Analytical validation of a novel comprehensive genomic profiling informed circulating tumor DNA monitoring assay for solid tumors.

Emerging technologies focused on the detection and quantification of circulating tumor DNA (ctDNA) in blood show extensive potential for managing patient treatment decisions, informing risk of recurrence, and predicting response to therapy. Currently available tissue-informed approaches are often limited by the need for additional sequencing of normal tissue or peripheral mononuclear cells to identify non-tumor-derived alterations while tissue-naïve approaches are often limited in sensitivity. Here we present the analytical validation for a novel ctDNA monitoring assay, FoundationOne®Tracker. The assay utilizes somatic alterations from comprehensive genomic profiling (CGP) of tumor tissue. A novel algorithm identifies monitorable alterations with a high probability of being somatic and computationally filters non-tumor-derived alterations such as germline or clonal hematopoiesis variants without the need for sequencing of additional samples. Monitorable alterations identified from tissue CGP are then quantified in blood using a multiplex polymerase chain reaction assay based on the validated SignateraTM assay. The analytical specificity of the plasma workflow is shown to be 99.6% at the sample level. Analytical sensitivity is shown to be >97.3% at ≥5 mean tumor molecules per mL of plasma (MTM/mL) when tested with the most conservative configuration using only two monitorable alterations. The assay also demonstrates high analytical accuracy when compared to liquid biopsy-based CGP as well as high qualitative (measured 100% PPA) and quantitative precision (<11.2% coefficient of variation).

COVID-19 Vaccine Booster Dose Acceptance: Systematic Review and Meta-Analysis.

The World Health Organization (WHO) recommended coronavirus disease 2019 (COVID-19) booster dose vaccination after completing the primary vaccination series for individuals ≥18 years and most-at-risk populations. This study aimed to estimate the pooled proportion of COVID-19 vaccine booster dose uptake and intention to get the booster dose among general populations and healthcare workers (HCWs). We searched PsycINFO, Scopus, EBSCO, MEDLINE Central/PubMed, ProQuest, SciELO, SAGE, Web of Science, Google Scholar, and ScienceDirect according to PRISMA guidelines. From a total of 1079 screened records, 50 studies were extracted. Meta-analysis was conducted using 48 high-quality studies according to the Newcastle-Ottawa Scale quality assessment tool. Using the 48 included studies, the pooled proportion of COVID-19 vaccine booster dose acceptance among 198,831 subjects was 81% (95% confidence interval (CI): 75-85%, I2 = 100%). The actual uptake of the booster dose in eight studies involving 12,995 subjects was 31% (95% CI: 19-46%, I2 = 100%), while the intention to have the booster dose of the vaccine was 79% (95% CI: 72-85%, I2 = 100%). The acceptance of the booster dose of COVID-19 vaccines among HCWs was 66% (95% CI: 58-74%), I2 = 99%). Meta-regression revealed that previous COVID-19 infection was associated with a lower intention to have the booster dose. Conversely, previous COVID-19 infection was associated with a significantly higher level of booster dose actual uptake. The pooled booster dose acceptance in the WHO region of the Americas, which did not include any actual vaccination, was 77% (95% CI: 66-85%, I2 = 100%). The pooled acceptance of the booster dose in the Western Pacific was 89% (95% CI: 84-92%, I2 = 100), followed by the European region: 86% (95% CI: 81-90%, I2 = 99%), the Eastern Mediterranean region: 59% (95% CI: 46-71%, I2 = 99%), and the Southeast Asian region: 52% (95% CI: 43-61%, I2 = 95). Having chronic disease and trust in the vaccine effectiveness were the significant predictors of booster dose COVID-19 vaccine acceptance. The global acceptance rate of COVID-19 booster vaccine is high, but the rates vary by region. To achieve herd immunity for the disease, a high level of vaccination acceptance is required. Intensive vaccination campaigns and programs are still needed around the world to raise public awareness regarding the importance of accepting COVID-19 vaccines needed for proper control of the pandemic.

Circulating Tumor DNA in Stage III Colorectal Cancer, beyond Minimal Residual Disease Detection, toward Assessment of Adjuvant Therapy Efficacy and Clinical Behavior of Recurrences.

