Serum levels of stem cell factor for predicting embryo quality.

We evaluated whether serum stem cell factor (s-SCF) levels just prior to ovulation induction could indicate the ability to develop a top-quality (TQ) blastocyst by day 5. We investigated patients with normal ovarian reserve (NOR), polycystic ovary syndrome (PCOS), diminished ovarian reserve (DOR), or mild endometriosis. Our pilot research suggests a correlation between s-SCF levels and the ability to form TQ blastocysts in patients with mild endometriosis. This significant statistical difference (p < 0.05) was noted between mild endometriosis patients for whom a TQ blastocyst was obtained and those for whom it was not possible, as measured on the 8th day of stimulation and the day of oocyte retrieval. The mean SCF levels in the serum of these women on the 8th day were at 28.07 (± 2.67) pg/ml for the TQ subgroup and 53.32 (± 16.02) pg/ml for the non-TQ subgroup (p < 0.05). On oocyte retrieval day it was 33.47 (± 3.93) pg/ml and 52.23 (± 9.72) pg/ml (p < 0.05), respectively.

Ensembling noisy segmentation masks of blurred sperm images.

BACKGROUND: Sperm tail morphology and motility have been demonstrated to be important factors in determining sperm quality for in vitro fertilization. However, many existing computer-aided sperm analysis systems leave the sperm tail out of the analysis, as detecting a few tail pixels is challenging. Moreover, some publicly available datasets for classifying morphological defects contain images limited only to the sperm head. This study focuses on the segmentation of full sperm, which consists of the head and tail parts, and appear alone and in groups. METHODS: We re-purpose the Feature Pyramid Network to ensemble an input image with multiple masks from state-of-the-art segmentation algorithms using a scale-specific cross-attention module. We normalize homogeneous backgrounds for improved training. The low field depth of microscopes blurs the images, easily confusing human raters in discerning minuscule sperm from large backgrounds. We thus propose evaluation protocols for scoring segmentation models trained on imbalanced data and noisy ground truth. RESULTS: The neural ensembling of noisy segmentation masks outperforms all single, state-of-the-art segmentation algorithms in full sperm segmentation. Human raters agree more on the head than tail masks. The algorithms also segment the head better than the tail. CONCLUSIONS: The extensive evaluation of state-of-the-art segmentation algorithms shows that full sperm segmentation is challenging. We release the SegSperm dataset of images from Intracytoplasmic Sperm Injection procedures to spur further progress on full sperm segmentation with noisy and imbalanced ground truth. The dataset is publicly available at https://doi.org/10.34808/6wm7-1159.

X-chromosome inactivation patterns depend on age and tissue but not conception method in humans.

Female somatic X-chromosome inactivation (XCI) balances the X-linked transcriptional dosages between the sexes, randomly silencing the maternal or paternal X chromosome in each cell of 46,XX females. Skewed XCI toward one parental X has been observed in association with ageing and in some female carriers of X-linked diseases. To address the problem of non-random XCI, we quantified the XCI skew in different biological samples of naturally conceived females of different age groups and girls conceived after in vitro fertilization (IVF). Generally, XCI skew differed between saliva, blood, and buccal swabs, while saliva and blood had the most similar XCI patterns in individual females. XCI skew increased with age in saliva, but not in other tissues. We showed no significant differences in the XCI patterns in tissues of naturally conceived and IVF females. The gene expression profile of the placenta and umbilical cord blood was determined depending on the XCI pattern. The increased XCI skewing in the placental tissue was associated with the differential expression of several genes out of 40 considered herein. Notably, skewed XCI patterns (> 80:20) were identified with significantly increased expression levels of four genes: CD44, KDM6A, PHLDA2, and ZRSR2. The differences in gene expression patterns between samples with random and non-random XCI may shed new light on factors contributing to the XCI pattern outcome and indicate new paths in future research on the phenomenon of XCI skewing.

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.

Chromosome errors in human eggs shape natural fertility over reproductive life span.

Chromosome errors, or aneuploidy, affect an exceptionally high number of human conceptions, causing pregnancy loss and congenital disorders. Here, we have followed chromosome segregation in human oocytes from females aged 9 to 43 years and report that aneuploidy follows a U-curve. Specific segregation error types show different age dependencies, providing a quantitative explanation for the U-curve. Whole-chromosome nondisjunction events are preferentially associated with increased aneuploidy in young girls, whereas centromeric and more extensive cohesion loss limit fertility as women age. Our findings suggest that chromosomal errors originating in oocytes determine the curve of natural fertility in humans.

