Noninvasive Prenatal Diagnosis of Fetal RHD Status Using Cell-free Fetal DNA in Maternal Plasma.

Background: The main cause of hemolytic disease of the fetus and newborn (HDFN) is the incompatibility of the RHD antigen between mother and fetus. Following the discovery of cell-free fetal DNA (cffDNA), noninvasive fetal RHD genotyping also became possible, which will help in the better management of immunized RHD negative mothers and in the targeted prenatal injection of Rho(D) immune globulin (RhIG). The objective of this study was to establish a reliable method with high accuracy to determine the fetal RHD genotype. Methods: The project was a prospective observational cohort study. After cell-free DNA (cfDNA) extraction from maternal plasma, fetal RHD genotyping was performed by duplex real-time polymerase chain reaction (PCR) and exons 5, 7, and 10 of the RHD gene were examined. SRY and RASSF1A genes were used as internal controls to confirm the presence of cffDNA in maternal plasma. Results: Out of 40 samples, 33 were RhD positive heterozygous mothers and 7 cases were RHD negative. In three cases where both the fetal RHD and SRY genotypes were negative, RASSF1A was amplified in cell-free DNA sample treated with the BstUI enzyme, and the presence of cffDNA was confirmed. Conclusion: The findings reveal that the strategy used in this study is reliable and it is possible to determine the fetal RHD status with high accuracy. The strategy can help targeted injection of RhIG and prevent unnecessary injection in RhD negative mothers who carry an RhD negative fetus.

QuCo: quartet-based co-estimation of species trees and gene trees.

MOTIVATION: Phylogenomics faces a dilemma: on the one hand, most accurate species and gene tree estimation methods are those that co-estimate them; on the other hand, these co-estimation methods do not scale to moderately large numbers of species. The summary-based methods, which first infer gene trees independently and then combine them, are much more scalable but are prone to gene tree estimation error, which is inevitable when inferring trees from limited-length data. Gene tree estimation error is not just random noise and can create biases such as long-branch attraction. RESULTS: We introduce a scalable likelihood-based approach to co-estimation under the multi-species coalescent model. The method, called quartet co-estimation (QuCo), takes as input independently inferred distributions over gene trees and computes the most likely species tree topology and internal branch length for each quartet, marginalizing over gene tree topologies and ignoring branch lengths by making several simplifying assumptions. It then updates the gene tree posterior probabilities based on the species tree. The focus on gene tree topologies and the heuristic division to quartets enables fast likelihood calculations. We benchmark our method with extensive simulations for quartet trees in zones known to produce biased species trees and further with larger trees. We also run QuCo on a biological dataset of bees. Our results show better accuracy than the summary-based approach ASTRAL run on estimated gene trees. AVAILABILITY AND IMPLEMENTATION: QuCo is available on https://github.com/maryamrabiee/quco. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SODA: multi-locus species delimitation using quartet frequencies.

MOTIVATION: Species delimitation, the process of deciding how to group a set of organisms into units called species, is one of the most challenging problems in computational evolutionary biology. While many methods exist for species delimitation, most based on the coalescent theory, few are scalable to very large datasets, and methods that scale tend to be not accurate. Species delimitation is closely related to species tree inference from discordant gene trees, a problem that has enjoyed rapid advances in recent years. RESULTS: In this article, we build on the accuracy and scalability of recent quartet-based methods for species tree estimation and propose a new method called SODA for species delimitation. SODA relies heavily on a recently developed method for testing zero branch length in species trees. In extensive simulations, we show that SODA can easily scale to very large datasets while maintaining high accuracy. AVAILABILITY AND IMPLEMENTATION: The code and data presented here are available on https://github.com/maryamrabiee/SODA. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A comparison of the effects of Two suture materials on isthmocele formation: A cohort study.

OBJECTIVE: Cesarean scar defects (CSD) are a problem that may lead to complications and excessive cost. The optimal way to suture the uterus is a matter of debate. The aim of this study was to evaluate the effect of two suture materials on cesarean scar niches. STUDY DESIGN: This was a cohort study that allocated women into two groups: uterotomy closure with vicryl or catgut sutures. Transvaginal ultrasound (TVUS) was performed six months after the cesarean section (CS) to assess the scar. RESULTS: Totally, 250 patients enrolled in this study. After six months, 20 (18.2 %) patients in the catgut suture group and 13 (9.3 %) patients in the vicryl group had isthmocele according to their sonography reports. The prevalence of isthmocele was higher in the catgut group (p = 0.03). The residual myometrial thickness was greater in the vicryl group (4.98 cm ± 2.18) compared to the catgut suture group (3.70 cm ± 1.50; p = 0.001). The prevalence of postoperative gynecological sequelae such as postmenstrual spotting and pain were similar between the two groups. CONCLUSION: Vicryl sutures were associated with a lower risk of CSD formation in comparison with catgut sutures.

Forcing external constraints on tree inference using ASTRAL.

