Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server.

Antisense oligomers (ASOs), such as peptide nucleic acids (PNAs), designed to inhibit the translation of essential bacterial genes, have emerged as attractive sequence- and species-specific programmable RNA antibiotics. Yet, potential drawbacks include unwanted side effects caused by their binding to transcripts other than the intended target. To facilitate the design of PNAs with minimal off-target effects, we developed MASON (make antisense oligomers now), a web server for the design of PNAs that target bacterial mRNAs. MASON generates PNA sequences complementary to the translational start site of a bacterial gene of interest and reports critical sequence attributes and potential off-target sites. We based MASON's off-target predictions on experiments in which we treated Salmonella enterica serovar Typhimurium with a series of 10-mer PNAs derived from a PNA targeting the essential gene acpP but carrying two serial mismatches. Growth inhibition and RNA-sequencing (RNA-seq) data revealed that PNAs with terminal mismatches are still able to target acpP, suggesting wider off-target effects than anticipated. Comparison of these results to an RNA-seq data set from uropathogenic Escherichia coli (UPEC) treated with eleven different PNAs confirmed that our findings are not unique to Salmonella We believe that MASON's off-target assessment will improve the design of specific PNAs and other ASOs.

A Combined DNA/RNA-based Next-Generation Sequencing Platform to Improve the Classification of Pancreatic Cysts and Early Detection of Pancreatic Cancer Arising From Pancreatic Cysts.

OBJECTIVE: We report the development and validation of a combined DNA/RNA next-generation sequencing (NGS) platform to improve the evaluation of pancreatic cysts. BACKGROUND AND AIMS: Despite a multidisciplinary approach, pancreatic cyst classification, such as a cystic precursor neoplasm, and the detection of high-grade dysplasia and early adenocarcinoma (advanced neoplasia) can be challenging. NGS of preoperative pancreatic cyst fluid improves the clinical evaluation of pancreatic cysts, but the recent identification of novel genomic alterations necessitates the creation of a comprehensive panel and the development of a genomic classifier to integrate the complex molecular results. METHODS: An updated and unique 74-gene DNA/RNA-targeted NGS panel (PancreaSeq Genomic Classifier) was created to evaluate 5 classes of genomic alterations to include gene mutations (e.g., KRAS, GNAS, etc.), gene fusions and gene expression. Further, CEA mRNA ( CEACAM5 ) was integrated into the assay using RT-qPCR. Separate multi-institutional cohorts for training (n=108) and validation (n=77) were tested, and diagnostic performance was compared to clinical, imaging, cytopathologic, and guideline data. RESULTS: Upon creation of a genomic classifier system, PancreaSeq GC yielded a 95% sensitivity and 100% specificity for a cystic precursor neoplasm, and the sensitivity and specificity for advanced neoplasia were 82% and 100%, respectively. Associated symptoms, cyst size, duct dilatation, a mural nodule, increasing cyst size, and malignant cytopathology had lower sensitivities (41-59%) and lower specificities (56-96%) for advanced neoplasia. This test also increased the sensitivity of current pancreatic cyst guidelines (IAP/Fukuoka and AGA) by >10% and maintained their inherent specificity. CONCLUSIONS: PancreaSeq GC was not only accurate in predicting pancreatic cyst type and advanced neoplasia but also improved the sensitivity of current pancreatic cyst guidelines.

Electronic Health Record Work Demands for Gastroenterology and Hepatology Providers: A Prospective Use Analysis and Survey Study.

