A systematic assessment of the impact of rare canonical splice site variants on splicing using functional and in silico methods.

Canonical splice site variants (CSSVs) are often presumed to cause loss-of-function (LoF) and are assigned very strong evidence of pathogenicity (according to American College of Medical Genetics/Association for Molecular Pathology criterion PVS1). The exact nature and predictability of splicing effects of unselected rare CSSVs in blood-expressed genes are poorly understood. We identified 168 rare CSSVs in blood-expressed genes in 112 individuals using genome sequencing, and studied their impact on splicing using RNA sequencing (RNA-seq). There was no evidence of a frameshift, nor of reduced expression consistent with nonsense-mediated decay, for 25.6% of CSSVs: 17.9% had wildtype splicing only and normal junction depths, 3.6% resulted in cryptic splice site usage and in-frame insertions or deletions, 3.6% resulted in full exon skipping (in frame), and 0.6% resulted in full intron inclusion (in frame). Blind to these RNA-seq data, we attempted to predict the precise impact of CSSVs by applying in silico tools and the ClinGen Sequence Variant Interpretation Working Group 2018 guidelines for applying PVS1 criterion. The predicted impact on splicing using (1) SpliceAI, (2) MaxEntScan, and (3) AutoPVS1, an automatic classification tool for PVS1 interpretation of null variants that utilizes Ensembl Variant Effect Predictor and MaxEntScan, was concordant with RNA-seq analyses for 65%, 63%, and 61% of CSSVs, respectively. In summary, approximately one in four rare CSSVs did not show evidence for LoF based on analysis of RNA-seq data. Predictions from in silico methods were often discordant with findings from RNA-seq. More caution may be warranted in applying PVS1-level evidence to CSSVs in the absence of functional data.

A comparative medical genomics approach may facilitate the interpretation of rare missense variation.

PURPOSE: To determine the degree to which likely causal missense variants of single-locus traits in domesticated species have features suggestive of pathogenicity in a human genomic context. METHODS: We extracted missense variants from the Online Mendelian Inheritance in Animals database for nine animals (cat, cattle, chicken, dog, goat, horse, pig, rabbit and sheep), mapped coordinates to the human reference genome and annotated variants using genome analysis tools. We also searched a private commercial laboratory database of genetic testing results from >400 000 individuals with suspected rare disorders. RESULTS: Of 339 variants that were mappable to the same residue and gene in the human genome, 56 had been previously classified with respect to pathogenicity: 31 (55.4%) pathogenic/likely pathogenic, 1 (1.8%) benign/likely benign and 24 (42.9%) uncertain/other. The odds ratio for a pathogenic/likely pathogenic classification in ClinVar was 7.0 (95% CI 4.1 to 12.0, p<0.0001), compared with all other germline missense variants in these same 220 genes. The remaining 283 variants disproportionately had allele frequencies and REVEL scores that supported pathogenicity. CONCLUSION: Cross-species comparisons could facilitate the interpretation of rare missense variation. These results provide further support for comparative medical genomics approaches that connect big data initiatives in human and veterinary genetics.

Telomeres and replicative cellular aging of the human placenta and chorioamniotic membranes.

Recent hypotheses propose that the human placenta and chorioamniotic membranes (CAMs) experience telomere length (TL)-mediated senescence. These hypotheses are based on mean TL (mTL) measurements, but replicative senescence is triggered by short and dysfunctional telomeres, not mTL. We measured short telomeres by a vanguard method, the Telomere shortest length assay, and telomere-dysfunction-induced DNA damage foci (TIF) in placentas and CAMs between 18-week gestation and at full-term. Both the placenta and CAMs showed a buildup of short telomeres and TIFs, but not shortening of mTL from 18-weeks to full-term. In the placenta, TIFs correlated with short telomeres but not mTL. CAMs of preterm birth pregnancies with intra-amniotic infection showed shorter mTL and increased proportions of short telomeres. We conclude that the placenta and probably the CAMs undergo TL-mediated replicative aging. Further research is warranted whether TL-mediated replicative aging plays a role in all preterm births.

Preoperative cystoscopy could determine the severity of placenta accreta spectrum disorders: An observational study.

