MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection.

SUMMARY: DNA methylation patterns in a cell are associated with gene expression and the phenotype of a cell, including disease states. Bisulphite PCR sequencing is commonly used to assess the methylation profile of genomic regions between different cells. Here we have developed MethPanel, a computational pipeline with an interactive graphical interface to rapidly analyse multiplex bisulphite PCR sequencing data. MethPanel comprises a complete analysis workflow from genomic alignment to DNA methylation calling and supports an unlimited number of PCR amplicons and input samples. MethPanel offers important and unique features, such as calculation of an epipolymorphism score and bisulphite PCR bias correction capabilities, and is designed so that the methylation data from all samples can be processed in parallel. The outputs are automatically forwarded to a shinyApp for convenient display, visualization and remotely sharing data with collaborators and clinicians. AVAILABILITYAND IMPLEMENTATION: MethPanel is freely available at https://github.com/thinhong/MethPanel. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

HLA-DRB1 and DQB1 genetic susceptibility to pemphigus vulgaris and pemphigus foliaceus in Vietnamese patients.

Pemphigus is a group of rare, lifethreatening bullous autoimmune diseases that affect the skin and mucous membranes and are associated with high morbidity and morbidity. HLA class II genes, particularly HLA-DRB1 and HLA-DQB1, play roles in pemphigus. The aim of this paper is to investigate the susceptibility of HLA class II DRB1 and DQB1 alleles in Vietnamese patients with pemphigus vulgaris (PV) or pemphigus foliaceus (PF). The study enrolled 31 participants (22 with PV, 9 with PF) with diagnoses confirmed by clinical manifestations, histopathology, and direct immunofluorescence from November 2019 to June 2020. The HLA polymorphisms were determined by Sanger sequencing. The HLA-DRB1 and HLA-DQB1 profiles of the 101 healthy individuals in the control group have been published previously. The frequencies of HLA-DRB1*14, DRB1*13:07, DRB1*04:04, DRB1*03:02, DQB1*02:02, and DQB1*05:03 were significantly higher, whereas those of DRB1*09:01, DRB1*12:02, DQB1*03:03, DQB1*05:01, and DQB1*06:01 were significantly lower, in the PV group than in the controls. The frequencies of DRB1*14:54, DRB1*13:07, and HLA-DQB1*03:02 were significantly higher in the PF group than in the controls. Alleles HLA-DRB1*14:54, DRB1*14:04, DRB1*14:03, DRB1*14:01, DRB1*14:12, DRB1*13:07, DRB1*04:04, DRB1*03:02, DQB1*02:02, and DQB1*05:03 were associated with an increased risk of PV, whereas alleles DRB1*09:01, DRB1*12:02, DQB1*03:03, DQB1*05:01, and DQB1*06:01 might protect against PV. In PF, DRB1*14:54, DRB1*13:07, and HLA-DQB1*03:02 are promising susceptibility alleles.

Fresh versus elective frozen embryo transfer: Cumulative live birth rates of 7,236 IVF cycles.

