Improvement in neoantigen prediction via integration of RNA sequencing data for variant calling

IntroductionNeoantigen-based immunotherapy has emerged as a promising strategy for improving the life expectancy of cancer patients. This therapeutic approach heavily relies on accurate identification of cancer mutations using DNA sequencing (DNAseq) data. However, current workflows tend to provide a large number of neoantigen candidates, of which only a limited number elicit efficient and immunogenic T-cell responses suitable for downstream clinical evaluation. To overcome this limitation and increase the number of high-quality immunogenic neoantigens, we propose integrating RNA sequencing (RNAseq) data into the mutation identification step in the neoantigen prediction workflow.MethodsIn this study, we characterize the mutation profiles identified from DNAseq and/or RNAseq data in tumor tissues of 25 patients with colorectal cancer (CRC). Immunogenicity was then validated by ELISpot assay using long synthesis peptides (sLP).ResultsWe detected only 22.4% of variants shared between the two methods. In contrast, RNAseq-derived variants displayed unique features of affinity and immunogenicity. We further established that neoantigen candidates identified by RNAseq data significantly increased the number of highly immunogenic neoantigens (confirmed by ELISpot) that would otherwise be overlooked if relying solely on DNAseq data.DiscussionThis integrative approach holds great potential for improving the selection of neoantigens for personalized cancer immunotherapy, ultimately leading to enhanced treatment outcomes and improved survival rates for cancer patients

The influence of human genetic variation on early transcriptional responses and protective immunity following immunization with Rotarix vaccine in infants in Ho Chi Minh City in Vietnam : a study protocol for an open single-arm interventional trial [awaiting peer review]

Background: Rotavirus (RoV) remains the leading cause of acute gastroenteritis in infants and children aged under five years in both high- and low-middle-income countries (LMICs). In LMICs, RoV infections are associated with substantial mortality. Two RoV vaccines (Rotarix and Rotateq) are widely available for use in infants, both of which have been shown to be highly efficacious in Europe and North America. However, for unknown reasons, these RoV vaccines have markedly lower efficacy in LMICs. We hypothesize that poor RoV vaccine efficacy across in certain regions may be associated with genetic heritability or gene expression in the human host. Methods/design: We designed an open-label single-arm interventional trial with the Rotarix RoV vaccine to identify genetic and transcriptomic markers associated with generating a protective immune response against RoV. Overall, 1,000 infants will be recruited prior to Expanded Program on Immunization (EPI) vaccinations at two months of age and vaccinated with oral Rotarix vaccine at two and three months, after which the infants will be followed-up for diarrheal disease until 18 months of age. Blood sampling for genetics, transcriptomics, and immunological analysis will be conducted before each Rotarix vaccination, 2-3 days post-vaccination, and at each follow-up visit (i.e. 6, 12 and 18 months of age). Stool samples will be collected during each diarrheal episode to identify RoV infection. The primary outcome will be Rotarix vaccine failure events (i.e. symptomatic RoV infection despite vaccination), secondary outcomes will be antibody responses and genotypic characterization of the infection virus in Rotarix failure events. Discussion: This study will be the largest and best powered study of its kind to be conducted to date in infants, and will be critical for our understanding of RoV immunity, human genetics in the Vietnam population, and mechanisms determining RoV vaccine-mediated protection. Registration: ClinicalTrials.gov, ID: NCT03587389. Registered on 16 July 2018

Patients’ perspectives and experiences of patient-centered care in some communes of Thua Thien Hue Province

Patient-centered care is widely acknowledged as an important goal in healthcare delivery. Research has demonstrated that patient perceptions of patient-centred care can be linked to clinical and long-term outcomes in addition to being a useful metric for quality improvement efforts. Objectives: 1) To identify patients' perspectives and experiences of patient-centered care in some communes in Thua Thien Hue province; 2) To determine the association between the patients' perspectives, experiences on patient-centered care and utilization of the health services. Methods: A cross sectional descriptive study was conducted in 313 patients living in Thua Thien Hue province. A structured questionnaire was used to investigate 4 main domains of patient-centered care: Information and Education, Relationships with doctors and other health professionals, making decisions, motivating patients about self-management. We used ANOVA test to analyze the association between patient-centered care and health care utilization among participants (p < 0.05). Results: The percentage of good patient-centered care (≥ 3.75 points) was 43.1% (Mean = 3.58 (0.57)). Patients using health services at the commune health centers had a higher experience in patient-centered care compared to district, province and central hospital (p < 0.005). Domains “Encourage patients to take care of themselves” and “Relationship factor with doctors” were evaluated low. There were significant associations between patient-centered care and primary health care facilities, quality of life utilization of periodic health checkup, and patient activation in health care (p < 0.05). Conclusion: Out study illustrates that patients' perspectives and experiences of patient-centered care are still low. There is a need to improve communication and counseling skills of health care providers and increase patient motivation for self-car

Early Essential Newborn Care Is Associated With Reduced Adverse Neonatal Outcomes in a Tertiary Hospital in Da Nang, Viet Nam: A Pre- Post- Intervention Study

