Adding α,α-disubstituted and ß-linked monomers to the genetic code of an organism.

The genetic code of living cells has been reprogrammed to enable the site-specific incorporation of hundreds of non-canonical amino acids into proteins, and the encoded synthesis of non-canonical polymers and macrocyclic peptides and depsipeptides1-3. Current methods for engineering orthogonal aminoacyl-tRNA synthetases to acylate new monomers, as required for the expansion and reprogramming of the genetic code, rely on translational readouts and therefore require the monomers to be ribosomal substrates4-6. Orthogonal synthetases cannot be evolved to acylate orthogonal tRNAs with non-canonical monomers (ncMs) that are poor ribosomal substrates, and ribosomes cannot be evolved to polymerize ncMs that cannot be acylated onto orthogonal tRNAs-this co-dependence creates an evolutionary deadlock that has essentially restricted the scope of translation in living cells to α-L-amino acids and closely related hydroxy acids. Here we break this deadlock by developing tRNA display, which enables direct, rapid and scalable selection for orthogonal synthetases that selectively acylate their cognate orthogonal tRNAs with ncMs in Escherichia coli, independent of whether the ncMs are ribosomal substrates. Using tRNA display, we directly select orthogonal synthetases that specifically acylate their cognate orthogonal tRNA with eight non-canonical amino acids and eight ncMs, including several ß-amino acids, α,α-disubstituted-amino acids and ß-hydroxy acids. We build on these advances to demonstrate the genetically encoded, site-specific cellular incorporation of ß-amino acids and α,α-disubstituted amino acids into a protein, and thereby expand the chemical scope of the genetic code to new classes of monomers.

RBBP6 activates the pre-mRNA 3' end processing machinery in humans.

3' end processing of most human mRNAs is carried out by the cleavage and polyadenylation specificity factor (CPSF; CPF in yeast). Endonucleolytic cleavage of the nascent pre-mRNA defines the 3' end of the mature transcript, which is important for mRNA localization, translation, and stability. Cleavage must therefore be tightly regulated. Here, we reconstituted specific and efficient 3' endonuclease activity of human CPSF with purified proteins. This required the seven-subunit CPSF as well as three additional protein factors: cleavage stimulatory factor (CStF), cleavage factor IIm (CFIIm), and, importantly, the multidomain protein RBBP6. Unlike its yeast homolog Mpe1, which is a stable subunit of CPF, RBBP6 does not copurify with CPSF and is recruited in an RNA-dependent manner. Sequence and mutational analyses suggest that RBBP6 interacts with the WDR33 and CPSF73 subunits of CPSF. Thus, it is likely that the role of RBBP6 is conserved from yeast to humans. Overall, our data are consistent with CPSF endonuclease activation and site-specific pre-mRNA cleavage being highly controlled to maintain fidelity in mRNA processing.

Total synthesis of Escherichia coli with a recoded genome.

Nature uses 64 codons to encode the synthesis of proteins from the genome, and chooses 1 sense codon-out of up to 6 synonyms-to encode each amino acid. Synonymous codon choice has diverse and important roles, and many synonymous substitutions are detrimental. Here we demonstrate that the number of codons used to encode the canonical amino acids can be reduced, through the genome-wide substitution of target codons by defined synonyms. We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis. Our synthetic genome implements a defined recoding and refactoring scheme-with simple corrections at just seven positions-to replace every known occurrence of two sense codons and a stop codon in the genome. Thus, we recode 18,214 codons to create an organism with a 61-codon genome; this organism uses 59 codons to encode the 20 amino acids, and enables the deletion of a previously essential transfer RNA.

Edetate Disodium-Based Chelation for Patients With a Previous Myocardial Infarction and Diabetes: TACT2 Randomized Clinical Trial.

