Robust embryo identification using first polar body single nucleotide polymorphism microarray-based DNA fingerprinting

The number of biopsied trophectoderm cells may affect pregnancy outcomes

OBJECTIVE

To study if the number of trophectoderm (TE) biopsied cells has an impact on implantation rates.

DESIGN

A retrospective cohort study in a single-center study.

SETTING

In vitro fertilization center.

PATIENTS

Patients who underwent PGT-A from January 2013 to March 2016. In total, 482 vitrified/warmed single embryo transfers were included.

INTERVENTIONS

None.

MAIN OUTCOME MEASURES

Clinical pregnancies rate, implantation rate.

RESULTS

Overall, clinical pregnancies per embryo transfer were higher when a regular TE were biopsied compared to larger size biopsy cells (66% (175/267) vs 53% (115/215) (p < 0.005) respectively). Pregnancy rates were also analyzed according to embryo morphology at the moment of embryo biopsy, when a good-quality embryo was transferred the clinical outcome was 75% (81/108) in group 1 and 61% (60/99) in group 2 (p < 0.05). Data was also stratified by age in patients ≤ 35 years and > 35 years. The clinical pregnancy was 67% (51/76) in women ≤ 35 years and 65% (124/191) in women > 35 years when a regular size biopsy was performed. These results significantly reduced when a larger size biopsy was performed 54% (49/91) and 53% (66/124), respectively (p < 0.05). Further investigation indicated that miscarriage rate was similar between these groups (4% (7/182) in group 1 and 5% (6/121) in group 2).

CONCLUSIONS

These findings underscore that when a large amount of TE cells are biopsied, it may negatively affect implantation rates, but once implanted, the embryos have the same chance to miscarry or reach term.

Preimplantation genetic diagnosis: an update on current technologies and ethical considerations

The aim of reproductive medicine is to support the birth of healthy children. Advances in assisted reproductive technologies and genetic analysis have led to the introduction of preimplantation genetic diagnosis (PGD) for embryos. Indications for PGD have been a major topic in the fields of ethics and law. Concerns vary by nation, religion, population, and segment, and the continued rapid development of new technologies. In contrast to the ethical augment, technology has been developing at an excessively rapid speed. The most significant recent technological development provides the ability to perform whole genome amplification and sequencing of single embryonic cells by microarray or next-generation sequencing methods. As new affordable technologies are introduced, patients are presented with a growing variety of PGD options. Simultaneously, the ethical guidelines for the indications for testing and handling of genetic information must also rapidly correspond to the changes.

Trophectoderm DNA fingerprinting by quantitative real-time PCR successfully distinguishes sibling human embryos

PURPOSE

To validate a novel and more practical system for trophectoderm DNA fingerprinting which reliably distinguishes sibling embryos from each other.

METHODS

In this prospective and blinded study two-cell and 5-cell samples from commercially available sibling cell lines and excess DNA from trophectoderm biopsies of sibling human blastocysts were evaluated for accurate assignment of relationship using qPCR-based allelic discrimination from 40 single nucleotide polymorphisms (SNPs) with low allele frequency variation and high heterozygosity.

RESULTS

Cell samples with self relationships averaged 95.1 ± 5.9 % similarity. Sibling relationships averaged 57.2 ± 5.9 % similarity for all 40 SNPs, and 40.8 ± 8.2 % similarity for the 25 informative SNPs. Assignment of relationships was accomplished with 100 % accuracy for cell lines and embryos.

CONCLUSIONS

These data demonstrate the first trophectoderm qPCR-based DNA fingerprinting technology capable of unequivocal discrimination of sibling human embryos. This methodology will empower research and development of new markers of, and interventions that influence embryonic reproductive potential.

Simultaneous assessment of aneuploidy, polymorphisms, and mitochondrial DNA content in human polar bodies and embryos with the use of a novel microarray platform

OBJECTIVE

To develop a microarray platform that allows simultaneous assessment of aneuploidy and quantification of mitochondrial DNA (mtDNA) in human polar bodies and embryos.

