Test performance and clinical utility of expanded non-invasive prenatal test: Experience on 71,883 unselected routine cases from one single center

OBJECTIVE

The balance between benefits and risks of discordant outcomes makes the Genome-Wide Non-Invasive Prenatal Test (GW-NIPT) controversial. This study aims to evaluate performance and clinical utility in a wide cohort of unselected clinical cases from a single center when a standardized protocol is applied and integrated with a secondary algorithm for data interpretation.

METHOD

In 2 years, over 70,000 pregnant patients underwent GW-NIPT for fetal common trisomies, sex chromosome aneuploidies, rare autosomal aneuploidies, segmental abnormalities (CNVs ≥ 7 Mb) and microdeletions (CNVs < 7 Mb). All samples were uniformly processed with Veriseq NIPT Solution v2 and analyzed using all data metrics along with a home-made algorithm for sequencing data analysis. Results were retrospectively reviewed for clinical outcomes.

RESULTS

Among 71,883 eligible cases including twin pregnancies, 1011 (1.4%) received a positive result and 781 were confirmed by invasive prenatal diagnosis. Clinical sensitivity ranged from 99.65% for common trisomy (T21, T18, T13) to 83.33% for microdeletions, while specificity remained high (99.98%) for each class of fetal abnormalities detected.

CONCLUSIONS

Integrating a standardized protocol with an internal algorithm allowed discordant results to be reduced, yielding high accuracy. Observed reliability in detecting genome-wide chromosomal conditions reinforced the expanded NIPT utility in clinical practice.

Combined TP53 status in tumor-free resection margins and circulating microRNA profiling predicts the risk of locoregional recurrence in head and neck cancer

Locoregional recurrences represent a frequently unexpected problem in head and neck squamous cell carcinoma (HNSCC). Relapse often (10-30%) occurs in patients with histologically negative resection margins (RMs), probably due to residual tumor cells or hidden pre-cancerous lesions in normal mucosa, both missed by histopathological examination. Therefore, definition of a 'clean' or tumor-negative RM is controversial, demanding for novel approaches to be accurately explored. Here, we evaluated next generation sequencing (NGS) and digital PCR (dPCR) as tools to profile TP53 mutational status and circulating microRNA expression aiming at scoring the locoregional risk of recurrence by means of molecular analyses. Serial monitoring of these biomarkers allowed identifying patients at high risk, laying the ground for accurate tracking of disease evolution and potential intensification of post-operative treatments. Additionally, our pipeline demonstrated its applicability into the clinical routine, being cost-effective and feasible in terms of patient sampling, holding promise to accurately (re)-stage RMs in the era of precision medicine.

The mosaic embryo: what it means for the doctor and the patient

INTRODUCTION

Mosaic embryos are embryos that on preimplantation genetic analysis are found to be composed of euploid and aneuploid cells. Although most of these embryos do not implant when transferred into the uterus following IVF treatment, some may implant and are capable of giving rise to babies.

EVIDENCE ACQUISITION

There is currently an increasing number of reports of live births following the transfer of mosaic embryos. Compared to euploid, mosaic embryos have lower implantation rates and higher rates of miscarriage, and occasionally aneuploid component persists. However, their outcome is better than that obtained after the transfer of embryos consisting entirely of aneuploid cells. After implantation, the ability to develop into a full-term pregnancy is influenced by the amount and type of chromosomal mosaicism present in a mosaic embryo. Nowadays many experts in the reproductive field consider mosaic transfers as an option when no euploid embryos are available. Genetic counseling is an important part of educating patients about the likelihood of having a pregnancy with healthy baby but also on the risk that mosaicism could persist and result in liveborn with chromosomal abnormality. Each situation needs to be assessed on a case-by-case basis and counseled accordingly.

EVIDENCE SYNTHESIS

So far, the transfers of 2155 mosaic embryos have been documented and 440 live births resulting in healthy babies have been reported. In addition, in the literature to date, there are 6 cases in which embryonic mosaicism persisted.

CONCLUSIONS

In conclusion, the available data indicate that mosaic embryos have the potential to implant and develop into healthy babies, albeit with lower success rates than euploids. Further clinical outcomes should be collected to better establish a refined ranking of embryos to transfer.

Chromosomal, gestational, and neonatal outcomes of embryos classified as a mosaic by preimplantation genetic testing for aneuploidy

OBJECTIVE

To understand the clinical risks associated with the transfer of embryos classified as a mosaic using preimplantation genetic testing for aneuploidy.

DESIGN

Analysis of data collected between 2017 and 2023.

SETTING

Multicenter.

PATIENTS

Patients of infertility treatment.

INTERVENTION

Comparison of pregnancies resulting from embryos classified as euploid or mosaic using the 20%-80% interval in chromosomal intermediate copy numbers to define a mosaic result.

MAIN OUTCOME MEASURES

Rates of spontaneous abortion, birth weight, length of gestation, incidence of birth defects, and chromosomal status during gestation.

RESULTS

Implanted euploid embryos had a significantly lower risk of spontaneous abortion compared with mosaic embryos (8.9% [n = 8,672; 95% confidence interval {CI95} 8.3, 9.5] vs. 22.2% [n = 914; CI95 19.6, 25.0]). Embryos with mosaicism affecting whole chromosomes (not segmental) had the highest risk of spontaneous abortion (27.6% [n = 395; CI95 23.2, 32.3]). Infants born from euploid, mosaic, and whole chromosome mosaic embryos had average birth weights and lengths of gestation that were not statistically different (3,118 g and 267 days [n = 488; CI95 3,067, 3,169, and 266, 268], 3052 g and 265 days [n = 488; CI95 2,993, 3,112, and 264,267], 3,159 g and 268 days [n = 194; CI95 3,070, 3,249, and 266,270], respectively). Out of 488 infants from mosaic embryo transfers (ETs), one had overt gross abnormalities as defined by the Centers for Disease Control and Prevention. Most prenatal tests performed on pregnancies from mosaic ETs had normal results, and only three pregnancies produced prenatal test results reflecting the mosaicism detected at the embryonic stage (3 out of 250, 1.2%; CI95 0.25, 3.5).

CONCLUSION

Although embryos classified as mosaic experience higher rates of miscarriage than euploid embryos (with a particularly high frequency shortly after implantation), infants born of mosaic ETs are similar to infants of euploid ETs. Prenatal testing indicates that mosaicism resolves during most pregnancies, although this process is not perfectly efficient. In a small percentage of cases, the mosaicism persists through gestation. These findings can serve as risk-benefit considerations for mosaic ETs in the fertility clinic.

Two clinical case reports of embryonic mosaicism identified with PGT-A persisting during pregnancy as true fetal mosaicism

The health risks associated with transferring embryos classified as mosaic by preimplantation genetic testing for aneuploidies (PGT-A) are currently unknown. Such embryos produce PGT-A results indicating the presence of both euploid and aneuploid cells and have historically been deselected from transfer and grouped with uniformly aneuploid embryos as 'abnormal'. In recent years, numerous groups have reported the intentional transfer of mosaic embryos in the absence of uniformly euploid embryos, largely observing births of seemingly healthy babies. However, it remains to be understood whether the embryonic mosaicism invariably becomes resolved during the ensuing pregnancy, or whether the placenta and/or fetal tissues retain aneuploid cells, and if so to what potential clinical effect. Here, we report two cases of mosaicism persisting from the embryonic stage to the established pregnancy. Case 1 involved an embryonic low-level segmental mosaic loss in Chromosome (Chr) 1, which was confirmed in amniocentesis as well as in brain tissue of the products of conception. This pregnancy was terminated due to the chromosomal pathologies associated with 1p36 deletion syndrome, such as severe intellectual disability. Case 2 involved a low-level mosaic Chr 21 trisomy, which was confirmed with chorionic villus sampling and amniocentesis. The ensuing pregnancy was terminated after ultrasound identification of severe abnormalities in the placenta and fetus. Together, these two cases should be taken into account for risk-benefit assessments of prospective mosaic embryo transfers.

Decision-making process about prenatal genetic screening: how deeply do moms-to-be want to know from Non-Invasive Prenatal Testing?

BACKGROUND

Prenatal information may be obtained through invasive diagnostic procedures and non-invasive screening procedures. Several psychological factors are involved in the decision to undergo a non-invasive prenatal testing (NIPT) but little is known about the decision-making strategies involved in choosing a specific level of in-depth NIPT, considering the increased availability and complexity of NIPT options. The main aim of this work is to assess the impact of psychological factors (anxiety about pregnancy, perception of risk in pregnancy, intolerance to uncertainty), and COVID-19 pandemic on the type of NIPT chosen, in terms of the number of conditions that are tested.

