The impact of next-generation sequencing technology on preimplantation genetic diagnosis and screening

Experts' perspectives on human gene editing in Switzerland

Despite many specialized studies on the views of the public or stakeholders who face inherited conditions that may be treatable by HGE, limited studies have focused on experts' views towards Human Gene Editing (HGE). Therefore, in this study we conducted exploratory interviews with 14 experts (scientists, clinicians, social scientists, lawyers) in Switzerland to assess their views towards HGE and how they expect the Swiss public to view HGE. We found general acceptance of Somatic Gene Editing (SGE), but opinions towards Germline Gene Editing (GGE) were more divided. Participants emphasized patient autonomy and informed decision-making in pursuing gene editing treatments, and described a need for regulation, as with any other new therapy. Only a few participants (mostly lawyers and ethicists) described the regulations that currently prohibit GGE in Switzerland. Some expressed concern that restrictive regulations would lead to healthcare outsourcing and medical tourism to other nearby countries, as it has in the past with other restricted technologies. The analysis explored the unique Swiss context that is shaped by cultural diversity, conservative attitudes towards new medical technologies, and a democratic system that engages the public in policy and law making. Given that our findings identify areas of difference from that published in other countries, we emphasize the value in conducting similar research across different countries in order to achieve a global sense of attitudes towards HGE, so that regulations can be tailored to the diverse needs of citizens around the world.

Genetics in reproductive endocrinology and infertility

Tremendous advances in genetics have transformed the field of reproductive endocrinology and infertility over the last few decades. One of the most prominent advances is preimplantation genetic testing (PGT), which allows for the screening of embryos obtained during in vitro fertilization before transfer. Moreover, PGT can be performed for aneuploidy screening, detection of monogenic disorders, or exclusion of structural rearrangements. Refinement of biopsy techniques, such as obtaining samples at the blastocyst rather than the cleavage stage, has helped optimize results from PGT, and technological advances, including next-generation sequencing, have made PGT more efficient and accurate. The continued evolution of the approach to PGT has the potential to further enhance the accuracy of results, expand the application to other conditions, and increase access by reducing cost and improving efficiency.

To mask or not to mask mosaicism? The impact of reporting embryo mosaicism on reproductive potential

PURPOSE

To evaluate euploidy rates and probability of having at least one euploid embryo for transfer per cycle when mosaicism is reported compared to when it is masked.

METHODS

Women age 18-46 years who underwent PGT-A with next generation sequencing of blastocyst biopsies were analyzed. When reported, mosaic embryos were classified as low-level, 20-40% mosaic, or high-level, 41-80% mosaic. When masked, low-level mosaics were categorized as euploid and high-level mosaics were considered aneuploid. Comparative analyses were performed with χ2 tests and t-tests.

RESULTS

A total of 22,504 PGT-A biopsy cycles from 18,401 patients were included. These cycles were from 293 different clinics with a mean of 1.22 cycles per patient. The majority of cycles (94.8%) reported mosaicism, and only 5.2% cycles were masked. The euploidy rate was significantly lower when mosaicism was reported versus masked (38.7% v 47.4%, p < 0.0001), which remained significant for age 40 years old and younger. The mosaic reporting cohort was less likely to have at least one euploid embryo for transfer (68.8%) compared to the masked cohort (75.7%) (p < 0.0001); however, this was no longer significant after stratification by age.

CONCLUSION

Mosaicism reporting shows an overall expected reduction in euploidy rate. In turn, the probability of having a euploid embryo to transfer depends on clinic transfer practices and patient preference. If mosaic embryos are not transferred, we observe a reduction in probability of having an embryo for transfer. Although the magnitude of these differences is small, our data show that mosaic reporting may contribute to embryo attrition rate.

Mitochondrial DNA Copy Number in Cleavage Stage Human Embryos-Impact on Infertility Outcome

A retrospective case control study was undertaken at the molecular biology department of a private center for reproductive medicine in order to determine whether any correlation exists between mitochondrial DNA (mtDNA) content of cleavage-stage preimplantation embryos and their developmental potential. A total of 69 couples underwent IVF treatment (averaged women age: 36.5, SD 4.9) and produced a total of 314 embryos. A single blastomere was biopsied from each embryo at the cleavage stage (day-3 post-fertilization) subjected to low-pass next generation sequencing (NGS), for the purpose of detecting aneuploidy. For each sample, the number of mtDNA reads obtained after analysis using NGS was divided by the number of reads attributable to the nuclear genome. The mtDNA copy number amount was found to be higher in aneuploid embryos than in those that were euploid (mean mtDNA ratio ± SD: 6.3 ± 7.5 versus 7.1 ± 5.8, p < 0.004; U Mann−Whitney test), whereas no statistically significant differences in mtDNA content were seen in relation to embryo morphology (6.6 ± 4.8 vs. 8.5 ± 13.6, p 0.09), sex (6.6 ± 4.1 vs. 6.2 ± 6.8, p 0.16), maternal age (6.9 ± 7.8 vs. 6.7 ± 4.5, p 0.14) or its ability to implant (7.4 ± 6.6 vs. 5.1 ± 4.6, p 0.18). The mtDNA content cannot serve as a useful biomarker at this point in development. However, further studies investigating both quantitative and qualitative aspects of mtDNA are still required to fully evaluate the relationship between mitochondrial DNA and human reproduction.

