Preimplantation Genetic Testing for Monogenic Conditions: Is Cell-Free DNA Testing the Next Step?

Rogers, Alice P; Menezes, Melody; Kane, Stefan C.; Zander-Fox, Deirdre; Hardy, Tristan

doi:10.1007/s40291-021-00556-0

Cited by 6 publications

(4 citation statements)

References 72 publications

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“…Currently, most studies have focused on niPGT for aneuploides, or niPGT-A. However, the next challenge for niPGT, that is already under investigation by some research groups, is to extent the indication not only for genetic assessment of the chromosome copy number but even to do embryonic analysis of segmental rearrangement, for monogenic conditions (Rogers et al, 2021) or diagnostic reassessment of putative mosaicism .…”

Section: Non-invasive Pgtamentioning

confidence: 99%

The embryo non-invasive pre-implantation diagnosis era: how far are we?

del Collado,

Andrade,

Gonçalves

et al. 2023

Anim. Reprod.

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Advancements in assisted reproduction (AR) methodologies have allowed significant improvements in live birth rates of women who otherwise would not be able to conceive. One of the tools that allowed this improvement is the possibility of embryo selection based on genetic status, performed via preimplantation genetic testing (PGT). Even though the widespread use of PGT from TE biopsy helped to decrease the interval from the beginning of the AR intervention to pregnancy, especially in older patients, in AR, there are still many concerns about the application of this invasive methodology in all cycles. Therefore, recently, researchers started to study the use of cell free DNA (cfDNA) released by the blastocyst in its culture medium to perform PGT, in a method called non-invasive PGT (niPGT). The development of a niPGT would bring the diagnostics power of conventional PGT, but with the advantage of being potentially less harmful to the embryo. Its implementation in clinical practice, however, is under heavy discussion since there are many unknowns about the technique, such as the origin of the cfDNA or if this genetic material is a true representative of the actual ploidy status of the embryo. Available data indicates that there is high correspondence between results observed in TE biopsies and the ones observed from cfDNA, but these results are still contradictory and highly debatable. In the present review, the advantages and disadvantages of niPGT are presented and discussed in relation to tradition TE biopsy-based PGT. Furthermore, there are also presented some other possible non-invasive tools that could be applied in the selection of the best embryo, such as quantification of other molecules as quality biomarkers, or the use artificial intelligence (AI) to identify the best embryos based on morphological and/or morphokitetic parameters.

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Section: Non-invasive Pgtamentioning

confidence: 99%

The embryo non-invasive pre-implantation diagnosis era: how far are we?

del Collado,

Andrade,

Gonçalves

et al. 2023

Anim. Reprod.

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“…Discrepancies have been found regarding the concordance of the embryonic genetic state obtained from SECM and other DNA sources, including polar bodies, embryos, and TE biopsies, and whole embryos. There have been many discussions and suggestions on standardization and validation methods in several review papers on this issue [90,113,[122][123][124][125]. With the latest advanced methods, such as NGS and mass spectrometry, which have recently emerged as superior analysis methods, it has become possible to verify the source of the genetic sample used for analysis and assess the probability of accurately estimating the genetic state of the embryo [126].…”

Section: Clinical Outcomes Of Tlms and Secm Analysis In Human Ivf-et ...mentioning

confidence: 99%

Non-invasive evaluation of embryo quality for the selection of transferable embryos in human in vitro fertilization-embryo transfer

Kim

Lee

Jun

2022

Clin Exp Reprod Med

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The ultimate goal of human assisted reproductive technology is to achieve a healthy pregnancy and birth, ideally from the selection and transfer of a single competent embryo. Recently, techniques for efficiently evaluating the state and quality of preimplantation embryos using time-lapse imaging systems have been applied. Artificial intelligence programs based on deep learning technology and big data analysis of time-lapse monitoring system during in vitro culture of preimplantation embryos have also been rapidly developed. In addition, several molecular markers of the secretome have been successfully analyzed in spent embryo culture media, which could easily be obtained during in vitro embryo culture. It is also possible to analyze small amounts of cell-free nucleic acids, mitochondrial nucleic acids, miRNA, and long non-coding RNA derived from embryos using real-time polymerase chain reaction (PCR) or digital PCR, as well as next-generation sequencing. Various efforts are being made to use non-invasive evaluation of embryo quality (NiEEQ) to select the embryo with the best developmental competence. However, each NiEEQ method has some limitations that should be evaluated case by case. Therefore, an integrated analysis strategy fusing several NiEEQ methods should be urgently developed and confirmed by proper clinical trials.