METHODS

A self-administered survey evaluated the decision-making process about NIPT. The final sample comprised 191 women (M_age = 35.53; SD = 4.79) who underwent a NIPT from one private Italian genetic company. Based on the test date, the sample of women was divided between "NIPT before COVID-19" and "NIPT during COVID-19".

RESULTS

Almost all of the participants reported being aware of the existence of different types of NIPT and more than half reported having been informed by their gynecologist. Results showed no significant association between the period in which women underwent NIPT (before COVID-19 or during COVID-19) and the preferences for more expanded screening panel. Furthermore, regarding psychological variables, results showed a significant difference between perceived risk for the fetus based on the NIPT type groups, revealing that pregnant women who underwent the more expanded panel had a significantly higher level of perceived risk for the fetus than that reported by pregnant women who underwent the basic one. There was no statistically significant difference between the other psychological variables and NIPT type.

CONCLUSIONS

Our findings indicate the paramount role of gynecologist and other health care providers, such as geneticists and psychologists, is to support decision-making process in NIPT, in order to overcome people's deficits in genetic knowledge, promote awareness about their preferences, and control anxiety related to the unborn child. Decision-support strategies are critical during the onset of prenatal care, according to the advances in prenatal genomics and to parent's needs.

ESHRE PGT Consortium data collection XXI: PGT analyses in 2018

STUDY QUESTION

What are the trends and developments in preimplantation genetic testing (PGT) in 2018 as compared to previous years?

SUMMARY ANSWER

The main trends observed in this 21st dataset on PGT are that the implementation of trophectoderm biopsy with comprehensive whole-genome testing is most often applied for PGT-A and concurrent PGT-M/SR/A, while for PGT-M and PGT-SR, single-cell testing with PCR and FISH still prevail.

WHAT IS KNOWN ALREADY

Since it was established in 1997, the ESHRE PGT Consortium has been collecting and analysing data from mainly European PGT centres. To date, 20 datasets and an overview of the first 10 years of data collections have been published.

STUDY DESIGN SIZE DURATION

The data for PGT analyses performed between 1 January 2018 and 31 December 2018 with a 2-year follow-up after analysis were provided by participating centres on a voluntary basis. Data were collected using an online platform, which is based on genetic analysis and has been in use since 2016.

PARTICIPANTS/MATERIALS SETTING METHODS

Data on biopsy method, diagnostic technology, and clinical outcome were submitted by 44 centres. Records with analyses for more than one PGT for monogenic disorders (PGT-M) and/or PGT for chromosomal structural rearrangements (PGT-SR), or with inconsistent data regarding the PGT modality, were excluded. All transfers performed within 2 years after the analysis were included, enabling the calculation of cumulative pregnancy rates. Data analysis, calculations, and preparation of figures and tables were carried out by expert co-authors.

MAIN RESULTS AND THE ROLE OF CHANCE

The current data collection from 2018 covers a total of 1388 analyses for PGT-M, 462 analyses for PGT-SR, 3003 analyses for PGT for aneuploidies (PGT-A), and 338 analyses for concurrent PGT-M/SR with PGT-A.The application of blastocyst biopsy is gradually rising for PGT-M (from 19% in 2016-2017 to 33% in 2018), is status quo for PGT-SR (from 30% in 2016-2017 to 33% in 2018) and has become the most used biopsy stage for PGT-A (from 87% in 2016-2017 to 98% in 2018) and for concurrent PGT-M/SR with PGT-A (96%). The use of comprehensive, whole-genome amplification (WGA)-based diagnostic technology showed a small decrease for PGT-M (from 15% in 2016-2017 to 12% in 2018) and for PGT-SR (from 50% in 2016-2017 to 44% in 2018). Comprehensive testing was, however, the main technology for PGT-A (from 93% in 2016-2017 to 98% in 2018). WGA-based testing was also widely used for concurrent PGT-M/SR with PGT-A, as a standalone technique (74%) or in combination with PCR or FISH (24%). Trophectoderm biopsy and comprehensive testing strategies are linked with higher diagnostic efficiencies and improved clinical outcomes per embryo transfer.

LIMITATIONS REASONS FOR CAUTION

The findings apply to the data submitted by 44 participating centres and do not represent worldwide trends in PGT. Details on the health of babies born were not provided in this manuscript.

WIDER IMPLICATIONS OF THE FINDINGS

The Consortium datasets provide a valuable resource for following trends in PGT practice.

STUDY FUNDING/COMPETING INTERESTS

The study has no external funding, and all costs are covered by ESHRE. There are no competing interests declared.

TRIAL REGISTRATION NUMBER

N/A.

The number and rate of euploid blastocysts in women undergoing IVF/ICSI cycles are strongly dependent on ovarian reserve and female age

STUDY QUESTION

Can the possibility of having at least one euploid blastocyst for embryo transfer and the total number of euploid blastocysts be predicted for couples before they enter the IVF programme?

SUMMARY ANSWER

Ovarian reserve and female age are the most important predictors of having at least one euploid blastocyst and the total number of euploid blastocysts.

WHAT IS KNOWN ALREADY

The blastocyst euploidy rate among women undergoing ART has already been shown to significantly decrease with increasing female age, and the total number of euploid embryos is dependent on the blastocyst cohort size. However, the vast majority of published studies are based on retrospective analysis of data.

STUDY DESIGN, SIZE, DURATION

This prospective analysis included 847 consecutively enrolled couples approaching their first preimplantation genetic testing for aneuploidies (PGT-A) cycle between 2017 and 2020. Only couples for whom ejaculated sperm was available and women with a BMI of <35 kg/m2 were included in the study. Only the first cycle was included for each patient.

PARTICIPANTS/MATERIALS, SETTING, METHODS

The study was conducted at an IVF centre where, for all patients, the planned treatment was to obtain embryos at the blastocyst stage for the PGT-A programme. The impact of the following covariates was investigated: a woman's serum AMH level, age, height, weight and BMI and a man's age, height, weight, BMI, sperm volume and sperm motility and morphology. The analysis was performed with a machine learning (ML) approach. Models were fit on the training set (677 patients) and their predictive performance was then evaluated on the test set (170 patients).

MAIN RESULTS AND ROLE OF CHANCE

After ovarian stimulation and oocyte insemination, 40.1% of couples had at least one blastocyst available for the PGT-A. Of 1068 blastocysts analysed, 33.6% were euploid. Two distinct ML models were fit: one for the probability of having at least one euploid blastocyst and one for the number of euploid blastocysts obtained. In the training set of patients, the variable importance plots of both models indicated that AMH and the woman's age are by far the most important predictors. Specifically, a positive association between the outcome and AMH and a negative association between the outcome and female age appeared. Gradient-boosted modelling offers a greater predictive performance than generalized additive models (GAMs).

LIMITATIONS, REASONS FOR CAUTION

The study was performed based on data from a single centre. While this provides a robust set of data with a constant ART process and laboratory practice, the model might be suitable only for the evaluated population, which may limit the generalization of the model to other populations.

WIDER IMPLICATIONS OF THE FINDINGS

ML models indicate that for couples entering the IVF/PGT-A programme, ovarian reserve, which is known to vary with age, is the most important predictor of having at least one euploid embryo. According to the GAM, the probability of a 30-year-old woman having at least one euploid embryo is 28% or 47% if her AMH level is 1 or 3 ng/ml, respectively; if the woman is 40 years old, this probability is 18% with an AMH of 1 ng/ml and 30% with an AMH of 3 ng/ml.

STUDY FUNDING/COMPETING INTEREST(S)

This study was supported by an unrestricted grant from Gedeon Richter. The authors declared no conflict of interests.

TRIAL REGISTRATION NUMBER

N/A.

