Seroprevalence and placental transfer of SARS-CoV-2 antibodies in unvaccinated pregnant women.

PURPOSE: Pregnant women are at risk of severe SARS-CoV-2 infection, potentially leading to obstetric and neonatal complications. Placental transfer of antibodies directed to SARS-CoV-2 may be protective against neonatal COVID-19, but this remains to be studied. We aimed to determine the seroprevalence of SARS-CoV-2 antibodies in a population of unvaccinated pregnant women and to determine the placental transfer of these antibodies. METHODOLOGY: A total of 1197 unvaccinated women with mostly unknown pre-study SARS-CoV-2 infection status, were tested at delivery for SARS-CoV-2 spike protein IgG antibodies during the first year of the pandemic. Umbilical cord samples were collected and assessed for seropositivity if the mother was seropositive. Maternal characteristics, pregnancy and neonatal outcomes and data on SARS-CoV-2 infection were extracted from medical records. RESULTS: Specific IgG were detected in 258 women (21.6%). A significant placental transfer to the newborn was observed in 81.3% of cases. The earlier in the 2nd and 3rd trimesters that the mother had contracted the disease and the more symptomatic she was, the greater the likelihood of transplacental transfer of IgG to her newborn. CONCLUSION: Approximately one in five women had detectable anti-SARS-CoV-2 spike protein IgG antibodies at delivery during the first year of the pandemic, and these antibodies were significantly transferred to their fetuses. This research provides further evidence to better understand the dynamics of the placental transfer of SARS-CoV-2 IgG antibodies from mothers to their newborns, which is necessary to improve vaccination strategies.

Influence of organizational factors on the offer and success rate of a trial of labor after cesarean section in Belgium: an ecological study.

BACKGROUND: Trial of Labor After Cesarean is an important strategy for reducing the overall rate of cesarean delivery. Offering the option of vaginal delivery to a woman with a history of cesarean section requires the ability to manage a potential uterine rupture quickly and effectively. This requires infrastructure and organization of the maternity unit so that the decision-to-delivery interval is as short as possible when uterine rupture is suspected. We hypothesize that the organizational characteristics of maternity units in Belgium have an impact on their proposal and success rates of trial of labour after cesarean section. METHODS: We collected data on the organizational characteristics of Belgian maternity units using an online questionnaire. Data on the frequency of cesarean section, trial of labor and vaginal birth after cesarean section were obtained from regional perinatal registries. We analyzed the determinants of the proposal and success of trial of labor after cesarean section and report the associations as mean proportions. RESULTS: Of the 101 maternity units contacted, 97 responded to the questionnaire and data from 95 was included in the analysis. Continuous on-site presence of a gynecologist and an anesthetist was associated with a higher proportion of trial of labor after cesarean section, compared to units where staff was on-call from home (51% versus 46%, p = 0.04). There is a non-significant trend towards more trial of labor after cesarean section in units with an operating room in or near the delivery unit and a shorter transfer time, in larger units (> 1500 deliveries/year) and in units with a neonatal intensive care unit. The proposal of trial of labor after cesarean section and its success was negatively correlated to the number of cesarean section in the maternity unit (Spearman' rho = 0.50 and 0.42, p value < 0.001). CONCLUSIONS: Organizational differences in maternity units appear to affect the proposal of trial of labor after cesarean section. Addressing these organizational factors may not be sufficient to change practice, given that general tendency to perform a cesarean section in the maternity unit is the main contributor to the percentage of trial of labor after cesarean.

Late miscarriage and stillbirth in asymptomatic and symptomatic hospitalised pregnant women in Belgium during the first and second waves of COVID-19: a prospective nationwide population-based study.