Importance: In 2013, the Trial to Assess Chelation Therapy (TACT) reported that edetate disodium (EDTA)-based chelation significantly reduced cardiovascular disease (CVD) events by 18% in 1708 patients with a prior myocardial infarction (MI). Objective: To replicate the finding of TACT in individuals with diabetes and previous MI. Design, Setting, and Participants: A 2 × 2 factorial, double-masked, placebo-controlled, multicenter trial at 88 sites in the US and Canada, involving participants who were 50 years or older, had diabetes, and had experienced an MI at least 6 weeks before recruitment compared the effect of EDTA-based chelation vs placebo infusions on CVD events and compared the effect of high doses of oral multivitamins and minerals with oral placebo. This article reports on the chelation vs placebo infusion comparisons. Interventions: Eligible participants were randomly assigned to 40 weekly infusions of an EDTA-based chelation solution or matching placebo and to twice daily oral, high-dose multivitamin and mineral supplements or matching placebo for 60 months. This article addresses the chelation study. Main Outcomes and Measures: The primary end point was the composite of all-cause mortality, MI, stroke, coronary revascularization, or hospitalization for unstable angina. Median follow-up was 48 months. Primary comparisons were made from patients who received at least 1 assigned infusion. Results: Of the 959 participants (median age, 67 years [IQR, 60-72 years]; 27% females; 78% White, 10% Black, and 20% Hispanic), 483 received at least 1 chelation infusion and 476 at least 1 placebo infusion. A primary end point event occurred in 172 participants (35.6%) in the chelation group and in 170 (35.7%) in the placebo group (adjusted hazard ratio [HR], 0.93; 95% CI, 0.76-1.16; P = .53). The 5-year primary event cumulative incidence rates were 45.8% for the chelation group and 46.5% for the placebo group. CV death, MI, or stroke events occurred in 89 participants (18.4%) in the chelation group and in 94 (19.7%) in the placebo group (adjusted HR, 0.89; 95% CI, 0.66-1.19). Death from any cause occurred in 84 participants (17.4%) in the chelation group and in 84 (17.6%) in the placebo group (adjusted HR, 0.96; 95% CI, 0.71-1.30). Chelation reduced median blood lead levels from 9.03 µg/L at baseline to 3.46 µg/L at infusion 40 (P < .001). Corresponding levels in the placebo group were 9.3 µg/L and 8.7 µg/L, respectively. Conclusions and Relevance: Despite effectively reducing blood lead levels, EDTA chelation was not effective in reducing cardiovascular events in stable patients with coronary artery disease who have diabetes and a history of MI. Trial Registration: ClinicalTrials.gov Identifier: NCT02733185.

Serum Urate Lowering with Allopurinol and Kidney Function in Type 1 Diabetes.

BACKGROUND: Higher serum urate levels are associated with an increased risk of diabetic kidney disease. Lowering of the serum urate level with allopurinol may slow the decrease in the glomerular filtration rate (GFR) in persons with type 1 diabetes and early-to-moderate diabetic kidney disease. METHODS: In a double-blind trial, we randomly assigned participants with type 1 diabetes, a serum urate level of at least 4.5 mg per deciliter, an estimated GFR of 40.0 to 99.9 ml per minute per 1.73 m2 of body-surface area, and evidence of diabetic kidney disease to receive allopurinol or placebo. The primary outcome was the baseline-adjusted GFR, as measured with iohexol, after 3 years plus a 2-month washout period. Secondary outcomes included the decrease in the iohexol-based GFR per year and the urinary albumin excretion rate after washout. Safety was also assessed. RESULTS: A total of 267 patients were assigned to receive allopurinol and 263 to receive placebo. The mean age was 51.1 years, the mean duration of diabetes 34.6 years, and the mean glycated hemoglobin level 8.2%. The mean baseline iohexol-based GFR was 68.7 ml per minute per 1.73 m2 in the allopurinol group and 67.3 ml per minute per 1.73 m2 in the placebo group. During the intervention period, the mean serum urate level decreased from 6.1 to 3.9 mg per deciliter with allopurinol and remained at 6.1 mg per deciliter with placebo. After washout, the between-group difference in the mean iohexol-based GFR was 0.001 ml per minute per 1.73 m2 (95% confidence interval [CI], -1.9 to 1.9; P = 0.99). The mean decrease in the iohexol-based GFR was -3.0 ml per minute per 1.73 m2 per year with allopurinol and -2.5 ml per minute per 1.73 m2 per year with placebo (between-group difference, -0.6 ml per minute per 1.73 m2 per year; 95% CI, -1.5 to 0.4). The mean urinary albumin excretion rate after washout was 40% (95% CI, 0 to 80) higher with allopurinol than with placebo. The frequency of serious adverse events was similar in the two groups. CONCLUSIONS: We found no evidence of clinically meaningful benefits of serum urate reduction with allopurinol on kidney outcomes among patients with type 1 diabetes and early-to-moderate diabetic kidney disease. (Funded by the National Institute of Diabetes and Digestive and Kidney Diseases and others; PERL ClinicalTrials.gov number, NCT02017171.).