AIM: In the surgical treatment of placenta accreta spectrum disorders, cystoscopy for prophylactic stent placement is performed to protect the ureters from potential injury. Despite its frequent use, the use of cystoscopy in assessing the severity of these disorders has not been explored. Our objective was to find out if the abnormal findings documented during cystoscopy are associated with disease severity. METHODS: In this retrospective, observational cohort study (n = 56), the bladder wall was evaluated at the time of ureteral stent placement via cystoscopy in prenatally diagnosed placenta accreta spectrum cases. Three abnormal findings were commonly present in these cases: bulging of the posterior bladder wall, neovascularization and arterial pulsatility in the area of neovascularization. These findings were stratified according to severity in histologically confirmed specimens. Continuous variables were compared via two-tailed t-tests and Wilcoxon rank sum tests. Categorical data were evaluated using logistic regression analysis. RESULTS: Neovascularization affected 84%, bulging 71% and pulsatility 54% of the cases. Bulging and neovascularization increased with disease severity. Pulsatility occurred exclusively in percretas. Bulging was associated with a 12-fold (OR = 11.6, 95% CI 2.94-46.33, P = 0.0005) increased likelihood of percreta and neovascularization with a 17-fold (OR = 17.06, 95% CI 2.98-97.79, P = 0.0014) increase. Neovascularization and/or the presence of bulging of the bladder have high positive predictive value for placenta increta and percreta (91.5% and 95.0%, respectively). Cystoscopy can be used to assess the severity of placenta accreta spectrum cases preoperatively, especially when placentation is over the previous uterine scar and is in proximity to the bladder wall.

Genital tract GBS and rate of histologic chorioamnionitis in patients with preterm premature rupture of membrane.

INTRODUCTION: Histologic chorioamnionitis (HC) is a common finding in the placenta from patients with preterm premature rupture of membranes (PPROM). The purpose of this study is to determine if HC differs based on the Group B streptococcus (GBS) status in patients managed expectantly with PPROM <34 weeks gestation. METHODS: A retrospective study was performed of patients admitted with PPROM between 23 0/7 and 33 6/7 weeks from 2003 to 2014 at one institution. Patients were excluded if in labor, evidence of clinical chorioamnionitis, nonreassuring fetal status, multifetal gestation, HIV positive, or if GBS specimens or placental histology were not available. Placental pathology results were compared using Fisher's exact test. RESULTS: One hundred eighty-one patients met inclusion criteria and 55 (30.3%) were GBS positive. The prevalence of HC did not differ between the GBS positive and GBS negative groups (69 versus 64.2%, respectively; p = .62). Clinical chorioamnionitis, endomyometritis, wound infection, maternal and neonatal sepsis did not differ between the two groups. CONCLUSIONS: Vaginal-rectal colonization with GBS on admission does not appear to affect the rate of HC nor neonatal outcome in patients managed conservatively with PPROM <34 weeks gestation.

Telomere length dynamics in early life: the blood-and-muscle model.

Telomere length (TL) trajectories in somatic tissues during human growth and development are poorly understood. We examined a blood-and-muscle model during early life, focusing on TL trajectories in leukocytes, representing the highly proliferative hematopoietic system, and skeletal muscle, a minimally proliferative tissue. Leukocyte TL (LTL) and skeletal muscle TL (MTL) were measured in 28 fetuses and 73 children. LTL and MTL were highly variable across individuals (sd: fetal LTL = 0.72 kb, MTL = 0.72 kb; children LTL = 0.81 kb, MTL = 0.82 kb) but were highly correlated within individuals (fetuses, r = 0.76, P < 0.0001; children, r = 0.87, P < 0.0001). LTL was shorter than MTL in fetuses (10.63 vs. 11.01 kb; P = 0.0004) and children (8.46 vs. 9.40 kb; <0.0001). The LTL-MTL gap was smaller in fetuses than children. TL in children was inversely correlated with body mass index (BMI) (LTL: -0.047 ± 0.016 kb/BMI, P < 0.005; MTL: -0.037 ± 0.017 kb/BMI, P = 0.03). We conclude that variations in TL across adults and differences in TL between somatic tissues are largely established in early life. Because TL plays a significant role in aging-related diseases, insight into the factors that fashion TL in somatic tissues during early development should contribute to an understanding of the relationship of TL with these disease and longevity in humans.-Sabharwal, S., Verhulst, S., Guirguis, G., Kark, J. D., Labat, C., Roche, N. E., Martimucci, K., Patel, K., Heller, D. S., Kimura, M., Chuang, D., Chuang, A., Benetos, A., Aviv, A. Telomere length dynamics in early life: the blood-and-muscle model.