P-563 The effect of embryo culture time on concordance rates between invasive and non-invasive preimplantation genetic testing for aneuploidies (niPGT-A) in spent culture media (SCM) analysis

Study question

To evaluate different embryo culture times (day5 versus day6) to understand the ideal time-frame for the performance of concordance analysis between invasive and non-invasive PGT-A(niPGT-A)

Summary answer

Different levels of ploidy concordance rates were observed between day5 and day6 groups: 72,6% versus 84,8%, respectively

What is known already

The recent data supports that a non-invasive approach for evaluating embryo ploidy status may be an alternative to standard invasive methods. Embryo cell-free DNA(cfDNA) released into culture media during in-vitro embryo development represents the potential source for this analysis. The release of cfDNA from embryos is expected to be directly proportional to embryo culture time and late-stage released cfDNA may be more representative of the embryo. Therefore, it is important to estimate the most effective time frame of the culture that will provide the most conclusive data from spent-culture-media(SCM) without adversely affecting the development of the embryo

Study design, size, duration

A total of 334 SCM from blastocyst stage embryos have been included in this study. The SCM samples were divided in 2 subgroups according to the embryo culture time as day5 (n = 154) and day6 (n = 180). The cfDNA of SCM samples were amplified by whole genome amplification(WGA) and analyzed by next generation sequencing(NGS) in parallel to day5 or day6 trophectodermal(TE) biopsied samples of their corresponding embryos. Ploidy status and concordance were compared between two groups

Participants/materials, setting, methods

Day3 embryos were washed and transferred in 20µl fresh culture media until the biopsy. SCM samples were collected in PCR tubes and stored at -20 °C while embryos were biopsied for standard PGT-A analysis. Both SCM and corresponding TE biopsy samples were amplified by Sureplex(Vitrolife). Then TE and SCM samples were analyzed by next-generation sequencing(NGS) using MiSeq® System (Illumina). Data analysis has been done by Bluefuse Multi Software 4.5(Illumina) for all SCM and TE samples

Main results and the role of chance

A successful DNA amplification rate (&gt;30ng/µl) was obtained in both day5 and day6 groups with 95,5% (147/154) and 99,4% (179/180) respectively. The DNA concentration after WGA was ranging between 30.1-122.5ng/µl and 38.5-123.2ng/µl in day5 and day6 groups respectively. Not conclusive (NC) results including a noisy NGS profile and chaotic chromosome aneuploidies (&gt;5 chromosomes) were excluded in both groups. Therefore, 64,6% (95/147) of SCM samples in day5 group and 81,0% (145/179) of SCM samples in day6 group were conclusive for NGS analysis. The ploidy concordance rate between SCM and TE samples (euploid vs euploid, aneuploid vs aneuploid) was 72,6% (69/95) in day5 and 84,8% (123/145) in day6 group. In day5 group, the false-negative rate was 10.5% (10/95), and false-positive rate was 16.8% (16/95) while in day6 group the false-negative rate was 6,8% (10/145), and false-positive rate was 8,2% (12/145). Sensitivity and specificity were calculated as 83,6% and 52,9% in day5 group, and 90,9% and 65,7 in day6 group respectively

Limitations, reasons for caution

We have high number of samples in our study, but larger prospective studies may change the significance of ploidy concordance. One of the important issues in SCM analysis is the maternal DNA contamination risk which cannot be revealed always. Therefore the use of molecular markers would increase the reliability

Wider implications of the findings

A non-invasive approach for aneuploidy screening may be an alternative to standard PGT-A procedure with invasive embryo biopsy but the evaluation of ideal culture time is crucial for the performance of niPGT-A method. Our study demonstrates that the late collection time of SCM provides significantly better ploidy concordance rates

Trial registration number

Not applicable

O-041 Data from the ESHRE PGT consortium – year 2020

Study question

Which are the trends shown in data collection XXII of the European Society of Human Reproduction and Embryology (ESHRE) PGT Consortium compared with previous years?

Summary answer

Data collection XXII, year 2020, represents valuable data on PGT activity in (mainly) Europe and reports on the main trends observed, being the further expansion of comprehensive testing technology in PGT-SR and PGT-A.

What is known already

The ESHRE PGT Consortium was set up in 1997 and from that time has been collecting data on PGT and PGT-A. The PGT database comprises the world’s largest collection of PGT / PGT-A data providing a valuable resource for data mining and for following trends in PGT practice. So far, up to the year 2015, data collections were carried out in a retrospective data way, from 2016 onwards a prospective cycle-by-cycle data collection was in place.

Study design, size, duration

As the nature of PGT/ PGT-A treatments has changed significantly over the last years and IVF cycle management and genetic analysis techniques are getting more complex, ESHRE uses an online data collection system in which data are collected prospectively from oocyte retrieval to analysis, embryo transfer and pregnancy / live birth. Data are collected cycle by cycle on a voluntary basis.

Participants/materials, settings, method

For the 2020 data, individual centres (37) from 20 countries directly entered the data into the PGT database through software developed by ESHRE. Data were analysed at ESHRE headquarters and include all aspects of PGT/PGT-A cycles.

Main results and the role of chance

The Consortium has analysed the PGT analyses (n = 2809) performed in 2020. The indications for PGT included inherited chromosomal abnormalities (n = 331 analyses), monogenic disorders (n = 987 analyses), aneuploidy testing for infertility (n = 1417 analyses) or combinations of the above (n = 74 analyses). In addition, 704 clinical pregnancies and 335 deliveries have been analysed in detail. The methods used for biopsy were polar body (2%), cleavage stage biopsy (20%) and blastocyst biopsy (78%), showing a further increase of blastocyst biopsy compared to 2019. The methodology used for diagnosis is what is evolving most over the last years, with data set XXII (2020) showing around 4% of FISH, 28% of PCR and 68% of WGA. Within WGA 95% of the analysis were done using NGS, in 4% of the cases SNP arrays were used and in 1% array-CGH was used. The overall clinical pregnancy rate is about 25% per analysis. The baby data show that it is difficult for most centres to have a detailed follow-up.

Limitations, reasons for caution

The findings apply to the 37 participating centres and may not represent worldwide trends in PGT. Data were collected prospectively, but details of the follow-up on PGT pregnancies and babies born were limited.

Wider implications of the findings

The ESHRE PGD Consortium continues its activities as an important forum for PGT practitioners to share data and exchange experiences. The information extracted from the data collections helps to monitor quality issues in PGT and survey the introduction and effectiveness of new PGT technologies and methods.

Trial registration number

Genetic testing users in Italy and Germany: Health orientation, health-related habits, and psychological profile

Background

Rapid advances in genomic knowledge and widespread access to the web contributed to the development of genetic services by private companies or medical laboratories. In the European landscape, though, there is not a single coherent regulatory approach to genetic testing (GT). The study aimed to investigate differences and similarities between two populations of GT users, Italians and Germans, in terms of health‐related behaviors, psychological characteristics, and attitudes toward genetic information.

Methods

Ninety‐nine Italian GT users from one private genetic company and 64 Germans GT users from one medical laboratory, completed an ad hoc self‐administered questionnaire.

Results

Results showed significant differences in health‐related behaviors (unhealthy eating behaviors, smoking behaviors, and frequency in medical check‐ups), with Germans reporting higher levels of unhealthy eating habits and smoking behaviors than Italians; Italian users also were more medically controlled. Furthermore, German participants were less willing to change their lifestyle following the GT results compared to Italian participants. Regarding psychological variables, German users felt more confident about their physical well‐being and they seemed more motivated than Italians to avoid becoming unhealthy. Finally, two samples differed in the way they accessed genetic testing (with the Italians guided predominately by a physician in contrast with the Germans who were recommended by friends) and managed genetic testing results (with Italian participants significantly more willing to share results with doctors than German participants, who preferred sharing with the family).

Conclusion

The analysis of cultural and organizational differences could help in defining adequate guidelines for counseling, and provide inputs for regulators in different European contexts.

Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects

Objectives

Despite extensive efforts to monitor the diffusion of COVID-19, the actual wave of infection is worldwide characterized by the presence of emerging SARS-CoV-2 variants. The present study aims to describe the presence of yet undiscovered SARS-CoV-2 variants in Italy.

Methods

Next Generation Sequencing was performed on 16 respiratory samples from occasionally employed within the Bangladeshi community present in Ostia and Fiumicino towns. Computational strategy was used to identify all potential epitopes for reference and mutated Spike proteins. A simulation of proteasome activity and the identification of possible cleavage sites along the protein guided to a combined score involving binding affinity, peptide stability and T-cell propensity.

Results

Retrospective sequencing analysis revealed a double Spike D614G/S939F mutation in COVID-19 positive subjects present in Ostia while D614G mutation was evidenced in those based in Fiumicino. Unlike D614G, S939F mutation affects immune response by the slight but significant modulation of T-cell propensity and the selective enrichment of potential binding epitopes for some HLA alleles.

