Comprehensive Characterization of Cancer Driver Genes and Mutations.

Identifying molecular cancer drivers is critical for precision oncology. Multiple advanced algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on large datasets are few. We report a PanCancer and PanSoftware analysis spanning 9,423 tumor exomes (comprising all 33 of The Cancer Genome Atlas projects) and using 26 computational tools to catalog driver genes and mutations. We identify 299 driver genes with implications regarding their anatomical sites and cancer/cell types. Sequence- and structure-based analyses identified >3,400 putative missense driver mutations supported by multiple lines of evidence. Experimental validation confirmed 60%-85% of predicted mutations as likely drivers. We found that >300 MSI tumors are associated with high PD-1/PD-L1, and 57% of tumors analyzed harbor putative clinically actionable events. Our study represents the most comprehensive discovery of cancer genes and mutations to date and will serve as a blueprint for future biological and clinical endeavors.

Clarke Error Grid Analysis for Performance Evaluation of Glucometers in a Tertiary Care Referral Hospital.

Glucometer is the most commonly used POCT device and guides monitoring of blood glucose level in both clinical settings and outside. Inaccurate glucometer readings resulting in erroneous therapeutic intervention has critical consequences on patient care. Regulatory guidelines for performance evaluation of glucometers are not available in many countries. A robust program implemented by the hospital is essential to ensure accuracy and precision of glucometers to produce optimal results. The objective of this study was to design a quality assurance program for the evaluation of glucometers in a high volume tertiary care referral hospital and evaluate the results from July'18 to July'19. Seventy three glucometers used across the hospital were subjected to Internal Quality Control checks and Proficiency Testing performed once a month and every 3 months respectively. The results were reviewed and plotted on a Bland Altman Graph. Clarke Error Grid Analysis was done to evaluate the clinical significance of inaccuracies in the measurement of blood glucose concentration as per ISO 15197: 2013. Eight devices were identified as unacceptable by ISO standards and replaced subsequently. 96.83% and 3.17% of the values were in Zone A and B of Clarke Error Grid Analysis. The study complied with the standard which requires that 99% of the values fall within zones A and B. The review of the program after one year and its ability to identify defective glucometers has validated the efficacy of the model. The method used may be suggested as a prototype for quality management of glucometers in a clinical setting.

Retrospective Analysis of Clinical Laboratory Parameters, Therapeutics and Outcome in Patients Infected with SARS-CoV2.

SARS-CoV-2 is the third coronavirus to have caused severe disease in humans in the last two decades, with approximately 5% of all patients and 20% of hospitalized patients experiencing severe symptoms, necessitating intensive care. The occurrence of Cytokine Storm has been implicated in the immune-pathogenesis of severe COVID-19. This is associated with cardiac injury, precipitated by cytokine mediated imbalance of coagulation and fibrinolysis, in the lung alveoli. In the absence of proven therapeutic agents, combinations of anti-viral drugs, immune-modulators and other adjunctive therapies have been tried in different clinical settings. A total of 128 confirmed cases of severe COVID-19 admitted to BLK-MAX Super Speciality Hospital between 16th of June to 31st of July, 2020 were included in this study. The correlation of age, gender, first value (on admission) of serum IL-6 and D-dimer, and impact of Tocilizumab and Remdesivir therapy on clinical outcome (28-day mortality), was evaluated in confirmed cases of severe COVID-19. The mortality rate was highest in the age group above 70 years. The incidence of death was significantly higher in males above 50 years, when age and gender were considered together. IL-6 and D-dimer levels >70 pg/mL and > 0.5µg FEU/mL respectively, were associated with poor outcome. 85.3% of patients treated with Remdesivir showed clinical improvement. When Tocilizumab and Remdisivir were administered together, 44.0% of patients survived while 56% expired. 79.7% of patients survived while 20.3% expired when neither Tocilizumab nor Remdesivir was administered.

Database of evidence for precision oncology portal.