BACKGROUND: To account for genome-wide discordance among gene trees, several widely-used methods seek to find a species tree with the minimum distance to input gene trees. To efficiently explore the large space of species trees, some of these methods, including ASTRAL, use dynamic programming (DP). The DP paradigm can restrict the search space, and thus, ASTRAL and similar methods use heuristic methods to define a restricted search space. However, arbitrary constraints provided by the user on the output tree cannot be trivially incorporated into such restrictions. The ability to infer trees that honor user-defined constraints is needed for many phylogenetic analyses, but no solution currently exists for constraining the output of ASTRAL. RESULTS: We introduce methods that enable the ASTRAL dynamic programming to infer constrained trees in an effective and scalable manner. To do so, we adopt a recently developed tree completion algorithm and extend it to allow multifurcating input and output trees. In simulation studies, we show that the approach for honoring constraints is both effective and fast. On real data, we show that constrained searches can help interrogate branches not recovered in the optimal ASTRAL tree to reveal support for alternative hypotheses. CONCLUSIONS: The new algorithm is added ASTRAL to all user-provided constraints on the species tree.

Noninvasive Fetal Sex Determination by Real-Time PCR and TaqMan Probes.

BACKGROUND: Noninvasive fetal sex determination by analyzing Y chromosome-specific sequences is very useful in the management of cases related to sex-linked genetic diseases. The aim of this study was to establish a non-invasive fetal sex determination test using Real-Time PCR and specific probes. METHODS: The study was a prospective observational cohort study conducted from August 2018 to September 2019. Venous blood samples were collected from 25 Iranian pregnant women at weeks 7 to 25 of gestation. Cell-free DNA (cfDNA) was isolated from the plasma of samples and fetal sex was determined by SRY gene analysis using the Real-Time PCR technique. In the absence of SRY detection, the presence of fetal DNA was investigated using cfDNA treated with BstUI enzyme and PCR for the epigenetic marker RASSF1A. RESULTS: Of the total samples analyzed, 48% were male and 52% female. The RASSF1A assay performed on SRY negative cases also confirmed the presence of cell-free fetal DNA. Genotype results were in full agreement with neonate gender, and the accuracy of noninvasive fetal sex determination was 100%. CONCLUSION: Fetal sex determination using the strategy applied in this study is noninvasive and highly accurate and can be exploited in the management of sex-linked genetic diseases.

INSTRAL: Discordance-Aware Phylogenetic Placement Using Quartet Scores.

Phylogenomic analyses have increasingly adopted species tree reconstruction using methods that account for gene tree discordance using pipelines that require both human effort and computational resources. As the number of available genomes continues to increase, a new problem is facing researchers. Once more species become available, they have to repeat the whole process from the beginning because updating species trees is currently not possible. However, the de novo inference can be prohibitively costly in human effort or machine time. In this article, we introduce INSTRAL, a method that extends ASTRAL to enable phylogenetic placement. INSTRAL is designed to place a new species on an existing species tree after sequences from the new species have already been added to gene trees; thus, INSTRAL is complementary to existing placement methods that update gene trees. [ASTRAL; ILS; phylogenetic placement; species tree reconstruction.].

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.

Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer "core" genes, such as the ribosomal proteins. The robustness of the results was tested with respect to several variables, including taxon and site sampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, and the impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide an updated view of domain-level relationships.

Knowledge of Prenatal Screening, Down Syndrome, Amniocentesis, and Related Factors among Iranian Pregnant Women: A Cross-Sectional Study.

BACKGROUND: The primary goal of prenatal aneuploidy screening is the early detection of pregnancies at high risk of Down syndrome (DS). The present study aimed to assess the knowledge about the prenatal screening test (PST), DS, and amniotic fluid test (AFT) among Iranian pregnant women. METHODS: The present cross-sectional study was conducted from April 2013 to July 2014 in Mostafa Khomeini Educational Hospital, Tehran, Iran. The participants were recruited among pregnant women referred to the Obstetrics and Gynecology Clinic of the hospital for their routine medical evaluations. A total of 471 consecutive women fulfilling the inclusion criteria were enrolled in the study. The data collection instruments included a 9-item socio-demographic information form and a 23-item knowledge questionnaire. The latter included 9 items on DS, 10 items on PST, and 4 items on AFT. The data were analyzed using the SPSS software (version 20.0) with the Kruskal-Wallis and Mann-Whitney tests. P<0.05 was considered statistically significant. RESULTS: The mean score of total knowledge, PST, DS, and AFT was 9.93±4.86, 5.26±2.19, 3.25±2.42, and 1.41±1.39, respectively. There was a significant correlation between the mean score of total knowledge and the age of the mother (P=0.019), gestational age (P=0.001), educational level of the mother and spouse (P=0.001), history of birth abnormality (P=0.03), history of birth abnormality in the family (P=0.02), and sources of information (P=0.001). CONCLUSION: The results showed that the mean score of knowledge in pregnant women was less than half of the total scores, and total score was related to various parameters. Intervention factors that could contribute to improved knowledge and informed decision-making among pregnant women should be considered.