BACKGROUND: Stillbirth has been recognized as a possible complication of a SARS-CoV-2 infection during pregnancy, probably due to destructive placental lesions (SARS-CoV-2 placentitis). The aim of this work is to analyse stillbirth and late miscarriage cases in unvaccinated pregnant women infected with SARS-CoV-2 during the first two waves (wild-type period) in Belgium. METHODS: Stillbirths and late miscarriages in our prospective observational nationwide registry of SARS-CoV-2 infected pregnant women (n = 982) were classified by three authors using a modified WHO-UMC classification system for standardized case causality assessment. RESULTS: Our cohort included 982 hospitalised pregnant women infected with SARS-CoV-2, with 23 fetal demises (10 late miscarriages from 12 to 22 weeks of gestational age and 13 stillbirths). The stillbirth rate was 9.5‰ for singleton pregnancies and 83.3‰ for multiple pregnancies, which seems higher than for the background population (respectively 5.6‰ and 13.8‰). The agreement between assessors about the causal relationship with SARS-Cov-2 infection was fair (global weighted kappa value of 0.66). Among these demises, 17.4% (4/23) were "certainly" attributable to SARS-CoV-2 infection, 13.0% (3/23) "probably" and 30.4% (7/23) "possibly". Better agreement in the rating was noticed when pathological examination of the placenta and identification of the virus were available, underlining the importance of a thorough investigation in case of intra-uterine fetal demise. CONCLUSIONS: SARS-CoV-2 causality assessment of late miscarriage and stillbirth cases in our Belgian nationwide case series has shown that half of the fetal losses could be attributable to SARS-CoV-2. We must consider in future epidemic emergencies to rigorously investigate cases of intra-uterine fetal demise and to store placental tissue and other material for future analyses.

Implementation of fetal clinical exome sequencing: Comparing prospective and retrospective cohorts.

PURPOSE: We compared the diagnostic yield of fetal clinical exome sequencing (fCES) in prospective and retrospective cohorts of pregnancies presenting with anomalies detected using ultrasound. We evaluated factors that led to a higher diagnostic efficiency, such as phenotypic category, clinical characterization, and variant analysis strategy. METHODS: fCES was performed for 303 fetuses (183 ongoing and 120 ended pregnancies, in which chromosomal abnormalities had been excluded) using a trio/duo-based approach and a multistep variant analysis strategy. RESULTS: fCES identified the underlying genetic cause in 13% (24/183) of prospective and 29% (35/120) of retrospective cases. In both cohorts, recessive heterozygous compound genotypes were not rare, and trio and simplex variant analysis strategies were complementary to achieve the highest possible diagnostic rate. Limited prenatal phenotypic information led to interpretation challenges. In 2 prospective cases, in-depth analysis allowed expansion of the spectrum of prenatal presentations for genetic syndromes associated with the SLC17A5 and CHAMP1 genes. CONCLUSION: fCES is diagnostically efficient in fetuses presenting with cerebral, skeletal, urinary, or multiple anomalies. The comparison between the 2 cohorts highlights the importance of providing detailed phenotypic information for better interpretation and prenatal reporting of genetic variants.

[Trial of labour after c-section in 2022: a narrative review of the literature]. / Accouchement vaginal après une césarienne en 2022 : revue narrative de la littérature.

One in three women in Switzerland gives birth by c-section. This high incidence of c-section frequently exposes obstetricians and midwives to the management of women and their deliveries with a scarred uterus. The decision of couples is multifactorial, but the information that will be delivered by their gynaecologist will necessarily influence the delivery route choice. We propose to review the international recommendations and the literature on the subject, to provide the couple and the attending physician with elements of reflection to guide the choice of delivery route or to monitor adequately when attempting vaginal delivery after a caesarean section.

En Suisse, une femme sur trois donne naissance à son enfant par césarienne. Cette forte incidence de la césarienne expose régulièrement les obstétriciens et les sages-femmes à la gestion de femmes et de leur accouchement avec un utérus cicatriciel. La décision des couples est multifactorielle, mais l'information qui sera délivrée par leur gynécologue va nettement influencer le choix de la voie d'accouchement. Nous proposons ici de passer en revue les recommandations internationales et la littérature sur le sujet, afin de procurer les éléments de réflexion au couple et au médecin traitant afin de guider le choix de la voie d'accouchement et de monitorer adéquatement au cours d'une tentative d'accouchement par voie basse.