Summary: A database of curated genomic variants with clinically supported drug therapies and other oncological annotations is described. The accompanying web portal provides a search engine with two modes: one that allows users to query gene, cancer type, variant type or position for druggable mutations, and another to search for and to visualize, on three-dimensional protein structures, putative druggable sites that cluster with known druggable mutations. Availability and implementation: http://dinglab.wustl.edu/depo.

Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.

The advent of next-generation sequencing has dramatically decreased the cost for whole-genome sequencing and increased the viability for its application in research and clinical care. The Personal Genome Project (PGP) provides unrestricted access to genomes of individuals and their associated phenotypes. This resource enabled the Critical Assessment of Genome Interpretation (CAGI) to create a community challenge to assess the bioinformatics community's ability to predict traits from whole genomes. In the CAGI PGP challenge, researchers were asked to predict whether an individual had a particular trait or profile based on their whole genome. Several approaches were used to assess submissions, including ROC AUC (area under receiver operating characteristic curve), probability rankings, the number of correct predictions, and statistical significance simulations. Overall, we found that prediction of individual traits is difficult, relying on a strong knowledge of trait frequency within the general population, whereas matching genomes to trait profiles relies heavily upon a small number of common traits including ancestry, blood type, and eye color. When a rare genetic disorder is present, profiles can be matched when one or more pathogenic variants are identified. Prediction accuracy has improved substantially over the last 6 years due to improved methodology and a better understanding of features.

A Novel Experimental Approach to Understand the Transport of Nanodrugs.

Nanoparticle-based drugs offer attractive advantages like targeted delivery to the diseased site and size and shape-controlled properties. Therefore, understanding the particulate flow of the nanodrugs is important for effective delivery, accurate prediction of required dosage, and developing efficient drug delivery platforms for nanodrugs. In this study, the transport of nanodrugs including flow velocity and deposition is investigated using three model metal oxide nanodrugs of different sizes including iron oxide, zinc oxide, and combined Cu-Zn-Fe oxide synthesized via a modified polyol approach. The hydrodynamic size, size, morphology, chemical composition, crystal phase, and surface functional groups of the water-soluble nanodrugs were characterized via dynamic light scattering, transmission electron microscopy, scanning electron microscopy-energy dispersive X-ray, X-ray diffraction, and fourier transform infrared spectroscopy, respectively. Two different biomimetic flow channels with customized surfaces are developed via 3D printing to experimentally monitor the velocity and deposition of the different nanodrugs. A diffusion dominated mechanism of flow is seen in size ranges 92 nm to 110 nm of the nanodrugs, from the experimental velocity and mass loss profiles. The flow velocity analysis also shows that the transport of nanodrugs is controlled by sedimentation processes in the larger size ranges of 110-302 nm. However, the combined overview from experimental mass loss and velocity trends indicates presence of both diffusive and sedimentation forces in the 110-302 nm size ranges. It is also discovered that the nanodrugs with higher positive surface charges are transported faster through the two test channels, which also leads to lower deposition of these nanodrugs on the walls of the flow channels. The results from this study will be valuable in realizing reliable and cost-effective in vitro experimental approaches that can support in vivo methods to predict the flow of new nanodrugs.

HIV interventions to reduce HIV/AIDS stigma: a systematic review.

We reviewed the literature to determine the effectiveness of HIV-related interventions in reducing HIV/AIDS stigma. Studies selected had randomized controlled trial (RCT), pretest-posttest with a non-randomized control group, or pretest-posttest one group study designs in which HIV-related interventions were being evaluated, and in which HIV/AIDS stigma was one of the outcomes being measured. A checklist was used to extract data from accepted studies, assess their internal validity, and overall quality. Data were extracted from 19 studies, and 14 of these studies demonstrated effectiveness in reducing HIV/AIDS stigma. Only 2 of these 14 effective studies were considered good studies, based on quality, the extent to which the intervention focused on reducing HIV/AIDS stigma, and the statistics reported to demonstrate effectiveness. Future studies to reduce HIV/AIDS stigma could improve by designing interventions that pay greater attention to internal validity, use validated HIV/AIDS stigma instruments, and achieve both statistical and public health significance.