Feasibility study of using unbalanced embryos as a reference to distinguish euploid carrier from noncarrier embryos by single nucleotide polymorphism array for reciprocal translocations

OBJECTIVES

To study the feasibility of using unbalanced embryos as a reference in distinguishing euploid carrier and noncarrier embryos by single nucleotide polymorphism (SNP) array-based preimplantation genetic testing (PGT) for reciprocal translocations.

METHODS

After comprehensive chromosome screening (CCS), euploid embryos were identified as normal or carriers using a family member as a reference. Next, unbalanced embryos were used as a reference, and the results were compared with the previous ones. Karyotypes of transferred embryos were validated by prenatal diagnosis.

RESULTS

Of 995 embryos from 110 couples, 288 were found to be euploid. Using a family member as a reference, 142 and 144 embryos were tested to be euploid noncarrier and carrier respectively, and the remaining 2 embryos were undetermined. When unbalanced embryos were selected as references, all the results were consistent with the previous ones. A total of 107 embryos were transferred, resulting in 66 clinical pregnancies. Karyotypes of prenatal diagnosis were all in accordance with the results of tested embryos.

CONCLUSIONS

SNP array-based haplotyping is a rapid and effective way to distinguish between euploid carrier and noncarrier embryos. In case no family member is available as a reference, unbalanced embryos can be used for identification of euploid carrier and noncarrier embryos.

A systematic review exploring the patient decision-making factors and attitudes towards pre-implantation genetic testing for aneuploidy and gender selection

INTRODUCTION

Pre-implantation genetic testing for aneuploidy (PGT-A) is in high demand worldwide, with ongoing debate among medical societies as to which patient groups it should be offered. The psychological aspects for patients regarding its use, lag behind the genomic technological advances, leaving couples with limited decision-making support. The development of this technology also leads to the possibility for its utilization in gender selection. Despite the controversy surrounding these issues, very few studies have investigated the psychological aspects of patients using PGT-A.

MATERIAL AND METHODS

This systematic review provides an up-to-date analysis of the psychosocial aspects surrounding PGT for aneuploidy and sex selection, as well as decision-making factors. A systematic search of English peer-reviewed journals of three computerized databases were undertaken following PRISMA guidelines. The qualitative data were extracted using thematic analysis. PROSPERO Registration number: CRD42019126439.

RESULTS

The main outcome measures were patients' motivations, decision-making factors, attitudes and experiences surrounding the use of PGT for aneuploidy and sex selection. Ten studies were included, four for PGT-A and six for sex selection. Attitudes towards PGT-A were positive, with the main motivating factors being decreasing miscarriage rate, reducing the risk of termination of pregnancy and reducing the time to pregnancy. Consistently raised concerns regarding PGT-A were the financial burden and moral beliefs. The vast majority of patients felt sufficiently knowledgeable to make the decision; however, studies did reveal that a minority mis-interpreted certain potential benefits of PGT-A. Studies investigating PGT for sex selection predominantly reported the main motivation was to achieve gender balance within the family dynamic, with most studies finding no difference between couples using PGT for gender selection to have male or female offspring.

CONCLUSIONS

Although this systematic review was limited by the small number of studies investigating this topic, a significant minority of patients appeared to misunderstand certain benefits and limitations of PGT-A. Fertility clinics must ensure they provide adequate counseling to all patients using PGT-A. With the use of PGT-A on the rise globally, there is a need to develop decision support tools for couples who have an increasing number of genetic testing options becoming available to them.

Preimplantation Genetic Testing for Aneuploidy: A Review

Importance

Preimplantation genetic testing for aneuploidy (PGT-A) has undergone many technical developments over recent years, including changes in biopsy timings, methodology, and genetic analysis techniques. The evidence surrounding the efficaciousness of PGT-A is sporadic and inconsistent; as such, significant doubt and concern remain regarding its widespread implementation.

Objective

This review seeks to describe the historical development of PGT-A and to analyze and summarize the current published literature.

Conclusions

At times during its infancy, PGT-A failed to display conclusive improvements in results; with newer technologies, PGT-A appears to yield superior outcomes, including reductions in miscarriages and multiple gestations. Clinicians and patients should assess the use of PGT-A on a case-by-case basis, with laboratories encouraged to utilize blastocyst biopsy and next-generation sequencing when conducting PGT-A. Further studies providing cumulative live birth rates and time to live birth are required if PGT-A is to be proven as producing superior outcomes.

Relevance

PGT-A has the potential ability to impact in vitro fertilization success rates, and as it is increasingly adopted worldwide, it is crucial that clinicians are aware of the evidence for its continued use.

