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).

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A printed edition of this Special Issue is available here.

Special Issue Editors

Prof. Carlos Simón
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Guest Editor
1. Deparrtment of Obstetrics & Gynecology, Valencia University, Valencia, Spain
2. BIDMC Harvard University, Boston, MA, USA
3. Department of Ob/Gyn, Baylor College of Medicine, Houston, TX, USA
Dr. Carmen Rubio
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Co-Guest Editor
Director of Embryo Genetics Research, Igenomix, 46980 Valencia, 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 (11 papers)

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Editorial

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Editorial
Embryo Genetics
Genes 2021, 12(1), 118; https://doi.org/10.3390/genes12010118 - 19 Jan 2021
Viewed by 842
Abstract
Advances in embryo and reproductive genetics have influenced clinical approaches to overcome infertility. Since the 1990s, many attempts have been made to decipher the genetic causes of infertility and to understand the role of chromosome aneuploidies in embryo potential. At the embryo stage, [...] Read more.
Advances in embryo and reproductive genetics have influenced clinical approaches to overcome infertility. Since the 1990s, many attempts have been made to decipher the genetic causes of infertility and to understand the role of chromosome aneuploidies in embryo potential. At the embryo stage, preimplantation genetic testing for chromosomal abnormalities and genetic disorders has offered many couples the opportunity to have healthy offspring. Recently, the application of new technologies has resulted in more comprehensive and accurate diagnoses of chromosomal abnormalities and genetic conditions to improve clinical outcome. In this Special Issue, we include a collection of reviews and original articles covering many aspects of embryo diagnosis, genome editing, and maternal–embryo cross-communication during the implantation process. Full article
(This article belongs to the Special Issue EmbryoGenetics)