Factors associated with utilization of a free HIV VCT clinic by female sex workers in Jinan City, Northern China.

Based on our previous qualitative exploration, this research presents the second phase in our study of factors associated with utilization of a free HIV VCT clinic in Jinan City, Northern China, by female sex workers (FSWs). A total of 970 FSWs from entertainment venues were interviewed and prospectively followed to determine who ultimately sought and received VCT at the clinic, compared to those who did not. Simple and multiple logistic regressions were performed on factors drawn from the Ecological Perspective, hypothesized to be associated with utilization of testing at the VCT clinic. Despite 69% of FSWs expressing willingness to attend the VCT clinic, only 11% were actually tested. The multiple logistic regression model that provided best goodness of fit included the covariates of willingness to attend the VCT clinic (Adjusted OR 3.13, 95% CI: 1.62-6.59), low perceived HIV infection risk (Adjusted OR 0.64, 95% CI: 0.35-1.11), low fear of FSWs status disclosure in the clinic (Adjusted OR 0.55, 95% CI: 0.31-0.94) and influence of acquaintances (Adjusted OR 0.52, 95% CI: 0.29-0.89) and peers (Adjusted OR 2.45, 95% CI: 1.40-4.50). This is the first study in China to follow FSWs longitudinally to measure factors related to VCT utilization. The low utilization of VCT services by participants in our study is similar to prior reports throughout China. FSWs' access to VCT service is associated with intrapersonal, institutional, and particularly, interpersonal factors. Based on these findings, we recommend emphasis on confidentiality of services, VCT education for influential peers, and introduction of HIV rapid testing on site.

Pilot study demonstrating effectiveness of targeted education to improve informed consent understanding in AIDS clinical trials.

Assessing and improving informed consent understanding is equally important as obtaining consent from participants in clinical trial research, but developing interventions to target gaps in participants' informed consent understanding remains a challenge. We used a randomized controlled study design to pilot test an educational intervention to improve actual informed consent understanding of new enrollees in the Adult AIDS Clinical Trial Group (AACTG). Questionnaires were administered to 24 enrollees to assess their baseline understanding on eight elements of informed consent associated with AIDS clinical trials. Enrollees who scored 18/21(85%) or less were randomly assigned to in-person, targeted education (intervention), or delayed education (control). Two follow-up assessments were administered. Repeated measures ANOVA was performed to determine intervention effectiveness in improving actual informed consent understanding over time. Actual understanding improved at the immediate post-intervention time point with a significant score difference of 2.5 when comparing the intervention and delayed groups. In addition, there was a significant score difference of 3.2 when comparing baseline to three-month follow-up for the two groups, suggesting a statistically significant intervention effect to improve actual understanding of the basic elements of informed consent. The findings demonstrated that one-time targeted education can improve actual informed consent understanding one week after the intervention, but retention of these concepts may require periodic monitoring to ensure comprehension throughout the course of a clinical trial.

Socio-demographic and AIDS-related factors associated with tuberculosis stigma in southern Thailand: a quantitative, cross-sectional study of stigma among patients with TB and healthy community members.