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“…Traditionally, the approach to PGT-M has been to develop patient-specific assays, typically a composite of the mutation and nearby short tandem repeat (STR) markers, which are then used to directly analyze embryonic DNA for the causative parental single-gene mutation(s), with linked STRs enabling accurate embryo genotyping ( Rechitsky et al, 2015 ). As an alternative indirect approach, SNP-based genome-wide karyomapping has been developed ( Chang et al, 2023 ) to enable PGT-M to be successfully performed directly on embryonic multiple displacement amplification (MDA) products for almost any monogenic disease ( Rogers et al, 2021 ; Ou et al, 2022 ). More recently, whole exome and whole genome haplotype sequencing methods have been shown to provide accurate embryo genotyping for PGT-M cases ( Masset et al, 2019 ; Rogers et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

“…As an alternative indirect approach, SNP-based genome-wide karyomapping has been developed ( Chang et al, 2023 ) to enable PGT-M to be successfully performed directly on embryonic multiple displacement amplification (MDA) products for almost any monogenic disease ( Rogers et al, 2021 ; Ou et al, 2022 ). More recently, whole exome and whole genome haplotype sequencing methods have been shown to provide accurate embryo genotyping for PGT-M cases ( Masset et al, 2019 ; Rogers et al, 2021 ). Even more recently, proof of concept for PGT-M in an alpha thalassemia deletion was demonstrated by direct third-generation sequencing of embryonic MDA products ( Liu et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Proband-independent haplotyping based on NGS-based long-read sequencing for detecting pathogenic variant carrier status in preimplantation genetic testing for monogenic diseases

Zhang,

Zhao,

et al. 2024

Front. Mol. Biosci.

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Preimplantation genetic testing for monogenic diseases (PGT-M) can be used to select embryos that do not develop disease phenotypes or carry disease-causing genes for implantation into the mother’s uterus, to block disease transmission to the offspring, and to increase the birth rate of healthy newborns. However, the traditional PGT-M technique has some limitations, such as its time consumption, experimental procedural complexity, and the need for a complete family or reference embryo to construct the haplotype. In this study, proband-independent haplotyping based on NGS-based long-read sequencing (Phbol-seq) was used to effectively construct haplotypes. By targeting the mutation sites of single gene disease point mutations and small fragment deletion carriers, embryos carrying parental disease-causing mutations were successfully identified by linkage analysis. The efficiency of embryo resolution was then verified by classical Sanger sequencing, and it was confirmed that the construction of haplotype and SNP linkage analysis by Phbol-seq could accurately and effectively detect whether embryos carried parental pathogenic mutations. After the embryos confirmed to be nonpathogenic by Phbol-seq-based PGT-M and confirmed to have normal copy number variation by Phbol-seq-based PGT-A were transplanted into the uterus, gene detection in amniotic fluid of the implanted embryos was performed, and the results confirmed that Phbol-seq technology could accurately distinguish normal genotype embryos from genetically modified carrier embryos. Our results suggest that Phbol-seq is an effective strategy for accurately locating mutation sites and accurately distinguishing between embryos that inherit disease-causing genes and normal embryos that do not. This is critical for Phbol-seq-based PGT-M and could help more single-gene disease carriers with incomplete families, de novo mutations or suspected germline mosaicism to have healthy babies with normal phenotypes. It also helps to reduce the transmission of monogenic genetic diseases in the population.

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Preimplantation Genetic Testing for Monogenic Conditions: Is Cell-Free DNA Testing the Next Step?

Cited by 6 publications

References 72 publications

The embryo non-invasive pre-implantation diagnosis era: how far are we?

The embryo non-invasive pre-implantation diagnosis era: how far are we?

Non-invasive evaluation of embryo quality for the selection of transferable embryos in human in vitro fertilization-embryo transfer

Proband-independent haplotyping based on NGS-based long-read sequencing for detecting pathogenic variant carrier status in preimplantation genetic testing for monogenic diseases

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