Bench Research Informed by GWAS Results.
Ontology highlight
ABSTRACT:
SUBMITTER: Kondratyev NV
PROVIDER: S-EPMC8623533 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundPatient and Public Involvement (PPI) in research is increasingly being utilized to better connect patients and researchers. The Patient Engagement Studio (PES) supports PPI in research by working directly with researchers throughout various stages of their projects. Recently, two researchers presented to the PES for assistance with their project, Embryo+™. The purpose of Embryo+™ is to decrease miscarriage rates using RNA sequencing technology that screens for the most viable embryos. To date, no examples of PPI directly in the planning or implementation of bench research concerning in vitro fertilization and embryo transfer have been identified.Main bodyEmbryo+™ researchers met in-person with the PES two times (fall 2019; each meeting had 9 PES members in attendance) for initial feedback and protocol development. After these meetings, PES leadership and Embryo+™ researchers decided that the unique nature of the project merited a PPI evaluation. Subsequent evaluation of engagement efforts occurred by reviewing the PES reports for the Embryo+™ researchers, conducting two recorded web-based discussion meetings with the PES (summer 2020; meeting 1 n = 7; meeting 2 n = 6), and a brief survey (n = 13). The discussion meetings provided an opportunity for the PES members to define engagement themes through consensus via verbal agreement to the studio director's periodic summaries during the discussions. Combining survey results and PES themes allowed for a broad discussion for meaningful engagement. The Embryo+™ researchers established trust with the patients by changing some of their language in response to patient suggestions, allowing for unintended ethical conversations, and implementing the patient developed protocols. Overall, the patient experts thought this project was very meaningful and valuable, quantified by a mean loyalty score 89.43 (s.d. 10.29).ConclusionBench science researchers may need additional PPI training prior to engaging with patient groups. PPI in this project was successful in large part due to this training, where the director emphasized the importance of gaining trust with the patients. The researchers applied what they learned and several examples of how to develop trust with patients are discussed. If trust is established, PPI in an ethically charged, basic science research study can be both valuable and successful.
| S-EPMC8115861 | biostudies-literature
Project description:After more than 10 years of accumulated efforts, genome-wide association studies (GWAS) have led to many findings, most of which have been deposited into the GWAS Catalog. Between GWAS's inception and March 2017, the GWAS Catalog has collected 2429 studies, 1818 phenotypes, and 28,462 associated SNPs. We reclassified the psychology-related phenotypes into 217 reclassified phenotypes, which accounted for 514 studies and 7052 SNPs. In total, 1223 of the SNPs reached genome-wide significance. Of these, 147 were replicated for the same psychological trait in different studies. Another 305 SNPs were replicated within one original study. The SNPs rs2075650 and rs4420638 were linked to the most replications within a single reclassified phenotype or very similar reclassified phenotypes; both were associated with Alzheimer's disease (AD). Schizophrenia was associated with 74 within-phenotype SNPs reported in independents studies. Alzheimer's disease and schizophrenia were both linked to some physical phenotypes, including cholesterol and body mass index, through common GWAS signals. Alzheimer's disease also shared risk SNPs with age-related phenotypes such as age-related macular degeneration and longevity. Smoking-related SNPs were linked to lung cancer and respiratory function. Alcohol-related SNPs were associated with cardiovascular and digestive system phenotypes and disorders. Two separate studies also identified a shared risk SNP for bipolar disorder and educational attainment. This review revealed a list of reproducible SNPs worthy of future functional investigation. Additionally, by identifying SNPs associated with multiple phenotypes, we illustrated the importance of studying the relationships among phenotypes to resolve the nature of their causal links. The insights within this review will hopefully pave the way for future evidence-based genetic studies.