Background: To accelerate reductions in neonatal mortality, Viet Nam rolled out early essential newborn care (EENC) using clinical coaching, quality improvement assessments in hospitals, and updated protocols. Da Nang Hospital for Women and Children, a tertiary referral hospital in central Viet Nam, compared outcomes pre- and post-EENC introduction. Methods: Records of live births and NICU admissions were reviewed pre- (November 2013–October 2014) and post- (November 2014–October 2015) EENC implementation. Delivery room practices, NICU admissions and adverse outcomes on NICU admission were compared using descriptive statistics. Findings: A total of 13,201 live births were delivered pre- and 14,180 live births post-EENC introduction. Post-EENC, delivery practice scores, rates of early and prolonged skin-to-skin contact and early breastfeeding rose significantly. There was a significant reduction in risk of NICU admissions (relative risk [RR] 0.68; 95% confidence interval [CI] 0.64–0.71; p < 0.0001), hypothermia on NICU admission (RR 0.72; 95% CI 0.65–0.81, p < 0.0001) and sepsis (RR 0.28; 95% CI 0.23–0.35, p < 0.0001). Exclusive breastfeeding rates in NICU increased from 49% to 88% (p < 0.0001) and of kangaroo mother care (KMC) from 52% to 67% (p < 0.0001). Reduced formula use resulted in decreased monthly costs. Interpretation: EENC introduction, including staff coaching, quality improvement assessments and changes in hospital protocols and environments, were associated with improved clinical practices, reduced NICU admissions, admissions with hypothermia and sepsis and increased rates of exclusive breastfeeding and KMC in the NICU. Funding: Data collection was funded by the World Health Organization Western Pacific Regional Office and Newborns Vietnam. Outstanding Questions: • What is the impact of the package of early essential newborn care interventions on newborn mortality? • What are the total direct and indirect cost savings of early essential newborn care implementation? • What is the cost effectiveness of kangaroo mother care for preterm and low birth weight babies? • What strategies can help reduce unnecessary cesarean sections in hospitals? Keywords: Early essential newborn care, Neonatal care unit, Newborn health outcomes, Clinical practice, Quality of care, Viet Na

Multimodal analysis of genome-wide methylation, copy number aberrations, and end motif signatures enhances detection of early-stage breast cancer

IntroductionBreast cancer causes the most cancer-related death in women and is the costliest cancer in the US regarding medical service and prescription drug expenses. Breast cancer screening is recommended by health authorities in the US, but current screening efforts are often compromised by high false positive rates. Liquid biopsy based on circulating tumor DNA (ctDNA) has emerged as a potential approach to screen for cancer. However, the detection of breast cancer, particularly in early stages, is challenging due to the low amount of ctDNA and heterogeneity of molecular subtypes.MethodsHere, we employed a multimodal approach, namely Screen for the Presence of Tumor by DNA Methylation and Size (SPOT-MAS), to simultaneously analyze multiple signatures of cell free DNA (cfDNA) in plasma samples of 239 nonmetastatic breast cancer patients and 278 healthy subjects.ResultsWe identified distinct profiles of genome-wide methylation changes (GWM), copy number alterations (CNA), and 4-nucleotide oligomer (4-mer) end motifs (EM) in cfDNA of breast cancer patients. We further used all three signatures to construct a multi-featured machine learning model and showed that the combination model outperformed base models built from individual features, achieving an AUC of 0.91 (95% CI: 0.87-0.95), a sensitivity of 65% at 96% specificity.DiscussionOur findings showed that a multimodal liquid biopsy assay based on analysis of cfDNA methylation, CNA and EM could enhance the accuracy for the detection of early- stage breast cancer

Multimodal analysis of methylomics and fragmentomics in plasma cell-free DNA for multi-cancer early detection and localization

Despite their promise, circulating tumor DNA (ctDNA)-based assays for multi-cancer early detection face challenges in test performance, due mostly to the limited abundance of ctDNA and its inherent variability. To address these challenges, published assays to date demanded a very high-depth sequencing, resulting in an elevated price of test. Herein, we developed a multimodal assay called SPOT-MAS (screening for the presence of tumor by methylation and size) to simultaneously profile methylomics, fragmentomics, copy number, and end motifs in a single workflow using targeted and shallow genome-wide sequencing (~0.55×) of cell-free DNA. We applied SPOT-MAS to 738 non-metastatic patients with breast, colorectal, gastric, lung, and liver cancer, and 1550 healthy controls. We then employed machine learning to extract multiple cancer and tissue-specific signatures for detecting and locating cancer. SPOT-MAS successfully detected the five cancer types with a sensitivity of 72.4% at 97.0% specificity. The sensitivities for detecting early-stage cancers were 73.9% and 62.3% for stages I and II, respectively, increasing to 88.3% for non-metastatic stage IIIA. For tumor-of-origin, our assay achieved an accuracy of 0.7. Our study demonstrates comparable performance to other ctDNA-based assays while requiring significantly lower sequencing depth, making it economically feasible for population-wide screening