Classification of PTEN missense VUS through exascale simulations.

Phosphatase and tensin homolog (PTEN), a tumor suppressor with dual phosphatase properties, is a key factor in PI3K/AKT signaling pathway. Pathogenic germline variation in PTEN can abrogate its ability to dephosphorylate, causing high cancer risk. Lack of functional evidence lets numerous PTEN variants be classified as variants of uncertain significance (VUS). Utilizing Molecular Dynamics (MD) simulations, we performed a thorough evaluation for 147 PTEN missense VUS, sorting them into 66 deleterious and 81 tolerated variants. Utilizing replica exchange molecular dynamic (REMD) simulations, we further assessed the variants situated in the catalytic core of PTEN's phosphatase domain and uncovered conformational alterations influencing the structural stability of the phosphatase domain. There was a high degree of agreement between our results and the variants classified by Variant Abundance by Massively Parallel Sequencing, saturation mutagenesis, multiplexed functional data and experimental assays. Our extensive analysis of PTEN missense VUS should benefit their clinical applications in PTEN-related cancer. SIGNIFICANCE STATEMENT: Classification of PTEN variants affecting its lipid phosphatase activity is important for understanding the roles of PTEN variation in the pathogenesis of hereditary and sporadic malignancies. Of the 3000 variants identified in PTEN, 1296 (43%) were assigned as VUS. Here, we applied MD and REMD simulations to investigate the effects of PTEN missense VUS on the structural integrity of the PTEN phosphatase domain consisting the WPD, P and TI active sites. We classified a total of 147 missense VUS into 66 deleterious and 81 tolerated variants by referring to the control group comprising 54 pathogenic and 12 benign variants. The classification was largely in concordance with these classified by experimental approaches.

Classification of MLH1 Missense VUS Using Protein Structure-Based Deep Learning-Ramachandran Plot-Molecular Dynamics Simulations Method.

Pathogenic variation in DNA mismatch repair (MMR) gene MLH1 is associated with Lynch syndrome (LS), an autosomal dominant hereditary cancer. Of the 3798 MLH1 germline variants collected in the ClinVar database, 38.7% (1469) were missense variants, of which 81.6% (1199) were classified as Variants of Uncertain Significance (VUS) due to the lack of functional evidence. Further determination of the impact of VUS on MLH1 function is important for the VUS carriers to take preventive action. We recently developed a protein structure-based method named "Deep Learning-Ramachandran Plot-Molecular Dynamics Simulation (DL-RP-MDS)" to evaluate the deleteriousness of MLH1 missense VUS. The method extracts protein structural information by using the Ramachandran plot-molecular dynamics simulation (RP-MDS) method, then combines the variation data with an unsupervised learning model composed of auto-encoder and neural network classifier to identify the variants causing significant change in protein structure. In this report, we applied the method to classify 447 MLH1 missense VUS. We predicted 126/447 (28.2%) MLH1 missense VUS were deleterious. Our study demonstrates that DL-RP-MDS is able to classify the missense VUS based solely on their impact on protein structure.

Ethnic-specificity, evolution origin and deleteriousness of Asian BRCA variation revealed by over 7500 BRCA variants derived from Asian population.

Pathogenic variation in BRCA1 and BRCA2 (BRCA) causes high risk of breast and ovarian cancer, and BRCA variation data are important markers for BRCA-related clinical cancer applications. However, comprehensive BRCA variation data are lacking from the Asian population despite its large population size, heterogenous genetic background and diversified living environment across the Asia continent. We performed a systematic study on BRCA variation in Asian population including extensive data mining, standardization, annotation and characterization. We identified 7587 BRCA variants from 685 592 Asian individuals in 40 Asia countries and regions, including 1762 clinically actionable pathogenic variants and 4915 functionally unknown variants (https://genemutation.fhs.um.edu.mo/Asian-BRCA/). We observed the highly ethnic-specific nature of Asian BRCA variants between Asian and non-Asian populations and within Asian populations, highlighting that the current European descendant population-based BRCA data is inadequate to reflect BRCA variation in the Asian population. We also provided archeological evidence for the evolutionary origin and arising time of Asian BRCA variation. We further provided structural-based evidence for the deleterious variants enriched within the functionally unknown Asian BRCA variants. The data from our study provide a current view of BRCA variation in the Asian population and a rich resource to guide clinical applications of BRCA-related cancer for the Asian population.