BACKGROUND: Tuberculosis (TB) remains one of the most important infectious diseases worldwide. A comprehensive approach towards disease control that addresses social factors including stigma is now advocated. Patients with TB report fears of isolation and rejection that may lead to delays in seeking care and could affect treatment adherence. Qualitative studies have identified socio-demographic, TB knowledge, and clinical determinants of TB stigma, but only one prior study has quantified these associations using formally developed and validated stigma scales. The purpose of this study was to measure TB stigma and identify factors associated with TB stigma among patients and healthy community members. METHODS: A cross-sectional study was performed in southern Thailand among two different groups of participants: 480 patients with TB and 300 healthy community members. Data were collected on socio-demographic characteristics, TB knowledge, and clinical factors. Scales measuring perceived TB stigma, experienced/felt TB stigma, and perceived AIDS stigma were administered to patients with TB. Community members responded to a community TB stigma and community AIDS stigma scale, which contained the same items as the perceived stigma scales given to patients. Stigma scores could range from zero to 30, 33, or 36 depending on the scale. Three separate multivariable linear regressions were performed among patients with TB (perceived and experience/felt stigma) and community members (community stigma) to determine which factors were associated with higher mean TB stigma scores. RESULTS: Only low level of education, belief that TB increases the chance of getting AIDS, and AIDS stigma were associated with higher TB stigma scores in all three analyses. Co-infection with HIV was associated with higher TB stigma among patients. All differences in mean stigma scores between index and referent levels of each factor were less than two points, except for incorrectly believing that TB increases the chance of getting AIDS (mean difference of 2.16; 95% CI: 1.38, 2.94) and knowing someone who died from TB (mean difference of 2.59; 95% CI: 0.96, 4.22). CONCLUSION: These results suggest that approaches addressing the dual TB/HIV epidemic may be needed to combat TB stigma and that simply correcting misconceptions about TB may have limited effects.

Silent endurance and profound loneliness: socioemotional suffering in African Americans living with HIV in the rural south.

We explored how community responses to HIV contribute to distress in African Americans living with HIV in the rural South of the United States. We listened to the voices of community members through focus groups and African Americans with HIV through interviews. Community avoidance of HIV, negative views of HIV, and discriminatory behavior powerfully affected the distress of people living with HIV (PLWH). Ongoing distress, coupled with limited support, led to a life in which many PLWH endured their pain in silence and experienced profound loneliness. We conceptualized their experiences as socioemotional suffering--the hidden emotional burden and inner distress of not only living with HIV, a complex serious illness, but also with the societal attitudes and behaviors that are imposed on the illness and on PLWH. To improve the quality of life and health of PLWH, we cannot focus solely on the individual, but must also focus on the local community and society as a whole.

Spatially interacting phosphorylation sites and mutations in cancer.

Advances in mass-spectrometry have generated increasingly large-scale proteomics datasets containing tens of thousands of phosphorylation sites (phosphosites) that require prioritization. We develop a bioinformatics tool called HotPho and systematically discover 3D co-clustering of phosphosites and cancer mutations on protein structures. HotPho identifies 474 such hybrid clusters containing 1255 co-clustering phosphosites, including RET p.S904/Y928, the conserved HRAS/KRAS p.Y96, and IDH1 p.Y139/IDH2 p.Y179 that are adjacent to recurrent mutations on protein structures not found by linear proximity approaches. Hybrid clusters, enriched in histone and kinase domains, frequently include expression-associated mutations experimentally shown as activating and conferring genetic dependency. Approximately 300 co-clustering phosphosites are verified in patient samples of 5 cancer types or previously implicated in cancer, including CTNNB1 p.S29/Y30, EGFR p.S720, MAPK1 p.S142, and PTPN12 p.S275. In summary, systematic 3D clustering analysis highlights nearly 3,000 likely functional mutations and over 1000 cancer phosphosites for downstream investigation and evaluation of potential clinical relevance.

How researchers define vulnerable populations in HIV/AIDS clinical trials.

In this study, we interviewed researchers, asking them to define vulnerable populations in HIV/AIDS clinical trials, and provide feedback on the federal regulations for three vulnerable populations. Interview data informed a conceptual framework, and were content analyzed to identify acceptability or disagreement with the regulations. Beginning with several characteristics of vulnerable enrollees identified by researchers, the conceptual framework illustrates possible scenarios of how enrollees could be considered vulnerable in clinical research. Content analysis identified barriers affecting HIV/AIDS researchers' ability to conduct clinical trials with pregnant women, prisoners, and children, for which the regulations specify additional protections. This study challenges current thinking about federal regulations' group-based approach to defining vulnerable populations.

Reported willingness and associated factors related to utilization of voluntary counseling and testing services by female sex workers in Shandong Province, China.