The trial to assess chelation therapy 2 (TACT2): Rationale and design.

BACKGROUND: Intravenous edetate disodium-based infusions reduced cardiovascular events in a prior clinical trial. The Trial to Assess Chelation Therapy 2 (TACT2) will replicate the initial study design. METHODS: TACT2 is an NIH-sponsored, randomized, 2x2 factorial, double masked, placebo-controlled, multicenter clinical trial testing 40 weekly infusions of a multi-component edetate disodium (disodium ethylenediamine tetra-acetic acid, or Na2EDTA)-based chelation solution and twice daily oral, high-dose multivitamin and mineral supplements in patients with diabetes and a prior myocardial infarction (MI). TACT2 completed enrollment of 1000 subjects in December 2020, and infusions in December 2021. Subjects are followed for 2.5 to 5 years. The primary endpoint is time to first occurrence of all-cause mortality, MI, stroke, coronary revascularization, or hospitalization for unstable angina. The trial has >;85% power to detect a 30% relative reduction in the primary endpoint. TACT2 also includes a Trace Metals and Biorepository Core Lab, to test whether benefits of treatment, if present, are due to chelation of lead and cadmium from patients. Design features of TACT2 were chosen to replicate selected features of the first TACT, which demonstrated a significant reduction in cardiovascular outcomes in the EDTA chelation arm compared with placebo among patients with a prior MI, with the largest effect in patients with diabetes. RESULTS: Results are expected in 2024. CONCLUSION: TACT2 may provide definitive evidence of the benefit of edetate disodiumbased chelation on cardiovascular outcomes, as well as the clinical importance of longitudinal changes in toxic metal levels of participants.

From clinic to community: A randomized controlled trial of a peer support model for adults with type 2 diabetes from specialty care settings in British Columbia.

AIMS: To examine the impact of a 12-month peer-led diabetes self-management support intervention delivered via telephone amongst adults with type 2 diabetes (T2D) from specialty care settings in British Columbia (BC). METHODS: One-hundred ninety-six adults with T2D were randomly assigned to either a 12-month Peer-Led, Empowerment-based, Approach, to Self-management Efforts in Diabetes (PLEASED) intervention or a usual care condition. PLEASED involved weekly telephone contacts from a peer leader (PL) in the first 3 months followed by bi-weekly telephone contacts in the last 9 months. Assessments were conducted at baseline, 3 and 12 months. The primary outcome was HbA1c ; secondary outcomes included diabetes distress (DD), ApoB, systolic and diastolic blood pressure (BP), body mass index, waist circumference and depressive symptoms. RESULTS: No within or between group changes were observed for HbA1c at 3 or 12 months. However, amongst participants with HbA1c  ≥ 69 mmol/mol (8.5%), the PLEASED group significantly lowered their HbA1c at 12 months [-11.7 mmol/mol (-1.07%); 95% CI: -20.7, -2.5 (-1.89, -0.23); p = 0.016] compared to usual care. Amongst secondary outcomes, within-group improvements in overall DD were found at 3 months (-0.21; 95% CI: -0.35, -0.08; p = 0.002) for the PLEASED group and at 12 months for both groups (PLEASED: -0.35; 95% CI: -0.49, -0.21; p < 0.001 and control: -0.33; 95% CI: -0.47, -0.19; p < 0.001), however, no between-group differences were observed. The PLEASED group improved systolic BP at 12 months (-5.4 mm Hg; 95% CI: -10.0, -0.8; p = 0.023) compared to usual care. CONCLUSIONS: Participation in a peer support intervention in diabetes delivered via telephone leads to long-term improvements in HbA1c amongst high-risk adults with T2D living in BC. TRIAL REGISTRATION: The study was registered on clinicaltrials.gov (NT02804620).