| S-EPMC6372350 | biostudies-literature
Project description:Over the last year, significant steps have been made toward understanding the pathogenesis of esophageal diseases and translating this knowledge to clinical practice. Gastroesophageal reflux disease (GERD) is the most common outpatient diagnosis in gastroenterology and has a high prevalence in the general population. As many as 40% of patients with GERD have incomplete response to medical therapy, and the pathophysiological mechanisms underlying lack of response are now better understood. Novel medical and minimally invasive interventions are available to optimize management of GERD. Esophageal cancer, regardless of the histological subtype, has among the worst survival statistics among all malignancies. Taking advantage of technological advances in genome sequencing, the mutational spectra in esophageal cancer are now emerging, offering novel avenues for targeted therapies. Early diagnosis is another strand for improving survival. While genome-wide association studies are providing insights into genetic susceptibility, novel approaches to early detection of cancer are being devised through the use of biomarkers applied to esophageal samples and as part of imaging technologies. Dysmotility and eosinophilic esophagitis are the differential diagnoses in patients with dysphagia. New pathophysiological classifications have improved the management of motility disorders. Meanwhile, exciting progress has been made in the endoscopic management of these conditions. Eosinophilic esophagitis is still a relatively new entity, and the pathogenesis remains poorly understood. However, it is now clear that an allergic reaction to food plays an important role, and dietary interventions as well as biologic agents to block the inflammatory cascade are novel, promising fields of clinical research.
| S-EPMC3790564 | biostudies-literature
Project description:ObjectiveTo determine the preferred means by which participants in a study of cardiac rehabilitation wish to be informed of the study's results.DesignPostal questionnaire survey of participants in a randomized controlled trial.SettingCornwall, southwest England.ParticipantsPatients recruited to the Cornwall Heart Attack Rehabilitation Management Study (CHARMS).MethodParticipants recruited to CHARMS who were alive 3 years and 9 months after the trial was completed were contacted by letter and invited to return a reply slip with four short questions indicating how they would prefer to be informed about the published results of the study.ResultsIn March 2008, 191/230 participants originally recruited to CHARMS were still alive. General practitioners deemed 166/191 (88%) survivors medically appropriate to be contacted through a postal survey, and 154/166 (93%) participants responded to the invitation to participate in the follow-up survey. 86% (143/166) of participants indicated that they wished to be informed about the results: 115 (80%) of these elected to receive information by letter and 25 (18%) of these preferred to attend a meeting. Men older than 65 years predominated in this latter group. Women respondents preferred to receive the study results by letter; none preferred communication by email or the web.ConclusionSurvivors of acute myocardial infarction who participated in a RCT of cardiac rehabilitation wanted to receive a summary of the aggregate study results. Participants had preferences regarding how they would wish to be informed about the results of the study. Most participants preferred to be informed by letter or email, but some preferred the interaction of a group or a meeting.
| S-EPMC5060540 | biostudies-literature
Project description:BackgroundThe use of research evidence in policy making is a complex and challenging process that has a long history in various fields, especially in healthcare. Different terms and concepts have been used to describe the relationship between research and policy, but they often lack clarity and consensus. To address this gap, several strategies and models have been proposed to facilitate evidence informed policy making and to identify the key factors and mechanisms involved. This study aims to critically review the existing models of evidence informed policy making (EIPM) in healthcare and to assess their strengths and limitations.MethodA systematic search and review conducted to identify and critically assess EIPM models in healthcare. We searched PubMed, Web of Science and Scopus databases as major electronic databases and applied predefined inclusion criteria to select the models. We also checked the citations of the included models to find other scholars' perspectives. Each model was described and critiqued each model in detail and discussed their features and limitations.ResultNine models of EIPM in healthcare were identified. While models had some strengths in comprehension, flexibility and theoretical foundations, analysis also identified limitations including: presupposing rational policymaking; lacking alternatives for time-sensitive situations; not capturing policy complexity; neglecting unintended effects; limited context considerations; inadequate complexity concepts; limited collaboration guidance; and unspecified evidence adaptations.ConclusionThe reviewed models provide useful frameworks for EIPM but need further improvement to address their limitations. Concepts from sociology of knowledge, change theory and complexity science can enrich the models. Future EIPM models should better account for the complexity of research-policy relationships and provide tailored strategies based on the policy context.