OBJECTIVE: To explore reported willingness and factors associated with utilization of voluntary counseling and testing services by female sex workers (FSWs) in China and to offer recommendations to optimize use of such services. METHODS: A questionnaire to explore willingness to use VCT was designed based on social ecological theory and formative qualitative research. A cross-sectional survey was conducted among FSWs from entertainment venues. Single and multiple logistic regression analyses were employed to examine factors associated with reported willingness to utilize VCT. RESULTS: A total of 970 FSWs provided valid questionnaires, with 69% (669) expressing willingness to utilize VCT. Factors at the interpersonal level associated with reported willingness included knowledge about VCT, desire to get help if diagnosed as HIV positive, ability to imagine life after an HIV positive diagnosis, and perceived support for VCT from peers, managers, and family members. Availability of free antiretroviral (ARV) treatment represented a factor at policy level. Other factors included intention to leave sex work in the near future, having had a previous HIV test, and lack of a suspected STD history. CONCLUSIONS: The rate of reported willingness to use VCT among FSWs was substantially higher than that of actual VCT utilization (11%). The next step is to explore the connection between reported willingness and actual use. Based on these findings, peer education, VCT knowledge dissemination, and free ARV treatment should be emphasized to increase FSWs' willingness to use VCT.

A conceptual model exploring the relationship between HIV stigma and implementing HIV clinical trials in rural communities of North Carolina.

BACKGROUND: HIV/AIDS disproportionately affects minority groups in the United States, especially in the rural southeastern states. Poverty and lack of access to HIV care, including clinical trials, are prevalent in these areas and contribute to HIV stigma. This is the first study to develop a conceptual model exploring the relationship between HIV stigma and the implementation of HIV clinical trials in rural contexts to help improve participation in those trials. METHODS: We conducted focus groups with HIV service providers and community leaders, and individual interviews with people living with HIV/AIDS in six counties in rural North Carolina. Themes related to stigma were elicited. We classified the themes into theoretical constructs and developed a conceptual model. RESULTS: HIV stigma themes were classified under the existing theoretical constructs of perceived, experienced, vicarious, and felt normative stigma. Two additional constructs emerged: causes of HIV stigma (e.g., low HIV knowledge and denial in the community) and consequences of HIV stigma (e.g., confidentiality concerns in clinical trials). The conceptual model illustrates that the causes of HIV stigma can give rise to perceived, experienced, and vicarious HIV stigma, and these types of stigma could lead to the consequences of HIV stigma that include felt normative stigma. LIMITATIONS: Understanding HIV stigma in rural counties of North Carolina may not be generalizeable to other rural US southeastern states. CONCLUSION: The conceptual model emphasizes that HIV stigma--in its many forms--is a critical barrier to HIV clinical trial implementation in rural North Carolina.

Ultrasound assessment of fetal hearing response to vibroacoustic stimulation.

Background: Assessment of fetal responses to external stimuli could be a vital clue for understanding development of fetal neurophysiology, which is extremely challenging to explore. To study hearing development in growing human fetus, we assessed sonographic fetal movement responses to external auditory stimulus at increasing period of gestation.Method: In 123 normal pregnant women between 16 and 40 weeks' gestation, sonographic assessment of fetal movements (gross body movement, isolated limb movement, breathing movement and startle response) was carried out before and after administering vibroacoustic stimulation (VAS). Types and number of fetal movements during 5-min period each - immediately before and after application of VAS - were compared.Results: With increasing gestational age, spontaneous gross body movement decreased significantly between 16-28 and 29-40 weeks of gestation (93.3 versus 66.6%; p < .001). However, VAS significantly increased gross body movement at 29-40 weeks of gestation (66.6 versus 93.6%; p < .001). Incidence of isolated limb movement was inversely related to increasing gestational age. However, VAS was associated with significantly increase in isolated limb movement during 29-40 weeks' gestation (57.1 versus 80.9%; p = .007). VAS induced almost similar pattern of response for both fetal startle and breathing movements.Conclusions: Fetal movement responses to VAS are consistent after 28 weeks' gestation. These findings suggest fetal hearing develops at or before 28 weeks of intrauterine life.