PURPOSE: Sensitive methods for risk stratification, monitoring therapeutic efficacy, and early relapse detection may have a major impact on treatment decisions and patient management for stage III colorectal cancer patients. Beyond assessing the predictive power of postoperative ctDNA detection, we explored the added benefits of serial analysis: assessing adjuvant chemotherapy (ACT) efficacy, early relapse detection, and ctDNA growth rates. EXPERIMENTAL DESIGN: We recruited 168 patients with stage III colorectal cancer treated with curative intent at Danish and Spanish hospitals between 2014 and 2019. To quantify ctDNA in plasma samples (n = 1,204), 16 patient-specific somatic single-nucleotide variants were profiled using multiplex-PCR, next-generation sequencing. RESULTS: Detection of ctDNA was a strong recurrence predictor postoperatively [HR = 7.0; 95% confidence interval (CI), 3.7-13.5; P < 0.001] and directly after ACT (HR = 50.76; 95% CI, 15.4-167; P < 0.001). The recurrence rate of postoperative ctDNA-positive patients treated with ACT was 80% (16/20). Only patients who cleared ctDNA permanently during ACT did not relapse. Serial ctDNA assessment after the end of treatment was similarly predictive of recurrence (HR = 50.80; 95% CI, 14.9-172; P < 0.001), and revealed two distinct rates of exponential ctDNA growth, slow (25% ctDNA-increase/month) and fast (143% ctDNA-increase/month; P < 0.001). The ctDNA growth rate was prognostic of survival (HR = 2.7; 95% CI, 1.1-6.7; P = 0.039). Serial ctDNA analysis every 3 months detected recurrence with a median lead-time of 9.8 months compared with standard-of-care computed tomography. CONCLUSIONS: Serial postoperative ctDNA analysis has a strong prognostic value and enables tumor growth rate assessment. The novel combination of ctDNA detection and growth rate assessment provides unique opportunities for guiding decision-making.See related commentary by Morris and George, p. 438.

Recent advances in nanomedicine-based delivery of histone deacetylase inhibitors for cancer therapy.

Histone deacetylase inhibitors (HDACi) are cancer therapeutics that operate at the epigenetic level and which have recently gained wide attention. However, the applications of HDACi are generally hindered by their poor physicochemical characteristics and unfavorable pharmacokinetic profile. Inspired by the approved nanomedicine-based drugs in the market, nanocarriers could provide a resort to circumvent the limitations imposed by HDACi. Enhanced tumor targeting, improved cellular uptake and reduced toxicity are major advantages offered by HDACi-loaded nanoparticles. More importantly, site-specific drug delivery can be achieved via engineered stimuli-responsive nanosystems. In this review we elucidate the anticancer mechanisms of HDACi and their structure-activity relationships, with a special focus on their nanomedicine-based delivery, different drug loading concepts and their implications.

Analysis of Plasma Cell-Free DNA by Ultradeep Sequencing in Patients With Stages I to III Colorectal Cancer.