Salmonella enterica Serotype Typhi Bacteremia Complicating Pregnancy in the Third Trimester.

Background. Salmonella enterica serotype Typhi (S. Typhi) is an anaerobic gram-negative enteric rod that causes infection when contaminated food or water is ingested and may cause illness in pregnancy. Case. This is a patient who presented at 31 weeks' gestation with abdominal pain and fever and was diagnosed with S. Typhi bacteremia. Conclusion. S. Typhi should be considered in febrile patients with recent travel presenting with abdominal discomfort with or without elevated liver enzymes.

Is there an association between assisted reproductive technologies and time and complications of the third stage of labor?

PURPOSE: To determine if vaginal deliveries exposed to assisted reproductive technologies (ART) are associated with an increased time between delivery of the neonate and placenta and select complications. METHODS: A retrospective cohort of patients enrolled in an infertility practice who had term, singleton, vaginal deliveries at two academic hospitals from 2008 to 2013 was analyzed. Controls were patients with spontaneous conceptions after infertility consultations. The exposure groups were patients with controlled ovarian hyper-stimulation (COH) with in vivo fertilization, COH with in vitro fertilization and fresh embryo transfer (COH/IVF), and frozen embryo transfer or oocyte donation recipients without COH (non-COH ET). Multiple gestations and stillbirths were excluded. Median time of third stage was compared using the Mann-Whitney U test. Secondary outcomes of retained placenta, manual placental extraction, and post-partum hemorrhage (PPH) were compared using Chi-square or Fisher's exact analyses. RESULTS: A total of 769 patients met criteria and were analyzed. While there were no differences in time of third stage of labor, retained placenta, or PPH, manual extraction was significantly more common among non-COH ET [age-adjusted OR 5.6 (95 % CI 2.2-13.8); p < 0.001]. CONCLUSIONS: Patients who conceived after non-COH ET were at increased risk for manual placental extraction. This association was not influenced by age differences between groups. Further research must be done to determine which elements of the ART process are responsible for these differences.

Is preeclampsia an independent predictor of diastolic dysfunction? A retrospective cohort study.

OBJECTIVE: To determine if preeclampsia is an independent predictor of diastolic dysfunction and what factors among patients with preeclampsia are associated with diastolic dysfunction. METHODS: This is a retrospective cohort study of patients who delivered between 2008 and 2013 at a single institution who had a maternal echocardiogram during their pregnancy or within 5months of delivery. Patients with structural heart disease, ejection fraction less than 45%, pulmonary embolus, or age over 45years were excluded. Medical records were reviewed for medical and obstetric complications and echocardiogram findings. Demographic characteristics and rate of diastolic dysfunction were compared between patients with preeclampsia and without preeclampsia. Multivariate logistic regression was performed controlling for age, ethnicity, gestational age at delivery, diabetes, preeclampsia, intrauterine growth restriction (IUGR), antihypertensive use and magnesium sulfate administration. RESULTS: Sixty-six patients were identified, of which 39 (59%) had preeclampsia. Past history of preeclampsia, IUGR in the current pregnancy, antihypertensive use and magnesium sulfate use were higher in the preeclampsia group. Fifteen patients (39%) in the preeclampsia group were African-American compared to 2 (3%) in the control group (p<0.01). Seventeen (44%) of the patients with preeclampsia were found to have diastolic dysfunction compared to 3 (11%) controls (OR=6.18, 95% CI 1.59,24.02; p=0.006). Logistic regression analysis did not reveal other independent predictors of diastolic dysfunction. In the patients with preeclampsia, history of preeclampsia with severe features and IUGR were not associated with diastolic dysfunction. CONCLUSIONS: Our study supports previous findings that preeclampsia is associated with diastolic dysfunction.