Factors related to female sex workers' willingness to utilize VCT service: a qualitative study in Jinan city, northern China.

While national HIV prevalence remains low in China, female sex workers (FSWs) have become infected at high rates. Free voluntary HIV counseling and testing (VCT) has been offered in recent years; however, its utilization rate is low. This study explored factors related to FSWs' willingness to utilize a VCT clinic. Qualitative interviews informed by the Ecological Perspective were conducted to interview 17 FSWs and 12 managers from 23 selected entertainment establishments in Jinan, the capital of Shandong province in northern China. While the majority of FSWs professed willingness to use VCT services, they described barriers to actual utilization of services which included: misunderstandings about HIV; low perceived risk and HIV prevalence; mistrust of the free VCT; and especially anxiety about the implications of possible test results. This research suggests that increasing FSWs' utilization of VCT will require increased knowledge of HIV and VCT, and acceptance of testing and on-site VCT services.

Measuring stigma associated with tuberculosis and HIV/AIDS in southern Thailand: exploratory and confirmatory factor analyses of two new scales.

OBJECTIVE: To develop scales to measure tuberculosis and HIV/AIDS stigma in a developing world context. METHODS: Cross-sectional study of tuberculosis patients in southern Thailand, who were asked to rate their agreement with items measuring TB and HIV/AIDS stigma. Developing the scales involved exploratory and confirmatory factor analyses, internal consistency, construct validity, test-retest reliability and standardized summary scores. RESULTS: Factor analyses identified two sub-scales associated with both tuberculosis and HIV/AIDS stigma: community and patient perspectives. Goodness-of-fit was good (TLI = 94, LFI = 0.88 and RMSEA = 0.11), internal consistency was excellent (Cronbach's alphas 0.82-0.91), test-retest reliability was moderate, and construct validity showed an inverse correlation with social support. CONCLUSION: Our scales have good psychometric properties that measure stigma associated with tuberculosis and HIV/AIDS and allow assessment of stigma from community and patient perspectives. Their use will help document the burden of stigma, guide the development of interventions and evaluate stigma reduction programmes in areas with a high HIV/AIDS and tuberculosis burden.

2007 costs and coverage of antiretrovirals under Medicare Part D for people with HIV/AIDS living in North Carolina.

BACKGROUND: Effective January 1, 2006 Medicare Part D became a new source of prescription drug coverage for people with HIV/AIDS in the United States. The implementation of Part D has affected access to antiretrovirals for people with HIV/AIDS. In North Carolina, access can be difficult because of the state's struggling safety net programs and the growing HIV-infected populations among Blacks and in poor rural counties. This analysis examines Medicare Part D antiretroviral coverage in 2007 for beneficiaries with HIV/AIDS in North Carolina, particularly those who did not qualify as dual eligibles or for a full low-income subsidy. METHODS: Data describing program coverage were obtained from the Web site www.medicare.gov and descriptive analyses were performed to assess changes in antiretroviral coverage in Part D prescription drug plans in North Carolina. RESULTS: Most of the 26 antiretrovirals are covered in some way by 76 North Carolina prescription drug plans. There may be variability in coverage however associated with (a) antiretroviral classification within formularies; (b) drug premiums; (c) whether premiums can be waived; (d) annual deductibles; and (e) whether coverage is provided in the "doughnut hole." LIMITATIONS: The data may not reflect actual patterns of drug use and realized access to the drugs. The findings are limited to antiretroviral coverage in North Carolina's Part D offerings but could be generalized to other states with similar prescription drug plan costs and coverage. CONCLUSION: These concerns continue to pose significant challenges to accessing antiretrovirals for Part D beneficiaries with HIV/AIDS in North Carolina. Variability demonstrated within prescription drug plans will continue, and beneficiaries with HIV/AIDS who do not qualify as dual eligibles or for low-income subsidies will need to evaluate these issues when selecting a prescription drug plan in future enrollment periods.