Conclusion

Collectively, our findings mirror further the importance of deep sequencing of SARS-CoV-2 genome as a unique approach to monitor the appearance of specific mutations as for those herein reported for Spike protein. This might have implications on both the type of immune response triggered by the viral infection and the severity of the related illness.

Let the data do the talking: the need to consider mosaicism during embryo selection

Chromosomal mosaicism, the coexistence of cells with different chromosomal content, has been documented in human embryos for 3 decades. Early versions of preimplantation genetic testing for aneuploidy (PGT-A) did not measure mosaicism, either because typically only a single cell was assessed or because the technique could not accurately identify it. Although this led to a straightforward diagnosis (an embryo was considered either normal or abnormal), it simply avoided the issue and, in hindsight, may have led to numerous misdiagnoses with negative clinical consequences. Modern PGT-A evaluates a multicellular biopsy specimen with techniques capable of recognizing intermediate copy number signals for chromosomes or subchromosomal regions. We are, therefore, inevitably confronted with the issue of mosaicism and the challenge of managing embryos producing such results in the clinic. Here we discuss recent data showing that not only mosaicism in general, but specific features of mosaicism detected with PGT-A, are associated with variable clinical outcomes. The conclusion is evident: mosaicism should be considered for more informed and improved embryo selection in the clinic.

Search for Lepton Number and Flavor Violation in K^{+} and π^{0} Decays

Searches for the lepton number violating K^{+}→π^{-}μ^{+}e^{+} decay and the lepton flavor violating K^{+}→π^{+}μ^{-}e^{+} and π^{0}→μ^{-}e^{+} decays are reported using data collected by the NA62 experiment at CERN in 2017-2018. No evidence for these decays is found and upper limits of the branching ratios are obtained at 90% confidence level: B(K^{+}→π^{-}μ^{+}e^{+})<4.2×10^{-11}, B(K^{+}→π^{+}μ^{-}e^{+})<6.6×10^{-11} and B(π^{0}→μ^{-}e^{+})<3.2×10^{-10}. These results improve by 1 order of magnitude over previous results for these decay modes.

O-009 Data from the ESHRE PGT consortium – year 2019

Study question

Which are the trends shown in data collection XXI of the European Society of Human Reproduction and Embryology (ESHRE) PGT Consortium compared with previous years?

Summary answer

Data collection XXI, year 2019, represents valuable data on PGT activity in (mainly) Europe and reports on the main trends observed, being the further expansion of comprehensive testing technology in PGT-SR and PGT-A.

What is known already

The ESHRE PGT Consortium was set up in 1997 and from that time has been collecting data on PGT and PGT-A. The PGT database comprises the world’s largest collection of PGT / PGT-A data providing a valuable resource for data mining and for following trends in PGT practice. So far, up to the year 2015, data collections were carried out in a retrospective data way, from 2016 onwards a prospective data collection was in place.

Study design, size, duration

As the nature of PGT/ PGT-A treatments has changed significantly over the last years and IVF cycle management and genetic analysis techniques are getting more complex, ESHRE uses an online data collection system in which data are collected prospectively from oocyte retrieval to analysis, embryo transfer and pregnancy / live birth. Data are collected cycle by cycle on a voluntary basis.

Participants/materials, settings, method

For the 2019 data, individual centres (31) from 19 countries directly entered the data into the PGT database through software developed by ESHRE. Data were analysed at ESHRE headquarters and include all aspects of PGT/PGT-A cycles.

Main results and the role of chance

The Consortium has analysed the PGT analyses (n = 2735) performed in 2019. The indications for PGT included inherited chromosomal abnormalities (n = 253 analyses), monogenic disorders (n = 1105 analyses), aneuploidy testing for infertility (n = 1111 analyses) or combinations of the above (n = 266 analyses). In addition, 662 clinical pregnancies and 216 deliveries have been analysed in detail. The methods used for biopsy were polar body (2%), cleavage stage biopsy (35%) and blastocyst biopsy (61%; comparable with data from 2018). The methodology used for diagnosis is what is evolving most over the last years, with data set XXI (2019) showing around 7% of FISH, 37% of PCR and 55% of WGA. Within WGA 90.6% of the analysis were done using NGS, in 4.4% cases SNP arrays were used and in 2.4% array-CGH was used. The overall clinical pregnancy rate is about 24% per analysis. The baby data show that it is difficult for most centres to have a detailed follow-up.

Limitations, reasons for caution

The findings apply to the 31 participating centres and may not represent worldwide trends in PGT. Data were collected prospectively, but details of the follow-up on PGT pregnancies and babies born were limited.

Wider implications of the findings

The ESHRE PGD Consortium continues its activities as an important forum for PGT practitioners to share data and exchange experiences. The information extracted from the data collections helps to monitor quality issues in PGT and survey the introduction and effectiveness of new PGT technologies and methods.

O-201 Prenatal and postnatal outcome of mosaic embryo transfers: multicentric study of one thousand mosaic embryos diagnosed by preimplantation genetic testing with trophectoderm biopsy

Study question

To explore the effect of chromosomal mosaicism detected in preimplantation genetic testing (PGT-A) on prenatal and postnatal outcome of mosaic embryo pregnancies

Summary answer

No significant difference between euploid and mosaic embryos was observed in terms of weeks of gestation, average weight, and developmental defect of the babies born

What is known already

Mosaic embryos have the potential to implant and develop into healthy babies. Transfer of these embryos is now offered as an option for women who undergo IVF resulting in no euploid embryos. While, prenatal diagnosis has shown the depletion of chromosomal mosaicism in mosaic embryos, several concerns remain. For instance, the direct effects of different kind of mosaicism on prenatal/postnatal outcome and the possibility that intra-biopsy mosaicism in the TE is a poor predictor of the ploidy status of the ICM. Thus, there is certainly a need for comprehensive analyses of obstetrical and neonatal outcome data of transferred mosaic embryos.

Study design, size, duration

Compiled analysis from multicenter data on transfers of mosaic embryos (n = 1,000) and their outcome, with comparison to a euploid control group (n = 5,561). To explore the effect of embryonic mosaicism on newborns, we matched mosaic embryos resulting in a birth with a euploid embryo by a series of parameters (maternal age, embryo morphology, and indication for PGT-A). Prenatal tests and birth characteristics of &gt; 200 neonates from mosaic embryo transfers were compared to &gt; 200 euploid embryos.

Participants/materials, setting, methods

PGT-A was performed on blastocyst-stage embryos with 24-Chromosome whole genome amplification (WGA)-based Next Generation Sequencing (NGS). In accordance with established guidelines, embryos were categorized as mosaic when PGT-A results indicated 20-80% aneuploid content. Prenatal testing where performed in 30% of pregnancies with amniocentesis, 4% did an extra analysis for potential UPD for the suspected mosaic chromosome, and an additional 16% performed chorionic villus sampling (CVS) and 9.5% performed noninvasive prenatal testing (NIPT).

Main results and the role of chance

Of the 465 mosaic embryos that implanted, about 20% miscarried, and out of those, 75% were early spontaneous abortions. Of the pregnancies, 3 out of 368 were stillborn (2 out of them were twins that were extremely premature at 23 weeks, and the other died during pregnancy from a heart defect). The remaining 99% of those have been born or are late ongoing pregnancies at the time of analysis. Prenatal tests were performed in &gt; 200 pregnancies and the vast majority tested normal. All 5 abnormal cases were amniocentesis tests showing microdeletions or insertions of sizes smaller than the resolution used during PGT-A, so they were unrelated to the mosaicism detected with PGT-A. In fact, in none of the cases did the prenatal test reflect the mosaicism detected at the embryonic stage. Matching each of the 162 mosaic embryos resulting in a birth with a euploid embryo, we found that the length of gestation was similar on average, and so was the average weight of the babies at birth. We also gathered information on the routine physical examination performed on babies at birth, and of those 162 babies from mosaic embryo transfers, none had obvious developmental defects or gross abnormalities.

Limitations, reasons for caution

Even though newborns resulting from mosaic embryo transfers in this study invariably appeared healthy by routine examination, concerns for long-term health cannot yet be entirely dispelled. The question must therefore be carefully considered by each clinic and patient situation.

Wider implications of the findings

Prenatal testing of &gt; 200 pregnancies from mosaic embryo transfers showed no incidence of mosaicism that matched the PGT-A findings, indicating the involvement of self-corrective mechanisms. Pregnancy and obstetric data indicates that mosaic embryos prevailing through gestation and birth have similar chromosomal and physiological health compared to euploid embryos.

