Identifying risk variants for embryo aneuploidy using ultra-low coverage whole-genome sequencing from preimplantation genetic testing

Aneuploidy frequently arises during human meiosis and is the primary cause of early miscarriage and in vitro fertilization (IVF) failure. Individuals undergoing IVF exhibit significant variability in aneuploidy rates, although the exact genetic causes of the variability in aneuploid egg production remain unclear. Preimplantation genetic testing for aneuploidy (PGT-A) using next-generation sequencing is a standard test for identifying and selecting IVF-derived euploid embryos. The wealth of embryo aneuploidy data and ultra-low coverage whole-genome sequencing (ulc-WGS) data from PGT-A have the potential to discover variants in parental genomes that are associated with aneuploidy risk in their embryos. Using ulc-WGS data from ∼10,000 PGT-A biopsies, we imputed genotype likelihoods of genetic variants in embryo genomes. We then used the imputed variants and embryo aneuploidy calls to perform a genome-wide association study of aneuploidy incidence. Finally, we carried out functional evaluation of the identified candidate gene in a mouse oocyte system. We identified one locus on chromosome 3 that is significantly associated with meiotic aneuploidy risk. One candidate gene, CCDC66, encompassed by this locus, is involved in chromosome segregation during meiosis. Using mouse oocytes, we showed that CCDC66 regulates meiotic progression and chromosome segregation fidelity, especially in older mice. Our work extended the research utility of PGT-A ulc-WGS data by allowing robust association testing and improved the understanding of the genetic contribution to maternal meiotic aneuploidy risk. Importantly, we introduce a generalizable method that has potential to be leveraged for similar association studies that use ulc-WGS data.

Identifying risk genes for embryo aneuploidy using ultra-low coverage whole-genome sequencing

Background

Aneuploidy, the state of a cell containing extra or missing chromosomes, frequently arises during human meiosis and is the primary cause of early miscarriage and maternal age-related in vitro fertilization (IVF) failure. IVF patients exhibit significant variability in aneuploidy rates, although the exact genetic causes of the variability in aneuploid egg production remain unclear. Preimplantation genetic testing for aneuploidy (PGT-A) using ultra-low coverage whole-genome sequencing (ulc-WGS) is a standard test for identifying and selecting IVF-derived embryos with a normal chromosome complement. The wealth of embryo aneuploidy data and ulc-WGS data from PGT-A has potential for discovering variants in paternal genomes that are associated with aneuploidy risk in their embryos.

Methods

Using ulc-WGS data from ∼10,000 PGT-A biopsies, we imputed genotype likelihoods of genetic variants in parental genomes. We then used the imputed variants and aneuploidy calls from the embryos to perform a genome-wide association study of aneuploidy incidence. Finally, we carried out functional evaluation of the identified candidate gene in a mouse oocyte system.

Results

We identified one locus on chromosome 3 that is significantly associated with maternal meiotic aneuploidy risk. One candidate gene, CCDC66, encompassed by this locus, is involved in chromosome segregation during meiosis. Using mouse oocytes, we showed that CCDC66 regulates meiotic progression and chromosome segregation fidelity, especially in older mice.

Conclusions

Our work extended the research utility of PGT-A ulc-WGS data by allowing robust association testing and improved the understanding of the genetic contribution to maternal meiotic aneuploidy risk. Importantly, we introduce a generalizable method that can be leveraged for similar association studies using ulc-WGS data.

Reproductive outcome is optimized by genomic embryo screening, vitrification, and subsequent transfer into a prepared synchronous endometrium

PURPOSE

The aim of this study is to compare implantation and live birth rates (LBR) between fresh euploid embryo transfers versus cryo-all cycles with a subsequent embryo transfer into a prepared endometrium.

