Recent advances and future developments in PGD

New insights regarding origin of monosomy occurrence in early developing embryos as demonstrated in preimplantation genetic testing

Introduction

Analyses of miscarriage products indicate that the majority of aneuploidies in early developing embryos derive from errors occurring during maternal meiosis and the paternal contribution is less than 10%. Our aim was to assess the aneuploidy (mainly monosmies) frequencies at the earliest stages of embryo development, 3 days following fertilization during In vitro fertilization (IVF) treatments and to elucidate their parental origin. Later, we compared monosomies rates of day 3 to those of day 5 as demonstrated from Preimplantation Genetic Testing for Structural chromosomal Rearrangement (PGT-SR) results.

Methods

For a retrospective study, we collected data of 210 Preimplantation Genetic Testing for Monogenic Disorder (PGT-M) cycles performed between years 2008 and 2019.This study includes 2083 embryos, of 113 couples. It also included 432 embryos from 90 PGT-SR cycles of other 45 patients, carriers of balanced translocations. Defining the parental origin of aneuploidy in cleavage stage embryos was based on haplotypes analysis of at least six informative markers flanking the analyzed gene. For comprehensive chromosomal screening (CCS), chromosomal microarray (CMA) and next generation sequencing (NGS) was used.

Results

We inspected haplotype data of 40 genomic regions, flanking analyzed genes located on 9 different chromosomes.151 (7.2%) embryos presented numerical alterations in the tested chromosomes. We found similar paternal and maternal contribution to monosomy at cleavage stage. We demonstrated paternal origin in 51.5% of the monosomy, and maternal origin in 48.5% of the monosomies cases.

Conclusion

In our study, we found equal parental contribution to monosomies in cleavage-stage embryos. Comparison to CCS analyses of PGT-SR patients revealed a lower rate of monosomy per chromosome in embryos at day 5 of development. This is in contrast to the maternal dominancy described in studies of early miscarriage. Mitotic errors and paternal involvement in chemical pregnancies and IVF failure should be re-evaluated. Our results show monosomies are relatively common and may play a role in early development of ART embryos.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13039-022-00582-5.

Whole genome amplification in preimplantation genetic diagnosis

Preimplantation genetic diagnosis (PGD) refers to a procedure for genetically analyzing embryos prior to implantation, improving the chance of conception for patients at high risk of transmitting specific inherited disorders. This method has been widely used for a large number of genetic disorders since the first successful application in the early 1990s. Polymerase chain reaction (PCR) and fluorescent in situ hybridization (FISH) are the two main methods in PGD, but there are some inevitable shortcomings limiting the scope of genetic diagnosis. Fortunately, different whole genome amplification (WGA) techniques have been developed to overcome these problems. Sufficient DNA can be amplified and multiple tasks which need abundant DNA can be performed. Moreover, WGA products can be analyzed as a template for multi-loci and multi-gene during the subsequent DNA analysis. In this review, we will focus on the currently available WGA techniques and their applications, as well as the new technical trends from WGA products.

The role of preimplantation genetic diagnosis in diagnosing embryo aneuploidy

PURPOSE OF REVIEW

Use of preimplantation genetic diagnosis to improve in-vitro fertilization outcomes is reviewed.

RECENT FINDINGS

Many embryos produced in vitro contain chromosomal abnormalities and have little potential for forming a viable pregnancy. The most commonly used method for preimplantation genetic diagnosis involves embryo biopsy on day 3 of development, followed by fluorescence in-situ hybridization analysis of 5-12 chromosomes. However, positive results have been more common with single-cell biopsy and the analysis of nine or more chromosomes, including 15, 16, 21, and 22. Comparative genomic hybridization, array-comparative genomic hybridization, and single-nucleotide polymorphism arrays analyze all chromosomes and, although technically demanding and requiring experience for successful use, improve the selection potential of preimplantation genetic diagnosis and minimize error rates. Recent data suggest that biopsy at the blastocyst stage may allow sampling of representative genetic material without compromising embryo viability. The optimal strategy for aneuploidy screening using preimplantation genetic diagnosis seems to be blastocyst biopsy at 5 days and comprehensive chromosome analysis (comparative genomic hybridization, array-comparative genomic hybridization, single-nucleotide polymorphism array).