DESIGN

Optimization and validation applied to cell lines and clinical samples (polar bodies, blastomeres, and trophectoderm biopsies).

SETTING

University research laboratory and a preimplantation genetic diagnosis (PGD) reference laboratory.

PATIENT(S)

Samples from 65 couples who underwent PGD for aneuploidy and/or a single-gene disorder.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

1) Comparison of aneuploidy screening results obtained with the use of the new microarray with those derived from two well established cytogenetic techniques. 2) mtDNA quantification. 3) Analysis of single-nucleotide polymorphisms.

RESULT(S)

The fully optimized microarray was estimated to have an accuracy of ≥97% for the detection of individual aneuploidies and to detect 99% of chromosomally abnormal embryos. The microarray was shown to accurately determine relative quantities of mtDNA. Information provided from polymorphic loci was sufficient to allow confirmation that an embryo was derived from specific parents.

CONCLUSION(S)

It is hoped that methods such as those reported here, which provide information on several aspects of oocyte/embryo genetics, could lead to improved strategies for identifying viable embryos, thereby increasing the likelihood of successful implantation. Additionally, the provision of genotyping information has the potential to reveal DNA contaminants and confirm parental origin of embryos.

OMICS: Current and future perspectives in reproductive medicine and technology

Many couples present fertility problems at their reproductive age, and although in the last years, the efficiency of assisted reproduction techniques has increased, these are still far from being 100% effective. A key issue in this field is the proper assessment of germ cells, embryos and endometrium quality, in order to determine the actual likelihood to succeed. Currently available analysis is mainly based on morphological features of oocytes, sperm and embryos and although these strategies have improved the results, there is an urgent need of new diagnostic and therapeutic tools. The emergence of the - OMICS technologies (epigenomics, genomics, transcriptomics, proteomics and metabolomics) permitted the improvement on the knowledge in this field, by providing with a huge amount of information regarding the biological processes involved in reproductive success, thereby getting a broader view of complex biological systems with a relatively low cost and effort.

Single cell segmental aneuploidy detection is compromised by S phase

BACKGROUND

Carriers of balanced translocations are at high risk for unbalanced gametes which can result in recurrent miscarriages or birth defects. Preimplantation genetic diagnosis (PGD) is often offered to select balanced embryos. This selection is currently mainly performed by array CGH on blastomeres. Current methodology does not take into account the phase of the cell cycle, despite the variable copy number status of different genomic regions in S phase.

RESULTS

Cell lines derived from 3 patients with different chromosomal imbalances were used to evaluate the accuracy of single cell array CGH. The different cell cycle phases were sorted by flow cytometry and 10 single cells were picked per cell line per cell cycle phase, whole genome amplified and analyzed by BAC arrays, the most commonly used platform for PGD purposes. In contrast to G phase, where the imbalances were efficiently identified, less than half of the probes in the regions of interest indicated the presence of the aberration in 17 S-phase cells, resulting in reduced accuracy.

CONCLUSIONS

The results demonstrate that the accuracy to detect segmental chromosomal imbalances is reduced in S-phase cells, which could be a source of misdiagnosis in PGD. Hence, the cell cycle phase of the analyzed cell is of great importance and should be taken into account during the analysis. This knowledge may guide future technological improvements.

Assisted reproductive techniques

Assisted reproductive technologies (ART) encompass fertility treatments, which involve manipulations of both oocyte and sperm in vitro. This chapter provides a brief overview of ART, including indications for treatment, ovarian reserve testing, selection of controlled ovarian hyperstimulation (COH) protocols, laboratory techniques of ART including in vitro fertilization (IVF), and intracytoplasmic sperm injection (ICSI), embryo transfer techniques, and luteal phase support. This chapter also discusses potential complications of ART, namely ovarian hyperstimulation syndrome (OHSS) and multiple gestations, and the perinatal outcomes of ART.