MATERIAL AND METHODS

This is a retrospective cohort study. Patients who underwent an IVF cycle with PGS with trophectoderm biopsy from January 2011 to July 2015 were included. Patients were divided into three groups: "Fresh Only," "Frozen Embryo Transfer ('FET) Only," and "Fresh ET then FET." For "Fresh Only" group (n = 345), PGS results were received within 24 h. For "FET Only" group (n = 514), results were expected after 24 h, and embryos were cryopreserved after biopsy; only FET was performed in this group (no fresh transfer). For "FET with a previous fresh ET" (n = 139) group, patients underwent a fresh ET with a subsequent FET, in which the same cohort of embryos was utilized. The main outcome measures were pregnancy rate (PR), clinical PR, implantation rate (IR), LBR, and early pregnancy loss rate.

RESULTS

IRs were statistically higher in the "FET Only" group when compared to the "Fresh Only" group (59.5 vs. 50.6%, p < 0.01) and the "FET with a previous fresh ET" (59.5 vs. 50.6%, p < 0.05). LBR was statistically significant in the "FET Only" group when compared to the "Fresh Only" group (57.6 vs. 46.5 %, p < 0.005) but not when compared to "FET with a previous fresh ET" group (57.6 vs. 47.7%, p = 0.07).

CONCLUSIONS

This analysis suggests euploid embryos to be more likely to implant and achieve a LBR in a synthetic FET cycle than in a fresh cycle.

Effects on specific promoter DNA methylation in zebrafish embryos and larvae following benzo[a]pyrene exposure

Benzo[a]pyrene (BaP) is an established carcinogen and reproductive and developmental toxicant. BaP exposure in humans and animals has been linked to infertility and multigenerational health consequences. DNA methylation is the most studied epigenetic mechanism that regulates gene expression, and mapping of methylation patterns has become an important tool for understanding pathologic gene expression events. The goal of this study was to investigate aberrant changes in promoter DNA methylation in zebrafish embryos and larvae following a parental and continued embryonic waterborne BaP exposure. A total of 21 genes known for their role in human diseases were selected to measure percent methylation by multiplex deep sequencing. At 96hpf (hours post fertilization) compared to 3.3hpf, dazl, nqo1, sox3, cyp1b1, and gstp1 had higher methylation percentages while c-fos and cdkn1a had decreased CG methylation. BaP exposure significantly reduced egg production and offspring survival. Moreover, BaP decreased global methylation and altered CG, CHH, and CHG methylation both at 3.3 and 96hpf. CG methylation changed by 10% or more due to BaP in six genes (c-fos, cdkn1a, dazl, nqo1, nrf2, and sox3) at 3.3hpf and in ten genes (c-fos, cyp1b1, dazl, gstp1, mlh1, nqo1, pten, p53, sox2, and sox3) at 96hpf. BaP also induced gene expression of cyp1b1 and gstp1 at 96hpf which were found to be hypermethylated. Further studies are needed to link aberrant CG, CHH, and CHG methylation to heritable epigenetic consequences associated with disease in later life.

Should ICSI be recommended routinely in patients with four or fewer oocytes retrieved?

PURPOSE

To determine if patients with a low response to controlled ovarian hyperstimulation during IVF benefit from intracytoplasmic sperm injection (ICSI) METHODS: Retrospective analysis of 350 IVF cycles in which four or fewer oocytes were retrieved. Severe male factor cases were excluded from analysis. Conventional insemination (CI) and ICSI were compared, with primary outcome measures of fertilization rate, implantation rate, clinical pregnancy rate per embryo transfer, and pregnancy loss rate.

RESULT(S)

Fertilization rates per oocyte retrieved for CI and ICSI were comparable (51.5% vs. 51.8%). Parallel implantation rates (22% vs. 25%), clinical pregnancy rates (32.8% vs. 33.3%), and loss rates (26.7% vs. 39.5%) were also noted. No difference in cancelled cycles was reported.

CONCLUSION(S)

Our results demonstrate that in the presence of normal semen parameters, low egg number is not an indication to perform ICSI.