SUMMARY

The use of preimplantation genetic diagnosis to assist the identification and preferential transfer of healthy euploid embryos should improve implantation rates, reduce miscarriages and trisomic offspring, and ultimately lead to an increase in live birth rates.

Technology requirements for preimplantation genetic diagnosis to improve assisted reproduction outcomes

Preimplantation genetic diagnosis has been proposed as a method to improve assisted reproduction technology outcomes, but different techniques have produced conflicting results. The use of appropriate techniques may provide positive outcomes.

Microarray Technology for Mutation Analysis of Low-Template DNA Samples

Microarrays containing oligonucleotide mutation probes are emerging as useful platforms for the diagnosis of genetic disease. Herein, we describe the development and validation of an in-house microarray suitable for the diagnosis of common cystic fibrosis (CF) mutations in low-template DNA samples such as those taken for preimplantation genetic diagnosis and prenatal diagnosis. The success of the CF microarray was based on the ability to generate sufficient target DNA for hybridization to the array probes using either direct polymerase chain reaction (PCR) amplification or whole-genome amplification followed by PCR. From replicate experiments using target DNA carrying known CF mutations, it was possible to define strict diagnostic parameters for the accurate diagnosis of CF. This protocol serves as a general guide for DNA-testing laboratories to develop other microarray platforms that may eventually replace traditional PCR-based genetic testing in the near future.

Preimplantation genetic diagnosis: technological promise and ethical perils

OBJECTIVE

To describe the ethical issues inherent to the current and foreseeable uses of preimplantation genetic diagnosis (PGD).

DESIGN

Review of ethical principles and their application to PGD.

SETTING

Academic medical center.

PATIENT(S)

None.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

A discussion of the current ethical perils surrounding the use of PGD, and a prediction of future ethical quandaries that will arise from the use of this technology.

RESULT(S)

Although PGD may be used to predict and prevent disease, it may also be used to determine nondisease traits. The ever-expanding ability of genetics to determine qualities of the preimplantation embryo continues to open up new ethical questions relating to the use of PGD for preimplantation diagnosis.

CONCLUSION(S)

Preimplantation genetic diagnosis is a powerful technique with many positive applications. As with all such new technologies, care should be taken to ponder the ethical implications of its use before routinely accepting PGD as a tool in the reproductive armamentarium.

Cytogénétique des ovocytes humains : 40 ans de progrès

Chromosomal abnormalities account for the majority of pre- and post- implantation embryo wastage in humans. Most of these abnormalities result from maternal meiotic errors, which preferentially occur during the first meiotic division. Consequently, the cytogenetic analysis of human oocytes has then been considered as a highly valuable source of data for the investigation of both the occurrence and the origin of chromosomal abnormalities in human. During the last 4 decades, the cytogenetic analysis of human oocytes has never stopped progressing, according to the advents of new technologies. Both karyotyping and molecular cytogenetic studies have been reported to date, providing a large body of data on the incidence and the distribution of chromosomal abnormalities in human female gametes. However, these studies display a great variability in results, which may be essentially attributable to the limitations of these techniques when applied to human oocytes. The most relevant analysis have led to the estimate that 15-20% of human oocytes present chromosome abnormalities, and they have emphasized the implication of both whole chromosome non-disjunction and chromatid separation in the occurrence of aneuploidy in human oocytes. The effect of advanced maternal age on the incidence of aneuploidy in human oocytes has also been clearly evidenced by recent reports based on large sample of oocytes or polar bodies.