IMPORTANCE: Novel sensitive methods for detection and monitoring of residual disease can improve postoperative risk stratification with implications for patient selection for adjuvant chemotherapy (ACT), ACT duration, intensity of radiologic surveillance, and, ultimately, outcome for patients with colorectal cancer (CRC). OBJECTIVE: To investigate the association of circulating tumor DNA (ctDNA) with recurrence using longitudinal data from ultradeep sequencing of plasma cell-free DNA in patients with CRC before and after surgery, during and after ACT, and during surveillance. DESIGN, SETTING, AND PARTICIPANTS: In this prospective, multicenter cohort study, ctDNA was quantified in the preoperative and postoperative settings of stages I to III CRC by personalized multiplex, polymerase chain reaction-based, next-generation sequencing. The study enrolled 130 patients at the surgical departments of Aarhus University Hospital, Randers Hospital, and Herning Hospital in Denmark from May 1, 2014, to January 31, 2017. Plasma samples (n = 829) were collected before surgery, postoperatively at day 30, and every third month for up to 3 years. MAIN OUTCOMES AND MEASURES: Outcomes were ctDNA measurement, clinical recurrence, and recurrence-free survival. RESULTS: A total of 130 patients with stages I to III CRC (mean [SD] age, 67.9 [10.1] years; 74 [56.9%] male) were enrolled in the study; 5 patients discontinued participation, leaving 125 patients for analysis. Preoperatively, ctDNA was detectable in 108 of 122 patients (88.5%). After definitive treatment, longitudinal ctDNA analysis identified 14 of 16 relapses (87.5%). At postoperative day 30, ctDNA-positive patients were 7 times more likely to relapse than ctDNA-negative patients (hazard ratio [HR], 7.2; 95% CI, 2.7-19.0; P < .001). Similarly, shortly after ACT ctDNA-positive patients were 17 times (HR, 17.5; 95% CI, 5.4-56.5; P < .001) more likely to relapse. All 7 patients who were ctDNA positive after ACT experienced relapse. Monitoring during and after ACT indicated that 3 of the 10 ctDNA-positive patients (30.0%) were cleared by ACT. During surveillance after definitive therapy, ctDNA-positive patients were more than 40 times more likely to experience disease recurrence than ctDNA-negative patients (HR, 43.5; 95% CI, 9.8-193.5 P < .001). In all multivariate analyses, ctDNA status was independently associated with relapse after adjusting for known clinicopathologic risk factors. Serial ctDNA analyses revealed disease recurrence up to 16.5 months ahead of standard-of-care radiologic imaging (mean, 8.7 months; range, 0.8-16.5 months). Actionable mutations were identified in 81.8% of the ctDNA-positive relapse samples. CONCLUSIONS AND RELEVANCE: Circulating tumor DNA analysis can potentially change the postoperative management of CRC by enabling risk stratification, ACT monitoring, and early relapse detection.

Early Detection of Metastatic Relapse and Monitoring of Therapeutic Efficacy by Ultra-Deep Sequencing of Plasma Cell-Free DNA in Patients With Urothelial Bladder Carcinoma.

PURPOSE: Novel sensitive methods for early detection of relapse and for monitoring therapeutic efficacy may have a huge impact on risk stratification, treatment, and ultimately outcome for patients with bladder cancer. We addressed the prognostic and predictive impact of ultra-deep sequencing of cell-free DNA in patients before and after cystectomy and during chemotherapy. PATIENTS AND METHODS: We included 68 patients with localized advanced bladder cancer. Patient-specific somatic mutations, identified by whole-exome sequencing, were used to assess circulating tumor DNA (ctDNA) by ultra-deep sequencing (median, 105,000×) of plasma DNA. Plasma samples (n = 656) were procured at diagnosis, during chemotherapy, before cystectomy, and during surveillance. Expression profiling was performed for tumor subtype and immune signature analyses. RESULTS: Presence of ctDNA was highly prognostic at diagnosis before chemotherapy (hazard ratio, 29.1; P = .001). After cystectomy, ctDNA analysis correctly identified all patients with metastatic relapse during disease monitoring (100% sensitivity, 98% specificity). A median lead time over radiographic imaging of 96 days was observed. In addition, for high-risk patients (ctDNA positive before or during treatment), the dynamics of ctDNA during chemotherapy was associated with disease recurrence (P = .023), whereas pathologic downstaging was not. Analysis of tumor-centric biomarkers showed that mutational processes (signature 5) were associated with pathologic downstaging (P = .024); however, no significant correlation for tumor subtypes, DNA damage response mutations, and other biomarkers was observed. Our results suggest that ctDNA analysis is better associated with treatment efficacy compared with other available methods. CONCLUSION: ctDNA assessment for early risk stratification, therapy monitoring, and early relapse detection in bladder cancer is feasible and provides a basis for clinical studies that evaluate early therapeutic interventions.

Personalized Detection of Circulating Tumor DNA Antedates Breast Cancer Metastatic Recurrence.