Early cost-utility analysis of genetically guided therapy for patients with drug-resistant epilepsy.

OBJECTIVE: Existing gene panels were developed to understand the etiology of epilepsy, and further benefits will arise from an effective pharmacogenomics panel for personalizing therapy and achieving seizure control. Our study assessed the cost-effectiveness of a pharmacogenomics panel for patients with drug-resistant epilepsy, compared with usual care. METHODS: A cost-utility analysis was employed using a discrete event simulation model. The microsimulation model aggregated the costs and benefits of genetically guided treatment versus usual care for 5000 simulated patients. The 10-year model combined data from various sources including genomic databases on prevalence of variants, population-level pharmaceutical claims on antiseizure medications, published long-term therapy retention rates, patient-level cost data, and systematic reviews. Incremental cost per quality-adjusted life-year (QALY) gained was computed. Deterministic and probabilistic sensitivity analyses were undertaken to address uncertainty in model parameters. RESULTS: The mean cost of the genetically guided treatment option was AU$98 199 compared with AU$95 386 for usual care. Corresponding mean QALYs were 4.67 compared with 4.28 for genetically guided and usual care strategies, respectively. The incremental cost per QALY gained was AU$7381. In probabilistic sensitivity analyses, the incremental cost per QALY gained was AU$6321 (95% uncertainty interval = AU$3604-AU$9621), with a 100% likelihood of being cost-effective in the Australian health care system. The most influential drivers of the findings were the monthly health care costs associated with reduced seizures, costs when seizures continued, and the quality-of-life estimates under genetically guided and usual care strategies. SIGNIFICANCE: This early economic evaluation of a pharmacogenomics panel to guide treatment for drug-resistant epilepsy could potentially be cost-effective in the Australian health care system. Clinical trial evidence is necessary to confirm these findings.

Primary care clinicians' opinions before and after implementation of cancer screening and prevention clinical decision support in a clinic cluster-randomized control trial: a survey research study.

BACKGROUND: Electronic health record (EHR)-linked clinical decision support (CDS) may impact primary care clinicians' (PCCs') clinical care opinions. As part of a clinic cluster-randomized control trial (RCT) testing a cancer prevention and screening CDS system with patient and PCC printouts (with or without shared decision-making tools [SDMT]) for patients due for breast, cervical, colorectal, and lung cancer screening and/or human papillomavirus (HPV) vaccination compared to usual care (UC), we surveyed PCCs at study clinics pre- and post-CDS implementation. Our primary aim was to learn if PCCs' opinions changed over time within study arms. Secondary aims including examining whether PCCs' opinions in study arms differed both pre- and post-implementation, and gauging PCCs' opinions on the CDS in the two intervention arms. METHODS: This study was conducted within a healthcare system serving an upper Midwestern population. We administered pre-implementation (11/2/2017-1/24/2018) and post-implementation (2/2/2020-4/9/2020) cross-sectional electronic surveys to PCCs practicing within a RCT arm: UC; CDS; or CDS + SDMT. Bivariate analyses compared responses between study arms at both time periods and longitudinally within study arms. RESULTS: Pre-implementation (53%, n = 166) and post-implementation (57%, n = 172) response rates were similar. No significant differences in PCC responses were seen between study arms on cancer prevention and screening questions pre-implementation, with few significant differences found between study arms post-implementation. However, significantly fewer intervention arm clinic PCCs reported being very comfortable with discussing breast cancer screening options with patients compared to UC post-implementation, as well as compared to the same intervention arms pre-implementation. Other significant differences were noted within arms longitudinally. For intervention arms, these differences related to CDS areas like EHR alerts, risk calculators, and ordering screening. Most intervention arm PCCs noted the CDS provided overdue screening alerts to which they were unaware. Few PCCs reported using the CDS, but most would recommend it to colleagues, expressed high CDS satisfaction rates, and thought patients liked the CDS's information and utility. CONCLUSIONS: While appreciated by PCCs with high satisfaction rates, the CDS may lower PCCs' confidence regarding discussing patients' breast cancer screening options and may be used irregularly. Future research will evaluate the impact of the CDS on cancer prevention and screening rates. TRIAL REGISTRATION: clinicaltrials.gov , NCT02986230, December 6, 2016.