The chromosomal analysis of human oocytes. An overview of established procedures

The cytogenetic survey of mature human oocytes has been and remains a subject of great interest because of the prevalence of aneuploidy of maternal origin in abnormal human conceptuses, and the lack of understanding about the non-disjunction processes in human meiosis. The first attempts to analyse the chromosomal content of human female gametes were made in the early 1970s, and led to limited data because of the paucity of materials and the inadequacy of the procedure used. The years to follow brought a resurgence of interest in this field, because of the development of human IVF techniques which made oocytes unfertilized in vitro available for cytogenetic analysis. Numerous studies have since been performed. However, the difficulties in obtaining good chromosome preparations and of performing accurate chromosome identification have reduced the viability of these studies, resulting in large variations in the reported incidences of chromosomal abnormalities. The further introduction of new procedures for oocyte fixation and the screening of large oocyte samples have allowed more reliable data to be obtained and to identify premature chromatid separation as a major mechanism in aneuploidy occurrence. The last decade has been privileged to witness the adaptation of molecular cytogenetic techniques to human oocytes, and thus various powerful procedures have been tried not only on female gametes, but also on polar bodies, involving sequential and multicolour fluorescent in situ hybridization (FISH) labelling, comparative genomic hybridization (CGH), spectral karyotyping and alternative methods such as primed in situ labelling (PRINS) and peptide nucleic acid (PNA) techniques. A large body of data has been obtained, but these studies also display a great variability in the frequency of abnormalities, which may be essentially attributable to the technical limitations of these in situ methods when applied to human oocytes. However, molecular cytogenetic approaches have also evidenced the co-existence of both whole chromosome non-disjunction and chromatid separation in maternal aneuploidy. In addition, the extension of these techniques to oocyte polar body materials has provided additional data on the mechanism of meiotic malsegregation. Improvements of some of these techniques have already been reported. The further development of new approaches for the in situ analysis of human meiosis will increase the impact of cytogenetic investigation of human oocytes in the understanding of aneuploidy processes in humans.

Population genetic screening programmes: principles, techniques, practices, and policies

This paper examines the professional and scientific views on the principles, techniques, practices, and policies that impact on the population genetic screening programmes in Europe. This paper focuses on the issues surrounding potential screening programmes, which require further discussion before their introduction. It aims to increase, among the health-care professions and health policy-makers, awareness of the potential screening programmes as an issue of increasing concern to public health. The methods comprised primarily the review of the existing professional guidelines, regulatory frameworks and other documents related to population genetic screening programmes in Europe. Then, the questions that need debate, in regard to different types of genetic screening before and after birth, were examined. Screening for conditions such as cystic fibrosis, Duchenne muscular dystrophy, familial hypercholesterolemia, fragile X syndrome, hemochromatosis, and cancer susceptibility was discussed. Special issues related to genetic screening were also examined, such as informed consent, family aspects, commercialization, the players on the scene and monitoring genetic screening programmes. Afterwards, these questions were debated by 51 experts from 15 European countries during an international workshop organized by the European Society of Human Genetics Public and Professional Policy Committee in Amsterdam, The Netherlands, 19-20, November, 1999. Arguments for and against starting screening programmes have been put forward. It has been questioned whether genetic screening differs from other types of screening and testing in terms of ethical issues. The general impression on the future of genetic screening is that one wants to 'proceed with caution', with more active impetus from the side of patients' organizations and more reluctance from the policy-makers. The latter try to obviate the potential problems about the abortion and eugenics issues that might be perceived as a greater problem than it is in reality. However, it seems important to maintain a balance between a 'professional duty of care' and 'personal autonomy'.

Towards preimplantation diagnosis of cystic fibrosis using microarrays

Cystic fibrosis (CF) is a common indication for preimplantation genetic diagnosis (PGD). A 3-bp deletion (DeltaF508) in the cftr gene, which accounts for approximately 80% of all CF mutations in the Caucasian population, is normally diagnosed in IVF embryos using fluorescent PCR (FL-PCR) and allelic sizing. In PGD, the possibility of using microarrays for genetic diagnosis is largely unexplored. Therefore, the aim of this study was to prove the diagnostic capability of microarrays for PGD, using DeltaF508 as a model mutation. To this end, oligonucleotide probes representing both the normal and DeltaF508 disease alleles were used to construct a single microarray platform. Target DNA, which was generated by PCR and labelled with the fluorescent dye Cy3, was hybridized to the array and the DeltaF508 genotypes assigned from the fluorescence bound to each allelic probe. The performance of the array was evaluated by its ability to detect DeltaF508 mutations in target DNA. Strong binding of the target to the probes was observed, allowing the expected DeltaF508 genotypes to be assigned. The reliability and accuracy of the microarray diagnosis for DeltaF508 was blindly assessed on 10 samples with either a homozygous normal, homozygous affected or heterozygous genotype. All samples were correctly genotyped. In addition, PCR products from a previous PGD case involving DeltaF508 were re-evaluated on the array, with results in complete concordance with allelic sizing methods used to make the original diagnosis. Together, these findings prove the concept that the DeltaF508 mutation of CF can be reliably and accurately diagnosed at the single cell level using microarray analysis. The availability of more cost-effective array platforms comprising mutation probes for common single-gene disorders and a reliable method of whole genome amplification (WGA) would allow PGD to be offered to the majority of PGD patients with minimal or no change to methodology.