SerpinB2 deficiency modulates Th1⁄Th2 responses after schistosome infection

SerpinB2, also known as plasminogen activator inhibitor type-2, is a major product of macrophages and is upregulated during many infections. Although SerpinB2 inhibits urokinase plasminogen activator in vitro, evidence that this represents its physiological role in vivo is not compelling. We have recently shown that SerpinB2-/-mice generate enhanced Th1 responses after immunization with a Th1 immunogen. Herein,we show that Schistosoma japonicum granulomas induced liver SerpinB2 mRNA expression by >600-fold in wild-type mice. In SerpinB2-/- mice, worm and egg burden, and granuloma number and volume were unaffected. However, granulomas in these mice were associated with reduced fibrosis (as determined by Sirius red staining and image analysis) and increased iNOS, IL-6, IL-10 and TNFa and decreased Arg 1 and IL-13 mRNA expression. SerpinB2-/- mice immunized with soluble egg antigen (SEA) also showed reduced levels of SEA-specific IgG1. SerpinB2 deficiency thus promoted certain Th1 and reduced certain Th2 responses in response to this Th2 immunogen.

Human blastocyst morphological quality is significantly improved in embryos classified as fast on day 3 (≥10 cells), bringing into question current embryological dogma

OBJECTIVE

To evaluate developmental potential of fast cleaving day 3 embryos.

DESIGN

Retrospective analysis.

SETTING

Academic reproductive center.

PATIENT(S)

Three thousand five hundred twenty-nine embryos.

INTERVENTION(S)

Day 3 embryos were classified according to cell number: slow cleaving: <or=6 cells, intermediate cleaving: 7-9 cells, and fast cleaving: >or=10 cells, and further evaluated on day 5. The preimplantation genetic diagnosis (PGD) results of 43 fast cleaving embryos were correlated to blastocyst formation. Clinical outcomes of transfers involving only fast cleaving embryos (n = 4) were evaluated.

MAIN OUTCOME MEASURE(S)

Blastocyst morphology correlated to day 3 blastomere number. Relationship between euploidy and blastocyst formation of fast cleaving embryos. Implantation, pregnancy (PR), and birth rates resulting from fast embryo transfers.

RESULT(S)

Blastocyst formation rate was significantly greater in the intermediate cleaving (72.7%) and fast cleaving (54.2%) groups when compared to the slow cleaving group (38%). Highest quality blastocysts were formed significantly more often in the fast cleaving group. Twenty fast cleaving embryos that underwent PGD, formed blastocysts, of which 45% (9/20) were diagnosed as euploid. Aneuploidy was diagnosed in 82.6% (19/23) of arrested embryos. A 50% implantation and 100% PR and birth rate were achieved with embryo transfers involving fast cleaving embryos.

CONCLUSION(S)

Fast cleaving embryos not only reach the blastocyst stage at a similar rate to intermediate cleaving embryos, but also exceed morphological quality criteria on day 5. Fast cleaving embryo transfers demonstrated a high clinical potential.

The morphology of extracted testicular sperm correlates with fertilization but not pregnancy rates

OBJECTIVE

To investigate sperm morphology on the day of fresh testicular sperm extraction (TESE) with intracytoplasmic sperm injection (ICSI), and its effect on fertilization and pregnancy rates, as TESE in conjunction with ICSI results in high fertilization and pregnancy rates in most patients, but to our knowledge only one small study has assessed the morphology of retrieved sperm and found no correlation with the success of fertilization.

PATIENTS AND METHODS

In a retrospective database analysis in a large academic centre, 68 men had 75 cycles of TESE combined with ICSI from January 2004 until April 2006. Sperm obtained by TESE was morphologically analysed at high (x 400-600) magnification and used for ICSI on the day of tissue retrieval. Sperm were classified as being either normal, having an amorphous head, having a mid-piece defect or having multiple defects. The calculated percentage of abnormal sperm injected was compared with the normal fertilization rate using Pearson's correlation coefficient, and pregnancy rates between groups were compared using chi-square analysis.

