Special Issue "EmbryoGenetics"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (4 May 2020).

Special Issue Editors

Prof. Carlos Simón

Guest Editor
1) Professor of Obstetrics & Gynecology, Valencia University, Valencia, Spain
2) Senior Lecturer PT, BIDMC Harvard University, Boston, MA, USA
3) Adjunct Clinical Professor, Department of Ob/Gyn, Baylor College of Medicine, Houston, TX, USA
Dr. Carmen Rubio

Co-Guest Editor
Director of Embryo Genetics Research, Igenomix, Spain

Special Issue Information

Dear Colleagues,

The science of human genetics has advanced at an exponential pace since the double-helix structure of DNA was identified in 1953. Within only 25 years of that discovery, the first gene was sequenced. Subsequent efforts in the span of a few decades have brought advanced next-generation sequencing and new tools for genome editing, allowing scientists to write and rewrite the code of life. We are now realizing that genetics represents yet another system of information technology that follows Moore’s law, stating that computer processing power roughly doubles every two years. Importantly, with such rapid and sophisticated advancements, any tools or studies applicable for adult genetics can now also be applied in embryos.

Genetic disorders affect 1% of live births and are responsible for 20% of pediatric hospitalizations and 20% of infant mortality. Many disorders are caused by recessive or X-linked genetic mutations carried by 85% of humans. Because assisted reproduction has armed us with technologies like in vitro fertilization that provide access to human embryos, we began to screen some genetic diseases simply by selecting sex. The first live births following preimplantation genetic testing (PGT) to identify sex in X-linked disease were reported by Alan Handyside in 1990. This groundbreaking work used the identification of male embryos and selective transfer of unaffected normal or carrier females as proof-of-concept to avoid genetic diseases, paving the way to extend the concept to PGT for monogenic diseases (PGT-M), including Mendelian single-gene defects (autosomal dominant/recessive, X-linked dominant/recessive), severe childhood lethality or early-onset disease, cancer predisposition, and HLA typing for histocompatible cord-blood stem cells transplantation. Later we moved to the identification and selection of euploid embryos by analyzing all 23 pairs of chromosomes in 4–8 cells from the trophectoderm, called PGT for aneuploidy (PGT-A). PGT-A currently leverages next-generation sequencing technologies to uncover meiotic- and mitotic-origin aneuploidies affecting whole chromosomes, as well as duplications/deletions of small chromosome regions. A step forward was the use of structural chromosome rearrangements (PGT-SR) to identify Robertsonian and reciprocal translocations, inversions, and balanced vs. unbalanced rearrangements. Another advancement came with PGT for polygenic risk scoring (PGT-P). This technique takes us from learning how to read simple words to starting to understand poetry (i.e., evolving from PGT-M/A/SR to PGT-P for multifactorial, polygenic risk prediction). Common multifactorial diseases like diabetes, coronary heart disease, and cancer are caused by a combination of environmental, lifestyle, and genetic factors; risk scores are now being generated to predict in embryos the likelihood of such complex, later-life diseases. Moreover, we are moving from embryo selection to intervention because the genetic code is not only readable, but also re-writeable. Indeed, gene editing is now possible using tools like CRISPR/Cas9 applicable to all species, including human embryos.

In this Special Issue, we invite reviews, primers, and original research papers that contribute to our understanding of human embryo genetics. Specifically, we would like to compile the current knowledge in PGT for monogenic diseases (PGT-M), PGT for aneuploidy (PGT-A) including mosaicism, PGT for polygenic risk scoring (PGT-P), and gene editing in human embryos. Manuscripts can target both basic science as well as the clinical impact of embryogenetics in reproductive medicine, maternal-fetal medicine, and pediatrics. We look forward to your submissions.

Prof. Carlos Simón
Dr. Carmen Rubio
Guest Editor

Manuscript Submission Information

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Keywords

  • embryos
  • genetics
  • PGT
  • human
  • monogenic diseases
  • aneuploidy
  • mosaicism
  • polygenic risk scoring
  • gene editing

Published Papers (6 papers)