Successful clinical application of pre-implantation genetic diagnosis for infantile neuroaxonal dystrophy

Infantile neuroaxonal dystrophy (INAD) is a rare, lethal, autosomal recessive neurodegenerative disease and leads to progressive impairment of movement and cognition. A couple with a proband child with calcium-independent group VI phospholipase A2 (PLA2G6)-associated INAD and a previous affected pregnancy sought pre-implantation genetic diagnosis (PGD) to bear a healthy child. Intracytoplasmic sperm injection treatment was performed and 15 blastocystic embryos were obtained at days 5 and 6, and these biopsies were amplified. PGD was performed by next-generation sequencing-based linkage analysis in conjunction with aneuploidy screening. Only two embryos were considered for transfer. In the second frozen-thawed embryo transfer cycle, transfer of a mosaic PLA2G6 c.692G>T heterozygous embryo resulted in a singleton ongoing pregnancy. Prenatal diagnosis was performed using amniotic fluid cells, providing results consistent with those of PGD. The aneuploidy screen and karyotype analysis indicated that the chromosomes of the fetus were normal without any mosaicism. The present study reported the first successful PGD for INAD. For parents at risk, this strategy may successfully lead to pregnancies with embryos unlikely to develop INAD, thus providing valuable experience in reproductive management regarding INAD and potentially other single-gene disorders.

The evolving role of genetic tests in reproductive medicine

Infertility is considered a major public health issue, and approximately 1 out of 6 people worldwide suffer from infertility during their reproductive lifespans. Thanks to technological advances, genetic tests are becoming increasingly relevant in reproductive medicine. More genetic tests are required to identify the cause of male and/or female infertility, identify carriers of inherited diseases and plan antenatal testing. Furthermore, genetic tests provide direction toward the most appropriate assisted reproductive techniques. Nevertheless, the use of molecular analysis in this field is still fragmented and cumbersome. The aim of this review is to highlight the conditions in which a genetic evaluation (counselling and testing) plays a role in improving the reproductive outcomes of infertile couples. We conducted a review of the literature, and starting from the observation of specific signs and symptoms, we describe the available molecular tests. To conceive a child, both partners' reproductive systems need to function in a precisely choreographed manner. Hence to treat infertility, it is key to assess both partners. Our results highlight the increasing importance of molecular testing in reproductive medicine.

High Throughput Sequencing and Assessing Disease Risk

High-throughput sequencing has dramatically improved our ability to determine and diagnose the underlying causes of human disease. The use of whole-genome and whole-exome sequencing has facilitated faster and more cost-effective identification of new genes implicated in Mendelian disease. It has also improved our ability to identify disease-causing mutations for Mendelian diseases whose associated genes are already known. These benefits apply not only in cases in which the objective is to assess genetic disease risk in adults and children, but also for prenatal genetic testing and embryonic testing. High-throughput sequencing has also impacted our ability to assess risk for complex diseases and will likely continue to influence this area of disease research as more and more individuals undergo sequencing and we better understand the significance of variation, both rare and common, across the genome. Through these activities, high-throughput sequencing has the potential to revolutionize medicine.

Preimplantation genetic diagnosis as a strategy to prevent having a child born with an heritable eye disease

BACKGROUND

In developed countries, genetically inherited eye diseases are responsible for a high percentage of childhood visual impairment. We aim to report our experience using preimplantation genetic diagnostics (PGD) in order to avoid transmitting a genetic form of eye disease associated with childhood visual impairment and ocular cancer.

MATERIAL AND METHODS

Retrospective case series of women who underwent in vitro fertilization (IVF) and PGD due to a familial history of inherited eye disease and/or ocular cancer, in order to avoid having a child affected with the known familial disease. Each family underwent genetic testing in order to identify the underlying disease-causing mutation. IVF and PGD treatment were performed; unaffected embryos were implanted in their respective mothers.

RESULTS

Thirty-five unrelated mothers underwent PGD, and the following hereditary conditions were identified in their families: albinism (10 families); retinitis pigmentosa (7 families); retinoblastoma (4 families); blue cone monochromatism, achromatopsia, and aniridia (2 families each); and Hermansky-Pudlak syndrome, Leber congenital amaurosis, Norrie disease, papillorenal syndrome, primary congenital cataract, congenital glaucoma, Usher syndrome type 1F, and microphthalmia with coloboma (1 family each). Following a total of 88 PGD cycles, 18 healthy (i.e., unaffected) children were born.

CONCLUSIONS

Our findings underscore the importance an ophthalmologist plays in informing patients regarding the options now available for using prenatal and preimplantation genetic diagnosis to avoid having a child with a potentially devastating genetic form of eye disease or ocular cancer. This strategy is highly relevant, particularly given the limited options currently available for treating these conditions.

Preimplantation Genetic Diagnosis of Multiple Endocrine Neoplasia Type 2A Using Informative Markers Identified by Targeted Sequencing

BACKGROUND

The revised guidelines for the management of medullary thyroid carcinoma recommend that genetic counseling regarding reproductive options, including preimplantation genetic diagnosis (PGD), be considered for all RET mutation carriers of reproductive age to avoid the transmission of multiple endocrine neoplasia type 2 (MEN2). However, the high complexity and cost of PGD have hindered its widespread use. Thus, it is necessary to establish a simple and relatively inexpensive method to facilitate the PGD of MEN2.