A Tutsi family harbouring two new RHCE variant alleles and a new haplotype in the Rh blood group system.

BACKGROUND: RHCE*ceEK is a rare RH allele mostly encountered in people of African descent. This allele is defined by four single nucleotide substitutions: c.48G>C, c.712A>G, c.787A>G and c.800T>A. Until now, it has only been reported to segregate with either RHD*01N.01 or RHD*DAR1.00. MATERIALS AND METHODS: Blood samples were drawn from a 32-year-old Tutsi pregnant woman during an antenatal visit in order to perform her type and screen. To further investigate the results found in the patient, a family study was conducted. Standard haemagglutination methods were used to investigate the subjects' red blood cells and plasma. Molecular workup on RHD and RHCE genes was carried out by DNA microarray, real-time PCR and DNA sequencing techniques. RESULTS: The patient was phenotyped as group B, D+C-E-c+e+, Hr-. A complex mixture of anti-E, anti-c, anti-Hr and anti-hrS was detected in her plasma. She was found to carry a normal RHD gene, a conventional RHCE*ceEK allele and an alternative RHCE*ceEK allele (RHCE*ceEK without c.48G>C). The family study showed that the conventional RHCE*ceEK and the alternative RHCE*ceEK alleles were associated with a RHD*01 allele and a RHD*01N.01 allele, respectively. Molecular analysis performed in the proband's mother showed a novel RHCE*ce variant allele on a RHCE*ceS -like background (RHCE*ceS with c.609G>A). CONCLUSIONS: This case study brought out new associations between RHD and RHCE alleles encoding the rare Hr- phenotype: the conventional RHCE*ceEK allele linked to the RHD*01 allele and an alternative RHCE*ceEK allele associated with the RHD*01N.01 allele. A novel RHCE*ce variant (RHCE*ceS with c.609G>A) was also reported.

The "Cocoon," first alongside midwifery-led unit within a Belgian hospital: Comparison of the maternal and neonatal outcomes with the standard obstetric unit over 2 years.

OBJECTIVES: Our aim was to compare maternal and neonatal outcomes of women with a low-risk pregnancy attending the "Cocoon," an alongside midwifery-led birth center and care pathway, with women with a low-risk pregnancy attending the traditional care pathway in a tertiary care hospital in Belgium. METHODS: We performed a retrospective cohort study of maternal and neonatal outcomes of women with a low-risk pregnancy who chose to adhere to the Cocoon pathway of care (n = 590) and women with a low-risk pregnancy who chose the traditional pathway of care (n = 394) from March 1, 2014, to February 29, 2016. We performed all analyses using an intention-to-treat approach. RESULTS: In this setting, the cesarean birth rate was 10.3% compared with 16.0% in the traditional care pathway (adjusted odds ratios [aOR] 0.42 [95% CI 0.25-0.69]), the induction rate was 16.3% compared with 30.5% (0.46 [0.30-0.69]), the epidural analgesia rate was 24.9% compared with 59.1% (0.15 [0.09-0.22]), and the episiotomy rate was 6.8% compared with 14.5% (0.31 [0.17-0.56]). There was no increase in adverse neonatal outcomes. Intrapartum and postpartum transfer rates to the traditional pathway of care were 21.1% and 7.1%, respectively. CONCLUSIONS: Women planning their births in the midwifery-led unit, the Cocoon, experienced fewer interventions with no increase in adverse neonatal outcomes. Our study gives initial support for the introduction of similar midwifery-led care pathways in other hospitals in Belgium.

Change in prevalence of gestational diabetes and obstetric complications when applying IADPSG screening criteria in a Belgian French speaking University Hospital. A retrospective cohort study.