Preimplantation genetic diagnosis for aneuploidy and translocations using array comparative genomic hybridization

At least 50% of human embryos are abnormal, and that increases to 80% in women 40 years or older. These abnormalities result in low implantation rates in embryos transferred during in vitro fertilization procedures, from 30% in women <35 years to 6% in women 40 years or older. Thus selecting normal embryos for transfer should improve pregnancy results. The genetic analysis of embryos is called Preimplantation Genetic Diagnosis (PGD) and for chromosome analysis it was first performed using FISH with up to 12 probes analyzed simultaneously on single cells. However, suboptimal utilization of the technique and the complexity of fixing single cells produced conflicting results. PGD has been invigorated by the introduction of microarray testing which allows for the analysis of all 24 chromosome types in one test, without the need of cell fixation, and with staggering redundancy, making the test much more robust and reliable. Recent data published and presented at scientific meetings has been suggestive of increased implantation rates and pregnancy rates following microarray testing, improvements in outcome that have been predicted for quite some time. By using markers that cover most of the genome, not only aneuploidy can be detected in single cells but also translocations. Our validation results indicate that array CGH has a 6Mb resolution in single cells, and thus the majority of translocations can be analyzed since this is also the limit of karyotyping. Even for translocations with smaller exchanged fragments, provided that three out of the four fragments are above 6Mb, the translocation can be detected.

Embryos whose polar bodies contain isolated reciprocal chromosome aneuploidy are almost always euploid

STUDY QUESTION

When a chromosome aneuploidy is detected in the first polar body and a reciprocal loss or gain of the same chromosome is detected in the second polar body, is the resulting embryo usually aneuploid for that chromosome?

SUMMARY ANSWER

When reciprocal aneuploidy occurs in polar bodies, the resulting embryo is usually normal for that chromosome, indicating that premature separation of sister chromatids (PSSC)—not non-disjunction—likely occurred in meiosis I.

WHAT IS KNOWN ALREADY

Single-nucleotide polymorphism-based microarray analysis can be used to accurately determine the chromosomal status of polar bodies and embryos. Sometimes, the only abnormality found is a reciprocal gain or loss of one or two chromosomes in the two polar bodies. Prediction of the status of the resulting embryo in these cases is problematic.

STUDY DESIGN, SIZE, DURATION

Blinded microarray analysis of previously diagnosed aneuploid embryos that had reciprocal polar body aneuploidy.

MATERIALS, SETTING, METHODS

IVF cycles were performed between 2008 and 2011 in patients aged 40 ± 3 years (range 35–47 years) with an indication for polar body-based aneuploidy screening. Thirty-five aneuploid vitrified Day 3 embryos were warmed, cultured to Day 5 and biopsied for microarray analysis. Predictions were made for the ploidy status of the embryo if PSSC or non-disjunction had occurred. The signal intensity for the aneuploid chromosome in the first polar body was compared between those that resulted in euploid and aneuploid embryos.

MAIN RESULTS AND THE ROLE OF CHANCE

Among 34 embryos with evaluable results, 31 were euploid on re-analysis. Of 43 chromosomes that had reciprocal aneuploidy in the polar bodies, 41 were disomic in the embryo, indicating that PSSC was likely to have occurred 95% (95% confidence interval 85–99%) of the time. The log 2 ratio signal intensity from the chromosomes that underwent non-disjunction, resulting in unbalanced embryos, were outliers when compared with those that underwent PSSC.

LIMITATIONS, REASONS FOR CAUTION

Although most embryos with reciprocal aneuploid polar bodies were euploid, it is unknown whether they maintain equivalent reproductive potential when transferred. Further study is needed to determine whether these embryos should be re-biopsied and considered for transfer.

WIDER IMPLICATIONS OF THE FINDINGS

This study is consistent with increasing evidence that PSSC is the primary cause of meiosis I errors in embryos from women of advanced reproductive age. Clinicians should be cautious in interpreting results from polar body aneuploidy screening, especially when only the first polar body is tested.