PURPOSE: Up to 30% of patients with breast cancer relapse after primary treatment. There are no sensitive and reliable tests to monitor these patients and detect distant metastases before overt recurrence. Here, we demonstrate the use of personalized circulating tumor DNA (ctDNA) profiling for detection of recurrence in breast cancer. EXPERIMENTAL DESIGN: Forty-nine primary patients with breast cancer were recruited following surgery and adjuvant therapy. Plasma samples (n = 208) were collected every 6 months for up to 4 years. Personalized assays targeting 16 variants selected from primary tumor whole-exome data were tested in serial plasma for the presence of ctDNA by ultradeep sequencing (average >100,000X). RESULTS: Plasma ctDNA was detected ahead of clinical or radiologic relapse in 16 of the 18 relapsed patients (sensitivity of 89%); metastatic relapse was predicted with a lead time of up to 2 years (median, 8.9 months; range, 0.5-24.0 months). None of the 31 nonrelapsing patients were ctDNA-positive at any time point across 156 plasma samples (specificity of 100%). Of the two relapsed patients who were not detected in the study, the first had only a local recurrence, whereas the second patient had bone recurrence and had completed chemotherapy just 13 days prior to blood sampling. CONCLUSIONS: This study demonstrates that patient-specific ctDNA analysis can be a sensitive and specific approach for disease surveillance for patients with breast cancer. More importantly, earlier detection of up to 2 years provides a possible window for therapeutic intervention.

Association Between Purpose in Life and Glucose Control Among Older Adults.

Background: Greater purpose in life is associated with lower rates of certain chronic diseases. Whether purpose in life can protect against development of prediabetes or type 2 diabetes is unknown. Purpose: To examine the association between purpose in life and blood glucose control among adults ≥50 years. Methods: We conducted a longitudinal cohort study of 3,907 participants of the Health and Retirement Study who at baseline did not have type 2 diabetes or prediabetes. Baseline purpose in life was measured using the Ryff and Keyes' Scales of Psychological Well-Being and grouped into tertiles (high, medium, and low). We used multivariable linear regression to examine the association between baseline purpose in life and HbA1c over 4 years. Multivariable logistic regression was used to examine the association between baseline purpose and incident prediabetes or type 2 diabetes over the same period. Results: After adjusting for sociodemographic factors, body mass index, physical activity, and physical and mental health factors, HbA1c was 0.07 percentage points lower among participants with high purpose than those with low purpose (95% confidence interval [CI] -0.12 to -0.02; p = .011). Participants with high purpose had lower odds of developing prediabetes or type 2 diabetes than those with low purpose (adjusted odds ratio 0.78; 95% CI 0.62 to 0.98; p = .037). Conclusions: Among older adults, greater purpose in life is associated with a lower incidence of prediabetes or type 2 diabetes. Strategies to promote greater purpose in life should be tested as a part of type 2 diabetes prevention efforts.

Ambulatory care-sensitive emergency visits among patients with medical home access.

OBJECTIVES: To characterize patterns of emergency department (ED) utilization for ambulatory care-sensitive conditions (ACSCs) among patients with established care within a patient-centered medical home. STUDY DESIGN: Retrospective chart review using Michigan Medicine's (formerly University of Michigan Health System) electronic health record. METHODS: Ten general medicine (GM) physicians reviewed 256 ambulatory care-sensitive ED encounters that occurred between January 1, 2014, and December 31, 2014, among patients of a GM medical home. Physician reviewers abstracted from the medical record the day and time of ED presentation and the source of ED referral (eg, patient self-referral vs physician referral). Physicians assessed the appropriateness of the care location (eg, ED vs primary care). Interrater reliability was assessed using the kappa statistic, and the χ2 test was used to assess differences in the appropriateness of the care location according to ED referral source. RESULTS: Compared with all other days of the week, the fewest number of ED visits occurred on weekend days, and nearly half of patients (48%) presented to the ED after daytime hours, which were defined as 8 am to 3:59 pm. The majority (n = 185; 72%) of patients were self-referred to the ED. The ED was considered the appropriate care location in more than half (53%) of the reviewed cases. Among the 119 cases considered appropriate for GM management, the majority (86%) were self-referred to the ED. CONCLUSIONS: Patients with ACSCs often presented to the ED without contacting their medical home. Frequently, the ED is the most appropriate location given symptoms at presentation.

Corrigendum: Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution.