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Research

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Open AccessArticle
Optimized NGS Approach for Detection of Aneuploidies and Mosaicism in PGT-A and Imbalances in PGT-SR
Genes 2020, 11(7), 724; https://doi.org/10.3390/genes11070724 - 29 Jun 2020
Cited by 1
Abstract
The detection of chromosomal aneuploidies and mosaicism degree in preimplantation embryos may be essential for achieving pregnancy. The aim of this study was to determine the robustness of diagnosing homogenous and mosaic aneuploidies using a validated algorithm and the minimal resolution for de [...] Read more.
The detection of chromosomal aneuploidies and mosaicism degree in preimplantation embryos may be essential for achieving pregnancy. The aim of this study was to determine the robustness of diagnosing homogenous and mosaic aneuploidies using a validated algorithm and the minimal resolution for de novo and inherited deletions and duplications (Del/Dup). Two workflows were developed and validated: (a,b) preimplantation genetic testing for uniform whole and segmental aneuploidies, plus mixtures of euploid/aneuploid genomic DNA to develop an algorithm for detecting mosaicism; and (c) preimplantation genetic testing for structural rearrangements for detecting Del/Dup ≥ 6 Mb. Next-generation sequencing (NGS) was performed with automatic library preparation and multiplexing up to 24–96 samples. Specificity and sensitivity for PGT-A were both 100% for whole chromosomes and segmentals. The thresholds stablished for mosaicism were: euploid embryos (<30% aneuploidy), low mosaic (from 30% to <50%), high mosaic (50–70%) or aneuploid (>70%). In the PGT-SR protocol, changes were made to increase the detection level to ≥6 Mb. This is the first study reporting an accurate assessment of semiautomated-NGS protocols using Reproseq on pools of cells. Both protocols allow for the analysis of homogeneous and segmental aneuploidies, different degrees of mosaicism, and small Del/Dup with high sensitivity and specificity. Full article
(This article belongs to the Special Issue EmbryoGenetics)
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Open AccessFeature PaperArticle
Combined Preimplantation Genetic Testing for Autosomal Dominant Polycystic Kidney Disease: Consequences for Embryos Available for Transfer
Genes 2020, 11(6), 692; https://doi.org/10.3390/genes11060692 - 24 Jun 2020
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary kidney disease and presents with genetic and clinical heterogeneity. ADPKD can also manifest extra-renally, and seminal cysts have been associated with male infertility in some cases. ADPKD-linked male infertility, along with female [...] Read more.
Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary kidney disease and presents with genetic and clinical heterogeneity. ADPKD can also manifest extra-renally, and seminal cysts have been associated with male infertility in some cases. ADPKD-linked male infertility, along with female age, have been proposed as factors that may influence the clinical outcomes of preimplantation genetic testing (PGT) for monogenic disorders (PGT-M). Large PGT for aneuploidy assessment (PGT-A) studies link embryo aneuploidy to increasing female age; other studies suggest that embryo aneuploidy is also linked to severe male-factor infertility. We aimed to assess the number of aneuploid embryos and the number of cycles with transferable embryos in ADPKD patients after combined-PGT. The combined-PGT protocol, involving PGT-M by PCR and PGT-A by next-generation sequencing, was performed in single trophectoderm biopsies from 289 embryos in 83 PGT cycles. Transferable embryos were obtained in 69.9% of cycles. The number of aneuploid embryos and cycles with transferable embryos did not differ when the male or female had the ADPKD mutation. However, a significantly higher proportion of aneuploid embryos was found in the advanced maternal age (AMA) group, but not in the male factor (MF) group, when compared to non-AMA and non-MF groups, respectively. Additionally, no significant differences in the percentage of cycles with transferable embryos were found in any of the groups. Our results indicate that AMA couples among ADPKD patients have an increased risk of aneuploid embryos, but ADPKD-linked male infertility does not promote an increased aneuploidy rate. Full article
(This article belongs to the Special Issue EmbryoGenetics)
Open AccessArticle
Preimplantation Genetic Testing for Polygenic Disease Relative Risk Reduction: Evaluation of Genomic Index Performance in 11,883 Adult Sibling Pairs
Genes 2020, 11(6), 648; https://doi.org/10.3390/genes11060648 - 12 Jun 2020
Abstract
Preimplantation genetic testing for polygenic disease risk (PGT-P) represents a new tool to aid in embryo selection. Previous studies demonstrated the ability to obtain necessary genotypes in the embryo with accuracy equivalent to in adults. When applied to select adult siblings with known [...] Read more.
Preimplantation genetic testing for polygenic disease risk (PGT-P) represents a new tool to aid in embryo selection. Previous studies demonstrated the ability to obtain necessary genotypes in the embryo with accuracy equivalent to in adults. When applied to select adult siblings with known type I diabetes status, a reduction in disease incidence of 45–72% compared to random selection was achieved. This study extends analysis to 11,883 sibling pairs to evaluate clinical utility of embryo selection with PGT-P. Results demonstrate simultaneous relative risk reduction of all diseases tested in parallel, which included diabetes, cancer, and heart disease, and indicate applicability beyond patients with a known family history of disease. Full article
(This article belongs to the Special Issue EmbryoGenetics)
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Open AccessArticle
Identification and Characterization of Extracellular Vesicles and Its DNA Cargo Secreted During Murine Embryo Development
Genes 2020, 11(2), 203; https://doi.org/10.3390/genes11020203 - 17 Feb 2020
Cited by 1
Abstract
Extracellular vesicles (EVs) are known to transport DNA, but their implications in embryonic implantation are unknown. The aim of this study was to investigate EVs production and secretion by preimplantation embryos and assess their DNA cargo. Murine oocytes and embryos were obtained from [...] Read more.
Extracellular vesicles (EVs) are known to transport DNA, but their implications in embryonic implantation are unknown. The aim of this study was to investigate EVs production and secretion by preimplantation embryos and assess their DNA cargo. Murine oocytes and embryos were obtained from six- to eight-week-old females, cultured until E4.5 and analyzed using transmission electron microscopy to examine EVs production. EVs were isolated from E4.5-day conditioned media and quantified by nanoparticle tracking analysis, characterized by immunogold, and their DNA cargo sequenced. Multivesicular bodies were observed in murine oocytes and preimplantation embryos together with the secretion of EVs to the blastocoel cavity and blastocyst spent medium. Embryo-derived EVs showed variable electron-densities and sizes (20–500 nm) and total concentrations of 1.74 × 107 ± 2.60 × 106 particles/mL. Embryo secreted EVs were positive for CD63 and ARF6. DNA cargo sequencing demonstrated no differences in DNA between apoptotic bodies or smaller EVs, although they showed significant gene enrichment compared to control medium. The analysis of sequences uniquely mapping the murine genome revealed that DNA contained in EVs showed higher representation of embryo genome than vesicle-free DNA. Murine blastocysts secrete EVs containing genome-wide sequences of DNA to the medium, reinforcing the relevance of studying these vesicles and their cargo in the preimplantation moment, where secreted DNA may help the assessment of the embryo previous to implantation. Full article
(This article belongs to the Special Issue EmbryoGenetics)
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Review