Human follicular fluid proteomic and peptidomic composition quantitative studies by SWATH-MS methodology. Applicability of high pH RP-HPLC fractionation.

Analysis of proteomic composition of human follicular fluid (hFF) has been previously proposed as a potential tool of oocyte quality evaluation. In order to develop an efficient method to investigate the hFF proteome and peptidome components, we applied and tested a few prefractionation schemes of hFF material consisting of ultrafiltration, optional immunodepletion, and high pH RP-HPLC separation by building spectral libraries and comparing their quantification capabilities of unfractionated samples. Low Molecular-Weight Fraction peptides (LMWF, <10 kDa) and High Molecular-Weight Fraction proteins (HMWF, >10 kDa) resulting from ultrafiltration were analyzed separately. We identified 302 proteins in HMWF and 161 proteins in LMWF in all qualitative experiments. All LMWF peptidomic libraries turned out to be of poor quantification quality, however they enabled measurement of higher numbers of peptides with increasing input of experiment data, in contrast to HMWF proteomic libraries. We were able to quantify a total of 108 HMWF proteins and 250 LMWF peptides (from 84 proteins) in all experiments. Employment of high RP-HPLC fractionation allowed for identification of a much broader set of proteins, however did not significantly improve the quantification capabilities of the applied method. Data are available via ProteomeXchange with identifier PXD008073. SIGNIFICANCE: In the search of biomarkers for assessment of oocyte quality in assisted reproductive technology, many studies are devoted to analysis of follicular fluid composition. Candidates for such biomarkers can be located in both the proteome and the recently investigated peptidome of hFF. Reliable qualitative and especially quantitative analysis of complex mixtures such as hFF, requires development of a fast and preferably inexpensive analytical procedure. The powerful SWATH-MS technique is well suited for quantitative label-free analysis of complex protein and peptide mixtures. However, for efficient usage it needs well designed and constructed MS-spectral libraries as well as a proper protocol for sample preparation. We investigated the influence of the size and quality of MS-spectral libraries (different spectral libraries are constructed using various sample prefractionation protocols) on SWATH experiments on hFF proteome and peptidome. In the case of peptidome investigation, increasing the size of spectral libraries led to quantification of more peptides in a single experiment. For the proteome, increasing the size of spectral libraries improved quantification only to a limited extend, and further extension of spectral libraries even worsened results. Nevertheless, using the best selected prefractionation schemes and spectral libraries we were able to quantify as many as 79 proteins of hFF proteome and 106 peptides (from 53 proteins) of hFF peptidome in single experiments. The spectral libraries and prefractionation protocols we developed allow for a large scale fast scan of hundreds of clinical hFF samples in the search for biomarkers for evaluation of oocyte quality.

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.

Demographic characteristics and AMH levels in rural and urban women participating in an IVF programme.

OBJECTIVE: The primary aim of this preliminary study was to compare the IVF results of couples living in rural and urban areas. Additionally, the ovarian reserve parameters, such as AMH concentrations, were compared for the same groups. MATERIAL AND METHODS: The database of 1,265 women undergoing in vitro fertilization at the Invicta Fertility Center between May 2011-July 2012 were retrospectively analyzed. Women undergoing their first assisted reproductive technology cycle with ICSI, stimulated according to the long protocol, and whose AMH levels were measured using the same DSL kit, were selected. Ultimately, 651 women were included in the study. All participants were categorized based on the area where they live: rural areas, small towns (<100,000 inhabitants) and large cities (>100,000). RESULTS: The mean age of the patients living in large cities was significantly higher in comparison to those from rural areas and small towns. A significantly higher pregnancy body mass index (BMI) was found in women from rural areas in comparison to the women living in small and large towns. Serum AMH and inhibin B concentrations, number of ampules of gonadotropins, and antral follicle count (AFC), did not differ significantly among the groups. The study showed no significant differences among the groups in terms of clinical pregnancy rate, both per started cycle and per embryo transfer. CONCLUSIONS: No significant differences were found in IVF outcomes among the groups inhabiting rural areas, small and large cities.