RESULTS

Fifteen cycles had all morphologically normal sperm; 21 cycles had 50-99% normal forms and 39 cycles had <50% normal sperm. There was a highly significant correlation between the percentage of normal sperm used for ICSI and fertilization rates (P = 0.007). Overall, 43 clinical pregnancies resulted in this series, i.e. three among the group with all normal sperm injected, 12 in the group with 50-99% normal sperm and 28 in the group with <50% normal forms. There were also 11 pregnancies in cycles that used no normal forms. Pregnancy rates did not differ significantly among the groups (P = 0.08).

CONCLUSIONS

TESE with ICSI frequently results in successful pregnancy; normal morphology was highly and significantly associated with successful fertilization, but importantly there were still 10 clinical pregnancies in cycles where only abnormal sperm were used. Sperm morphology after TESE should be assessed at the time of the procedure, and whenever possible, morphologically normal sperm chosen for injection. However, it is reassuring that acceptable fertilization and pregnancy rates are still achievable in cases with no morphologically normal sperm available.

Inorganic membranes for hydrogen production and purification: A critical review and perspective

Hydrogen as a high-quality and clean energy carrier has attracted renewed and ever-increasing attention around the world in recent years, mainly due to developments in fuel cells and environmental pressures including climate change issues. In thermochemical processes for hydrogen production from fossil fuels, separation and purification is a critical technology. Where water-gas shift reaction is involved for converting the carbon monoxide to hydrogen, membrane reactors show great promises for shifting the equilibrium. Membranes are also important to the subsequent purification of hydrogen. For hydrogen production and purification, there are generally two classes of membranes both being inorganic: dense phase metal and metal alloys, and porous ceramic membranes. Porous ceramic membranes are normally prepared by sol-gel or hydrothermal methods, and have high stability and durability in high temperature, harsh impurity and hydrothermal environments. In particular, microporous membranes show promises in water gas shift reaction at higher temperatures. In this article, we review the recent advances in both dense phase metal and porous ceramic membranes, and compare their separation properties and performance in membrane reactor systems. The preparation, characterization and permeation of the various membranes will be presented and discussed. We also aim to examine the critical issues in these membranes with respect to the technical and economical advantages and disadvantages. Discussions will also be made on the relevance and importance of membrane technology to the new generation of zero-emission power technologies.

Identification of a diagnostic antibody-binding region on the immunogenic protein EpC1 from Echinococcus granulosus and its application in population screening for cystic echinococcosis

An Echinococcus granulosus cDNA sequence coding for EpC1, a proven serodiagnostic marker for cystic echinococcosis (CE, hydatid disease), has high amino acid sequence identity to a paralogue from Taenia solium, the cause of neurocysticercosis (NCC). To determine diagnostic antibody-binding regions on EpC1 recognized specifically by CE sera, 10 truncated regions (P1-10) of the immunogenic protein were expressed in Escherichia coli and subjected to immunoblotting. One peptide, designated peptide 5 [P5, fused with glutathione-S-transferase (GST)] was positively recognized by sera from mice experimentally infected with oncospheres of E. granulosus and sera from surgically confirmed CE patients. Sera from NCC patients did not react with any of the peptides used. There are four amino acid substitutions in P5 compared with the T. solium sequence and these may form part of the epitope inducing CE-specific antibody. Ninety-seven per cent (58 of 60) of sera from confirmed CE patients recognized P5-GST, which was higher than the parent EpC1 fused with GST which reacted with 92% (55 of 60) of the sera. A population screening survey showed that 424 human sera collected from communities in Xinjiang, an area in China endemic for CE, exhibited 4.5% and 3.3% positivity in immunoblotting analysis to EpC1 and P5, respectively; 19.8% of these sera reacted positively against hydatid cyst fluid (HCF) antigen B. Low numbers of surgical CE cases have been reported from this population, suggesting that HCF-based serology lacks specificity and that EpC1 or its contained P5 peptide may prove more accurate for seroepidemiological surveys of CE.