BACKGROUND: In April 2012 our institution chose to switch from a two- step criteria for Gestational Diabetes Mellitus (GDM) screening, to the International Association of Diabetes in Pregnancy Study Group (IADSPG) criteria. This shift led to an increased prevalence of GDM in our pregnant population. We designed a study in order to estimate the magnitude of the increase in GDM prevalence before and after the switch in screening strategy. As a secondary objective we wanted to evaluate if there was a significant difference between the two periods in the percentage of maternal and neonatal complications such as gestational hypertensive disorders (GHD), primary cesarean section (pCS), preterm birth, large for gestational age (LGA) newborns, macrosomia, shoulder dystocia, 5' Apgar score less than to 7 at birth, neonatal intensive care unit (NICU) transfer and neonatal hypoglycemia. METHODS: We selected retrospectively 3496 patients who delivered between January 2009 and December 2011 who were screened with the two-step criteria (group A), and compared them to 2555 patients who delivered between January 2013 and December 2014 and who were screened with IADPSG criteria (Group B). We checked patients' electronic files to establish GDM status, baseline characteristics (age, body mass index, nationality, parity) and the presence of maternal and neonatal complications. RESULTS: GDM prevalence increased significantly from group A (3.4%; 95%CI 2.8-4.06%) to group B (16.28%; 95%CI 14.8 -17.7%). In group B there were significantly more non-Belgian and primiparous patients. There was no statistically significant difference in maternal and neonatal complications between the two groups, even after adjustment for nationality and parity. There was a non-significant reduction of the proportion of macrosomic and of LGA babies. CONCLUSIONS: In our population the introduction of IADPSG screening criteria has increased the prevalence of GDM without having a statistically significant impact on pregnancy outcomes.

Severe X-linked chondrodysplasia punctata in nine new female fetuses.

OBJECTIVES: Conradi-Hünermann-Happle [X-linked dominant chondrodysplasia punctata 2 (CDPX2)] syndrome is a rare X-linked dominant skeletal dysplasia usually lethal in men while affected women show wide clinical heterogeneity. Different EBP mutations have been reported. Severe female cases have rarely been reported, with only six antenatal presentations. METHODS: To better characterize the phenotype in female fetuses, we included nine antenatally diagnosed cases of women with EBP mutations. All cases were de novo except for two fetuses with an affected mother and one case of germinal mosaicism. RESULTS: The mean age at diagnosis was 22 weeks of gestation. The ultrasound features mainly included bone abnormalities: shortening (8/9 cases) and bowing of the long bones (5/9), punctuate epiphysis (7/9) and an irregular aspect of the spine (5/9). Postnatal X-rays and examination showed ichthyosis (8/9) and epiphyseal stippling (9/9), with frequent asymmetric short and bowed long bones. The X-inactivation pattern of the familial case revealed skewed X-inactivation in the mildly symptomatic mother and random X-inactivation in the severe fetal case. Differently affected skin samples of the same fetus revealed different patterns of X-inactivation. CONCLUSION: Prenatal detection of asymmetric shortening and bowing of the long bones and cartilage stippling should raise the possibility of CPDX2 in female fetuses, especially because the majority of such cases involve de novo mutations.

Variations of cervical head entrapment in vaginal breech births: New insights on how to prevent, manage and resolve.

This paper presents a novel, systematic way to understand the causes of cervical head entrapment in vaginal breech births, and new insights into management. Three different types of cervical head entrapment are described, with detailed illustrations: unpredictable and potentially catastrophic, manageable, and preventable. The first affects preterm and growth-restricted fetuses. The second involves some degree of uterine prolapse. The third may result from prolonged head entrapment at the pelvic inlet, leaving time for cervical contraction or oedematous entrapment. Traditional and innovative strategies to resolve and prevent this complication are described and illustrated, with suggestions for further research.