PATIENTS AND METHODS

A customized Nimblegen EZ sequence capture array was designed to capture the targeted regions, including the RET gene, and 1 Mb range on each side of the RET gene. Targeted, capture-based next-generation sequencing of three members of one family with MEN2A (the couple and the paternal father) was conducted to identify the informative markers. The diagnosis of the embryos was achieved through haplotype analysis based on informative markers and causative mutation.

RESULTS

Based on the sequencing results, 173 informative markers were detected, which were sufficient for the subsequent use for PGD. Seven informative markers and the causative mutation (RET^C634Y) were selected and subjected to Sanger sequencing. Through haplotype analysis, four embryos without inheritance of the mutation haplotype of the RET gene were diagnosed as unaffected. One unaffected embryo was transferred, with one healthy baby born at 38 gestational weeks.

CONCLUSIONS

Targeted, capture-based next-generation sequencing for identification of informative markers together with Sanger sequencing is an easy and efficient method for the PGD of monogenic diseases such as MEN2.

Comparative study of single-nucleotide polymorphism array and next generation sequencing based strategies on triploid identification in preimplantation genetic diagnosis and screen

Triploidy occurred about 2-3% in human pregnancies and contributed to approximately 15% of chromosomally caused human early miscarriage. It is essential for preimplantation genetic diagnosis and screen to distinct triploidy sensitively. Here, we performed comparative investigations between MALBAC-NGS and MDA-SNP array sensitivity on triploidy detection. Self-correction and reference-correction algorism were used to analyze the NGS data. We identified 5 triploid embryos in 1198 embryos of 218 PGD and PGS cycles using MDA-SNP array, the rate of tripoidy was 4.17‰ in PGS and PGD patients. Our results indicated that the MDA-SNP array was sensitive to digyny and diandry triploidy, MALBAC-NGS combined with self and reference genome correction strategies analyze were not sensitive to detect triploidy. Our study demonstrated that triploidy occurred at 4.17‰ in PGD and PGS, MDA-SNP array could successfully identify triploidy in PGD and PGS and genomic DNA. MALBAC-NGS combined with self and reference genome correction strategies were not sensitive to triploidy.

Effect of next-generation sequencing in preimplantation genetic testing on live birth ratio

The present study analysed live birth ratios in frozen embryo transfer (FET) cycles where embryo ploidy status was determined with preimplantation genetic testing (PGT) using next-generation sequencing (NGS). PGT was performed on trophectoderm cells biopsied at the blastocyst stage. The present prospective cohort study included 112 women undergoing frozen embryo transfer, with NGS PGT. The control group consisted of 85 patients who underwent the IVF procedure with FET planned for a subsequent cycle. The live birth rate per cycle was higher by ~18.5 percentage points in the investigated compared with control group (42.0% vs 23.5% respectively; P = 0.012). The differences between the study and control groups were also significant for clinical pregnancy (42.0% vs 23.5% respectively; P = 0.012), implantation (41.2% vs 22.2% respectively; P = 0.001) and pregnancy loss rates (9.6% vs 28.6% respectively; P = 0.027). The results show that PGT NGS is a useful method for embryo selection and it may be implemented in routine clinical practice with propitious results.

Live births after polar body biopsy and frozen-thawed cleavage stage embryo transfer: case report

Pre-implantation genetic diagnosis (PGD) or screening (PGS) technology, has emerged and developed in the past few years, benefiting couples as it allows the selection and transfer of healthy embryos during IVF treatments. These techniques can be performed in oocytes (polar-body biopsy) or embryos (blastomere or trophectoderm biopsy). In this case report, we describe the first two live births to be published in Brazil after a polar-body (PB) biopsy. In case 1, a 42-year-old was submitted to PB biopsy with PGS due to advanced maternal age and poor ovarian reserve. Five MII oocytes underwent first and second polar body biopsy and four cleavage embryos were cryopreserved. The PGS analysis resulted in two euploid embryos (next generation sequence). A frozen-thawed embryo transfer (FET) was performed after endometrial priming and a healthy baby was delivered after a cesarean section (37 weeks, female, 3390g, 47.5 cm). In case 2, a 40-year old patient with balanced translocation and poor ovarian response was submitted to PB biopsy. Two MII oocytes underwent first and second polar body biopsy and two embryos were cryopreserved in cleavage stage. The analysis resulted in one euploid embryo that was transferred after endometrial priming. A preterm healthy baby (34 weeks, female, 2100g, 40 cm) was delivered via cesarean section. In conclusion, although the blastocyst biopsy is the norm when performing PGS/PGD during IVF treatments, other alternatives (as PB biopsy) should be considered in some specific situations.