Qualitative and Quantitative Analysis of Proteome and Peptidome of Human Follicular Fluid Using Multiple Samples from Single Donor with LC-MS and SWATH Methodology.

Human follicular fluid (hFF) is a natural environment of oocyte maturation, and some components of hFF could be used to judge oocyte capability for fertilization and further development. In our pilot small-scale study three samples from four donors (12 samples in total) were analyzed to determine which hFF proteins/peptides could be used to differentiate individual oocytes and which are patient-specific. Ultrafiltration was used to fractionate hFF to high-molecular-weight (HMW) proteome (>10 kDa) and low-molecular-weight (LMW) peptidome (<10 kDa) fractions. HMW and LMW compositions were analyzed using LC-MS in SWATH data acquisition and processing methodology. In total we were able to identify 158 proteins, from which 59 were never reported before as hFF components. 55 (45 not reported before) proteins were found by analyzing LMW fraction, 67 (14 not reported before) were found by analyzing HMW fraction, and 36 were identified in both fractions of hFF. We were able to perform quantitative analysis for 72 proteins from HMW fraction of hFF. We found that concentrations of 11 proteins varied substantially among hFF samples from single donors, and those proteins are promising targets to identify biomarkers useful in oocyte quality assessment.

Clinical utility of different anti-Müllerian hormone - AMH assays for the purpose of pregnancy prediction.

PURPOSE: Comparison of outcomes of IVF cycles where the AMH levels was measured with five different AMH kits: Immunotech (IOT), Beckman Coulter II Gen. RUO, Beckman Coulter II Gen. IVD (BC II IVD), Ansh Labs ultrasensitive (Ansh) and the automated Elecsys Roche assay. METHODS: Retrospective analysis of clinical data for 3693 cycles. RESULTS: In women < 35 years with low (<0.6 ng/ml) and high (>1.4 ng/ml) AMH concentrations, and in those > 39 years with medium (≥0.6 and ≤1.4 ng/ml) and high AMH concentrations the clinical pregnancy rate differed significantly among groups of patients whose AMH level was measured with different kits. In those subgroups, the highest rates were recorded for the BC II IVD and Ansh groups, while the lowest in the IOT group. AMH concentrations differed significantly between different kits in all age groups (the highest in each age group was for the IOT kit and the lowest for BC II IVD). AMH correlates positively with antral follicle count, MII and number of oocytes retrieved. CONCLUSIONS: This study demonstrated that we could expect very different pregnancy rates with the same AMH results depending on the AMH kit used. That would means, different values of AMH could similarly lead to misleading clinical decisions in IVF.

Granulocyte colony stimulating factor treatment of resistant thin endometrium in women with frozen-thawed blastocyst transfer.

The aim of the study was to assess the granulocyte-colony stimulating factor (G-CSF) effect on unresponsive thin (<7 mm) endometrium in women undergoing frozen-thawed embryo transfer at the blastocyst stage. A total of 62 women with thin unresponsive endometrium were included in the study, of which, 29 received a G-CSF infusion and 33 who opted out of the study served as controls. Patients in both groups had similar endometrial thickness at the time of the initial evaluation: 6.50 mm (5.50-6.80) in the G-CSF and 6.40 mm (5.50-7.0) in the control group. However, after the infusion endometrial thickness increased significantly in the G-CSF group in comparison with the controls (p=0.01), (Δ) 0.5 (0.02-1.2) (p=0.005). In the G-CSF group endometrium expanded to 7.90 mm (6.58-8.70) while in the control group to 6.90 mm (6.0-7.75). Five women in each group conceived. The clinical pregnancy rate was 5/29 (17.24%) in the G-CSF treated group and 5/33 (15.15%) in the control group (p>0.05). The live birth rate was 2/29 (6.89%) in the G-CSF group and 2/33 (6.06%) in the control group (p>0.05). We concluded that G-CSF infusion leads to an improvement in endometrium thickness but not to any improvement in the clinical pregnancy and live birth rates. Until more data is available G-CSF treatment should be considered to be of limited value in increasing pregnancy rate. ABBREVIATIONS: G-CSF: granulocyte colony-stimulating factor; M-CSF: macrophagecolony-stimulating factor; GM-CSF: granulocyte-macrophage colony-stimulating factor; FET: frozen embryo transfer; IVF: in vitro fertilization.

Current methods for preimplantation genetic diagnosis.