The impact of personalized clinical decision support on primary care patients' views of cancer prevention and screening: a cross-sectional survey.

BACKGROUND: Few studies have assessed the impact of clinical decision support (CDS), with or without shared decision-making tools (SDMTs), on patients' perceptions of cancer screening or prevention in primary care settings. This cross-sectional survey was conducted to understand primary care patient's perceptions on cancer screening or prevention. METHODS: We mailed surveys (10/2018-1/2019) to 749 patients aged 18 to 75 years within 15 days after an index clinical encounter at 36 primary care clinics participating in a clinic-randomized control trial of a CDS system for cancer prevention. All patients were overdue for cancer screening or human papillomavirus vaccination. The survey compared respondents' answers by study arm: usual care; CDS; or CDS + SDMT. RESULTS: Of 387 respondents (52% response rate), 73% reported having enough time to discuss cancer prevention options with their primary care provider (PCP), 64% reported their PCP explained the benefits of the cancer screening choice very well, and 32% of obese patients reported discussing weight management, with two-thirds reporting selecting a weight management intervention. Usual care respondents were significantly more likely to decide on colorectal cancer screening than CDS respondents (p < 0.01), and on tobacco cessation than CDS + SDMT respondents (p = 0.02) and both CDS and CDS + SDMT respondents (p < 0.001). CONCLUSIONS: Most patients reported discussing cancer prevention needs with PCPs, with few significant differences between the three study arms in patient-reported cancer prevention care. Upcoming research will assess differences in screening and vaccination rates between study arms during the post-intervention follow-up period. TRIAL REGISTRATION: clinicaltrials.gov , NCT02986230 , December 6, 2016.

Translational switching of Cry1 protein expression confers reversible control of circadian behavior in arrhythmic Cry-deficient mice.

The suprachiasmatic nucleus (SCN) is the principal circadian clock of mammals, coordinating daily rhythms of physiology and behavior. Circadian timing pivots around self-sustaining transcriptional-translational negative feedback loops (TTFLs), whereby CLOCK and BMAL1 drive the expression of the negative regulators Period and Cryptochrome (Cry). Global deletion of Cry1 and Cry2 disables the TTFL, resulting in arrhythmicity in downstream behaviors. We used this highly tractable biology to further develop genetic code expansion (GCE) as a translational switch to achieve reversible control of a biologically relevant protein, Cry1, in the SCN. This employed an orthogonal aminoacyl-tRNA synthetase/tRNACUA pair delivered to the SCN by adeno-associated virus (AAV) vectors, allowing incorporation of a noncanonical amino acid (ncAA) into AAV-encoded Cry1 protein carrying an ectopic amber stop codon. Thus, translational readthrough and Cry1 expression were conditional on the supply of ncAA via culture medium or drinking water and were restricted to neurons by synapsin-dependent expression of aminoacyl tRNA-synthetase. Activation of Cry1 translation by ncAA in neurons of arrhythmic Cry-null SCN slices immediately and dose-dependently initiated TTFL circadian rhythms, which dissipated rapidly after ncAA withdrawal. Moreover, genetic activation of the TTFL in SCN neurons rapidly and reversibly initiated circadian behavior in otherwise arrhythmic Cry-null mice, with rhythm amplitude being determined by the number of transduced SCN neurons. Thus, Cry1 does not specify the development of circadian circuitry and competence but is essential for its labile and rapidly reversible activation. This demonstrates reversible control of mammalian behavior using GCE-based translational switching, a method of potentially broad neurobiological interest.

Extreme Dimensionality Reduction with Quantum Modeling.

Effective and efficient forecasting relies on identification of the relevant information contained in past observations-the predictive features-and isolating it from the rest. When the future of a process bears a strong dependence on its behavior far into the past, there are many such features to store, necessitating complex models with extensive memories. Here, we highlight a family of stochastic processes whose minimal classical models must devote unboundedly many bits to tracking the past. For this family, we identify quantum models of equal accuracy that can store all relevant information within a single two-dimensional quantum system (qubit). This represents the ultimate limit of quantum compression and highlights an immense practical advantage of quantum technologies for the forecasting and simulation of complex systems.