Noninvasive chromosome screening of human embryos by genome sequencing of embryo culture medium for in vitro fertilization

Preimplantation genetic screening (PGS) is widely used to select in vitro-fertilized embryos free of chromosomal abnormalities and to improve the clinical outcome of in vitro fertilization (IVF). A disadvantage of PGS is that it requires biopsy of the preimplantation human embryo, which can limit the clinical applicability of PGS due to the invasiveness and complexity of the process. Here, we present and validate a noninvasive chromosome screening (NICS) method based on sequencing the genomic DNA secreted into the culture medium from the human blastocyst. By using multiple annealing and looping-based amplification cycles (MALBAC) for whole-genome amplification (WGA), we performed next-generation sequencing (NGS) on the spent culture medium used to culture human blastocysts (n = 42) and obtained the ploidy information of all 24 chromosomes. We validated these results by comparing each with their corresponding whole donated embryo and obtained a high correlation for identification of chromosomal abnormalities (sensitivity, 0.882, and specificity, 0.840). With this validated NICS method, we performed chromosome screening on IVF embryos from seven couples with balanced translocation, azoospermia, or recurrent pregnancy loss. Six of them achieved successful clinical pregnancies, and five have already achieved healthy live births thus far. The NICS method avoids the need for embryo biopsy and therefore substantially increases the safety of its use. The method has the potential of much wider chromosome screening applicability in clinical IVF, due to its high accuracy and noninvasiveness.

How do patient perceived determinants influence the decision-making process to accept or decline preimplantation genetic screening?

OBJECTIVE

Identify the determinants that influence the patient's decision-making process when deciding to accept or decline preimplantation genetic screening (PGS) in a given IVF cycle.

DESIGN

Pilot, retrospective, cross-sectional study that used a questionnaire containing a combination of quantitative and qualitative items.

SETTING

Private practice IVF clinic.

PATIENT(S)

Patients and partners initiating an IVF treatment cycle, both autologous and donor, between October 2012 and January 2015.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

Identification of patient perceived determinants and the importance of each on the decision to accept or decline PGS.

RESULT(S)

Responses from the questionnaire (N = 117) were returned, and of these, 60% accepted PGS. The female response rate was 75% (N = 88) and the male response rate was 25% (N = 29). Ninety-eight percent were Christian (N = 112) and 88% college educated (N = 102) with 39% (N = 40) having some postgraduate education. Sixty-eight percent (N = 79) had no knowledge of PGS before the IVF cycle; however, after provider education, 92% (N = 108) correctly identified that PGS was elective and 93% (N = 109) reported sufficient knowledge to make an informed decision to accept or decline PGS. The additional cost of screening, the provider information and influence, and social support or acceptance from partner, family, and/or friends, were the three statistically significant variables affecting the decision.

CONCLUSION(S)

This is the first study, to the authors' knowledge, to identify and assess the determinants of the patient decision-making process when presented with the choice of PGS. Several factors contribute to the patient-perceived determinants when choosing to accept or decline PGS, including cost, religious and ethical beliefs and values, social and family support, provider influences, and the past reproductive experience of the patient.

Preimplantation genetic diagnosis for cystic fibrosis: a case report

Cystic fibrosis is an autosomal recessive disorder caused by mutations in the cystic fibrosis transmembrane conductance regulator gene. This disorder produces a variable phenotype including lung disease, pancreatic insufficiency, and meconium ileus plus bilateral agenesis of the vas deferens causing obstructive azoospermia and male infertility. Preimplantation genetic diagnosis is an alternative that allows identification of embryos affected by this or other genetic diseases. We report a case of couple with cystic fibrosis; the woman had the I148 T mutation and the man had the Delta F508 gene mutation. The couple underwent in vitro fertilization, associated with preimplantation genetic diagnosis, and with subsequent selection of healthy embryos for uterine transfer. The result was an uneventful pregnancy and delivery of a healthy male baby.

Validation of a semiconductor next-generation sequencing-based protocol for preimplantation genetic diagnosis of reciprocal translocations

OBJECTIVE

We aim to validate a semiconductor next-generation sequencing (NGS)-based method to detect unbalanced chromosome translocation in preimplantation embryos.

METHODS

The study consisted of a blinded retrospective evaluation with NGS of 145 whole-genome amplification products obtained from biopsy of cleavage-stage embryos or blastocysts, derived from 33 couples carrying different balanced translocations. Consistency of NGS-based copy number assignments was evaluated and compared with the results obtained by array-comparative genomic hybridization.

RESULTS

Reliably identified with the NGS-based protocol were 162 segmental imbalances derived from 33 different chromosomal translocations, with the smallest detectable chromosomal segment being 5 Mb in size. Of the 145 embryos analysed, 20 (13.8%) were balanced, 43 (29.6%) were unbalanced, 53 (36.5%) were unbalanced and aneuploid, and 29 (20%) were balanced but aneuploid. NGS sensitivity for unbalanced/aneuploid chromosomal call (consistency of chromosome copy number assignment) was 99.75% (402/403), with a specificity of 100% (3077/3077). NGS specificity and sensitivity for unbalanced/aneuploid embryo call were 100%.

CONCLUSIONS

Next-generation sequencing can detect chromosome imbalances in embryos with the added benefit of simultaneous comprehensive aneuploidy screening. Given the high level of consistency with array-comparative genomic hybridization, NGS has been demonstrated to be a robust high-throughput technique ready for clinical application in preimplantation genetic diagnosis for chromosomal translocations, with potential advantages of automation, increased throughput and reduced cost.

Technical Update: Preimplantation Genetic Diagnosis and Screening

OBJECTIVE

To update and review the techniques and indications of preimplantation genetic diagnosis (PGD) and preimplantation genetic screening (PGS).