Research

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Article
Characteristics of the IVF Cycle that Contribute to the Incidence of Mosaicism
Genes 2020, 11(10), 1151; https://doi.org/10.3390/genes11101151 - 30 Sep 2020
Cited by 2 | Viewed by 795
Abstract
Highly sensitive next-generation sequencing (NGS) platforms applied to preimplantation genetic testing for aneuploidy (PGT-A) allow the classification of mosaicism in trophectoderm biopsies. However, the incidence of mosaicism reported by these tests can be affected by a wide number of analytical, biological, and clinical [...] Read more.
Highly sensitive next-generation sequencing (NGS) platforms applied to preimplantation genetic testing for aneuploidy (PGT-A) allow the classification of mosaicism in trophectoderm biopsies. However, the incidence of mosaicism reported by these tests can be affected by a wide number of analytical, biological, and clinical factors. With the use of a proprietary algorithm for automated diagnosis of aneuploidy and mosaicism, we retrospectively analyzed a large series of 115,368 trophectoderm biopsies from 27,436 PGT-A cycles to determine whether certain biological factors and in vitro fertilization (IVF) practices influence the incidence of overall aneuploidy, whole uniform aneuploidy, mosaicism, and TE biopsies with only segmental aneuploidy. Older female and male patients showed higher rates of high-mosaic degree and whole uniform aneuploidies and severe oligozoospermic patients had higher rates of mosaicism and only segmental aneuploidies. Logistic regression analysis identified a positive effect of female age but a negative effect of embryo vitrification on the incidence of overall aneuploid embryos. Female age increased whole uniform aneuploidy rates but decreased only segmental aneuploidy and mosaicism, mainly low-mosaics. Conversely, higher ovarian response decreased whole uniform aneuploidy rates but increased only segmental aneuploidies. Finally, embryo vitrification decreased whole uniform aneuploidy rates but increased mosaicism, mainly low-mosaics, compared to PGT-A cycles with fresh oocytes. These results could be useful for clinician’s management of the IVF cycles. Full article
(This article belongs to the Special Issue EmbryoGenetics)
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Article
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 10 | Viewed by 1328
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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Article
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
Cited by 3 | Viewed by 802
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)
Article
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
Cited by 6 | Viewed by 3960
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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Article
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 8 | Viewed by 1214
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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Review
The Reproductive Journey in the Genomic Era: From Preconception to Childhood
Genes 2020, 11(12), 1521; https://doi.org/10.3390/genes11121521 - 19 Dec 2020
Cited by 1 | Viewed by 759
Abstract
It is estimated that around 10–15% of the population have problems achieving a pregnancy. Assisted reproduction techniques implemented and enforced by personalized genomic medicine have paved the way for millions of infertile patients to become parents. Nevertheless, having a baby is just the [...] Read more.
It is estimated that around 10–15% of the population have problems achieving a pregnancy. Assisted reproduction techniques implemented and enforced by personalized genomic medicine have paved the way for millions of infertile patients to become parents. Nevertheless, having a baby is just the first challenge to overcome in the reproductive journey, the most important is to obtain a healthy baby free of any genetic condition that can be prevented. Prevention of congenital anomalies throughout the lifespan of the patient must be a global health priority. Congenital disorders can be defined as structural or functional anomalies that occur during intrauterine life and can be identified prenatally, at birth, or sometimes may only be detected later during childhood. It is considered a frequent group of disorders, affecting 3–6% of the population, and one of the leading causes of morbidity and mortality. Congenital anomalies can represent up to 30–50% of infant mortality in developed countries. Genetics plays a substantial role in the pathogenesis of congenital anomalies. This becomes especially important in some ethnic communities or populations where the incidence and levels of consanguinity are higher. The impact of genetic disorders during childhood is high, representing 20–30% of all infant deaths and 11.1% of pediatric hospital admissions. With these data, obtaining a precise genetic diagnosis is one of the main aspects of a preventive medicine approach in developed countries. The field of reproductive health has changed dramatically from traditional non-molecular visual microscope-based techniques (i.e., fluorescence in situ hybridization (FISH) or G-banding karyotype), to the latest molecular high-throughput techniques such as next-generation sequencing (NGS). Genome-wide technologies are applied along the different stages of the reproductive health lifecycle from preconception carrier screening and pre-implantation genetic testing, to prenatal and postnatal testing. The aim of this paper is to assess the new horizon opened by technologies such as next-generation sequencing (NGS), in new strategies, as a genomic precision diagnostic tool to understand the mechanisms underlying genetic conditions during the “reproductive journey”. Full article
(This article belongs to the Special Issue EmbryoGenetics)
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Review
Use of Customizable Nucleases for Gene Editing and Other Novel Applications
Genes 2020, 11(9), 976; https://doi.org/10.3390/genes11090976 - 22 Aug 2020
Cited by 5 | Viewed by 1187
Abstract
The development of novel genome editing tools has unlocked new opportunities that were not previously possible in basic and biomedical research. During the last two decades, several new genome editing methods have been developed that can be customized to modify specific regions of [...] Read more.
The development of novel genome editing tools has unlocked new opportunities that were not previously possible in basic and biomedical research. During the last two decades, several new genome editing methods have been developed that can be customized to modify specific regions of the genome. However, in the past couple of years, many newer and more exciting genome editing techniques have been developed that are more efficient, precise, and easier to use. These genome editing tools have helped to improve our understanding of genetic disorders by modeling them in cells and animal models, in addition to correcting the disease-causing mutations. Among the genome editing tools, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system has proven to be the most popular one due to its versatility and has been successfully used in a wide variety of laboratory animal models and plants. In this review, we summarize the customizable nucleases currently used for genome editing and their uses beyond the modification of genome. We also discuss the potential future applications of gene editing tools for both basic research and clinical purposes. Full article
(This article belongs to the Special Issue EmbryoGenetics)
Review
Preimplantation Genetic Testing for Monogenic Disorders
Genes 2020, 11(8), 871; https://doi.org/10.3390/genes11080871 - 31 Jul 2020
Cited by 5 | Viewed by 1396
Abstract
Preimplantation genetic testing (PGT) has evolved into a well-established alternative to invasive prenatal diagnosis, even though genetic testing of single or few cells is quite challenging. PGT-M is in theory available for any monogenic disorder for which the disease-causing locus has been unequivocally [...] Read more.
Preimplantation genetic testing (PGT) has evolved into a well-established alternative to invasive prenatal diagnosis, even though genetic testing of single or few cells is quite challenging. PGT-M is in theory available for any monogenic disorder for which the disease-causing locus has been unequivocally identified. In practice, the list of indications for which PGT is allowed may vary substantially from country to country, depending on PGT regulation. Technically, the switch from multiplex PCR to robust generic workflows with whole genome amplification followed by SNP array or NGS represents a major improvement of the last decade: the waiting time for the couples has been substantially reduced since the customized preclinical workup can be omitted and the workload for the laboratories has decreased. Another evolution is that the generic methods now allow for concurrent analysis of PGT-M and PGT-A. As innovative algorithms are being developed and the cost of sequencing continues to decline, the field of PGT moves forward to a sequencing-based, all-in-one solution for PGT-M, PGT-SR, and PGT-A. This will generate a vast amount of complex genetic data entailing new challenges for genetic counseling. In this review, we summarize the state-of-the-art for PGT-M and reflect on its future. Full article
(This article belongs to the Special Issue EmbryoGenetics)
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Review
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
Cited by 19 | Viewed by 2151
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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Review
Mother and Embryo Cross-Communication
Genes 2020, 11(4), 376; https://doi.org/10.3390/genes11040376 - 31 Mar 2020
Cited by 7 | Viewed by 1317
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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