Nationwide Analysis of Penetrating Thoracic Aortic Injury: Injury Patterns, Management, and Outcomes.

INTRODUCTION: Penetrating thoracic aortic injuries (PTAI) represent a rare form of thoracic trauma. Unlike blunt thoracic aortic injuries (BTAI), only scarce data, included in small case series, are currently available for PTAI. The purpose of this study was to describe injury patterns, surgical management, and outcomes of patients with PTAI and compare to those with BTAI. MATERIALS AND METHODS: A 9-y retrospective cohort study (2007-2015) was conducted using the National Trauma Data Bank. Patient demographics, injury profile, procedures performed, and patient outcomes were compared between the PTAI and BTAI group. RESULTS: A total of 2714 patients with PTAI and 14,037 patients with BTAI were identified. Compared to BTAI, PTAI patients were younger (28 versus 42 y, P < 0.001), more often male (89.1% versus 71.7%, P < 0.001), and more likely to arrive without signs of life (27.6% versus 7.5%, P < 0.001). PTAI patients had less associated injuries, overall, compared to those with BTAI; however, were more likely to have injuries to the esophagus, diaphragm, and heart. Patients with PTAI were less likely to undergo endovascular (5.8% versus 30.5%, P < 0.001) or open surgical repair (3.0% versus 4.2%, P < 0.001) compared to BTAI. While the large majority of PTAI patients expired before their hospital arrival or in the emergency department, the in-hospital mortality rate among those who survivedemergency department stay was 43.1%. CONCLUSIONS: Most patients with PTAI present to the hospital without any signs of life, and their overall mortality rate is extremely high. Only a small portion of PTAI patients who survived the initial resuscitation period underwent surgical interventions for thoracic aortic injuries. Further studies are still warranted to clarify the indications and types of surgical interventions for PTAI.

Prevalence and spectrum of DNA mismatch repair gene variation in the general Chinese population.

BACKGROUND: Identifying genetic disease-susceptible individuals through population screening is considered as a promising approach for disease prevention. DNA mismatch repair (MMR) genes including MLH1, MSH2, MSH6 and PMS2 play essential roles in maintaining microsatellite stability through DNA mismatch repair, and pathogenic variation in MMR genes causes microsatellite instability and is the genetic predisposition for cancer as represented by the Lynch syndrome. While the prevalence and spectrum of MMR variation has been extensively studied in cancer, it remains largely elusive in the general population. Lack of the knowledge prevents effective prevention for MMR variation-caused cancer. In the current study, we addressed the issue by using the Chinese population as a model. METHODS: We performed extensive data mining to collect MMR variant data from 18 844 ethnic Chinese individuals and comprehensive analyses for the collected MMR variants to determine its prevalence, spectrum and features of the MMR data in the Chinese population. RESULTS: We identified 17 687 distinct MMR variants. We observed substantial differences of MMR variation between the general Chinese population and Chinese patients with cancer, identified highly Chinese-specific MMR variation through comparing MMR data between Chinese and non-Chinese populations, predicted the enrichment of deleterious variants in the unclassified Chinese-specific MMR variants, determined MMR pathogenic prevalence of 0.18% in the general Chinese population and determined that MMR variation in the general Chinese population is evolutionarily neutral. CONCLUSION: Our study provides a comprehensive view of MMR variation in the general Chinese population, a resource for biological study of human MMR variation, and a reference for MMR-related cancer applications.

Organ Donation at the End of Life: Experiences From the 3 Wishes Project.