OPTIONS

Discussion about the genetic and technical aspects of preimplantation reproductive techniques, particularly those using new cytogenetic technologies and embryo-stage biopsy.

OUTCOMES

Clinical outcomes of reproductive techniques following the use of PGD and PGS are included. This update does not discuss in detail the adverse outcomes that have been recorded in association with assisted reproductive technologies.

EVIDENCE

Published literature was retrieved through searches of The Cochrane Library and Medline in April 2014 using appropriate controlled vocabulary (aneuploidy, blastocyst/physiology, genetic diseases, preimplantation diagnosis/methods, fertilization in vitro) and key words (e.g., preimplantation genetic diagnosis, preimplantation genetic screening, comprehensive chromosome screening, aCGH, SNP microarray, qPCR, and embryo selection). Results were restricted to systematic reviews, randomized controlled trials/controlled clinical trials, and observational studies published from 1990 to April 2014. There were no language restrictions. Searches were updated on a regular basis and incorporated in the update to January 2015. Additional publications were identified from the bibliographies of retrieved articles. Grey (unpublished) literature was identified through searching the websites of health technology assessment and health technology-related agencies, clinical practice guideline collections, clinical trial registries, and national and international medical specialty societies.

VALUES

The quality of evidence in this document was rated using the criteria described in the Report of the Canadian Task Force on Preventive Health Care. (Table 1) BENEFITS, HARMS, AND COSTS: This update will educate readers about new preimplantation genetic concepts, directions, and technologies. The major harms and costs identified are those of assisted reproductive technologies.

SUMMARY

Preimplantation genetic diagnosis is an alternative to prenatal diagnosis for the detection of genetic disorders in couples at risk of transmitting a genetic condition to their offspring. Preimplantation genetic screening is being proposed to improve the effectiveness of in vitro fertilization by screening for embryonic aneuploidy. Though FISH-based PGS showed adverse effects on IVF success, emerging evidence from new studies using comprehensive chromosome screening technology appears promising. Recommendations 1. Before preimplantation genetic diagnosis is performed, genetic counselling must be provided by a certified genetic counsellor to ensure that patients fully understand the risk of having an affected child, the impact of the disease on an affected child, and the benefits and limitations of all available options for preimplantation and prenatal diagnosis. (III-A) 2. Couples should be informed that preimplantation genetic diagnosis can reduce the risk of conceiving a child with a genetic abnormality carried by one or both parents if that abnormality can be identified with tests performed on a single cell or on multiple trophectoderm cells. (II-2B) 3. Invasive prenatal or postnatal testing to confirm the results of preimplantation genetic diagnosis is encouraged because the methods used for preimplantation genetic diagnosis have technical limitations that include the possibility of a false result. (II-2B) 4. Trophectoderm biopsy has no measurable impact on embryo development, as opposed to blastomere biopsy. Therefore, whenever possible, trophectoderm biopsy should be the method of choice in embryo biopsy and should be performed by experienced hands. (I-B) 5. Preimplantation genetic diagnosis of single-gene disorders should ideally be performed with multiplex polymerase chain reaction coupled with trophectoderm biopsy whenever available. (II-2B) 6. The use of comprehensive chromosome screening technology coupled with trophectoderm biopsy in preimplantation genetic diagnosis in couples carrying chromosomal translocations is recommended because it is associated with favourable clinical outcomes. (II-2B) 7. Before preimplantation genetic screening is performed, thorough education and counselling must be provided by a certified genetic counsellor to ensure that patients fully understand the limitations of the technique, the risk of error, and the ongoing debate on whether preimplantation genetic screening is necessary to improve live birth rates with in vitro fertilization. (III-A) 8. Preimplantation genetic screening using fluorescence in situ hybridization technology on day-3 embryo biopsy is associated with decreased live birth rates and therefore should not be performed with in vitro fertilization. (I-E) 9. Preimplantation genetic screening using comprehensive chromosome screening technology on blastocyst biopsy, increases implantation rates and improves embryo selection in IVF cycles in patients with a good prognosis. (I-B).

Evaluation of FTA ® paper for storage of oral meta-genomic DNA

AIM

The purpose of the present study was to evaluate the short-term storage of meta-genomic DNA from native oral biofilms on FTA(®) paper.

MATERIALS AND METHODS

Thirteen volunteers of both sexes received an acrylic splint for intraoral biofilm formation over a period of 48 hours. The biofilms were collected, resuspended in phosphate-buffered saline, and either stored on FTA(®) paper or directly processed by standard laboratory DNA extraction. The nucleic acid extraction efficiencies were evaluated by 16S rDNA targeted SSCP fingerprinting. The acquired banding pattern of FTA-derived meta-genomic DNA was compared to a standard DNA preparation protocol. Sensitivity and positive predictive values were calculated.

RESULTS

The volunteers showed inter-individual differences in their bacterial species composition. A total of 200 bands were found for both methods and 85% of the banding patterns were equal, representing a sensitivity of 0.941 and a false-negative predictive value of 0.059.

CONCLUSION

Meta-genomic DNA sampling, extraction, and adhesion using FTA(®) paper is a reliable method for storage of microbial DNA for a short period of time.