STUDY FUNDING/COMPETING INTEREST(S)

None.

Follicular fluid protein content (FSH, LH, PG4, E2 and AMH) and polar body aneuploidy

PURPOSE

Our objective was to identify a marker for oocyte aneuploidy in follicular fluid (FF) in women with an increased risk of oocyte aneuploidy after controlled ovarian hyperstimulation.

MATERIALS AND METHODS

Three groups of oocytes were constituted for polar body screening by FISH (chromosomes 13, 16, 18, 21 and 22): Group 1, advanced maternal age (n = 156); Group 2, implantation failure (i.e. no pregnancy after the transfer of more than 10 embryos; n = 101) and Group 3, implantation failure and advanced maternal age (n = 56). FSH and other proteins were assayed in the corresponding FF samples.

RESULTS

Of the 313 oocytes assessed, 35.78 % were abnormal. We found a significant difference between the follicular FSH levels in normal oocytes and abnormal oocytes (4.85 ± 1.75 IU/L vs. 5.41 ± 2.47 IU/L, respectively; p = 0.021). We found that the greater the number of chromosomal abnormalities per oocyte (between 0 and 3), the higher the follicular FSH level.

CONCLUSION

High FF FSH levels were associated with oocyte aneuploidy in women having undergone controlled ovarian hyperstimulation.

Delivery of a chromosomally normal child from an oocyte with reciprocal aneuploid polar bodies

Purpose

To demonstrate that a euploid embryo derived from an oocyte with reciprocal aneuploid polar bodies is capable of producing a chromosomally normal child.

Methods

A case report of maternal MI error compensation where single nucleotide polymorphism (SNP) microarray based comprehensive chromosome screening (CCS) was performed on the 1st and 2nd polar body, the resulting embryo, and newborn DNA.

Results

CCS performed after embryo transfer identified a chromosomally normal embryo that resulted from an oocyte with reciprocal aneuploid polar bodies. The first polar body was found to be missing a single chromatid derived from chromosome 21 and the second polar body possessed an extra chromatid derived from chromosome 21. Compensation of the maternal meiotic error was verified by CCS analysis of a trophectoderm biopsy from the resulting blastocyst which was euploid for all 23 pairs of chromosomes. DNA fingerprinting and CCS of the resulting newborn confirmed a chromosomally normal child, demonstrating the developmental potential of an oocyte with reciprocal aneuploid polar bodies.

Conclusions

This is the first case report demonstrating the reproductive potential of a chromosomally normal embryo derived from an oocyte which had undergone meiosis I error. Systematic investigation into the frequency of meiosis I error compensation and the negative predictive value of polar body aneuploidy screening for reproductive potential should be conducted in order to confirm clinical relevance.

Methods for comprehensive chromosome screening of oocytes and embryos: capabilities, limitations, and evidence of validity

Preimplantation aneuploidy screening of cleavage stage embryos using fluorescence in situ hybridization (FISH) may no longer be considered the standard of care in reproductive medicine. Over the last few years, there has been considerable development of novel technologies for comprehensive chromosome screening (CCS) of the human genome. Among the notable methodologies that have been incorporated are whole genome amplification, metaphase and array based comparative genomic hybridization, single nucleotide polymorphism microarrays, and quantitative real-time PCR. As these methods become more integral to treating patients with infertility, it is critical that clinicians and scientists obtain a better understanding of their capabilities and limitations. This article will focus on reviewing these technologies and the evidence of their validity.