Clinical and Economic Outcomes of Genome Sequencing Availability on Containing a Hospital Outbreak of Resistant Escherichia coli in Australia.

OBJECTIVES: To evaluate the outbreak size and hospital cost effects of bacterial whole-genome sequencing availability in managing a large-scale hospital outbreak. METHODS: We built a hybrid discrete event/agent-based simulation model to replicate a serious bacterial outbreak of resistant Escherichia coli in a large metropolitan public hospital during 2017. We tested the 3 strategies of using whole-genome sequencing early, late (actual outbreak), or not using it and assessed their associated outbreak size and hospital cost. The model included ward dynamics, pathogen transmission, and associated hospital costs during a 5-month outbreak. Model parameters were determined using data from the Queensland Hospital Admitted Patient Data Collection (N = 4809 patient admissions) and local clinical knowledge. Sensitivity analyses were performed to address model and parameter uncertainty. RESULTS: An estimated 197 patients were colonized during the outbreak, with 75 patients detected. The total outbreak cost was A$460 137 (US$317 117), with 6.1% spent on sequencing. Without sequencing, the outbreak was estimated to result in 352 colonized patients, costing A$766 921 (US$528 547). With earlier detection from use of routine sequencing, the estimated outbreak size was 3 patients and cost A$65 374 (US$45 054). CONCLUSIONS: Using whole-genome sequencing in hospital outbreak management was associated with smaller outbreaks and cost savings, with sequencing costs as a small fraction of total hospital costs, supporting the further investigation of the use of routine whole-genome sequencing in hospitals.

A hybrid simulation model approach to examine bacterial genome sequencing during a hospital outbreak.

BACKGROUND: Hospital infection control requires timely detection and identification of organisms, and their antimicrobial susceptibility. We describe a hybrid modeling approach to evaluate whole genome sequencing of pathogens for improving clinical decisions during a 2017 hospital outbreak of OXA-181 carbapenemase-producing Escherichia coli and the associated economic effects. METHODS: Combining agent-based and discrete-event paradigms, we built a hybrid simulation model to assess hospital ward dynamics, pathogen transmission and colonizations. The model was calibrated to exactly replicate the real-life outcomes of the outbreak at the ward-level. Seven scenarios were assessed including genome sequencing (early or late) and no sequencing (usual care). Model inputs included extent of microbiology and sequencing tests, patient-level data on length of stay, hospital ward movement, cost data and local clinical knowledge. The main outcomes were outbreak size and hospital costs. Model validation and sensitivity analyses were performed to address uncertainty around data inputs and calibration. RESULTS: An estimated 197 patients were colonized during the outbreak with 75 patients detected. The total outbreak cost was US$318,654 with 6.1% of total costs spent on sequencing. Without sequencing, the outbreak was estimated to result in 352 colonized patients costing US$531,109. Microbiology tests were the largest cost component across all scenarios. CONCLUSION: A hybrid simulation approach using the advantages of both agent-based and discrete-event modeling successfully replicated a real-life bacterial hospital outbreak as a foundation for evaluating clinical outcomes and efficiency of outbreak management. Whole genome sequencing of a potentially serious pathogen appears effective in containing an outbreak and minimizing hospital costs.

Estimating the costs of genomic sequencing in cancer control.