Application of next-generation sequencing for 24-chromosome aneuploidy screening of human preimplantation embryos

BACKGROUND

Aneuploidy is a leading cause of repeat implantation failure and recurrent miscarriages. Preimplantation genetic screening (PGS) enables the assessment of the numeral and structural chromosomal errors of embryos before transfer in patients undergoing in vitro fertilization. Array comparative genomic hybridization (aCGH) has been demonstrated to be an accurate PGS method and in present thought to be the gold standard, but new technologies, such as next-generation sequencing (NGS), continue to emerge. Validation of the new comprehensive NGS-based 24-chromosome aneuploidy screening technology is still needed to determine the preclinical accuracy before it might be considered as an alternative method for human PGS.

RESULTS

In the present study, 43 human trophectoderm (TE) biopsy samples and 5 cytogenetically characterized cell lines (Coriell Cell Repositories) were tested. The same whole genome amplified product of each sample was blindly assessed with Veriseq NGS and Agilent aCGH to identify the aneuploidy status. The result showed that the NGS identified all abnormalities identified in aCGH including the numeral chromosomal abnormalities (again or loss) in the embryo samples and the structural (partial deletion and duplication) in the Coriell cell lines. Both technologies can identify a segmental imbalance as small as 1.8 Mb in size. Among the 41 TE samples with abnormal karyotypes in this study, eight (19.5 %) samples presented as multiple chromosome abnormalities. The abnormalities occurred to almost all chromosomes, except chromosome 6, 7, 17 and Y chromosome.

CONCLUSIONS

Given its reliability and high level of consistency with an established aCGH methodology, NGS has demonstrated a robust high-throughput methodology ready for extensive clinical application in reproductive medicine, with potential advantages of reduced costs and enhanced precision. Then, a randomized controlled clinical trial confirming its clinical effectiveness is advisable to obtain a larger sequencing dataset and more evidence for the extensive use of NGS-based PGS.

Revised American Thyroid Association guidelines for the management of medullary thyroid carcinoma

INTRODUCTION

The American Thyroid Association appointed a Task Force of experts to revise the original Medullary Thyroid Carcinoma: Management Guidelines of the American Thyroid Association.

METHODS

The Task Force identified relevant articles using a systematic PubMed search, supplemented with additional published materials, and then created evidence-based recommendations, which were set in categories using criteria adapted from the United States Preventive Services Task Force Agency for Healthcare Research and Quality. The original guidelines provided abundant source material and an excellent organizational structure that served as the basis for the current revised document.

RESULTS

The revised guidelines are focused primarily on the diagnosis and treatment of patients with sporadic medullary thyroid carcinoma (MTC) and hereditary MTC.

CONCLUSIONS

The Task Force developed 67 evidence-based recommendations to assist clinicians in the care of patients with MTC. The Task Force considers the recommendations to represent current, rational, and optimal medical practice.

Recent advances and current issues in single-cell sequencing of tumors

Intratumoral heterogeneity is a recently recognized but important feature of cancer that underlies the various biocharacteristics of cancer tissues. The advent of next-generation sequencing technologies has facilitated large scale capture of genomic data, while the recent development of single-cell sequencing has allowed for more in-depth studies into the complex molecular mechanisms of intratumoral heterogeneity. In this review, the recent advances and current challenges in single-cell sequencing methodologies are discussed, highlighting the potential power of these data to provide insights into oncological processes, from tumorigenesis through progression to metastasis and therapy resistance.

Genetic considerations in recurrent pregnancy loss

Human reproduction is remarkably inefficient; nearly 70% of human conceptions do not survive to live birth. Spontaneous fetal aneuploidy is the most common cause for spontaneous loss, particularly in the first trimester of pregnancy. Although losses owing to de novo fetal aneuploidy occur at similar frequencies among women with sporadic and recurrent losses, some couples with recurrent pregnancy loss have additional associated genetic factors and some have nongenetic etiologies. Genetic testing of the products of conception from couples experiencing two or more losses may aid in defining the underlying etiology and in counseling patients about prognosis in a subsequent pregnancy. Parental karyotyping of couples who have experienced recurrent pregnancy loss (RPL) will detect some couples with an increased likelihood of recurrent fetal aneuploidy; this may direct interventions. The utility of preimplantation genetic analysis in couples with RPL is unproven, but new approaches to this testing show great promise.

A healthy delivery of twins by assisted reproduction followed by preimplantation genetic screening in a woman with X-linked dominant incontinentia pigmenti

The purpose of this study is to report a successful twin pregnancy and delivery in a female patient with X-linked dominant incontinentia pigmenti (IP) who underwent assisted reproductive technology followed by preimplantation genetic screening (PGS). A 29-year-old female with IP had a previous history of recurrent spontaneous abortion. A molecular analysis revealed the patient had a de novo mutation, 1308_1309insCCCCTTG(p.Ala438ProfsTer26), in the inhibitor of the kappa B kinase gamma gene located in the Xq28 region. IVF/ICSI and PGS was performed, in which male embryos were sexed using array-based comparative genomic hybridization (aCGH). After IVF/ICSI and PGS using aCGH on seven embryos, two euploid male blastocysts were transferred with a 50% probability of a viable male pregnancy. The dizygotic twin pregnancy was confirmed and the amniocentesis results of each twin were normal with regard to the mutation found in the mother. The patient delivered healthy twin babies during the 37th week of gestation. This case shows the beneficial role of PGS in achieving a successful pregnancy through euploid male embryo gender selection in a woman with X-linked dominant IP with a history of multiple male miscarriages.

