for chromosome copy number variation (CNV). Embryo transfers will rely solely on the results of PGT-A for trophectoderm biopsies.

Two types of samples (TE and SCM) will be collected for all blastocysts included in the study

Eligibility Criteria

• Age: 18 Years - 46 Years
• Sex: female
• Healthy Volunteers: Yes
• Age Groups: Adult (18-64)
• Sampling Method: Non-Probability Sample

Study Population

Day 6 blastocysts generated from couples undergoing fertility treatment with PGT-A and meeting the eligibility criteria

You may qualify if:

• Patients undergoing fertility treatment with PGT-A (Recombinant FSH antagonist protocol with dual trigger)
• Secondary infertility
• BMI 18- 35 kg/m2
• Sperm: fresh ejaculated sperm (abstinence: 2-3 days)
• At least one blastocyst biopsied on day 6

You may not qualify if:

• High progesterone on day of trigger (\>1.5ng/ml)
• Vitrified oocytes
• Frozen sperm
• Indications for PGT-SR and PGT-M

Sponsors & Collaborators

• ART Fertility Clinics LLC: lead

Related Publications (10)

• Shamonki MI, Jin H, Haimowitz Z, Liu L. Proof of concept: preimplantation genetic screening without embryo biopsy through analysis of cell-free DNA in spent embryo culture media. Fertil Steril. 2016 Nov;106(6):1312-1318. doi: 10.1016/j.fertnstert.2016.07.1112. Epub 2016 Aug 24.

  PMID: 27565258 BACKGROUND

• Xu J, Fang R, Chen L, Chen D, Xiao JP, Yang W, Wang H, Song X, Ma T, Bo S, Shi C, Ren J, Huang L, Cai LY, Yao B, Xie XS, Lu S. Noninvasive chromosome screening of human embryos by genome sequencing of embryo culture medium for in vitro fertilization. Proc Natl Acad Sci U S A. 2016 Oct 18;113(42):11907-11912. doi: 10.1073/pnas.1613294113. Epub 2016 Sep 29.

  PMID: 27688762 BACKGROUND

• Feichtinger M, Vaccari E, Carli L, Wallner E, Madel U, Figl K, Palini S, Feichtinger W. Non-invasive preimplantation genetic screening using array comparative genomic hybridization on spent culture media: a proof-of-concept pilot study. Reprod Biomed Online. 2017 Jun;34(6):583-589. doi: 10.1016/j.rbmo.2017.03.015. Epub 2017 Mar 28.

  PMID: 28416168 BACKGROUND

• Rubio C, Navarro-Sanchez L, Garcia-Pascual CM, Ocali O, Cimadomo D, Venier W, Barroso G, Kopcow L, Bahceci M, Kulmann MIR, Lopez L, De la Fuente E, Navarro R, Valbuena D, Sakkas D, Rienzi L, Simon C. Multicenter prospective study of concordance between embryonic cell-free DNA and trophectoderm biopsies from 1301 human blastocysts. Am J Obstet Gynecol. 2020 Nov;223(5):751.e1-751.e13. doi: 10.1016/j.ajog.2020.04.035. Epub 2020 May 26.

  PMID: 32470458 BACKGROUND

• Fang R, Yang W, Zhao X, Xiong F, Guo C, Xiao J, Chen L, Song X, Wang H, Chen J, Xiao X, Yao B, Cai LY. Chromosome screening using culture medium of embryos fertilised in vitro: a pilot clinical study. J Transl Med. 2019 Mar 8;17(1):73. doi: 10.1186/s12967-019-1827-1.

  PMID: 30849973 BACKGROUND

• Huang L, Bogale B, Tang Y, Lu S, Xie XS, Racowsky C. Noninvasive preimplantation genetic testing for aneuploidy in spent medium may be more reliable than trophectoderm biopsy. Proc Natl Acad Sci U S A. 2019 Jul 9;116(28):14105-14112. doi: 10.1073/pnas.1907472116. Epub 2019 Jun 24.

  PMID: 31235575 BACKGROUND

• Capalbo A, Romanelli V, Patassini C, Poli M, Girardi L, Giancani A, Stoppa M, Cimadomo D, Ubaldi FM, Rienzi L. Diagnostic efficacy of blastocoel fluid and spent media as sources of DNA for preimplantation genetic testing in standard clinical conditions. Fertil Steril. 2018 Oct;110(5):870-879.e5. doi: 10.1016/j.fertnstert.2018.05.031.

  PMID: 30316433 BACKGROUND

• Ho JR, Arrach N, Rhodes-Long K, Ahmady A, Ingles S, Chung K, Bendikson KA, Paulson RJ, McGinnis LK. Pushing the limits of detection: investigation of cell-free DNA for aneuploidy screening in embryos. Fertil Steril. 2018 Aug;110(3):467-475.e2. doi: 10.1016/j.fertnstert.2018.03.036. Epub 2018 Jun 28.

  PMID: 29960707 BACKGROUND

• Kuznyetsov V, Madjunkova S, Antes R, Abramov R, Motamedi G, Ibarrientos Z, Librach C. Evaluation of a novel non-invasive preimplantation genetic screening approach. PLoS One. 2018 May 10;13(5):e0197262. doi: 10.1371/journal.pone.0197262. eCollection 2018.

  PMID: 29746572 BACKGROUND

• Vera-Rodriguez M, Diez-Juan A, Jimenez-Almazan J, Martinez S, Navarro R, Peinado V, Mercader A, Meseguer M, Blesa D, Moreno I, Valbuena D, Rubio C, Simon C. Origin and composition of cell-free DNA in spent medium from human embryo culture during preimplantation development. Hum Reprod. 2018 Apr 1;33(4):745-756. doi: 10.1093/humrep/dey028.

  PMID: 29471395 BACKGROUND

Biospecimen

Retention: SAMPLES WITH DNA

Samples to be collected: * Saliva sample from female patient for maternal DNA contamination assessment * Spent culture media (SCM) collected on the day of biopsy * Trophectoderm (TE) biopsy for clinical PGT-A All samples collected for the study will be labelled with anonymised sample identifiers and cryopreserved until time of analysis. SCM samples will be stored at -80°C and TE biopsies at -20°C. Saliva samples will be stored at room temperature prior to DNA extraction. Extracted/amplified DNA will be stored at 4°C until completion of analysis, then at -20°C. Once the study is finalised, all stored samples will be destroyed.

Study Officials

• Souraya Jaroudi

  ART Fertility Clinics

  PRINCIPAL INVESTIGATOR

Study Design

• Study Type: observational
• Observational Model: COHORT
• Time Perspective: PROSPECTIVE
• Sponsor Type: OTHER
• Responsible Party: SPONSOR

Study Record Dates

• First Submitted: January 8, 2021
• First Posted: January 15, 2021
• Study Start: October 15, 2021
• Primary Completion: October 15, 2021
• Study Completion: October 15, 2021
• Last Updated: March 20, 2023

Record last verified: 2023-03