Karyotyping of human metaphase II oocytes by multifluor fluorescence in situ hybridization

OBJECTIVE

To quantify aneuploidy in inseminated, injected, and noninjected oocytes from infertility patients using Multifluor fluorescence in situ hybridization (M-FISH).

DESIGN

Prospective study.

SETTING

Reproductive biology group, academic unit of pediatrics, obstetrics, and gynecology.

PATIENT(S)

Forty-eight patients undergoing ovarian stimulation and either intracytoplasmic sperm injection (ICSI) or conventional in vitro fertilization (IVF).

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

M-FISH karyotyping of 67 metaphase II oocytes, including noninjected in vitro matured oocytes, and injected inseminated-failed fertilized oocytes.

RESULT(S)

Thirty-nine percent of oocytes were aneuploid, with nondisjunction of chromosomes in 34% of oocytes and predivision of chromatids in 10%. There was no difference in aneuploidy rates between ICSI noninjected in vitro matured oocytes and injected, failed fertilized oocytes. Chromosomes most frequently involved in aneuploidy were 15, 18, 19, 22, and X. In seven injected ICSI MII oocytes, the prematurely condensed sperm chromatin was karyotyped by M-FISH.

CONCLUSION(S)

M-FISH was used to diagnose aneuploidy at maternal meiosis I in 39% of oocytes, and M-FISH karyotyping of sperm was demonstrated.

Comparison between fluorescence in situ hybridization (FISH) and quantitative-fluorescent polymerase chain reaction (QF-PCR) for the detection of aneuploidies in single blastomeres

OBJECTIVES

The aim of our investigation was to compare the efficiencies of the fluorescence in situ hybridization (FISH) and the quantitative-fluorescent PCR (QF-PCR) methods for the detection of sexing and numerical chromosome disorders in single blastomeres collected from the same preimplantation human embryos.

METHODS

FISH analysis was carried out on 145 blastomeres from the 79 surplus embryos with probes specific for chromosomes 13, 18, 21, X, and Y. QF-PCR was performed with each one or two of the primers specific for the same chromosomes on 151 blastomeres from the same embryos obtained from patients undergoing IVF treatment.

RESULTS

Analyses were possible on 135 blastomeres (93%) by FISH and on 117 blastomeres (77%) by QF-PCR. Of 65 embryos, which could be analyzed by both methods, 20 embryos (31%) were diagnosed as abnormal.

CONCLUSION

The present study shows that FISH tests are more accurate than QF-PCR assays for the detection of numerical chromosome disorders when performed on single blastomeres.

Preimplantation genetic diagnosis

Preimplantation genetic diagnosis (PGD) is an evolving technique that provides a practical alternative to prenatal diagnosis and termination of pregnancy for couples who are at substantial risk of transmitting a serious genetic disorder to their offspring. Samples for genetic testing are obtained from oocytes or cleaving embryos after in vitro fertilization. Only embryos that are shown to be free of the genetic disorders are made available for replacement in the uterus, in the hope of establishing a pregnancy. PGD has provided unique insights into aspects of reproductive genetics and early human development, but has also raised important new ethical issues about assisted human reproduction.