Chromosomal disorders and male infertility

Infertility in humans is surprisingly common occurring in approximately 15% of the population wishing to start a family. Despite this, the molecular and genetic factors underlying the cause of infertility remain largely undiscovered. Nevertheless, more and more genetic factors associated with infertility are being identified. This review will focus on our current understanding of the chromosomal basis of male infertility specifically: chromosomal aneuploidy, structural and numerical karyotype abnormalities and Y chromosomal microdeletions. Chromosomal aneuploidy is the leading cause of pregnancy loss and developmental disabilities in humans. Aneuploidy is predominantly maternal in origin, but concerns have been raised regarding the safety of intracytoplasmic sperm injection as infertile men have significantly higher levels of sperm aneuploidy compared to their fertile counterparts. Males with numerical or structural karyotype abnormalities are also at an increased risk of producing aneuploid sperm. Our current understanding of how sperm aneuploidy translates to embryo aneuploidy will be reviewed, as well as the application of preimplantation genetic diagnosis (PGD) in such cases. Clinical recommendations where possible will be made, as well as discussion of the use of emerging array technology in PGD and its potential applications in male infertility.

Polar body morphology is not predictive of its cell division origin

PURPOSE

This study sought to determine whether morphology of simultaneously biopsied polar bodies is predictive of their cell division origin.

METHODS

Levels of heterozygosity were measured using single nucleotide polymorphism (SNP) microarrays in sequentially biopsied polar bodies to establish the predictive value on samples with known cell division origins. The validated method of predicting cell division origin of polar bodies using heterozygosity rates was then applied to simultaneously biopsied polar bodies which had origin predictions made by morphological assessment.

RESULTS

SNP microarray heterozygosity analysis was proven to be 94% predictive when tested against the known origin of sequentially biopsied polar bodies (n = 133). This methodology subsequently demonstrated that morphology was only 63% consistent when tested on simultaneously biopsied polar bodies (n = 455; P < 0.0001). Predictions of the origins of aneuploidy using morphology assignment were also significantly different than with heterozygosity assignment of polar body cell division origin (P = 0.0003).

CONCLUSIONS

Studies of the origin of aneuploidy utilizing morphological assignment of polar body cell division origin without heterozygosity analysis may be inaccurate and should be interpreted with caution.

Telomere DNA deficiency is associated with development of human embryonic aneuploidy

Aneuploidy represents the most prevalent form of genetic instability found in human embryos and is the leading genetic cause of miscarriage and developmental delay in newborns. Telomere DNA deficiency is associated with genomic instability in somatic cells and may play a role in development of aneuploidy commonly found in female germ cells and human embryos. To test this hypothesis, we developed a method capable of quantifying telomere DNA in parallel with 24-chromosome aneuploidy screening from the same oocyte or embryo biopsy. Aneuploid human polar bodies possessed significantly less telomere DNA than euploid polar bodies from sibling oocytes (-3.07 fold, P = 0.016). This indicates that oocytes with telomere DNA deficiency are prone to aneuploidy development during meiosis. Aneuploid embryonic cells also possessed significantly less telomere DNA than euploid embryonic cells at the cleavage stage (-2.60 fold, P = 0.002) but not at the blastocyst stage (-1.18 fold, P = 0.340). The lack of a significant difference at the blastocyst stage was found to be due to telomere DNA normalization between the cleavage and blastocyst stage of embryogenesis and not due to developmental arrest of embryos with short telomeres. Heterogeneity in telomere length within oocytes may provide an opportunity to improve the treatment of infertility through telomere-based selection of oocytes and embryos with reproductive competence.

Use of single nucleotide polymorphism microarrays to distinguish between balanced and normal chromosomes in embryos from a translocation carrier

OBJECTIVE

To prove the ability to distinguish between balanced and normal chromosomes in embryos from a translocation carrier.

DESIGN

Case report.

SETTING

Academic center for reproductive medicine.

PATIENT(S)

Woman with a balanced translocation causing Alagille syndrome seeking preimplantation genetic diagnosis (PGD).

INTERVENTION(S)

Blastocyst biopsy for PGD.

MAIN OUTCOME MEASURE(S)

Consistency of 3 methods of embryo genetic analysis (real-time polymerase chain reaction, single nucleotide polymorphism [SNP] microarray, and fluorescence in situ hybridization [FISH]) and normalcy in the newborn derived from PGD.