Trial registration number

none

P–582 High level of concordance between invasive and non-invasive preimplantation genetic testing for aneuploidies (niPGT-A) at day5 and day6–7

Study question

To explore ploidy concordance between invasive and non-invasive PGTA (niPGT-A) at different embryo culture time.

Summary answer

High level (&gt;84%) of concordance rate for ploidy and sex, sensitivity (&gt;88%), and specificity (76%) were obtained for both day6/7 samples and day5 samples.

What is known already

The analysis of embryo cell free DNA (cfDNA) that are released into culture media during in vitro embryo development has the potential to evaluate embryo ploidy status. However, obtaining sufficient quality and quantity of cfDNA is essential to achieve interpretable results for niPGT-A. More culture time is expected to be directly proportional to the release of more cfDNA. But embryo culture time is limited due to in-vitro embryo survival potential. Therefore, it is important to estimate the duration of the culture that will provide the maximum cfDNA that can be obtained without adversely affecting the development of the embryo.

Study design, size, duration

A total of 105 spent culture media (SCM) from day5-day7 blastocyst stage embryos have been included in this cohort study. The cfDNA of SCM samples were amplified and analyzed for niPGT-A by NGS analysis. The SCM samples were divided into 2 subgroups according the embryo culture hours (Day5 and Day6/7 group). The DNA concentration, informativity and euploidy results have then been compared with their corresponding embryos after trophectoderm biopsy (TE) and PGT-A analysis by NGS

Participants/materials, setting, methods

Embryos cultured until Day3 washed and cultured again in 20µl fresh culture media until embryo biopsy on Day5, 6, or 7. After biopsy SCM samples were immediately collected in PCR tubes and conserved at –20 °C until whole genome amplification by MALBAC® (Yicon Genomics). The TE and SCM samples were analyzed by next-generation sequencing (NGS) using Illumina MiSeq® System. NGS data analysis has been done by Bluefuse Multi Software 4.5 (Illumina) for SCM and TE samples

Main results and the role of chance

Only the SCM samples which have an embryo with a conclusive result were included in this cohort (n = 105). Overall 97.1% (102/105) of SCM samples gave a successful DNA amplification with a concentration ranging 32.4–128.5ng/µl. Non-informative (NI) results including a chaotic profile (&gt;5 chromosome aneuploidies) were observed in 17 samples, so 83.3%(85/102) of SCM samples were informative for NGS data analysis. Ploidy concordance rate with the corresponding TE biopsies (euploid vs euploid, aneuploid vs aneuploid) was 84.7% (72/85). Sensitivity and specificity were 92,8% and 76,7%, respectively with no significant difference for all parameters for day 6/7 samples compared with day 5 samples. The false-negative rate was 3.5% (3/85), and false-positive rate was 11.7% (10/85).

Limitations, reasons for caution

The sample size is relatively small. Larger prospective studies are needed. As this is a single-center study, the impact of the variations in embryo culture conditions can be underestimated. Maternal DNA contamination risk cannot be revealed in SCM, therefore the use of molecular markers would increase the reliability.

Wider implications of the findings: Non-invasive analysis of embryo cfDNA analyzed in spent culture media demonstrates high concordance with TE biopsy results in both early and late culture time. A non-invasive approach for aneuploidy screening offers important advantages such as avoiding invasive embryo biopsy and decreased cost, potentially increasing accessibility for a wider patient population.

Trial registration number

Not applicable

What people really change after genetic testing (GT) performed in private labs: results from an Italian study

Despite the widespread diffusion of direct-to-consumer genetic testing (GT), it is still unclear whether people who learn about their genetic susceptibility to a clinical condition change their behaviors, and the psychological factors involved. The aim of the present study is to investigate long-term changes in health-related choices, individual tendencies and risk attitudes in an Italian sample of GT users. In the context of the Mind the Risk study, which investigated a sample of Italian adults who underwent GT in a private laboratory, 99 clients participated in the follow up assessment. They completed a self-administered questionnaire investigating: (a) clinical history and motivation for testing, (b) lifestyle and risk behaviors, (c) individual tendencies toward health, and (d) risk-taking attitude and risk tolerance. Such variables were measured at three different time-points: T0—before GT, T1—at 6 months after genetic results, and T2—at 1 year from results. Results showed that, at baseline, participants who stated they intended to modify their behavior after GT results, effectively did so over time. This result held both for participants who received a positive or negative test result. In general, a healthier diet was the most frequently observed long-term behavioral change. As regards psychological variables, a risk-taking attitude and risk tolerance did not seem to affect the decision to change the lifestyle. Finally, we found an overall reduction in anxiety and worry over health over time, but also a reduction in the motivation for health promotion and prevention, health esteem, and positive expectations for their health in the future.

Cross-Validation of Next-Generation Sequencing Technologies for Diagnosis of Chromosomal Mosaicism and Segmental Aneuploidies in Preimplantation Embryos Model

Detection of mosaic embryos is crucial to offer more possibilities of success to women undergoing in vitro fertilization (IVF) treatment. Next Generation Sequencing (NGS)-based preimplantation genetic testing are increasingly used for this purpose since their higher capability to detect chromosomal mosaicism in human embryos. In the recent years, new NGS systems were released, however their performance for chromosomal mosaicism are variable. We performed a cross-validation analysis of two different NGS platforms in order to assess the feasibility of these techniques and provide standard parameters for the detection of such aneuploidies. The study evaluated the performance of Miseq^TM Veriseq (Illumina, San Diego, CA, USA) and Ion Torrent Personal Genome Machine PGM^TM ReproSeq (Thermo Fisher, Waltham, MA, USA) for the detection of whole and segmental mosaic aneuploidies. Reconstructed samples with known percentage of mosaicism were analyzed with both platforms and sensitivity and specificity were determined. Both platforms had high level of specificity and sensitivity with a Limit Of Detection (LOD) at ≥30% of mosaicism and a showed a ≥5.0 Mb resolution for segmental abnormalities. Our findings demonstrated that NGS methodologies are capable of accurately detecting chromosomal mosaicism and segmental aneuploidies. The knowledge of LOD for each NGS platform has the potential to reduce false-negative and false-positive diagnoses when applied to detect chromosomal mosaicism in a clinical setting.

Using outcome data from one thousand mosaic embryo transfers to formulate an embryo ranking system for clinical use

OBJECTIVE

To study how the attributes of mosaicism identified during preimplantation genetic testing for aneuploidy relate to clinical outcomes, in order to formulate a ranking system of mosaic embryos for intrauterine transfer.

DESIGN

Compiled analysis.

SETTING

Multi-center.

PATIENT(S)

A total of 5,561 euploid blastocysts and 1,000 mosaic blastocysts used in clinical transfers in patients undergoing fertility treatment.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

Implantation (gestational sac), ongoing pregnancy, birth, and spontaneous abortion (miscarriage before 20 weeks of gestation).

RESULT(S)

The euploid group had significantly more favorable rates of implantation and ongoing pregnancy/birth (OP/B) compared with the combined mosaic group or the mosaic group affecting only whole chromosomes (implantation: 57.2% vs. 46.5% vs. 41.8%; OP/B: 52.3% vs. 37.0% vs. 31.3%), as well as lower likelihood of spontaneous abortion (8.6% vs. 20.4% vs. 25%). Whole-chromosome mosaic embryos with level (percent aneuploid cells) <50% had significantly more favorable outcomes than the ≥50% group (implantation: 44.5% vs. 30.4%; OP/B: 36.1% vs. 19.3%). Mosaic type (nature of the aneuploidy implicated in mosaicism) affected outcomes, with a significant correlation between number of affected chromosomes and unfavorable outcomes. This ranged from mosaicism involving segmental abnormalities to complex aneuploidies affecting three or more chromosomes (implantation: 51.6% vs. 30.4%; OP/B: 43.1% vs. 20.8%). Combining mosaic level, type, and embryo morphology revealed the order of subcategories regarding likelihood of positive outcome.

CONCLUSION(S)

This compiled analysis revealed traits of mosaicism identified with preimplantation genetic testing for aneuploidy that affected outcomes in a statistically significant manner, enabling the formulation of an evidence-based prioritization scheme for mosaic embryos in the clinic.