Preimplantation Genetic Diagnosis (PGD) used in assisted reproduction techniques is designed to provide help for couples trying to conceive a child, as it helps deliver healthy offspring. After in vitro fertilization, material is collected from the oocyte (polar body), 3-day-old embryo, or increasingly often, from the trophectoderm of a blastocyst. Selection of the diagnostic method depends on the testing center, but methods such as aCGH (Comparative Genomic Hybridization Array) and NGS (Next-Generation Sequencing) are supposed to have the highest reliability and precision. This paper presents a review of the most important methods used in PGD, their advantages and disadvantages as well as efficacy in the procedures in which they are used.

[First in the world application of next generation sequencing in preimplantation genetic diagnostics in clinical practice - a case report]. / Pierwsze w swiecie zastosowanie sekwencjonowania nastepnej generacji w diagnostyce przedimplantacyjnej w praktyce klinicznej - opis przypadku.

Preimplantation genetic diagnosis (PGD) is a well established method for detecting genetic abnormalities during the course of infertility treatment, resulting in thousands of healthy newborns delivered worldwide. PGD with next generation sequencing (NGS) provides new possibilities for diagnosis and new parameters for evaluation. The use of next-generation DNA sequencing technique has lead to great progress in the human genome analysis. The aim of this study was molecular analysis using next generation sequencing technique of embryos from a couple suffering from recurrent pregnancy losses. As a result of in vitro fertilization procedure, seven embryos were created. Seven blastomeres, one from each embryo, were analyzed. Transfer of two blastocysts in a fresh cycle resulted in the singleton pregnancy. Healthy baby girl was delivered via caesarean section after 28 weeks of gestation (weight: 1250g, Apgar score: 8/9). The reason for the premature labor was likely caused by mother's pneumonia. This is the first case of clinical use of the NGS in PGD in fresh cycle after blastomere biopsy.

Next generation sequencing for preimplantation genetic testing of blastocysts aneuploidies in women of different ages.

Most of the current preimplantation genetic screening of aneuploidies tests are based on the low quality and low density comparative genomic hybridization arrays. The results are based on fewer than 2,700 probes. Our main outcome was the association of aneuploidy rates and the women's age. Between August-December 2013, 198 blastocysts from women (mean age 36.3+-4.6) undergoing in vitro fertilization underwent routine trophectoderm biopsy. NGS was performed on Ion Torrent PGM (Life Technologies). The results were analyzed in five age groups (<31, 31-35, 36-38, 39-40 and >40). 85 blastocysts were normal according to NGS results. The results in the investigated groups were (% of normal blastocyst in each group): <31 (41.9%), 31-35 (47.6%), 36-38 (47.8%), 39-40 (37.7%) and >40 (38.5%). Our study suggests that NGS PGD is applicable for routine preimplantation genetic testing. It allows also for easy customization of the procedure for each individual patient making personalized diagnostics a reality.

First Pregnancy, Somatic and Psychological Status of a 4-Year-Old Child Born following Annexin V TESA Sperm Separation.

Introduction Sperm DNA integrity is a crucial paternal factor affecting fertilization and pregnancy rates, as well as embryo development. Case The present case report describes the successful pregnancy after testicular sperm aspiration (TESA) combined with intracytoplasmic sperm injection (ICSI) (TESA-ICSI) in a couple where the male presented high sperm DNA fragmentation. In order to sort damaged sperm presenting DNA fragmentation, magnetic activated cell sorting (MACS) with annexin V microbeads (MACS Miltenyi Biotec, Teterow, Germany) was used. Conclusion The authors present the first description of a successful medical case using TESA-ICSI annexin V sperm sorting. Additionally, a follow-up of the child at the age of 4 years old was done.

Healthy Baby Born to a Robertsonian Translocation Carrier following Next-Generation Sequencing-Based Preimplantation Genetic Diagnosis: A Case Report.