This corrects the article DOI: 10.1038/nature22364.

McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes.

Transcriptional enhancers regulate spatio-temporal gene expression. While genomic assays can identify putative enhancers en masse, assigning target genes is a complex challenge. We devised a machine learning approach, McEnhancer, which links target genes to putative enhancers via a semi-supervised learning algorithm that predicts gene expression patterns based on enriched sequence features. Predicted expression patterns were 73-98% accurate, predicted assignments showed strong Hi-C interaction enrichment, enhancer-associated histone modifications were evident, and known functional motifs were recovered. Our model provides a general framework to link globally identified enhancers to targets and contributes to deciphering the regulatory genome.

A Scoping Review of Behavioral Economic Interventions for Prevention and Treatment of Type 2 Diabetes Mellitus.

PURPOSE OF REVIEW: The purpose of this paper was to review studies of behavioral economic interventions (financial incentives, choice architecture modifications, or commitment devices) to prevent type 2 diabetes mellitus (T2DM) among at-risk patients or improve self-management among patients with T2DM. RECENT FINDINGS: We found 15 studies that used varied study designs and outcomes to test behavioral economic interventions in clinical, workplace, or health plan settings. Of four studies that focused on prevention of T2DM, two found that financial incentives increased weight loss and completion of a fasting blood glucose test, and two choice architecture modifications had mixed effects in encouraging completion of tests to screen for T2DM. Of 11 studies that focused on improving self-management of T2DM, four of six tests of financial incentives demonstrated increased engagement in recommended care processes or improved biometric measures, and three of five tests of choice architecture modifications found improvements in self-management behaviors. Though few studies have tested behavioral economic interventions for prevention or treatment of T2DM, those that have suggested such approaches have the potential to improve patient behaviors and such approaches should be tested more broadly.

Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution.

The early detection of relapse following primary surgery for non-small-cell lung cancer and the characterization of emerging subclones, which seed metastatic sites, might offer new therapeutic approaches for limiting tumour recurrence. The ability to track the evolutionary dynamics of early-stage lung cancer non-invasively in circulating tumour DNA (ctDNA) has not yet been demonstrated. Here we use a tumour-specific phylogenetic approach to profile the ctDNA of the first 100 TRACERx (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy (Rx)) study participants, including one patient who was also recruited to the PEACE (Posthumous Evaluation of Advanced Cancer Environment) post-mortem study. We identify independent predictors of ctDNA release and analyse the tumour-volume detection limit. Through blinded profiling of postoperative plasma, we observe evidence of adjuvant chemotherapy resistance and identify patients who are very likely to experience recurrence of their lung cancer. Finally, we show that phylogenetic ctDNA profiling tracks the subclonal nature of lung cancer relapse and metastasis, providing a new approach for ctDNA-driven therapeutic studies.

Understanding type 2 diabetes mellitus screening practices among primary care physicians: a qualitative chart-stimulated recall study.

BACKGROUND: Early diagnosis and treatment of prediabetes and type 2 diabetes mellitus (T2DM) can prevent future health problems, yet many individuals with these conditions are undiagnosed. This could be due, in part, to primary care physicians' (PCP) screening practices, about which little is known. The objectives of this study were to identify factors that influence PCPs' decisions to screen patients for T2DM and to characterize their interpretation and communication of screening test results to patients. METHODS: We conducted semi-structured chart-stimulated recall interviews with 20 University of Michigan Health System (UMHS) primary care physicians. PCPs were asked about their recent decisions to screen or not screen 134 purposively sampled non-diabetic patients who met American Diabetes Association criteria for screening for T2DM. Interviews were audio-recorded, transcribed, and analyzed using qualitative directed content analysis. Data on patient demographic characteristics and comorbidities were abstracted from the electronic health record. RESULTS: The most common reasons PCPs gave for not screening 63 patients for T2DM were knowledge of a previously normal screening test (49%) and a visit for reasons other than a health maintenance examination (48%). The most common reasons PCPs gave for screening 71 patients for T2DM were knowledge of a previously abnormal screening test (49%), and patients' weight (42%) and age (38%). PCPs correctly interpreted 89% of screening test results and communicated 95% of test results to patients. Among 24 patients found to have prediabetes, PCPs usually (58%) recommended weight loss and increased physical activity but never recommended participation in a Diabetes Prevention Program or use of metformin. CONCLUSIONS: Previous screening test results, visit types, and patients' weight and age influenced PCPs' decisions to screen for T2DM. When patients were screened, test results were generally correctly interpreted and consistently communicated. Recommendations to patients with prediabetes could better reflect evidence-based strategies to prevent T2DM.