The complex relationship between female age and embryo euploidy

BACKGROUND

Female age is the strongest predictor of embryo chromosomal abnormalities and has a nonlinear relationship with the blastocyst euploidy rate: with advancing age there is an acceleration in the reduction of blastocyst euploidy. Aneuploidy was found to significantly increase with maternal age from 30% in embryos from young women to 70% in women older than 40 years old. The association seems mainly due to chromosomal abnormalities occurring in the oocyte. We aimed to elaborate a model for the blastocyst euploid rate for patients undergoing in-vitro fertilization/intra cytoplasmic sperm injection (IVF/ICSI) cycles using advanced machine learning techniques.

METHODS

This was a retrospective analysis of IVF/ICSI cycles performed from 2014 to 2016. In total, data of 3879 blastocysts were collected for the analysis. Patients underwent PGT-Aneuploidy analysis (PGT-A) at the Center for Reproductive Medicine of European Hospital (Rome, Italy) have been included in the analysis. The method involved whole-genome amplification followed by array comparative genome hybridization. To model the rate of euploid blastocysts, the data were split into a train set (used to fit and calibrate the models) and a test set (used to assess models' predictive performance). Three different models were calibrated: a classical linear regression; a gradient boosted tree (GBT) machine learning model; a model belonging to the generalized additive models (GAM).

RESULTS

The present study confirms that female age, which is the strongest predictor of embryo chromosomal abnormalities, and blastocyst euploidy rate have a nonlinear relationship, well depicted by the GBT and the GAM models. According to this model, the rate of reduction in the percentage of euploid blastocysts increases with age: the yearly relative variation is -10% at the age of 37 and -30% at the age of 45. Other factors including male age, female and male Body Mass Index, fertilization rate and ovarian reserve may only marginally impact on embryo euploidy rate.

CONCLUSIONS

Female age is the strongest predictor of embryo chromosomal abnormalities and has a non-linear relationship with the blastocyst euploidy rate. Other factors related to both the male and female subjects may only minimally affect this outcome.

The complex relationship between female age and embryo euploidy

BACKGROUND

Female age is the strongest predictor of embryo chromosomal abnormalities and has a nonlinear relationship with the blastocyst euploidy rate: with advancing age there is an acceleration in the reduction of blastocyst euploidy. Aneuploidy was found to significantly increase with maternal age from 30% in embryos from young women to 70% in women older than 40 years old. The association seems mainly due to chromosomal abnormalities occurring in the oocyte. We aimed to elaborate a model for the blastocyst euploid rate for patients undergoing in-vitro fertilization/intra cytoplasmic sperm injection (IVF/ICSI) cycles using advanced machine learning techniques.

METHODS

This was a retrospective analysis of IVF/ICSI cycles performed from 2014 to 2016. In total, data of 3879 blastocysts were collected for the analysis. Patients underwent PGT-Aneuploidy analysis (PGT-A) at the Center for Reproductive Medicine of European Hospital (Rome, Italy) have been included in the analysis. The method involved whole-genome amplification followed by array comparative genome hybridization. To model the rate of euploid blastocysts, the data were split into a train set (used to fit and calibrate the models) and a test set (used to assess models' predictive performance). Three different models were calibrated: a classical linear regression; a gradient boosted tree (GBT) machine learning model; a model belonging to the generalized additive models (GAM).

RESULTS

The present study confirms that female age, which is the strongest predictor of embryo chromosomal abnormalities, and blastocyst euploidy rate have a nonlinear relationship, well depicted by the GBT and the GAM models. According to this model, the rate of reduction in the percentage of euploid blastocysts increases with age: the yearly relative variation is -10% at the age of 37 and -30% at the age of 45. Other factors including male age, female and male Body Mass Index, fertilization rate and ovarian reserve may only marginally impact on embryo euploidy rate.

CONCLUSIONS

Female age is the strongest predictor of embryo chromosomal abnormalities and has a non-linear relationship with the blastocyst euploidy rate. Other factors related to both the male and female subjects may only minimally affect this outcome.

Genetic Testing Consumers in Italy: A Preliminary Investigation of the Socio-Demographic Profile, Health-Related Habits, and Decision Purposes

Aim of the study: Genetic testing is becoming increasingly common in clinical practice and health management; nonetheless, little is known about how the population approaches genetic services through private companies. Our study aims to describe socio-demographic aspects, health-related habits, and overall beliefs and knowledge about genetic risk and testing in a population of Italian citizens who decided to undergo a genetic examination through a private genetic company.

Study design: A sample of 152 clients from an Italian private genetic company completed an ad-hoc survey from September 2016 to February 2018, addressing socio-demographic data, health habits, psycho-physic condition, perceived utility of genetic results, decision purposes about data sharing, and behavioral changes after results.

Results: Participants (mean age 42.4) were predominantly female (82.2%) and were overall well-educated. Their main source of information were physicians (77%), and 41.1% entrusted the management of results to the same. Thirty-eight percentage underwent genetic analysis for cancer predisposition, 31.3% for fertility problems, 24% for dietary or intolerance issues in the period of enrolment. More than half of them (62.7%) reported a family history of the disease, and overall 69% had a current or past experience with a disease. Clients perceived the genetic screening as useful to adopt behaviors that may prevent disease onset (37.7%), to know their “real health status” (27.4%), and to adopt health-related behaviors (23.3%). 62.8% claimed they were motivated to change behaviors after results (healthier diet, practice exercise, medical checks), and they wanted to share results with their physician and family members.

Discussion/Conclusion: The overview of consumers' profiles in Italy and other European countries can contribute to tailoring and regulating genetic services in a way that could be efficient in terms of healthy choices, behaviors, and health resource expenditures for the general public.

TMPRSS2, a SARS-CoV-2 internalization protease is downregulated in head and neck cancer patients

Background

SARS-coronavirus-2 enters host cells through binding of the Spike protein to ACE2 receptor and subsequent S priming by the TMPRSS2 protease. We aim to assess differences in both ACE2 and TMPRSS2 expression in normal tissues from oral cavity, pharynx, larynx and lung tissues as well as neoplastic tissues from the same areas.

Methods

The study has been conducted using the TCGA and the Regina Elena Institute databases and validated by experimental model in HNSCC cells. We also included data from one COVID19 patient who went under surgery for HNSCC.

Results

TMPRSS2 expression in HNSCC was significantly reduced compared to the normal tissues. It was more evident in women than in men, in TP53 mutated versus wild TP53 tumors, in HPV negative patients compared to HPV positive counterparts. Functionally, we modeled the multivariate effect of TP53, HPV, and other inherent variables on TMPRSS2. All variables had a statistically significant independent effect on TMPRSS2. In particular, in tumor tissues, HPV negative, TP53 mutated status and elevated TP53-dependent Myc-target genes were associated with low TMPRSS2 expression. The further analysis of both TCGA and our institutional HNSCC datasets identified a signature anti-correlated to TMPRSS2. As proof-of-principle we also validated the anti-correlation between microRNAs and TMPRSS2 expression in a SARS-CoV-2 positive HNSCC patient tissues Finally, we did not find TMPRSS2 promoter methylation.

Conclusions

Collectively, these findings suggest that tumoral tissues, herein exemplified by HNSCC and lung cancers might be more resistant to SARS-CoV-2 infection due to reduced expression of TMPRSS2. These observations may help to better assess the frailty of SARS-CoV-2 positive cancer patients.

TRF2 and VEGF-A: an unknown relationship with prognostic impact on survival of colorectal cancer patients

BACKGROUND

Colorectal cancer is one of most common tumors in developed countries and, despite improvements in treatment and diagnosis, mortality rate of patients remains high, evidencing the urgent need of novel biomarkers to properly identify colorectal cancer high-risk patients that would benefit of specific treatments. Recent works have demonstrated that the telomeric protein TRF2 is over-expressed in colorectal cancer and it promotes tumor formation and progression through extra-telomeric functions. Moreover, we and other groups evidenced, both in vitro on established cell lines and in vivo on tumor bearing mice, that TRF2 regulates the vascularization mediated by VEGF-A. In the present paper, our data evidence a tight correlation between TRF2 and VEGF-A with prognostic relevance in colorectal cancer patients.

METHODS

For this study we sampled 185 colorectal cancer patients surgically treated and diagnosed at the Regina Elena National Cancer Institute of Rome and investigated the association between the survival outcome and the levels of VEGF-A and TRF2.