BACKGROUND: Despite the rapid uptake of genomic technologies within cancer care, few studies provide detailed information on the costs of sequencing across different applications. The objective of the study was to examine and categorise the complete costs involved in genomic sequencing for a range of applications within cancer settings. METHODS: We performed a cost-analysis using gross and micro-costing approaches for genomic sequencing performed during 2017/2018 across different settings in Brisbane, Australia. Sequencing was undertaken for patients with lung, breast, oesophageal cancers, melanoma or mesothelioma. Aggregated resource data were captured for a total of 1433 patients and point estimates of per patient costs were generated. Deterministic sensitivity analyses addressed the uncertainty in the estimates. Estimated costs to the public health system for resources were categorised into seven distinct activities in the sequencing process: sampling, extraction, library preparation, sequencing, analysis, data storage and clinical reporting. Costs were also aggregated according to labour, consumables, testing, equipment and 'other' categories. RESULTS: The per person costs were AU$347-429 (2018 US$240-297) for targeted panels, AU$871-$2788 (2018 US$604-1932) for exome sequencing, and AU$2895-4830 (2018 US$2006-3347) for whole genome sequencing. Cost proportions were highest for library preparation/sequencing materials (average 76.8% of total costs), sample extraction (8.1%), data analysis (9.2%) and data storage (2.6%). Capital costs for the sequencers were an additional AU$34-197 (2018 US$24-67) per person. CONCLUSIONS: Total costs were most sensitive to consumables and sequencing activities driven by commercial prices. Per person sequencing costs for cancer are high when tumour/blood pairs require testing. Using the natural steps involved in sequencing and categorising resources accordingly, future evaluations of costs or cost-effectiveness of clinical genomics across cancer projects could be more standardised and facilitate easier comparison of cost drivers.

Pre-implementation adaptation of primary care cancer prevention clinical decision support in a predominantly rural healthcare system.

BACKGROUND: Cancer is a leading cause of death in the United States. Primary care providers (PCPs) juggle patient cancer prevention and screening along with managing acute and chronic health problems. However, clinical decision support (CDS) may assist PCPs in addressing patients' cancer prevention and screening needs during short clinic visits. In this paper, we describe pre-implementation study design and cancer screening and prevention CDS changes made to maximize utilization and better fit a healthcare system's goals and culture. We employed the Consolidated Framework for Implementation Research (CFIR), useful for evaluating the implementation of CDS interventions in primary care settings, in understanding barriers and facilitators that led to those changes. METHODS: In a three-arm, pragmatic, 36 clinic cluster-randomized control trial, we integrated cancer screening and prevention CDS and shared decision-making tools (SDMT) into an existing electronic medical record-linked cardiovascular risk management CDS system. The integrated CDS is currently being tested within a predominately rural upper Midwestern healthcare system. Prior to CDS implementation, we catalogued pre-implementation changes made from 2016 to 2018 based on: pre-implementation site engagement; key informant interviews with healthcare system rooming staff, providers, and leadership; and pilot testing. We identified influential barriers, facilitators, and changes made in response through qualitative content analysis of meeting minutes and supportive documents. We then coded pre-implementation changes made and associated barriers and facilitators using the CFIR. RESULTS: Based on our findings from system-wide pre-implementation engagement, pilot testing, and key informant interviews, we made changes to accommodate the needs of the healthcare system based on barriers and facilitators that fell within the Intervention Characteristics, Inner Setting, and Outer Setting CFIR domains. Changes included replacing the expansion of medical assistant roles in one intervention arm with targeted SDMT, as well as altering cancer prevention CDS and study design elements. CONCLUSIONS: Pre-implementation changes to CDS may help meet healthcare systems' evolving needs and optimize the intervention by being responsive to real-world implementation barriers and facilitators. Frameworks like the CFIR are useful tools for identifying areas where pre-implementation barriers and facilitators may result in design changes, both to research studies and CDS systems. TRIAL REGISTRATION: NCT02986230.

Evaluating a risk assessment tool to improve triaging of patients to colonoscopies.

BACKGROUND: Colonoscopy is the gold standard in the diagnosis of significant bowel disease (SBD), including colorectal cancer, high-risk adenoma and inflammatory bowel disease. As the demand for colonoscopy services is placing significant pressure on hospital resources, new solutions are needed to manage patients more efficiently and effectively. AIM: We investigated the impact of using a risk assessment tool (RAT) to improve selection of patients for colonoscopy procedures to detect SBD. METHODS: A hybrid simulation model was constructed to replicate the current patient triage bookings and waiting times in a large metropolitan hospital. The model used data on 327 patients who were retrospectively assessed for risk of SBD. Risk assessment incorporated blood and faecal immunochemical test results, gender and age in addition to patient symptoms. The model was calibrated over 12 months to current outcomes and was compared with the RAT and a third scenario where low-risk patients did not proceed to a colonoscopy. One-way sensitivity analyses were undertaken. RESULTS: Using the RAT was expected to shorten waiting times by 153 days for moderately-urgent patients and 138 days for non-urgent patients. If low-risk patients did not proceed to colonoscopy, waiting times were expected to reduce for patients with SBD by 17 days producing cost-savings of AU$373 824 through avoided colonoscopies. CONCLUSIONS: A hybrid model that combines patient-level characteristics with hospital-level resource constraints can demonstrate improved efficiency in a hospital clinic. Further research on risk assessment is required to improve quality patient care and reduce low-value service delivery.