Clinical outcome of preimplantation genetic diagnosis and screening using next generation sequencing

Background

Next generation sequencing (NGS) is now being used for detecting chromosomal abnormalities in blastocyst trophectoderm (TE) cells from in vitro fertilized embryos. However, few data are available regarding the clinical outcome, which provides vital reference for further application of the methodology. Here, we present a clinical evaluation of NGS-based preimplantation genetic diagnosis/screening (PGD/PGS) compared with single nucleotide polymorphism (SNP) array-based PGD/PGS as a control.

Results

A total of 395 couples participated. They were carriers of either translocation or inversion mutations, or were patients with recurrent miscarriage and/or advanced maternal age. A total of 1,512 blastocysts were biopsied on D5 after fertilization, with 1,058 blastocysts set aside for SNP array testing and 454 blastocysts for NGS testing. In the NGS cycles group, the implantation, clinical pregnancy and miscarriage rates were 52.6% (60/114), 61.3% (49/80) and 14.3% (7/49), respectively. In the SNP array cycles group, the implantation, clinical pregnancy and miscarriage rates were 47.6% (139/292), 56.7% (115/203) and 14.8% (17/115), respectively. The outcome measures of both the NGS and SNP array cycles were the same with insignificant differences. There were 150 blastocysts that underwent both NGS and SNP array analysis, of which seven blastocysts were found with inconsistent signals. All other signals obtained from NGS analysis were confirmed to be accurate by validation with qPCR. The relative copy number of mitochondrial DNA (mtDNA) for each blastocyst that underwent NGS testing was evaluated, and a significant difference was found between the copy number of mtDNA for the euploid and the chromosomally abnormal blastocysts. So far, out of 42 ongoing pregnancies, 24 babies were born in NGS cycles; all of these babies are healthy and free of any developmental problems.

Conclusions

This study provides the first evaluation of the clinical outcomes of NGS-based pre-implantation genetic diagnosis/screening, and shows the reliability of this method in a clinical and array-based laboratory setting. NGS provides an accurate approach to detect embryonic imbalanced segmental rearrangements, to avoid the potential risks of false signals from SNP array in this study.

Electronic supplementary material

The online version of this article (doi:10.1186/2047-217X-3-30) contains supplementary material, which is available to authorized users.

[Update on preimplantation genetic diagnosis and screening]

Recent advancement in both human embryology and genomics has created a completely new situation for practical and widespread application of preimplantation genetic diagnosis and screening with a dramatic effect on assisted reproduction. The mapping of the first human genome and the advancement in sequencing technology and bioinformatics has led to the discovery of the exact genetic background of exponentially increasing number of diseases. In parallel, methods for culturing human embryos have also radically improved, enabling the late transfer, and the procedure of vitrification the safe cryopreservation. In consequence, refined genetic analyses have become available from blastocyst biopsy followed by the application of novel genomic methods. Furthermore, some studies suggest that by the selection of aneuploid embryos the pregnancy- and birth-rates can be increased. The amount and the depth of information obtainable from the embryos raise several technical and ethical questions that can be answered by further prospective randomized trials.

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.

Morphological good-quality embryo has higher nucleus spreading rate/signal resolution rate in fluorescence in situ hybridization

PURPOSE

To evaluate the relationship between day 3 embryo quality and nucleus spreading rate/signal resolution rate in Fluorescence in situ hybridization (FISH) during the PGD procedure.

METHODS

This study was a retrospective data analysis. 367 day-3 embryos were classified based on morphological scoring: grade 1 to grade 4 were defined from worse to better embryo quality. Day 3 embryos were classified as good quality when the number of blastomeres was between 6 and 10 and grade better than 2'. Nucleus spreading rate, signal rate and the full signal rate were compared between embryos with different morphological scoring.

RESULTS

Nucleus spreading rate of blastomeres from morphological high-quality embryos was significantly higher (86.25 %) than from poor-quality embryos (76.53 %) (p < 0.05). The rate of blastomeres with full signals was significantly higher (79.32 %) in the morphological high-quality group than in poor-quality group (64.54 %) (p < 0.05). Similar results were found from day 3 embryos with cell number between 6 cells and 10 cells (nucleus spreading rate 86.01 vs. 76.34 %, p < 0.05; full signal rate 78.72 vs. 62.71 %, p < 0.05). Both have no significant difference in the signal rate (82.67 vs. 89.66 %; 83.10 vs. 89.95 %).

CONCLUSIONS

Blastomeres from day 3 embryos with better morphological quality had higher nucleus spreading rate and higher full signal rate during FISH. Through this study, we speculate on whether it should reconsider the necessity of FISH application in embryos with poor quality.