RESULTS

Tissue microarray immunohistochemical analyses revealed that TRF2 positively correlates with VEGF-A expression in our cohort of patients. Moreover, analysis of patients' survival, confirmed in a larger dataset of patients from TCGA, demonstrated that co-expression of TRF2 and VEGF-A correlate with a poor clinical outcome in stage I-III colorectal cancer patients, regardless the mutational state of driver oncogenes.

CONCLUSIONS

Our results permitted to identify the positive correlation between high levels of TRF2 and VEGF-A as a novel prognostic biomarker for identifying the subset of high-risk colorectal cancer patients that could benefit of specific therapeutic regimens.

Health orientation and individual tendencies of a sample of Italian genetic testing consumers

Background

Over the last decade, genetic testing (GT) had markedly spread in European countries and struggled the debate concerning the psychological effects on the population. The aim of this study was to investigate the individual tendencies of GT consumers in a sample of Italian citizens.

Methods

A total of 152 Italian clients from GenomaLab, a private genetic company, were enrolled from February 2016 to September 2018 and completed an ad hoc survey.

Results

Results showed that GT consumers were motivated to preserve their well‐being, they felt responsible for their health, they were neither pessimistic nor optimistic toward negative occurrences, and poorly inclined to take high risks in their lives. Participants who had suffered from a disease in the past appear to be less tolerant to the uncertainty for future negative events.

Conclusion

Our results depict Italian GT consumers as health‐oriented, focused on prevention, who do not have a pessimistic perception of their condition but do not like to “bet” on their health, and probably their intention (and belief) is to acquire genetic information in order to reduce uncertainty and increase their decision‐making “power” related to their health. Taken together, all these results contribute to describe the population of GT users in European countries, to regulate the provision of GT results and to entail the communication of genetic risk information based on a consumers’ personal profile.

ESHRE PGT Consortium good practice recommendations for the detection of structural and numerical chromosomal aberrations

The field of preimplantation genetic testing (PGT) is evolving fast, and best practice advice is essential for regulation and standardisation of diagnostic testing. The previous ESHRE guidelines on best practice for PGD, published in 2005 and 2011, are considered outdated, and the development of new papers outlining recommendations for good practice in PGT was necessary. The current paper provides recommendations on the technical aspects of PGT for chromosomal structural rearrangements (PGT-SR) and PGT for aneuploidies (PGT-A) and covers recommendations on array-based comparative genomic hybridisation (aCGH) and next-generation sequencing (NGS) for PGT-SR and PGT-A and on fluorescence in situ hybridisation (FISH) and single nucleotide polymorphism (SNP) array for PGT-SR, including laboratory issues, work practice controls, pre-examination validation, preclinical work-up, risk assessment and limitations. Furthermore, some general recommendations on PGT-SR/PGT-A are formulated around training and general risk assessment, and the examination and post-examination process. This paper is one of a series of four papers on good practice recommendations on PGT. The other papers cover the organisation of a PGT centre, embryo biopsy and tubing and the technical aspects of PGT for monogenic/single-gene defects (PGT-M). Together, these papers should assist everyone interested in PGT in developing the best laboratory and clinical practice possible.

Comparison of euploidy rates of blastocysts in women treated with progestins or GnRH antagonist to prevent the luteinizing hormone surge during ovarian stimulation

STUDY QUESTION

Does the prevalence of euploid blastocysts differ between patients treated with progestin primed ovarian stimulation (PPOS) and those treated with conventional ovarian stimulation?

SUMMARY ANSWER

The numbers of blastocysts and euploid blastocysts per patient and the number of euploid embryos per injected oocyte are similar for patients undergoing progestin-primed ovarian stimulation and for those undergoing conventional ovarian stimulation with GnRH antagonist.

WHAT IS KNOWN ALREADY

New approaches to ovarian stimulation have been developed based on the use of drugs administrable by mouth instead of via injections. Attention has been dedicated to progestins to block the LH surge. Previous data regarding the number of oocytes retrieved and the number of good-quality embryos generated in PPOS have demonstrated similar outcomes when compared to conventional ovarian stimulation, even if some concerns regarding the quality of embryos have been advanced.

STUDY DESIGN, SIZE, DURATION

This is a prospective non-inferiority age-matched case–control study. In a period of 6 months, a total of 785 blastocysts from 1867 injected oocytes obtained from 192 patients were available for analysis.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Infertile women undergoing IVF and preimplanation genetic testing (PGT) cycles were included. Forty-eight patients were treated with PPOS, and for each of them three age-matched historical controls (n = 144) treated with a GnRH antagonist protocol were selected. PGT was performed according to next-generation sequencing technology.

MAIN RESULTS AND THE ROLE OF CHANCE

Basal characteristics were similar in the two groups; a substantial similarity of the main outcome measures in the two treatment groups has also been found. The rate of formation of euploid blastocysts per oocyte was 21% in both the two treatment groups. The percentage of patients with euploid embryos and the total number of euploid blastocysts per patient (median and interquartile range, IQR) in the PPOS group were 38.7 (25.5–52.9) and 2 (1.3–3.1), respectively. These figures were not significantly different in women treated with the GnRH antagonist protocol i.e. 42 (28–53.8) and 2.1 (1.3–2.9), respectively.

LIMITATIONS, REASONS FOR CAUTION

This was a case–control study which may limit the reliability of the main findings.

WIDER IMPLICATIONS OF THE FINDINGS

Our results encourage the use of PPOS, especially for oocyte donation, for fertility preservation and for patients in which total freezing of embryos is foreseen, for those expected to be high responders or candidates for preimplantation genetic testing. However, studies aiming to investigate the effect of PPOS on the live birth rate are warranted.

STUDY FUNDING/COMPETING INTEREST(S)

None.

Cross-sectional analysis of circulating tumor DNA in primary colorectal cancer at surgery and during post-surgery follow-up by liquid biopsy

BACKGROUND

Liquid biopsy (LB) in early-stage, non-metastatic colorectal cancer (CRC) must be sensitive enough to detect extremely low circulating tumor DNA (ctDNA) levels. This challenge has been seldom and non-systematically investigated.

METHODS

Next generation sequencing (NGS) and digital PCR (dPCR) were combined to test tumor DNAs (tDNAs) and paired ctDNAs collected at surgery from 39 patients, 12 of whom were also monitored during the immediate post-surgery follow up. Patients treated for metastatic disease (n = 14) were included as controls.

RESULTS

NGS and dPCR concordantly (100% agreement) called at least one single nucleotide variant (SNV) in 34 tDNAs, estimated differences in allelic frequencies being negligible (±1.4%). However, despite dPCR testing, SNVs were only detectable in 15/34 (44.1%) ctDNAs from patients at surgery, as opposed to 14/14 (100%) metastatic patients. This was likely due to striking differences (average 10 times, up to 500) in ctDNA levels between groups. NGS revealed blood-only SNVs, suggesting spatial heterogeneity since pre-surgery disease stages, and raising the combined NGS/dPCR sensitivity to 58.8%. ctDNA levels at surgery correlated with neither tumor size, stage, grade, or nodal status, nor with variant abundance in paired tDNA. LB sensitivity reached 63.6% when ctDNA was combined with CEA. Finally, persistence and absence of ctDNA on the first conventional (month 3) post-surgery follow-up were associated with fast relapse and a disease-free status in 3 and 7 patients, respectively.

CONCLUSIONS

A simple clinical NGS/dPCR/CEA combination effectively addresses the LB challenge in a fraction of non-metastatic CRC patients.

German and Italian Users of Web-Accessed Genetic Data: Attitudes on Personal Utility and Personal Sharing Preferences. Results of a Comparative Survey (n=192)

Genetic information is increasingly provided outside of the traditional clinical setting, allowing users to access it directly via specialized online platforms. This development is possibly resulting in changing ethical and social challenges for users of predictive genetic tests. Little is known about the attitudes and experiences of users of web-accessed genetic information. This survey analyzes data from two European countries with regard to the utility of genetic information, the users’ ways of making use of and dealing with information, and their sharing behavior. Particular focus is given to ethical and social questions regarding the motivation to share personal genetic results with others. Social factors tested for are national background, gender, and marital, parental, and educational status. This study will contribute to public discourse and offer ethical recommendations. The study will also serve to validate the developed questionnaire for use in population representative surveys.

Clinical outcomes after the transfer of blastocysts characterized as mosaic by high resolution Next Generation Sequencing- further insights

OBJECTIVE

To determine the pregnancy outcome potential of euploid, mosaic and aneuploid embryos.