Barriers and facilitators to implementing cancer prevention clinical decision support in primary care: a qualitative study.

BACKGROUND: In the United States, primary care providers (PCPs) routinely balance acute, chronic, and preventive patient care delivery, including cancer prevention and screening, in time-limited visits. Clinical decision support (CDS) may help PCPs prioritize cancer prevention and screening with other patient needs. In a three-arm, pragmatic, clinic-randomized control trial, we are studying cancer prevention CDS in a large, upper Midwestern healthcare system. The web-based, electronic health record (EHR)-linked CDS integrates evidence-based primary and secondary cancer prevention and screening recommendations into an existing cardiovascular risk management CDS system. Our objective with this study was to identify adoption barriers and facilitators before implementation in primary care. METHODS: We conducted semi-structured interviews guided by the Consolidated Framework for Implementation Research (CFIR) with 28 key informants employed by the healthcare organization in either leadership roles or the direct provision of clinical care. Transcribed interviews were analyzed using qualitative content analysis. RESULTS: EHR, CDS workflow, CDS users (providers and patients), training, and organizational barriers and facilitators were identified related to Intervention Characteristics, Outer Setting, Inner Setting, and Characteristics of Individuals CFIR domains. CONCLUSION: Identifying and addressing key informant-identified barriers and facilitators before implementing cancer prevention CDS in primary care may support a successful implementation and sustained use. The CFIR is a useful framework for understanding pre-implementation barriers and facilitators. Based on our findings, the research team developed and instituted specialized training, pilot testing, implementation plans, and post-implementation efforts to maximize identified facilitators and address barriers. TRIAL REGISTRATION: clinicaltrials.gov , NCT02986230 , December 6, 2016.

Understanding primary care providers' perceptions of cancer prevention and screening in a predominantly rural healthcare system in the upper Midwest.

BACKGROUND: Cancer is the leading cause of death in the United States, with the burden expected to rise in the coming decades, increasing the need for effective cancer prevention and screening options. The United States Preventive Services Task Force has suggested that a shared decision-making process be used when clinicians and patients discuss cancer screening. The electronic medical record (EMR) often provides only reminders or alerts to primary care providers (PCPs) when screenings are due, a strategy with limited efficacy. METHODS: We administered a cross-sectional electronic survey to PCPs (n = 165, 53% response rate) at 36 Essentia Health primary care clinics participating in a large, National Cancer Institute-funded study on a cancer prevention clinical decision support (CDS) tool. The survey assessed PCP demographics, perceptions of the EMR's ability to help assess and manage patients' cancer risk, and experience and comfort level discussing cancer screening and prevention with patients. RESULTS: In these predominantly rural clinics, only 49% of PCPs thought the EMR was well integrated to help assess and manage cancer risk. Both advanced care practitioners and physicians agreed that cancer screening and informed discussion of cancer risks are important; however, only 53% reported their patients gave cancer screening a high priority relative to other health issues. CONCLUSIONS: The impact of EMR-linked CDS delivered to both patients and PCPs may improve cancer screening, but only if it is easy to use and saves PCPs time.

Genetic code expansion in the mouse brain.

Site-specific incorporation of non-natural amino acids into proteins, via genetic code expansion with pyrrolysyl tRNA synthetase (PylRS) and tRNA(Pyl)CUA pairs (and their evolved derivatives) from Methanosarcina sp., forms the basis of powerful approaches to probe and control protein function in cells and invertebrate organisms. Here we demonstrate that adeno-associated viral delivery of these pairs enables efficient genetic code expansion in primary neuronal culture, organotypic brain slices and the brains of live mice.