Training for breech deliveries with the mother in an upright position: An innovative adaptation of a simulation model.

BACKGROUND: Delivery of a breech baby with the mother in an upright position or on all fours has gained a renewed interest. In these positions, the obstetrician or midwife needs to learn new landmarks and maneuvers. A realistic simulation model would be a valuable adjunct for breech on all fours teaching programs. MATERIAL AND METHODS: This article describes the simulation model and training program we have developed to train an interprofessional team to assist breech births when the mother is on all fours. A questionnaire was used to evaluate the realism of the adapted mannequin and the impact of training on the confidence level of the participants. RESULTS: On a Likert scale of 1 to 5, 92% of participants agreed or strongly agreed that the adapted mannequin used was realistic for training obstetric maneuvers for complicated breech births. After training, their confidence level supporting a breech birth in an upright position rose from an average of 2.5 to 5.7 on a scale of 1 to 10. CONCLUSION: Learning the skills for breech deliveries on all fours is made possible by targeted training with this adapted simulation model.

Internal podalic version of second twin: Improving feet identification using a simulation model.

BACKGROUND: Podalic version and breech extraction require high obstetrical expertise. Identifying fetal extremities is the first crucial step for trainees. When this skill is not polished enough, it increases the inter-twin delivery interval and can even jeopardize the whole manoeuver. MATERIAL AND METHODS: We present a model for simulating and training this specific skill, with obstetrical mannequin, and 3D printed hands and feet. Five feet and five hands (five rights and five lefts of each one) were printed in 3D after initial ultrasound acquisition of a near term fetus. Each foot and hand, was individually set in a condom filled with 100 cc of water and closed with a knot. A Sophie's Mum Birth Simulator Version 4.0 de MODEL-med was placed on the edge of the table. Each hand and foot was inserted into the pelvic mannequin. An evaluation of the students' skills using this model was performed. A significant reduction of the global mean to extract the first foot and all the feet was noticed at three month of interval. CONCLUSION: This model is an option to train and assess a crucial skill for version and breech extraction.

Using simulation team training with human's factors components in obstetrics to improve patient outcome: A review of the literature.

OBJECTIVE: to assess the evidence from multidisciplinary simulation team training in obstetrics that integrates human's factors components on patient outcome. INTRODUCTION: It has been stated that simulation-based education has the potential to improve technical and nontechnical skills. Reports from enquiries into maternal and newborn adverse outcomes, highlight that the majority of incidents are due to a breakdown of communication and a lack of crisis resource management skills (CRM). It is therefore reasonable to think that a better training on teamwork based on simulation will ultimately improve obstetrics care. In order to explore further that idea, we conducted a literature review on patient outcome after a multidisciplinary simulation training in obstetrics. METHOD: Pubmed, Advances in health sciences education, BMC in medical education, BMC in pregnancy and Childbirth, BMJ open, BMJ Simulation and technology enhanced learning were searched from inception to May 2020 for full-text publications in English on interprofessional, multidisciplinary, obstetrics, simulation training, non-technical skills, CRM. Searches were limited to studies with a report on patient outcome after a multidisciplinary simulation program that included elements of CRM. RESULT: Out of the ten studies selected in our review, five were single site before and after prospective studies and five were cluster before and after randomized trials. All the single site studies reported a positive outcome in low and high resource countries. Three single site studies reported a reduction between 41 and 50 % of blood transfusion after simulation team training. Two single studies reported a reduction of maternal mortality by 34 % and a decrease in an adverse obstetrics index outcome from 0.052 to 0.048 with a p-value of 0.05. Cluster studies showed either no change or some improvement in patient outcomes such as a 37 % improvement on weighted obstetrics adverse outcome, a 17 % reduction in the incidence of PPH and a 47 % reduction in the incidence of retained placenta. Stillbirths rate was reduced by 34 % while newborn deaths was down by 62 %. There was also a 15 % reduction of maternal mortality in favor of the trained team after adjustment to the secular mortality trend. Neonatal death from 24 weeks during the first 24 h was also reduced by 83 % in the intervention site compare with an increase by 18 % in the control site. CONCLUSION: There is evidence that simulation team training that includes CRM is associated with better patient outcome. In order to consolidate this finding, appropriate methodology should be used in future studies with the support of health authorities.