Multi-allele species reconstruction using ASTRAL.

Genome-wide phylogeny reconstruction is becoming increasingly common, and one driving factor behind these phylogenomic studies is the promise that the potential discordance between gene trees and the species tree can be modeled. Incomplete lineage sorting is one cause of discordance that bridges population genetic and phylogenetic processes. ASTRAL is a species tree reconstruction method that seeks to find the tree with minimum quartet distance to an input set of inferred gene trees. However, the published ASTRAL algorithm only works with one sample per species. To account for polymorphisms in present-day species, one can sample multiple individuals per species to create multi-allele datasets. Here, we introduce how ASTRAL can handle multi-allele datasets. We show that the quartet-based optimization problem extends naturally, and we introduce heuristic methods for building the search space specifically for the case of multi-individual datasets. We study the accuracy and scalability of the multi-individual version of ASTRAL-III using extensive simulation studies and compare it to NJst, the only other scalable method that can handle these datasets. We do not find strong evidence that using multiple individuals dramatically improves accuracy. When we study the trade-off between sampling more genes versus more individuals, we find that sampling more genes is more effective than sampling more individuals, even under conditions that we study where trees are shallow (median length: ≈1Ne) and ILS is extremely high.

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees.

BACKGROUND: Evolutionary histories can be discordant across the genome, and such discordances need to be considered in reconstructing the species phylogeny. ASTRAL is one of the leading methods for inferring species trees from gene trees while accounting for gene tree discordance. ASTRAL uses dynamic programming to search for the tree that shares the maximum number of quartet topologies with input gene trees, restricting itself to a predefined set of bipartitions. RESULTS: We introduce ASTRAL-III, which substantially improves the running time of ASTRAL-II and guarantees polynomial running time as a function of both the number of species (n) and the number of genes (k). ASTRAL-III limits the bipartition constraint set (X) to grow at most linearly with n and k. Moreover, it handles polytomies more efficiently than ASTRAL-II, exploits similarities between gene trees better, and uses several techniques to avoid searching parts of the search space that are mathematically guaranteed not to include the optimal tree. The asymptotic running time of ASTRAL-III in the presence of polytomies is [Formula: see text] where D=O(nk) is the sum of degrees of all unique nodes in input trees. The running time improvements enable us to test whether contracting low support branches in gene trees improves the accuracy by reducing noise. In extensive simulations, we show that removing branches with very low support (e.g., below 10%) improves accuracy while overly aggressive filtering is harmful. We observe on a biological avian phylogenomic dataset of 14K genes that contracting low support branches greatly improve results. CONCLUSIONS: ASTRAL-III is a faster version of the ASTRAL method for phylogenetic reconstruction and can scale up to 10,000 species. With ASTRAL-III, low support branches can be removed, resulting in improved accuracy.

The Adverse Effects of Pregnancies Complicated by Hemoglobin H (HBH) Disease.

Hemoglobin (Hb) H disease is a moderate form of α- thalassemia resulting from various genetic defects. HbH disease is not necessarily a benign disorder as has been generally thought. We present hereby a 25- year-old Iranian pregnant woman whom referred to our hospital for blood transfusion. She exhibited the clinical and hematological manifestation of HbH disease. Her father carries a common α-thalassemia deletion while her mother was normal in the hematological profile. The object of this report was to provide information about pregnancies affected by HbH disease.

Measurement of nitrite and nitrate in saliva of children with different caries activity.

OBJECTIVE OF THE STUDY: Recently, there has been growing interest in the role of salivary nitrate and nitrite in caries protection. Nitrate is a natural compound found in fruits and vegetables and when secreted in saliva, is reduced to nitrite through bacterial respiration and subsequently reduced to nitric oxide in acidic condition. Nitric oxide takes part in oral non-specific immune system and prevents bacterial growth. The aim of present study was to determine the concentration of nitrite and nitrate in saliva of children with different caries activity. MATERIALS AND METHODS: Ninety three children, 4 to 6 years old, enrolled in this case-control study and were divided into 3 groups; 31 caries free children, 31 with 5 10. Unstimulated saliva was collected and stored in 4°C. Measurement of nitrate and nitrite concentration was performed using Griess reaction. Data were analyzed by T-test, Chi-square, ANOVA and multiple comparisons using SPSS 18. p < 0.05 was considered significant. RESULTS: Mean value of DFS in the first, second and third were 0, 7.12 and 12.61 respectively. Mean value of nitrite and nitrate in the third group was significantly higher than two others (p < 0.05), but the difference between first and second group was not significant. CONCLUSION: Increase in DFS was associated by increase in salivary nitrite and nitrate concentration. CLINICAL SIGNIFICANCE: High concentration of nitrate and nitrite is not enough for caries prevention.