PURPOSE: The 3 Wishes Project (3WP) promotes holistic end-of-life care in the intensive care unit (ICU) to honor dying patients, support families, and encourage clinician compassion. Organ donation is a wish that is sometimes made by, or on behalf of, critically ill patients. Our objective was to describe the interface between the 3WP and organ donation as experienced by families, clinicians, and organ donation coordinators. METHODS: In a multicenter evaluation of the 3WP in 4 Canadian ICUs, we conducted a thematic analysis of transcripts from interviews and focus groups with clinicians, organ donation coordinators, and families of dying or died patients for whom donation was considered. RESULTS: We analyzed transcripts from 26 interviews and 2 focus groups with 18 family members, 17 clinicians, and 6 organ donation coordinators. The central theme describes the mutual goals of the 3WP and organ donation-emphasizing personhood and agency across the temporal continuum of care. During family decision-making, conversations encouraged by the 3WP can facilitate preliminary discussions about donation. During preparation for donation, memory-making activities supported by the 3WP redirect focus toward personhood. During postmortem family care, the 3WP supports families, including when donation is unsuccessful, and highlights aspirational pursuits of donation while encouraging reflections on other fulfilled wishes. CONCLUSIONS: Organ donation and the 3WP provide complementary opportunities to engage in value-based conversations during the dying process. The shared values of these programs may help to incorporate organ donation and death into a person's life narrative and incorporate new life into a person's death narrative.

Scale-up and sustainability of a personalized end-of-life care intervention: a longitudinal mixed-methods study.

BACKGROUND: Scaling-up and sustaining healthcare interventions can be challenging. Our objective was to describe how the 3 Wishes Project (3WP), a personalized end-of-life intervention, was scaled-up and sustained in an intensive care unit (ICU). METHODS: In a longitudinal mixed-methods study from January 12,013 - December 31, 2018, dying patients and families were invited to participate if the probability of patient death was > 95% or after a decision to withdraw life support. A research team member or bedside clinician learned more about each of the patients and their family, then elicited and implemented at least 3 personalized wishes for patients and/or family members. We used a qualitative descriptive approach to analyze interviews and focus groups conducted with 25 clinicians who cared for the enrolled patients. We used descriptive statistics to summarize patient, wish, and clinician characteristics, and analyzed outcome data in quarters using Statistical Process Control charts. The primary outcome was enrollment of terminally ill patients and respective families; the secondary outcome was the number of wishes per patient; tertiary outcomes included wish features and stakeholder involvement. RESULTS: Both qualitative and quantitative analyses suggested a three-phase approach to the scale-up of this intervention during which 369 dying patients were enrolled, having 2039 terminal wishes implemented. From a research project to clinical program to an approach to practice, we documented a three-fold increase in enrolment with a five-fold increase in total wishes implemented, without a change in cost. Beginning as a study, the protocol provided structure; starting gradually enabled frontline staff to experience and recognize the value of acts of compassion for patients, families, and clinicians. The transition to a clinical program was marked by handover from the research staff to bedside staff, whereby project catalysts mentored project champions to create staff partnerships, and family engagement became more intentional. The final transition involved empowering staff to integrate the program as an approach to care, expanding it within and beyond the organization. CONCLUSIONS: The 3WP is an end-of-life intervention which was implemented as a study, scaled-up into a clinical program, and sustained by becoming integrated into practice as an approach to care.

Compassionate End-of-Life Care: Mixed-Methods Multisite Evaluation of the 3 Wishes Project.