| S-EPMC11002157 | biostudies-literature
Project description:BackgroundSepsis is characterized by a dysregulated immune response and metabolic alterations, including decreased high-density lipoprotein cholesterol (HDL-C) levels. HDL exhibits beneficial properties, such as lipopolysaccharides (LPS) scavenging, exerting anti-inflammatory effects and providing endothelial protection. We investigated the effects of CER-001, an engineered HDL-mimetic, in a swine model of LPS-induced acute kidney injury (AKI) and a Phase 2a clinical trial, aiming to better understand its molecular basis in systemic inflammation and renal function.MethodsWe carried out a translational approach to study the effects of HDL administration on sepsis. Sterile systemic inflammation was induced in pigs by LPS infusion. Animals were randomized into LPS (n = 6), CER20 (single dose of CER-001 20 mg/kg; n = 6), and CER20 × 2 (two doses of CER-001 20 mg/kg; n = 6) groups. Survival rate, endothelial dysfunction biomarkers, pro-inflammatory mediators, LPS, and apolipoprotein A-I (ApoA-I) levels were assessed. Renal and liver histology and biochemistry were analyzed. Subsequently, we performed an open-label, randomized, dose-ranging (Phase 2a) study included 20 patients with sepsis due to intra-abdominal infection or urosepsis, randomized into Group A (conventional treatment, n = 5), Group B (CER-001 5 mg/kg BID, n = 5), Group C (CER-001 10 mg/kg BID, n = 5), and Group D (CER-001 20 mg/kg BID, n = 5). Primary outcomes were safety and efficacy in preventing AKI onset and severity; secondary outcomes include changes in inflammatory and endothelial dysfunction markers.ResultsCER-001 increased median survival, reduced inflammatory mediators, complement activation, and endothelial dysfunction in endotoxemic pigs. It enhanced LPS elimination through the bile and preserved liver and renal parenchyma. In the clinical study, CER-001 was well-tolerated with no serious adverse events related to study treatment. Rapid ApoA-I normalization was associated with enhanced LPS removal and immunomodulation with improvement of clinical outcomes, independently of the type and gravity of the sepsis. CER-001-treated patients had reduced risk for the onset and progression to severe AKI (stage 2 or 3) and, in a subset of critically ill patients, a reduced need for organ support and shorter ICU length of stay.ConclusionsCER-001 shows promise as a therapeutic strategy for sepsis management, improving outcomes and mitigating inflammation and organ damage.Trial registrationThe study was approved by the Agenzia Italiana del Farmaco (AIFA) and by the Local Ethic Committee (N° EUDRACT 2020-004202-60, Protocol CER-001- SEP_AKI_01) and was added to the EU Clinical Trials Register on January 13, 2021.
| S-EPMC10621167 | biostudies-literature
Project description:Exploration of genetic variant-to-gene relationships by quantitative trait loci such as expression QTLs is a frequently used tool in genome-wide association studies. However, the wide range of public QTL databases and the lack of batch annotation features complicate a comprehensive annotation of GWAS results. In this work, we introduce the tool "Qtlizer" for annotating lists of variants in human with associated changes in gene expression and protein abundance using an integrated database of published QTLs. Features include incorporation of variants in linkage disequilibrium and reverse search by gene names. Analyzing the database for base pair distances between best significant eQTLs and their affected genes suggests that the commonly used cis-distance limit of 1,000,000 base pairs might be too restrictive, implicating a substantial amount of wrongly and yet undetected eQTLs. We also ranked genes with respect to the maximum number of tissue-specific eQTL studies in which a most significant eQTL signal was consistent. For the top 100 genes we observed the strongest enrichment with housekeeping genes (P = 2 × 10-6) and with the 10% highest expressed genes (P = 0.005) after grouping eQTLs by r2 > 0.95, underlining the relevance of LD information in eQTL analyses. Qtlizer can be accessed via https://genehopper.de/qtlizer or by using the respective Bioconductor R-package ( https://doi.org/10.18129/B9.bioc.Qtlizer ).