The Effect of Technology-Mediated Diabetes Prevention Interventions on Weight: A Meta-Analysis.

BACKGROUND: Lifestyle interventions targeting weight loss, such as those delivered through the Diabetes Prevention Program, reduce the risk of developing type 2 diabetes. Technology-mediated interventions may be an option to help overcome barriers to program delivery, and to disseminate diabetes prevention programs on a larger scale. OBJECTIVE: We conducted a meta-analysis to evaluate the effect of such technology-mediated interventions on weight loss. METHODS: In this meta-analysis, six databases were searched to identify studies reporting weight change that used technology to mediate diet and exercise interventions, and targeted individuals at high risk for developing type 2 diabetes. Studies published between January 1, 2002 and August 4, 2016 were included. RESULTS: The search identified 1196 citations. Of those, 15 studies met the inclusion criteria and evaluated 18 technology-mediated intervention arms delivered to a total of 2774 participants. Study duration ranged from 12 weeks to 2 years. A random-effects meta-analysis showed a pooled weight loss effect of 3.76 kilograms (95% CI 2.8-4.7; P<.001) for the interventions. Several studies also reported improved glycemic control following the intervention. The small sample sizes and heterogeneity of the trials precluded an evaluation of which technology-mediated intervention method was most efficacious. CONCLUSIONS: Technology-mediated diabetes prevention programs can result in clinically significant amounts of weight loss, as well as improvements in glycaemia in patients with prediabetes. Due to their potential for large-scale implementation, these interventions will play an important role in the dissemination of diabetes prevention programs.

Workplace Interventions to Prevent Type 2 Diabetes Mellitus: a Narrative Review.

PURPOSE OF REVIEW: This study aims to summarize the recent peer-reviewed literature on workplace interventions for prevention of type 2 diabetes mellitus (T2DM), including studies that translate the Diabetes Prevention Program (DPP) curriculum to workplace settings (n = 10) and those that use different intervention approaches to achieve the specific objective of T2DM prevention among employees (n = 3). RECENT FINDINGS: Weight reduction was achieved through workplace interventions to prevent T2DM, though such interventions varied substantially in their effectiveness. The greatest weight loss was reported among intensive lifestyle interventions (i.e., at least 4 months in duration) that implemented the structured DPP curriculum (n = 3). Weight reduction was minimal among less intensive interventions, including those that substantially modified the DPP curriculum (n = 2) and those that used non-DPP intervention approaches to prevent T2DM (n = 3). Most studies (n = 12) reported increased levels of physical activity following the intervention. Implementation of the DPP in workplaces may be an effective strategy to prevent T2DM among employees.

Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy.

BACKGROUND: Polyadenylation is a key regulatory step in eukaryotic gene expression and one of the major contributors of transcriptome diversity. Aberrant polyadenylation often associates with expression defects and leads to human diseases. RESULTS: To better understand global polyadenylation regulation, we have developed a polyadenylation sequencing (PA-seq) approach. By profiling polyadenylation events in 13 human tissues, we found that alternative cleavage and polyadenylation (APA) is prevalent in both protein-coding and noncoding genes. In addition, APA usage, similar to gene expression profiling, exhibits tissue-specific signatures and is sufficient for determining tissue origin. A 3' untranslated region shortening index (USI) was further developed for genes with tandem APA sites. Strikingly, the results showed that different tissues exhibit distinct patterns of shortening and/or lengthening of 3' untranslated regions, suggesting the intimate involvement of APA in establishing tissue or cell identity. CONCLUSIONS: This study provides a comprehensive resource to uncover regulated polyadenylation events in human tissues and to characterize the underlying regulatory mechanism.