Background: The 3 Wishes Project (3WP) is an end-of-life program that aims to honor the dignity of dying patients by creating meaningful patient- and family-centered memories while promoting humanistic interprofessional care. Objective: To determine whether this palliative intervention could be successfully implemented-defined as demonstrating value, transferability, affordability, and sustainability-beyond the intensive care unit in which it was created. Design: Mixed-methods formative program evaluation. (ClinicalTrials.gov: NCT04147169). Setting: 4 North American intensive care units. Participants: Dying patients, their families, clinicians, hospital managers, and administrators. Intervention: Wishes from dying patients, family members, and clinicians were elicited and implemented. Measurements: Patient characteristics and processes of care; the number, type, and cost of each wish; and semistructured interviews and focus groups with family members, clinicians, and managers. Results: A total of 730 patients were enrolled, and 3407 wishes were elicited. Qualitative data were gathered from 75 family members, 72 clinicians, and 20 managers or hospital administrators. Value included intentional comforting of families as they honored the lives and legacies of their loved ones while inspiring compassionate clinical care. Factors promoting transferability included family appreciation and a collaborative intensive care unit culture committed to dignity-conserving end-of-life care. Staff participation evolved from passive support to professional agency. Program initiation required minimal investment for reusable materials; thereafter, the mean cost was $5.19 (SD, $17.14) per wish. Sustainability was demonstrated by the continuation of 3WP at each site after study completion. Limitation: This descriptive formative evaluation describes tertiary care center-specific experiences rather than aiming for generalizability to all jurisdictions. Conclusion: The 3WP is a transferrable, affordable, and sustainable program that provides value to dying patients, their families, clinicians, and institutions. Primary Funding Source: Greenwall Foundation.

Comprehensive Identification of Deleterious TP53 Missense VUS Variants Based on Their Impact on TP53 Structural Stability.

TP53 plays critical roles in maintaining genome stability. Deleterious genetic variants damage the function of TP53, causing genome instability and increased cancer risk. Of the large quantity of genetic variants identified in TP53, however, many remain functionally unclassified as variants of unknown significance (VUS) due to the lack of evidence. This is reflected by the presence of 749 (42%) VUS of the 1785 germline variants collected in the ClinVar database. In this study, we addressed the deleteriousness of TP53 missense VUS. Utilizing the protein structure-based Ramachandran Plot-Molecular Dynamics Simulation (RPMDS) method that we developed, we measured the effects of missense VUS on TP53 structural stability. Of the 340 missense VUS tested, we observed deleterious evidence for 193 VUS, as reflected by the TP53 structural changes caused by the VUS-substituted residues. We compared the results from RPMDS with those from other in silico methods and observed higher specificity of RPMDS in classification of TP53 missense VUS than these methods. Data from our current study address a long-standing challenge in classifying the missense VUS in TP53, one of the most important tumor suppressor genes.

Dual-Acting Small-Molecule Inhibitors Targeting Mycobacterial DNA Replication.

Mycobacterium tuberculosis (Mtb) is a pathogenic bacterium and a causative agent of tuberculosis (TB), a disease that kills more than 1.5 million people worldwide annually. One of the main reasons for this high mortality rate is the evolution of new Mtb strains that are resistant to available antibiotics. Therefore, new therapeutics for TB are in constant demand. Here, we report the development of small-molecule inhibitors that target two DNA replication enzymes of Mtb, namely DnaG primase and DNA gyrase (Gyr), which share a conserved TOPRIM fold near the inhibitors' binding site. The molecules were developed on the basis of previously reported inhibitors for T7 DNA primase that bind near the TOPRIM fold. To improve the physicochemical properties of the molecules as well as their inhibitory effect on primase and gyrase, 49 novel compounds have been synthesized as potential drug candidates in three stages of optimization. The last stage of chemical optimization yielded two novel inhibitors for both Mtb DnaG and Gyr that also showed inhibitory activity toward the fast-growing non-pathogenic model Mycobacterium smegmatis (Msmg).

Expanding the 3 Wishes Project for compassionate end-of-life care: a qualitative evaluation of local adaptations.