RESULT(S)

PGD was applied to 48 embryos. Real-time polymerase chain reaction, SNP microarray, and FISH demonstrated 100% consistency, although FISH failed to detect aneuploidies observed by comprehensive SNP microarray-based analyses. Two blastocysts were identified to be normal for all 3 factors using SNP microarray technology alone. The 2 normal embryos were transferred back to the patient, resulting in the delivery of a healthy boy with a normal karyotype.

CONCLUSION(S)

This is the first report of validation and successful clinical application of microarray-based PGD to distinguish between balanced and normal chromosomes in embryos from a translocation carrier.

Validation of microarray comparative genomic hybridization for comprehensive chromosome analysis of embryos

OBJECTIVE

To validate and determine the best array-comparative genomic hybridization (aCGH; array-CGH) protocols for preimplantation genetic screening (PGS).

DESIGN

Embryos had one cell removed as a biopsy specimen and analyzed by one of two array-CGH protocols. Abnormal embryos were reanalyzed by fluorescence in situ hybridization (FISH).

SETTING

Reference laboratory.

PATIENT(S)

Patients donating embryos or undergoing PGS.

INTERVENTION(S)

Embryo biopsy, array-CGH, FISH reanalysis.

MAIN OUTCOME MEASURE(S)

Diagnosis, no result rate and error rate.

RESULT(S)

Method one produced 11.2% of embryos with no results and a 9.1% error rate compared with 3% and 1.9% for method two, respectively. Thereafter, only method two was used clinically. The aneuploidy rate for cleavage-stage embryos was 63.2%, significantly increasing with maternal age. The chromosomes most involved in aneuploidy were 16, 22, 21, and 15. We report the first live births after array-CGH combined with single blastomere biopsy.

CONCLUSION(S)

Array-CGH is proved to be highly robust (2.9% no results) and specific (1.9% error rate) when applied to rapid (24-hour) analysis of single cells biopsied from cleavage-stage embryos. This comprehensive chromosome analysis technique is the first to be validated by reanalyzing the same embryos with another technique (e.g., FISH). Unlike some alternative techniques for comprehensive chromosome screening, array-CGH does not require prior testing of parental DNA and thus advance planning and careful scheduling are unnecessary.

SNP microarray-based 24 chromosome aneuploidy screening demonstrates that cleavage-stage FISH poorly predicts aneuploidy in embryos that develop to morphologically normal blastocysts

Although selection of chromosomally normal embryos has the potential to improve outcomes for patients undergoing IVF, the clinical impact of aneuploidy screening by fluorescence in situ hybridization (FISH) has been controversial. There are many putative explanations including sampling error due to mosaicism, negative impact of biopsy, a lack of comprehensive chromosome screening, the possibility of embryo self-correction and poor predictive value of the technology itself. Direct analysis of the negative predictive value of FISH-based aneuploidy screening for an embryo's reproductive potential has not been performed. Although previous studies have found that cleavage-stage FISH is poorly predictive of aneuploidy in morphologically normal blastocysts, putative explanations have not been investigated. The present study used a single nucleotide polymorphism (SNP) microarray-based 24 chromosome aneuploidy screening technology to re-evaluate morphologically normal blastocysts that were diagnosed as aneuploid by FISH at the cleavage stage. Mosaicism and preferential segregation of aneuploidy to the trophectoderm (TE) were evaluated by characterization of multiple sections of the blastocyst. SNP microarray technology also provided the first opportunity to evaluate self-correction mechanisms involving extrusion or duplication of aneuploid chromosomes resulting in uniparental disomy (UPD). Of all blastocysts evaluated (n = 50), 58% were euploid in all sections despite an aneuploid FISH result. Aneuploid blastocysts displayed no evidence of preferential segregation of abnormalities to the TE. In addition, extrusion or duplication of aneuploid chromosomes resulting in UPD did not occur. These findings support the conclusion that cleavage-stage FISH technology is poorly predictive of aneuploidy in morphologically normal blastocysts.