Iron Deficiency Is a Risk Factor for Thyroid Dysfunction During Pregnancy: A Population-Based Study in Belgium.

Background: Iron deficiency affects thyroid hormone synthesis by impairing the activity of the heme-dependent thyroid peroxidase. The prevalence of iron deficiency is elevated particularly in pregnant women. This study aimed to investigate the effects of iron status on thyroid function in a nationally representative sample of mildly iodine-deficient pregnant women. Methods: The study population comprised a sample of pregnant women in Belgium during the first and third trimesters of pregnancy (n = 1241). Women were selected according to a multistage proportional-to-size stratified and clustered sampling design. Urine and blood samples were collected, and a questionnaire was completed face to face with the study nurse. Concentrations of free thyroxine (fT4), total thyroxine (T4), free triiodothyronine, thyrotropin (TSH), thyroglobulin (Tg), thyroid peroxidase antibodies, Tg antibodies, hemoglobin, serum ferritin (SF), soluble transferrin receptor, urinary iodine concentrations (UICs) were measured and body iron stores (BIS) were calculated. Results: Median UICs were 117 and 132 µg/L in the first and third trimesters of pregnancy, respectively (p < 0.05). The frequency of SF <15 µg/L was 6.2% in the first trimester and 39.6% in the third trimester of pregnancy (p < 0.05). UIC was a significant predictor of serum Tg concentrations (p < 0.01) but not of thyroid hormone or TSH concentrations. The frequency of fT4

First trimester ultrasound prediction of velamentous cord insertions: a prospective study.

INTRODUCTION: The marginal and velamentous cord insertions complicate around 8% of pregnancies and are at higher risk of adverse perinatal outcomes. Their visualisation seems to decrease with advancing gestational age. Our aim was to analyse whether an umbilical cord insertion in the lower third of the uterus during the first trimester could predict abnormal cord insertions later in pregnancy. METHODS: This was a prospective multicentre study in two hospitals. During the first trimester, the cord insertions were inspected as well as their location (lower third of the uterus or not). Finally, all cord insertions were described at delivery. RESULTS: During the study period the cord insertion was described in 1620 patients of which 87.7% had a normal cord insertion, 11.9% (n = 192) a low cord insertion, and in 3.8% the insertion could not be situated. We find that 4.7% of those who have a low-lying cord insertion versus 0.7% in the normal cord insertion group during the first trimester will have a velamentous cord insertion subsequently (OR = 6.67; 95% CI = 2.67-16.63). CONCLUSION: The detection of a low lying umbilical cord insertion during the first-trimester ultrasound can help to predict an abnormal cord insertion at delivery particularly a velamentous cord insertion.

Maternal and perinatal outcomes in high compared to low risk pregnancies complicated by severe acute respiratory syndrome coronavirus 2 infection (phase 2): the World Association of Perinatal Medicine working group on coronavirus disease 2019.