Pre-implantation genetic diagnosis

Pre-implantation genetic diagnosis is an alternative to prenatal diagnosis for a select group of patients. Patients have to go through in vitro fertilization in order to produce embryos in vitro, from which one or two cells are removed at the 8-cell stage. A fluorescence in situ hybridization or polymerase chain reaction is carried out for the genetic diagnosis. Fluorescence in situ hybridization is used for the analysis of chromosomes for sexing for X-linked disease, chromosome abnormalities and aneuploidy screening. Aneuploidy screening is performed for infertile patients going through in vitro fertilization to try to improve their pregnancy rate. A polymerase chain reaction is used for the diagnosis of single-gene disorders. Since the risk of contamination and allele dropout is high with a polymerase chain reaction, linked or unlinked markers are usually used in a fluorescent multiplex polymerase chain reaction. New techniques, for example comparative genomic hybridization, allow the analysis of all of the chromosomes from one cell at one time. The ethical implications of pre-implantation genetic diagnosis are immense as the technique has already been used for social sexing and human leukocyte antigen matching.

Preimplantation genetic diagnosis for single gene disorders: experience with five single gene disorders

We report our experience of 14 preimplantation genetic diagnosis (PGD) cycles in eight couples carrying five different single gene disorders, during the last 18 months. Diagnoses were performed for myotonic dystrophy (DM), cystic fibrosis (CF) [Delta F508 and exon 4 (621+1 G>T)], fragile X and CF simultaneously, and two disorders for which PGD had not been previously attempted, namely neurofibromatosis type 2 (NF2) and Crouzon syndrome. Diagnoses for single gene disorders were carried out on ideally two blastomeres biopsied from Day 3 embryos. A highly polymorphic marker was included in each diagnosis to control against contamination. For the dominant disorders, where possible, linked polymorphisms provided an additional means of determining the genotype of the embryo hence reducing the risk of misdiagnosis due to allele dropout (ADO). Multiplex fluorescent polymerase chain reaction (F-PCR) was used in all cases, followed by fragment analysis and/or single-stranded conformation polymorphism (SSCP) for genotyping. Embryo transfer was performed in 13 cycles resulting in one biochemical pregnancy for CF, three normal deliveries (a twin and a singleton) and one early miscarriage for DM and a singleton for Crouzon syndrome. In each case the untransferred embryos were used to confirm the diagnoses performed on the biopsied cells. The results were concordant in all cases. The inclusion of a polymorphic marker allowed the detection of extraneous DNA contamination in two cells from one case. Knowing the genotype of the contaminating DNA allowed its origin to be traced. All five pregnancies were obtained from embryos in which two blastomeres were biopsied for the diagnosis. Our data demonstrate the successful strategy of using multiplex PCR to simultaneously amplify the mutation site and a polymorphic locus, fluorescent PCR technology to achieve greater sensitivity, and two-cell biopsy to increase the efficiency and success of diagnoses.

Comprehensive human genome amplification using multiple displacement amplification

Fundamental to most genetic analysis is availability of genomic DNA of adequate quality and quantity. Because DNA yield from human samples is frequently limiting, much effort has been invested in developing methods for whole genome amplification (WGA) by random or degenerate oligonucleotide-primed PCR. However, existing WGA methods like degenerate oligonucleotide-primed PCR suffer from incomplete coverage and inadequate average DNA size. We describe a method, termed multiple displacement amplification (MDA), which provides a highly uniform representation across the genome. Amplification bias among eight chromosomal loci was less than 3-fold in contrast to 4-6 orders of magnitude for PCR-based WGA methods. Average product length was >10 kb. MDA is an isothermal, strand-displacing amplification yielding about 20-30 microg product from as few as 1-10 copies of human genomic DNA. Amplification can be carried out directly from biological samples including crude whole blood and tissue culture cells. MDA-amplified human DNA is useful for several common methods of genetic analysis, including genotyping of single nucleotide polymorphisms, chromosome painting, Southern blotting and restriction fragment length polymorphism analysis, subcloning, and DNA sequencing. MDA-based WGA is a simple and reliable method that could have significant implications for genetic studies, forensics, diagnostics, and long-term sample storage.