| S-EPMC7687904 | biostudies-literature
Project description:PurposeThe dizzying pace of genomic discoveries is leading to an increasing number of clinical applications. In this report, we provide a method for horizon scanning and 1 year data on translational research beyond bench to bedside to assess the validity, utility, implementation, and outcomes of such applications.MethodsWe compiled cross-sectional results of ongoing horizon scanning of translational genomic research, conducted between 16 May 2012 and 15 May 2013, based on a weekly, systematic query of PubMed. A set of 505 beyond bench to bedside articles were collected and classified, including 312 original research articles; 123 systematic and other reviews; 38 clinical guidelines, policies, and recommendations; and 32 articles describing tools, decision support, and educational materials.ResultsMost articles (62%) addressed a specific genomic test or other health application; almost half of these (n = 180) were related to cancer. We estimate that these publications account for 0.5% of reported human genomics and genetics research during the same time.ConclusionThese data provide baseline information to track the evolving knowledge base and gaps in genomic medicine. Continuous horizon scanning of the translational genomics literature is crucial for an evidence-based translation of genomics discoveries into improved health care and disease prevention.
| S-EPMC4079725 | biostudies-literature
Project description:The assent procedure reflects an effort to enable the minor to understand, to the degree they are capable of, what their participation in the decision making process would involve. To evaluate the minors' ability to understand the information provided to them when obtaining assent and to evaluate the opinion of the parents regarding the importance of asking the child's assent. The sample included a total of 52 minors aged between 10 and 17 years who underwent exercise echocardiogram. The Quality of Informed Consent is divided into two parts: Part A was used to measure objective understanding and part B to measure subjective understanding. The results show that the minors have a high capacity to understand the information given to them when asking for assent. A positive relationship was found between the two parts of the questionnaire. No statistically significant relationship was found between age and sex and part A and part B or between both age groups (<14 years old and ≥14 years old) and the measure. In the case of the parents, 96.6% of parents consider assent as an advantage for the child's acceptance of health care. The opinion of the parents is not related to the age, sex or level of schooling. Minors showed a substantial level of understanding regarding the information provided to them. The parents considered the implementation of assent fundamental to the child's acceptance of health care.
| S-EPMC8307200 | biostudies-literature
Project description:BackgroundArtificial insemination and genetic selection are major factors contributing to population stratification in dairy cattle. In this study, we analyzed the effect of sample stratification and the effect of stratification correction on results of a dairy genome-wide association study (GWAS). Three methods for stratification correction were used: the efficient mixed-model association expedited (EMMAX) method accounting for correlation among all individuals, a generalized least squares (GLS) method based on half-sib intraclass correlation, and a principal component analysis (PCA) approach.ResultsHistorical pedigree data revealed that the 1,654 contemporary cows in the GWAS were all related when traced through approximately 10-15 generations of ancestors. Genome and phenotype stratifications had a striking overlap with the half-sib structure. A large elite half-sib family of cows contributed to the detection of favorable alleles that had low frequencies in the general population and high frequencies in the elite cows and contributed to the detection of X chromosome effects. All three methods for stratification correction reduced the number of significant effects. EMMAX method had the most severe reduction in the number of significant effects, and the PCA method using 20 principal components and GLS had similar significance levels. Removal of the elite cows from the analysis without using stratification correction removed many effects that were also removed by the three methods for stratification correction, indicating that stratification correction could have removed some true effects due to the elite cows. SNP effects with good consensus between different methods and effect size distributions from USDA's Holstein genomic evaluation included the DGAT1-NIBP region of BTA14 for production traits, a SNP 45kb upstream from PIGY on BTA6 and two SNPs in NIBP on BTA14 for protein percentage. However, most of these consensus effects had similar frequencies in the elite and average cows.ConclusionsGenetic selection and extensive use of artificial insemination contributed to overlapped genome, pedigree and phenotype stratifications. The presence of an elite cluster of cows was related to the detection of rare favorable alleles that had high frequencies in the elite cluster and low frequencies in the remaining cows. Methods for stratification correction could have removed some true effects associated with genetic selection.
| S-EPMC3496570 | biostudies-literature