OBJECTIVE: To determine whether elective frozen embryo transfer (eFET), or the 'freeze-all' strategy, associated with better cumulative clinical outcomes compared with fresh embryo transfer (ET). METHODS: A total of 7,236 IVF cycles that were followed by a fresh ET or eFET between 2013 and 2017. The patients were subjected to controlled ovarian stimulation (COS) with a gonadotropin-releasing hormone (GnRH) antagonist protocol and cleavage-stage ET. Embryo cryopreservation was performed on day 3 by vitrification using an open system. A comparison of cumulative outcomes between the eFET (n=4,065cycles) and the fresh ET groups (n=3,171cycles) were performed. The analysis was performed in four groups of patients based on the number of retrieved oocytes: Group 1: poor responders (1-3 oocytes); Group 2: suboptimal responders (4-9 oocytes); Group 3: normal responders (10-15 oocytes); and Group 4: hyper-responders (>15 oocytes). The primary outcome was the cumulative live birth rate (CLBR) per stimulated cycle. RESULTS: There were a total of 10,283 ETs (n=5,639 eFET group; n=4,644 fresh group). The freeze-all strategy is associated with improved CLBRs in normal and hyper-responders, but not in suboptimal and poor responders. In Group 1, there were 351 IVF cycles and 387 ETs in total, and the CLBR was 14.3% and 17.7% (p=0.584) for the eFET and fresh group, respectively. In Group 2, there were 2,074 IVF cycles and 2,465 ET in total, and the CLBR was 25.1% and 23.3% (p=0.083) in the eFET and fresh group, respectively. There was a significant difference in the CLBR in Groups 3 and 4, favouring the eFET strategy. In Group 3, 2226 IVF cycles and 3243 ET were performed. The CLBR was 40.5% in the eFET and 36.6% in the fresh group (p<0.001). In Group 4, there were 2547 IVF cycles and 3,188 ET in total, and the CLBR was 52.2% and 47.7% (p<0.001) in the eFET and fresh group, respectively. The number needed to treat to achieve one additional live birth was 25.9 in Group 3 and 22.3 in Group 4. CONCLUSIONS: The implementation of the freeze-all strategy should be individualized. The freeze-all strategy is associated with improved CLBRs in normal and hyper-responders, but not in suboptimal and poor responders.

Effectiveness of progesterone supplementation in women presenting low progesterone levels on the day of frozen embryo transfer: a randomised controlled trial.

INTRODUCTION: Progesterone is an essential hormone involved in the process of implantation and pregnancy maintenance. Evidence from recent studies has supported the importance of serum progesterone level around the time of embryo transfer in hormonal replacement therapy frozen embryo transfer cycles and recommended the need for individualised luteal support. Low progesterone around the time of embryo transfer is found to be associated with decreased rate of pregnancy after frozen embryo transfer. This single-centre, longitudinal, randomised, interventional controlled study aims to compare the rate of ongoing pregnancy between two groups of women with progesterone level below 10 ng/mL on the day of frozen embryo transfer: the study group using 800 mg vaginal micronised progesterone supplemented with 50 mg intramuscular progesterone per day and the control group using only 800 mg vaginal micronised progesterone. METHODS AND ANALYSIS: We enrol patients who are undergoing frozen embryo transfers with blastocyst-stage or cleavage-stage embryos and who satisfy the inclusion and exclusion criteria. After signing the informed consent, participants are randomised into two groups: the study group using vaginal micronised progesterone supplemented with progesterone intramuscular 50 mg per day and the control group using only vaginal micronised progesterone. Randomisation will be performed using R software at a 1:1 allocation ratio. Sequentially numbered, opaque sealed envelopes are used for allocation. The primary outcome is the rate of ongoing pregnancy. To demonstrate a difference of 10% with regard to rate of ongoing pregnancy, at least 370 participants per arm are required (type I error α=0.05, power=0.8). Assuming a dropout rate of 10%, a total of 824 patients (412 per group) will be invited. ETHICS AND DISSEMINATION: This study was approved by the Ethics Committee of Tu Du Hospital on 17 May 2021 (reference number: 1251/QD-BVTD). All participants provide informed consent before being enrolled in the study. The results of our study will be submitted to reproductive medicine conferences and journals. TRIAL REGISTRATION NUMBER: NCT04897269.

Diabetes-Related Distress Among People with Type 2 Diabetes in Ho Chi Minh City, Vietnam: Prevalence and Associated Factors.