BACKGROUND: The 3 Wishes Project (3WP) is an end-of-life program that honors the dignity of dying patients by fostering meaningful connections among patients, families, and clinicians. Since 2013, it has become embedded in the culture of end-of-life care in over 20 ICUs across North America. The purpose of the current study is to describe the variation in implementation of 3WP across sites, in order to ascertain which factors facilitated multicenter implementation, which factors remain consistent across sites, and which may be adapted to suit local needs. METHODS: Using the methodology of qualitative description, we collected interview and focus group data from 85 clinicians who participated in the successful initiation and sustainment of 3WP in 9 ICUs. We describe the transition between different models of 3WP implementation, from core clinical program to the incorporation of various research activities. We describe various sources of financial and in-kind resources accessed to support the program. RESULTS: Beyond sharing a common goal of improving end-of-life care, sites varied considerably in organizational context, staff complement, and resources. Despite these differences, the program was successfully implemented at each site and eventually evolved from a clinical or research intervention to a general approach to end-of-life care. Key to this success was flexibility and the empowerment of frontline staff to tailor the program to address identified needs with available resources. This adaptability was fueled by cross-pollination of ideas within and outside of each site, resulting in the establishment of a network of like-minded individuals with a shared purpose. CONCLUSIONS: The successful initiation and sustainment of 3WP relied on local adaptations to suit organizational needs and resources. The semi-structured nature of the program facilitated these adaptations, encouraged creative and important ways of relating within local clinical cultures, and reinforced the main tenet of the program: meaningful human connection at the end of life. Local adaptations also encouraged a team approach to care, supplementing the typical patient-clinician dyad by explicitly empowering the healthcare team to collectively recognize and respond to the needs of dying patients, families, and each other. TRIAL REGISTRATION: NCT04147169 , retrospectively registered with clinicaltrials.gov on October 31, 2019.

Prognostic accuracy of the Hamilton Early Warning Score (HEWS) and the National Early Warning Score 2 (NEWS2) among hospitalized patients assessed by a rapid response team.

BACKGROUND: Rapid response teams (RRTs) respond to hospitalized patients experiencing clinical deterioration and help determine subsequent management and disposition. We sought to evaluate and compare the prognostic accuracy of the Hamilton Early Warning Score (HEWS) and the National Early Warning Score 2 (NEWS2) for prediction of in-hospital mortality following RRT activation. We secondarily evaluated a subgroup of patients with suspected infection. METHODS: We retrospectively analyzed prospectively collected data (2012-2016) of consecutive RRT patients from two hospitals. The primary outcome was in-hospital mortality. We calculated the number needed to examine (NNE), which indicates the number of patients that need to be evaluated in order to detect one future death. RESULTS: Five thousand four hundred ninety-one patients were included, of whom 1837 (33.5%) died in-hospital. Mean age was 67.4 years, and 51.6% were male. A HEWS above the low-risk threshold (≥ 5) had a sensitivity of 75.9% (95% confidence interval (CI) 73.9-77.9) and specificity of 67.6% (95% CI 66.1-69.1) for mortality, with a NNE of 1.84. A NEWS2 above the low-risk threshold (≥ 5) had a sensitivity of 84.5% (95% CI 82.8-86.2), and specificity of 49.0% (95% CI: 47.4-50.7), with a NNE of 2.20. The area under the receiver operating characteristic curve (AUROC) was 0.76 (95% CI 0.75-0.77) for HEWS and 0.72 (95% CI: 0.71-0.74) for NEWS2. Among suspected infection patients (n = 1708), AUROC for HEWS was 0.79 (95% CI 0.76-0.81) and for NEWS2, 0.75 (95% CI 0.73-0.78). CONCLUSIONS: The HEWS has comparable clinical accuracy to NEWS2 for prediction of in-hospital mortality among RRT patients.

NMR-Fragment Based Virtual Screening: A Brief Overview.

Fragment-based drug discovery (FBDD) using NMR has become a central approach over the last twenty years for development of small molecule inhibitors against biological macromolecules, to control a variety of cellular processes. Yet, several considerations should be taken into account for obtaining a therapeutically relevant agent. In this review, we aim to list the considerations that make NMR fragment screening a successful process for yielding potent inhibitors. Factors that may govern the competence of NMR in fragment based drug discovery are discussed, as well as later steps that involve optimization of hits obtained by NMR-FBDD.

Radiofrequency Neurolysis of the Posterior Nasal Nerve: A Systematic Review and Meta-Analysis.