DESIGN

Retrospective study.

SETTING

Reference genetics laboratories.

PATIENT(S)

2654 PGT-A cycles with euploid characterized embryo transfers, 253 PGT-A cycles with transfer of embryos characterized as mosaic, and 10 PGT-A cycles with fully abnormal embryo transfers.

INTERVENTION(S)

Blastocysts were assessed by trophectoderm (TE) biopsy followed by PGT-A via array CGH or NGS.

MAIN OUTCOME MEASURE(S)

Implantation, miscarriage, ongoing implantation rates (OIR), and karyotype if available, were compared between different embryo groups, and between the two PGT-A techniques.

RESULTS

The Ongoing Pregnancy Rate (OPR)/transfer was significantly higher for NGS-classified euploid embryos (85%) than for aCGH ones (71%) (p < 0.001), but the OPR/cycle was similar (63% vs 59%). NGS-classified mosaic embryos resulted in 37% OPR/cycle (p < 0.001 compared to euploid). Mosaic aneuploid embryos with <40% abnormal cells in the TE sample had an OIR of 50% compared to 27% for mosaics with 40-80% abnormal cells in the TE, and 9% for complex mosaic embryos. All the karyotyped ongoing pregnancies (n = 29) were euploid. Transfers of embryos classified as aneuploid via aCGH (n = 10) led to one chromosomally abnormal pregnancy.

CONCLUSION(S)

NGS-classified euploid embryos yielded higher OIRs but similar OPRs/cycle compared to aCGH. NGS-classified mosaic embryos had reduced potential to reach term, compared to euploid embryos. If they did reach term, those with karyotype results available were euploid. Embryos carrying uniform aneuploidies affecting entire chromosomes were mostly unable to implant after transfer, and the one that implanted ended up in a chromosomally abnormal live birth.

NA62 and NA48/2 results on search for Heavy Neutral Leptons

In this paper we present new results on upper limits for the search of Heavy Neutral Leptons (HNL) with data collected by NA48/2 (2003-2004), NA62-RK (2007) and NA62 (2015) CERN experiments. The data collected with different trigger configuration allow to search for both long and short living heavy neutrinos in the mass range below the kaon mass. In addition the status of the search for K+ → π+vv with the NA62 detector will be briefly presented.

Correlation between aneuploidy, standard morphology evaluation and morphokinetic development in 1730 biopsied blastocysts: a consecutive case series study

STUDY QUESTION

Are there correlations among human blastocyst ploidy status, standard morphology evaluation and time-lapse kinetics?

SUMMARY ANSWER

Correlations were observed, in that euploid human blastocysts showed a higher percentage with top quality inner cell mass (ICM) and trophectoderm (TE), higher expansion grades and shorter time to start of blastulation, expansion and hatching, compared to aneuploid ones.

WHAT IS KNOWN ALREADY

Embryo quality has always been considered an important predictor of successful implantation and pregnancy. Nevertheless, knowledge of the relative impact of each morphological parameter at the blastocyst stage needs to be increased. Recently, with the introduction of time-lapse technology, morphokinetic parameters can also be evaluated. However, a large number of studies has reported conflicting outcomes.

STUDY DESIGN, SIZE, DURATION

This was a consecutive case series study. The morphology of 1730 blastocysts obtained in 530 PGS cycles performed from September 2012 to April 2014 that underwent TE biopsy and array comparative genomic hybridization was analyzed retrospectively. A total of 928 blastocysts were cultured in a time-lapse incubator allowing morphokinetic parameters to be analyzed.

PARTCIPANTS/MATERIALS, SETTING, METHOD

Mean female age was 36.8 ± 4.24 years. Four hunderd fifty-four couples were enrolled in the study: 384, 64 and 6 of them performed single, double or triple PGS cycles, respectively. In standard morphology evaluation, the expansion grade, and quality of the ICM and TE were analyzed. The morphokinetic parameters observed were second polar body extrusion, appearance of two pronuclei, pronuclear fading, onset of two- to eight-cell divisions, time between the two- and three-cell (cc2) and three- and four-cell (s2) stages, morulae formation time, starting blastulation, full blastocyst stage, expansion and hatching timing.

MAIN RESULTS AND THE ROLE OF CHANCE

Of the 1730 biopsied blastocysts, 603 were euploid and 1127 aneuploid. We observed that 47.2% of euploid and 32.8% of aneuploid blastocysts showed top quality ICM (P < 0.001), and 17.1% of euploid and 28.5% of aneuploid blastocysts showed poor quality ICM (P < 0.001). Top quality TE was present in 46.5% of euploid and 31.1% of aneuploid blastocysts (P < 0.001), while 26.6% of euploid and 38.1% of aneuploid blastocysts showed poor quality TE (P < 0.001). Regarding expansion grade, 81.1% of euploid and 72.4% of aneuploid blastocysts were fully expanded (Grade 5-6; P < 0.001). The timing of cleavage from the three- to four-cell stage, of reaching four-cell stage, of starting blastulation, reaching full blastocyst stage, blastocyst expansion and hatching were 2.6 (95% confidence interval (CI): 1.7-3.5), 40.0 (95% CI: 39.3-40.6), 103.4 (95% CI: 102.2-104.6), 110.2 (95% CI: 108.8-111.5), 118.7 (95% CI: 117.0-120.5) and 133.2 (95% CI: 131.2-135.2) hours in euploid blastocysts, and 4.2 (95% CI: 3.6-4.8), 41.1 (95% CI: 40.6-41.6), 105.0 (95% CI: 104.0-106.0), 112.8 (95% CI: 111.7-113.9), 122.1 (95% CI: 120.7-123.4) and 137.4 (95% CI: 135.7-139.1) hours in aneuploid blastocysts (P < 0.05 for early and P < 0.0001 for later stages of development), respectively. No statistically significant differences were found between euploid and aneuploid blastocysts for the remaining morphokinetic parameters.A total of 407 embryo transfers were performed (155 fresh, 252 frozen-thawed blastocysts). Higher clinical pregnancy, implantation and live birth rates were obtained in frozen-thawed compared to fresh embryo transfers (P = 0.0104, 0.0091 and 0.0148, respectively). The miscarriage rate was 16.1% and 19.6% in cryopreserved and fresh embryo transfer, respectively. The mean female age was lower in the euploid compared to aneuploid groups (35.0 ± 3.78 versus 36.7 ± 4.13 years, respectively), We found an increasing probability for aneuploidy with female age of 10% per year (odds ratio (OR) = 1.1, 95% CI: 1.1-1.2, P < 0.001).

LIMITATIONS, REASONS FOR CAUTION

The main limitation of morphology assessment is that it is a static system and can be operator-dependent. In this study, eight embryologists performed morphology assessments. The main limitation of the time-lapse technology is that it is impossible to rotate the embryos making it very difficult to observe them in case of blastomere overlapping or increased cytoplasmic fragmentation.

WIDER IMPLICATIONS OF THE FINDINGS

Although there seems to be a relationship between the ploidy status and blastocyst morphology/development dynamics, the evaluation of morphological and morphokinetic parameters cannot currently be improved upon, and therefore replace, PGS. Our results on ongoing pregnancy and miscarriage rates suggest that embryo evaluation by PGS or time-lapse imaging may not improve IVF outcome. However, time-lapse monitoring could be used in conjunction with PGS to choose, within a cohort, the blastocysts to analyze or, when more than one euploid blastocyst is available, to select which one should be transferred.

STUDY FUNDING/COMPETING INTERESTS

No specific funding was obtained for this study. None of the authors have any competing interests to declare.

Precision Measurement of the Helium Flux in Primary Cosmic Rays of Rigidities 1.9 GV to 3 TV with the Alpha Magnetic Spectrometer on the International Space Station

Knowledge of the precise rigidity dependence of the helium flux is important in understanding the origin, acceleration, and propagation of cosmic rays. A precise measurement of the helium flux in primary cosmic rays with rigidity (momentum/charge) from 1.9 GV to 3 TV based on 50 million events is presented and compared to the proton flux. The detailed variation with rigidity of the helium flux spectral index is presented for the first time. The spectral index progressively hardens at rigidities larger than 100 GV. The rigidity dependence of the helium flux spectral index is similar to that of the proton spectral index though the magnitudes are different. Remarkably, the spectral index of the proton to helium flux ratio increases with rigidity up to 45 GV and then becomes constant; the flux ratio above 45 GV is well described by a single power law.

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.