Mitochondrial disorders: genetics, counseling, prenatal diagnosis and reproductive options

Most patients with mitochondrial disorders are diagnosed by finding a respiratory chain enzyme defect or a mutation in the mitochondrial DNA (mtDNA). The provision of accurate genetic counseling and reproductive options to these families is complicated by the unique genetic features of mtDNA that distinguish it from Mendelian genetics. These include maternal inheritance, heteroplasmy, the threshold effect, the mitochondrial bottleneck, tissue variation, and selection. Although we still have much to learn about mtDNA genetics, it is now possible to provide useful guidance to families with an mtDNA mutation or a respiratory chain enzyme defect. We describe a range of current reproductive options that may be considered for prevention of transmission of mtDNA mutations, including the use of donor oocytes, prenatal diagnosis (by chorionic villus sampling or amniocentesis), and preimplantation genetic diagnosis, plus possible future options such as nuclear transfer and cytoplasmic transfer. For common mtDNA mutations associated with mitochondrial cytopathies (such as NARP, Leigh Disease, MELAS, MERRF, Leber's Hereditary Optic Neuropathy, CPEO, Kearns-Sayre syndrome, and Pearson syndrome), we summarize the available data on recurrence risk and discuss the relative advantages and disadvantages of reproductive options.

Preimplantation genetic diagnosis in clinical practice

Preimplantation genetic diagnosis (PGD) represents an alternative to prenatal diagnosis and allows selection of unaffected IVF embryos for establishing pregnancies in couples at risk for transmitting a genetic disorder.

Preimplantation genetic diagnosis: applications for molecular medicine

Preimplantation genetic diagnosis is an alternative to prenatal diagnosis for the detection of genetic disorders. Tests are conducted on single cells biopsied from embryos before they are implanted, allowing the selection of unaffected embryos before a pregnancy has been established. Thus, the issue of pregnancy termination is circumvented. The use of preimplantation genetic diagnosis might have a significant impact on in vitro fertilization success rates as well as allowing the diagnosis of inherited disease.

First specific preimplantation genetic diagnosis for ornithine transcarbamylase deficiency

Ornithine transcarbamylase (OTC) deficiency is an X-linked dominant metabolic disorder with partial penetrance in heterozygous females. Affected boys usually die from hyperammonemia in the first few days of life, while clinical expression in carrier females ranges from no symptoms to neonatal death. A young couple whose boy had died of OTC deficiency in the neonatal period was referred to our genetic department for their subsequent pregnancy. The fetus was found to be affected, and after genetic counseling the pregnancy was terminated. Prenatal diagnosis of the third pregnancy identified a heterozygous female, who died after a normal birth at age 11 days from hyperammonemia. After this, the couple asked for preimplantation genetic diagnosis (PGD). We have developed a duplex nested PCR assay allowing the amplification of both the mutation and an informative restriction fragment length polymorphism (RFLP) located in the 3' end of the OTC gene. After nested amplification, allele identification was carried out for both loci by double restriction digestion and electrophoresis gel analysis. The co-amplification of both loci provided a means of detecting potential allele dropout or incomplete digestion. Two PGD cycles were carried out, a total of 14 embryos were analysed and a diagnosis could be obtained in 13/14 embryos. There were four unaffected male embryos, four heterozygous females and four unaffected females; the final embryo was an affected one of undetermined gender. In both cycles, three unaffected embryos could be transferred early on Day 4 post-insemination. The second cycle resulted in the birth of a baby boy devoid of the OTC mutation. This constitutes the first birth following PGD carried out by a French team.

Pre-implantation genetic diagnosis

Pre-implantation genetic diagnosis (PGD) was developed in the UK over 10 years ago. There are now more than 40 centres worldwide carrying out PGD and 150 babies have been born after genetic testing on day 3 of development, at the cleavage stage. This review covers the current status of PGD, the technology used and the types of genetically determined diseases for which testing has been developed.

Preimplantation genetic diagnosis

Embryo biopsy for preimplantation genetic diagnosis can be performed on the oocyte/zygote, cleavage stage embryo, or blastocyst, but the majority of centres perform cleavage stage biopsy. Single-cell diagnosis is undertaken by the polymerase chain reaction or fluorescent in-situ hybridization. Technical difficulties have arisen with preimplantation genetic diagnosis, such as allele dropout and chromosomal mosaicism. However, it is hoped that these difficulties can be overcome in the future with the advent of new techniques.