BACKGROUND: Diabetes-related distress (DRD) refers to the condition of negative emotion as a result of living with diabetes and the burden of self-care. This study aims to evaluate the prevalence and associated factors of DRD among people with type 2 diabetes. METHODS: A cross-sectional study was carried out on people with Type 2 Diabetes at three hospitals in Ho Chi Minh City, between April and November 2020. The study used the Vietnamese version of the Diabetes Distress Scale (DDS) which includes 17 items. The mean total distress score was calculated on the average of the 17 items. A mean score of equal to 2.0 or higher was classified as moderate to severe distress. Descriptive statistics were performed by frequency and percentage, and the multivariate Logistic Regression Analysis was used to assess information where p-value <0.05 was considered statistically significant. RESULTS: A total of 517 participants, who were mainly over 60 years old (56.8%) with females being 65.0%, participated in the study. Results showed that 23.6% and 5.8% of them, respectively, were found as being moderately or highly distressed. Some factors that correlated with the total distress results included age, timescale of diabetes, and glycemic control level (HbA1c). The rate of total distress in those who were over 60 years old and had a HbA1c <7 were less prevalent than those who were under 60, and had a HbA1c ≥7 (OR 0.5 95% CI 0.3-0.7; OR 0.5 95% CI: 0.3-0.9, respectively, all p<0.05), whilst the timescale of diabetes between 5 and 10 years was significantly more prevalent than those who had a timescale less 5 years (OR 1.8 95% CI 1.1-2.9, p<0.05). CONCLUSION: A high rate of distress exists in people with diabetes. Therefore, combining the evaluation of distress as part of the regular diagnostic procedures of diabetes care, and recommending physicians apply a comprehensive approach to diabetes management, is necessary.

Benchmark study comparing liftover tools for genome conversion of epigenome sequencing data.

As reference genome assemblies are updated there is a need to convert epigenome sequence data from older genome assemblies to newer versions, to facilitate data integration and visualization on the same coordinate system. Conversion can be done by re-alignment of the original sequence data to the new assembly or by converting the coordinates of the data between assemblies using a mapping file, an approach referred to as 'liftover'. Compared to re-alignment approaches, liftover is a more rapid and cost-effective solution. Here, we benchmark six liftover tools commonly used for conversion between genome assemblies by coordinates, including UCSC liftOver, rtracklayer::liftOver, CrossMap, NCBI Remap, flo and segment_liftover to determine how they performed for whole genome bisulphite sequencing (WGBS) and ChIP-seq data. Our results show high correlation between the six tools for conversion of 43 WGBS paired samples. For the chromatin sequencing data we found from interval conversion of 366 ChIP-Seq datasets, segment_liftover generates more reliable results than USCS liftOver. However, we found some regions do not always remain the same after liftover. To further increase the accuracy of liftover and avoid misleading results, we developed a three-step guideline that removes aberrant regions to ensure more robust genome conversion between reference assemblies.

Clinical prognostic models for severe dengue: a systematic review protocol.

Background: Dengue is a common mosquito-borne, with high morbidity rates recorded in the annual. Dengue contributes to a major disease burden in many tropical countries. This demonstrates the urgent need in developing effective approaches to identify severe cases early. For this purpose, many multivariable prognostic models using multiple prognostic variables were developed to predict the risk of progression to severe outcomes. The aim of the planned systematic review is to identify and describe the existing clinical multivariable prognostic models for severe dengue as well as examine the possibility of combining them. These findings will suggest directions for further research of this field. Methods: This protocol has followed the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta - Analyses Protocol (PRISMA-P). We will conduct a comprehensive search of Pubmed, Embase, and Web of Science. Eligibility criteria include being published in peer-review journals, focusing on human subjects and developing the multivariable prognostic model for severe dengue, without any restriction on language, location and period of publication, and study design. The reference list will be captured and removed from duplications. We will use the Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modelling Studies (CHARMS) checklist to extract data and Prediction study risk of bias assessment tool (PROBAST) to assess the study quality. Discussion: This systematic review will describe the existing prediction models, summarize the current status of prognostic research on dengue, and report the possibility to combine the models to optimize the power of each paradigm. PROSPERO registration: CRD42018102907.