Preimplantation genetic diagnosis (PGD) is well established method for treatment of genetic problems associated with infertility. Moreover, PGD with next-generation sequencing (NGS) provide new possibilities for diagnosis and new parameters for evaluation in, for example, aneuploidy screening. The aim of the study was to report the successful pregnancy outcome following PGD with NGS as the method for 24 chromosome aneuploidy screening in the case of Robertsonian translocation. Day 3 embryos screening for chromosomal aneuploidy was performed in two consecutive in vitro fertilization (IVF) cycles, first with fluorescent in situ hybridization (FISH), and then with NGS-based protocol. In each IVF attempt, three embryos were biopsied. Short duration of procedures enabled fresh embryo transfer without the need for vitrification. First IVF cycle with the embryo selected using PGD analysis with the FISH method ended with pregnancy loss in week 8. The second attempt with NGS-based aneuploidy screening led to exclusion of the following two embryos: one embryo with 22 monosomy and one with multiple aneuploidies. The transfer of the only euploid blastocyst resulted in the successful pregnancy outcome. The identification of the euploid embryo based on the NGS application was the first successful clinical application of NGS-based PGD in the case of the Robertsonian translocation carrier couple.

Two new automated, compared with two enzyme-linked immunosorbent, antimüllerian hormone assays.

OBJECTIVE: To compare new automated antimüllerian hormone (AMH) assay performance characteristics from the new automated Elecsys AMH (Roche; Elecsys) and Access AMH (Beckman Coulter; Access) assays with the existing AMH Gen II ELISA (enzyme-linked immunosorbent assay; Gen II; Beckman Coulter) and AMH ELISA (Ansh Labs) assays. DESIGN: Prospective assay evaluation. SETTING: University-affiliated clinical chemistry laboratory. PATIENT(S): Patients referred for serum AMH measurement (n = 83) before start of in vitro fertilization cycle between September 2014 and October 2014. INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): Serum AMH concentration. RESULT(S): Intra-assay coefficients of variation were low; Ansh ≤ 9.0%; Gen II ≤ 5.8%; Access ≤ 10.7%; and Elecsys ≤ 2.8%. The Passing-Bablok regression equations (pmol/L) were y (Access) = 0.128 + (0.781 × Gen II); and y (Access) = 0.302 + (0.742 x Ansh). For y (Elecys) = 0.087 + (0.729 x Gen II) and y (Elecys) = 0.253 + (0.688 x Ansh Labs). For y (Elecys) = 0.943 - (0.037 × Access). For all the assays, AMH exhibited a moderate positive correlation with AFC (r = 0.62-0.64); number of cumulus oocyte complexes (r = 0.60-0.64); and metaphase II oocytes (r = 0.48-0.50). Accuracy of pregnancy prediction, as determined by area under the receiver operating characteristic curve, was uniformly low for all assays (0.62-0.63). CONCLUSION(S): The novel automated assays exhibit strong concordance in calibration, but derived values are substantially lower than those obtained from pre-existing assays, with assay-specific interpretation required for routine clinical use. These results highlight the need for an international standard of measurement of AMH.

Application of FISH method for preimplantation genetic diagnostics of reciprocal and Robertsonian translocations.

INTRODUCTION: Carriers of reciprocal (RCP) and Robertsonian (RT) translocations are known to be at risk for reproductive difficulties. Preimplantation genetic diagnosis (PGD) is one of the options these carriers have to try to fulfill their desire to have a child. The FISH technique is one of the best method to detect RCPs, and, together with the Next Generation Sequencing, to diagnose RTs. The aim of the present study was to assess the usefulness of the FISH method for rapid diagnosis of translocations in our center to improve the reproductive counseling. MATERIAL AND METHODS: From 2008 to 2012 one hundred and twenty seven fresh cycles of the in vitro fertilization (IVF; without freezing embryos) were performed in 42 couples with an RCP and 35 couples with an RT translocations. The patients were diagnosed before IVF as translocation carriers and therefore they opted for PGD. The classical FISH protocol has been applied with specific oligonucleotide probes. RESULTS: In total 521 blastomeres were tested in order to determine the presence or absence of genetic anomalies resulting from one of the parents being a translocation carrier. Despite the large number of abnormal embryos (407 embryos - 78.1% of all examined embryos), 19.4% of blastomeres appeared to come from a normal or balanced embryos that may have been transferred to the uterus. In 63 of the 127 cycles embryo transfer (ET) was feasible and 24 women had a successful singleton or twin pregnancy. Thus, a live delivery rate of 18.9% per started cycles and 38.1% per cycle with ET was obtained. CONCLUSION: FISH should be regarded as an optimal preimplantation genetic diagnosis method for specific RCP and RT translocation carriers to increase the chance of successful IVF procedure.