OBJECTIVE: Temperature-controlled radiofrequency neurolysis of the posterior nasal nerve (PNN) has been approved for use since 2020. This review synthesized the published data to assess its efficacy for treatment of chronic rhinitis. DATA SOURCES: Pubmed/Medline, Embase, Scopus, Web of Science. REVIEW METHODS: A systematic search was conducted with no restrictions on publication years in April 2023. RCTs and prospective investigations that reported the reflective Total Nasal Symptom Score (rTNSS) outcome of radiofrequency neurolysis as a single procedure in chronic rhinitis patients were included. Pooled estimates for change in rTNSS from baseline at 3 months and responder rates (≥30% reduction in baseline rTNSS) at 3 and 6 months were obtained. Other outcomes, such as postnasal drip and cough scores, quality of life (QoL) measures, and adverse events were included for qualitative review. RESULTS: Five studies were included in the systematic review, of which four were included in the meta-analysis. A total of 284 participants underwent treatment. The pooled change in rTNSS score at 3 months was -4.28 (95% CI, -5.10 to -3.46). The pooled responder rate at 3 months was 77.11% (95% CI, 68.21%-86.01%) and at 6 months 80.80% (95% CI, 70.85%-90.76%). Postnasal drip and cough scores and QoL also improved significantly at follow up. A total of 36 adverse events were reported in 21 (7.4%) patients. CONCLUSIONS: The findings from this review suggest that temperature-controlled radiofrequency neurolysis of the PNN is effective at treating chronic rhinitis symptoms and that it has an overall favorable safety profile. Laryngoscope, 134:507-516, 2024.

Efficacy of a RADA-16 peptide hydrogel versus chitosan-based polymer in improving patient comfort during postoperative debridement: A randomized controlled trial.

BACKGROUND: Bioresorbable nasal packing is associated with a decreased incidence of adhesions and bleeding postoperatively after endoscopic sinus surgery (ESS). However, discomfort during postoperative debridement is still a major area of concern for patients. Our objective was to compare the efficacy of a peptide hydrogel to that of a chitosan-based polymer in reducing pain during debridement after ESS. METHODS: A prospective, multicenter, randomized, blinded trial was conducted in adults undergoing bilateral total ethmoidectomy for chronic rhinosinusitis. Participants served as their own controls with each subject receiving the hydrogel in a randomized ethmoid cavity and chitosan-based polymer in the contralateral ethmoid cavity. Participants were evaluated at 1, 4, and 12 weeks postoperatively. Pain during debridement as well as endoscopic evaluation of mucosal healing and hemostasis were measured. RESULTS: Thirty patients who underwent ESS were included in this trial. During the week 1 postoperative debridement, patients reported significantly less pain on the hydrogel-treated side compared to the chitosan-based polymer-treated side. There were no significant differences in bleeding severity, Lund-Kennedy scores, debridement time, or need for further intervention between the two groups. CONCLUSION: This study demonstrated the efficacy of a peptide hydrogel in minimizing pain during postoperative debridement.

Gender-Specific Differences in Preoperative Concerns in Patients Undergoing Endoscopic Sinus Surgery for Chronic Rhinosinusitis.

OBJECTIVES: Among patients with chronic rhinosinusitis (CRS), gender differences in epidemiology as well as quality of life have been reported. However, whether gender differences in endoscopic sinus surgery (ESS) preoperative concerns exist is unclear. METHODS: CRS patients undergoing ESS at 3 tertiary care centers in Los Angeles completed the validated Western Surgical Concern Inventory - ESS assessing ESS preoperative concerns. RESULTS: Of the 75 patients included, female patients expressed greater concern than male patients in regard to nasal packing, undergoing anesthesia, impact of surgery on daily activities, and pain and discomfort following surgery. CONCLUSION: This study suggests there are gender differences in ESS preoperative concerns and otolaryngologists should be aware of these possible concerns during preoperative discussions.

Exploring a targeted approach for public health capacity restrictions during COVID-19 using a new computational model.