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Open AccessFeature PaperReview
Preimplantation Genetic Testing for Chromosomal Abnormalities: Aneuploidy, Mosaicism, and Structural Rearrangements
Genes 2020, 11(6), 602; https://doi.org/10.3390/genes11060602 - 29 May 2020
Abstract
There is a high incidence of chromosomal abnormalities in early human embryos, whether they are generated by natural conception or by assisted reproductive technologies (ART). Cells with chromosomal copy number deviations or chromosome structural rearrangements can compromise the viability of embryos; much of [...] Read more.
There is a high incidence of chromosomal abnormalities in early human embryos, whether they are generated by natural conception or by assisted reproductive technologies (ART). Cells with chromosomal copy number deviations or chromosome structural rearrangements can compromise the viability of embryos; much of the naturally low human fecundity as well as low success rates of ART can be ascribed to these cytogenetic defects. Chromosomal anomalies are also responsible for a large proportion of miscarriages and congenital disorders. There is therefore tremendous value in methods that identify embryos containing chromosomal abnormalities before intrauterine transfer to a patient being treated for infertility—the goal being the exclusion of affected embryos in order to improve clinical outcomes. This is the rationale behind preimplantation genetic testing for aneuploidy (PGT-A) and structural rearrangements (-SR). Contemporary methods are capable of much more than detecting whole chromosome abnormalities (e.g., monosomy/trisomy). Technical enhancements and increased resolution and sensitivity permit the identification of chromosomal mosaicism (embryos containing a mix of normal and abnormal cells), as well as the detection of sub-chromosomal abnormalities such as segmental deletions and duplications. Earlier approaches to screening for chromosomal abnormalities yielded a binary result of normal versus abnormal, but the new refinements in the system call for new categories, each with specific clinical outcomes and nuances for clinical management. This review intends to give an overview of PGT-A and -SR, emphasizing recent advances and areas of active development. Full article
(This article belongs to the Special Issue EmbryoGenetics)
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Open AccessReview
Mother and Embryo Cross-Communication
Genes 2020, 11(4), 376; https://doi.org/10.3390/genes11040376 - 31 Mar 2020
Abstract
Endometrial receptivity is a biosensor for embryo quality, as embryos with reduced developmental potential are rejected. However, embryo quality only accounts for an estimated one-third of implantation failures, with suboptimal endometrial receptivity accounting for the remaining two-thirds. As pregnancy progresses, a uterus continues [...] Read more.
Endometrial receptivity is a biosensor for embryo quality, as embryos with reduced developmental potential are rejected. However, embryo quality only accounts for an estimated one-third of implantation failures, with suboptimal endometrial receptivity accounting for the remaining two-thirds. As pregnancy progresses, a uterus continues to engage in close communication with an embryo/fetus, exchanging information in the form of endocrine, paracrine, and other cues. Given the long mammalian gestation period, this dialogue is intricate, diverse, and, currently, not fully understood. Recent progress and the availability of high-throughput techniques, including transcriptomics, proteomics, and metabolomics, has allowed the simultaneous examination of multiple molecular changes, enhancing our knowledge in this area. This review covers the known mechanisms of mother–embryo cross-communication gathered from animal and human studies. Full article
(This article belongs to the Special Issue EmbryoGenetics)
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