BACKGROUND: It has still to be ascertained whether severe acute respiratory syndrome coronavirus 2 infection in pregnancy is associated with worse maternal and fetal outcomes compared to low risk gestations. OBJECTIVE: This study aimed to evaluate maternal and perinatal outcomes in high- and low-risk pregnancies complicated by severe acute respiratory syndrome coronavirus 2 infection. STUDY DESIGN: This was a multinational retrospective cohort study involving women with laboratory-confirmed severe acute respiratory syndrome coronavirus 2 infection from 76 centers from 25 countries in Europe, the United States, South America, Asia, and Australia from April 4, 2020, to October 28, 2020. The primary outcome was a composite measure of maternal mortality and morbidity, including admission to the intensive care unit, use of mechanical ventilation, or death. The secondary outcome was a composite measure of adverse perinatal outcome, including miscarriage, fetal loss, neonatal and perinatal death, and admission to the neonatal intensive care unit. All outcomes were assessed in high- and low-risk pregnancies. Pregnancies were considered high risk in case of either preexisting chronic medical conditions in pregnancy or obstetrical disorders occurring in pregnancy. The Fisher exact test and logistic regression analysis were used to analyze the data. RESULTS: A total of 887 singleton pregnancies who tested positive for severe acute respiratory syndrome coronavirus 2 infection using reverse transcription-polymerase chain reaction of nasal and pharyngeal swab specimens were included in the study. The risk of composite adverse maternal outcomes was higher in high-risk pregnancies than in low-risk pregnancies (odds ratio, 1.52; 95% confidence interval, 1.03-2.24; P=.035). In addition, women carrying high-risk pregnancies were at higher risk of hospital admission (odds ratio, 1.48; 95% confidence interval, 1.07-2.04; P=.002), presence of severe respiratory symptoms (odds ratio, 2.13; 95% confidence interval, 0.41-3.21; P=.001), admission to the intensive care unit (odds ratio, 2.63; 95% confidence interval, 1.42-4.88), and invasive mechanical ventilation (odds ratio, 2.65; 95% confidence interval, 1.19-5.94; P=.002). When exploring perinatal outcomes, high-risk pregnancies were at high risk of adverse perinatal outcomes (odds ratio, 1.78; 95% confidence interval, 0.15-2.72; P=.009). However, such association was mainly because of the higher incidence of miscarriage in high-risk pregnancies compared with that in low-risk pregnancies (5.3% vs 1.6%, P=.008); furthermore, there was no difference in other explored outcomes between the 2 study groups. At logistic regression analysis, maternal age (odds ratio, 1.12; 95% confidence interval, 1.02-1.22; P=.023) and high-risk pregnancy (odds ratio, 4.21; 95% confidence interval, 3.90-5.11; P<.001) were independently associated with adverse maternal outcomes. CONCLUSION: High-risk pregnancies complicated by severe acute respiratory syndrome coronavirus 2 infection were at higher risk of adverse maternal outcomes than low-risk pregnancies complicated by severe acute respiratory syndrome coronavirus 2 infection.

Data analysis issues for allele-specific expression using Illumina's GoldenGate assay.

BACKGROUND: High-throughput measurement of allele-specific expression (ASE) is a relatively new and exciting application area for array-based technologies. In this paper, we explore several data sets which make use of Illumina's GoldenGate BeadArray technology to measure ASE. This platform exploits coding SNPs to obtain relative expression measurements for alleles at approximately 1500 positions in the genome. RESULTS: We analyze data from a mixture experiment where genomic DNA samples from pairs of individuals of known genotypes are pooled to create allelic imbalances at varying levels for the majority of SNPs on the array. We observe that GoldenGate has less sensitivity at detecting subtle allelic imbalances (around 1.3 fold) compared to extreme imbalances, and note the benefit of applying local background correction to the data. Analysis of data from a dye-swap control experiment allowed us to quantify dye-bias, which can be reduced considerably by careful normalization. The need to filter the data before carrying out further downstream analysis to remove non-responding probes, which show either weak, or non-specific signal for each allele, was also demonstrated. Throughout this paper, we find that a linear model analysis of the data from each SNP is a flexible modelling strategy that allows for testing of allelic imbalances in each sample when replicate hybridizations are available. CONCLUSIONS: Our analysis shows that local background correction carried out by Illumina's software, together with quantile normalization of the red and green channels within each array, provides optimal performance in terms of false positive rates. In addition, we strongly encourage intensity-based filtering to remove SNPs which only measure non-specific signal. We anticipate that a similar analysis strategy will prove useful when quantifying ASE on Illumina's higher density Infinium BeadChips.