This work introduces the Queen's University Agent-Based Outbreak Outcome Model (QUABOOM). This tool is an agent-based Monte Carlo simulation for modelling epidemics and informing public health policy. We illustrate the use of the model by examining capacity restrictions during a lockdown. We find that public health measures should focus on the few locations where many people interact, such as grocery stores, rather than the many locations where few people interact, such as small businesses. We also discuss a case where the results of the simulation can be scaled to larger population sizes, thereby improving computational efficiency.

Current otolaryngologic applications of the novel self-assembling RADA-16 peptide matrix.

A novel bioresorbable agent on the market is PuraGel® (3-D Matrix, Tokyo, Japan), a RADA-16 product that acts as a synthetic hemostatic and space-filling gel that promotes wound healing and prevents adhesion formation. Given the reported benefits of accelerated wound healing and scar tissue prevention, there are multiple otolaryngologic applications where RADA-16 might improve outcomes. Our study highlights current utilization and associated post-operative complications with this product.

DARVIC: Dihedral angle-reliant variant impact classifier for functional prediction of missense VUS.

BACKGROUND: Of the large number of genetic variants identified, the functional impact for most of them remains unknown. Mutations in DNA damage repair genes such as MUTYH, which is involved in repairing A:8-oxoG mismatches caused by reactive oxygen species, can cause a higher risk of cancer. Mutations happening in other key genes such as TP53 also pose huge health threats and risk of cancer. The interpretation of genetic variants' functional impact is a forefront issue that needs to be addressed. Many different in silico methods based on different principles have been developed and applied in interpreting genetic variants. However, a current challenge is that many existing methods tend to overpredict the pathogenicity of benign variants. A new approach is needed to tackle this issue to improve genetic variant interpretation through the use of in silico methods. METHODS: In this study, we developed another protein structural-based approach called Dihedral angle-reliant variant impact classifier (DARVIC) to predict the deleterious impact of the coding-changing missense variants. DARVIC uses Ramachandran's principle of protein stereochemistry as the theoretical foundation and uses molecular dynamics simulations coupled with a supervised machine learning algorithm XGBoost to determine the functional impact of missense variants on protein structural stability. RESULTS: We characterized the features of dihedral angles in dynamic protein structures. We also tested the performance of DARVIC in MUTYH and TP53 missense variants and achieved satisfactory results in reflecting the functional impacts of the variants on protein structure. The method achieved a balanced accuracy of 84% in a functionally validated MUTYH dataset containing both benign and pathogenic missense variants, higher than other existing in silico methods. Along with that, DARVIC was able to predict 119 (47%) deleterious variants from a dataset of 254 MUTYH VUS. Further application of DARVIC to a functionally validated TP53 dataset had a balanced accuracy of 94%, topping other methods, demonstrating DARVIC's robustness. CONCLUSION: DARVIC provides a valuable tool to predict the functional impacts of missense variants based on their effects on protein structural stability and motion. At its current state, DARVIC performed well in predicting the functional impact of the missense variants both in MUTYH and TP53. We expect its high potential to predict functional impact for the missense variants in other genes.

Integration of deep learning with Ramachandran plot molecular dynamics simulation for genetic variant classification.

Functional classification of genetic variants is a key for their clinical applications in patient care. However, abundant variant data generated by the next-generation DNA sequencing technologies limit the use of experimental methods for their classification. Here, we developed a protein structure and deep learning (DL)-based system for genetic variant classification, DL-RP-MDS, which comprises two principles: 1) Extracting protein structural and thermodynamics information using the Ramachandran plot-molecular dynamics simulation (RP-MDS) method, 2) combining those data with an unsupervised learning model of auto-encoder and a neural network classifier to identify the statistical significance patterns of the structural changes. We observed that DL-RP-MDS provided higher specificity than over 20 widely used in silico methods in classifying the variants of three DNA damage repair genes: TP53, MLH1, and MSH2. DL-RP-MDS offers a powerful platform for high-throughput genetic variant classification. The software and online application are available at https://genemutation.fhs.um.edu.mo/DL-RP-MDS/.