High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta.

BACKGROUND: Imprinted genes show expression from one parental allele only and are important for development and behaviour. This extreme mode of allelic imbalance has been described for approximately 56 human genes. Imprinting status is often disrupted in cancer and dysmorphic syndromes. More subtle variation of gene expression, that is not parent-of-origin specific, termed 'allele-specific gene expression' (ASE) is more common and may give rise to milder phenotypic differences. Using two allele-specific high-throughput technologies alongside bioinformatics predictions, normal term human placenta was screened to find new imprinted genes and to ascertain the extent of ASE in this tissue. RESULTS: Twenty-three family trios of placental cDNA, placental genomic DNA (gDNA) and gDNA from both parents were tested for 130 candidate genes with the Sequenom MassArray system. Six genes were found differentially expressed but none imprinted. The Illumina ASE BeadArray platform was then used to test 1536 SNPs in 932 genes. The array was enriched for the human orthologues of 124 mouse candidate genes from bioinformatics predictions and 10 human candidate imprinted genes from EST database mining. After quality control pruning, a total of 261 informative SNPs (214 genes) remained for analysis. Imprinting with maternal expression was demonstrated for the lymphocyte imprinted gene ZNF331 in human placenta. Two potential differentially methylated regions (DMRs) were found in the vicinity of ZNF331. None of the bioinformatically predicted candidates tested showed imprinting except for a skewed allelic expression in a parent-specific manner observed for PHACTR2, a neighbour of the imprinted PLAGL1 gene. ASE was detected for two or more individuals in 39 candidate genes (18%). CONCLUSIONS: Both Sequenom and Illumina assays were sensitive enough to study imprinting and strong allelic bias. Previous bioinformatics approaches were not predictive of new imprinted genes in the human term placenta. ZNF331 is imprinted in human term placenta and might be a new ubiquitously imprinted gene, part of a primate-specific locus. Demonstration of partial imprinting of PHACTR2 calls for re-evaluation of the allelic pattern of expression for the PHACTR2-PLAGL1 locus. ASE was common in human term placenta.

Prediction of severity of symptoms in iatrogenic ovarian hyperstimulation syndrome by follicle-stimulating hormone receptor Ser680Asn polymorphism.

The ovarian hyperstimulation syndrome (OHSS) is a potentially life-threatening complication of ovarian stimulation treatments for in vitro fertilization (i.v.f.). Recently, three different mutations of the FSH receptor (FSHr) have been identified in patients who presented recurrent spontaneous OHSS. This prompted us to study a possible association between coding polymorphisms of the FSHr and the occurrence of iatrogenic OHSS. We sequenced the region of the FSHr gene encompassing the A307T and S680N polymorphisms of exon 10 of FSHr in 37 Caucasian females who developed OHSS after an IVF cycle in our fertility clinic, 130 Caucasian female patients who were treated by i.v.f. but never developed OHSS, and 99 Caucasian female controls. The FSHr allele frequencies in the Caucasian control population were identical to what has already been published (39% S680 61% N680). The control i.v.f. population was enriched in the S680 allele compared with the Caucasian control population (51% S680; 49% N680; P = 0.016). The OHSS population had a even higher enrichment in the S680 allele compared with the Caucasian control population (57% S680; 43% N680; P = 0.010). These results were unexpected, because the frequency of the S680 allele was previously found to be increased among poor responders to FSH stimulation. In a second phase, we studied FSHr allele frequencies according to the severity of OHSS. Interestingly, a significant enrichment in the allele N680 was observed as the severity of OHSS increased (P = 0.034). Bearing in mind the limitations of the small number of patients studied and the possibility of sampling biases, these results suggest that the genotype in position 680 of the FSHr cannot predict which patients will develop OHSS, but could be a predictor of severity of symptoms among OHSS patients.