BACKGROUND AND AIMS: There is a paucity of research on the use of the electronic health record (EHR) by gastroenterology and hepatology providers and its effect on work-life balance. Our aim was to study the after-hour EHR work completed among providers within a multispecialty academic practice. METHODS: Time spent completing EHR tasks during evening hours (7p-7a) and days off was prospectively recorded for 35 providers over six consecutive months at a single center. Type and time of EHR tasks completed were compared based on subspecialty, academic degree, academic track category, identified gender, and number of weekly assigned clinical days worked. Prior to the data collection, providers filled out a survey regarding EHR use, work hours, and work-life balance. RESULTS: All providers used EHR during evening hours and during days off. The total mean after-hours time spent completing EHR tasks was 18.4 m (± 13.0) per day and 45.0 m (± 25.8) during days off. There was significant variation in the daily mean after-hours time spent completing EHR tasks among subspecialties, range 45.3 m (± 27.1) (advanced endoscopy)-28.7 m (± 22.7) (hepatology), and among providers who work clinically > 7.5 days per week versus those who do not, 42.1 m (± 25.7) vs 30.0 m (± 14.0). The most common after-hours EHR task was note completion. 83% providers reported being unable to complete EHR tasks during allotted workday time and 87% report that EHR tasks interfered with family life; 74% with social life. CONCLUSION: Gastroenterology and hepatology providers spend a significant amount of after-hour time completing EHR tasks which is perceived to interfere with family/social life.

Clear liquid diet before bowel preparation predicts successful chromoendoscopy in patients with inflammatory bowel disease.

BACKGROUND AND AIMS: Chromoendoscopy (CE) has been shown to generate both a superior diagnostic yield and dysplasia detection rate than conventional white-light endoscopy and requires a high-quality bowel preparation. The aim of this study was to identify predictors of the ability to perform CE in patients with inflammatory bowel disease (IBD). METHODS: We performed an observational study of patients with IBD undergoing colorectal cancer surveillance examinations with CE. Same-day colonoscopy surveys were used to collect patient and procedural variables. Multivariate logistic regression was used to establish odds ratios of successful completion of CE. RESULTS: Eighty-eight patients with IBD were enrolled. We found that patients who did not follow a clear liquid diet before colonoscopy had much lower odds of being able to undergo CE (odds ratio, 0.106; 95% confidence interval, 0.013-0.845; P < .034). Further, we found that previously identified risk factors (older age, history of diabetes mellitus, the timing and split dosing of preparation solution, and procedure time (AM or PM), chronic narcotic use, and history of constipation) for inadequate bowel preparation were not associated with the ability to perform CE. CONCLUSIONS: Following a clear liquid diet the entire day before the procedure was highly predictive of the ability to perform CE. However, established risk factors for inadequate bowel preparation did not inhibit the ability to perform CE in our population. Endoscopists performing CE should consider recommending that patients follow a clear liquid diet the entire day before their examination.

A Prospective Multicenter Study Evaluating Learning Curves and Competence in Endoscopic Ultrasound and Endoscopic Retrograde Cholangiopancreatography Among Advanced Endoscopy Trainees: The Rapid Assessment of Trainee Endoscopy Skills Study.

BACKGROUND & AIMS: On the basis of the Next Accreditation System, trainee assessment should occur on a continuous basis with individualized feedback. We aimed to validate endoscopic ultrasound (EUS) and endoscopic retrograde cholangiopancreatography (ERCP) learning curves among advanced endoscopy trainees (AETs) by using a large national sample of training programs and to develop a centralized database that allows assessment of performance in relation to peers. METHODS: ASGE recognized training programs were invited to participate, and AETs were graded on ERCP and EUS exams by using a validated competency assessment tool that assesses technical and cognitive competence in a continuous fashion. Grading for each skill was done by using a 4-point scoring system, and a comprehensive data collection and reporting system was built to create learning curves by using cumulative sum analysis. Individual results and benchmarking to peers were shared with AETs and trainers quarterly. RESULTS: Of the 62 programs invited, 20 programs and 22 AETs participated in this study. At the end of training, median number of EUS and ERCP performed/AET was 300 (range, 155-650) and 350 (125-500), respectively. Overall, 3786 exams were graded (EUS, 1137; ERCP-biliary, 2280; ERCP-pancreatic, 369). Learning curves for individual end points and overall technical/cognitive aspects in EUS and ERCP demonstrated substantial variability and were successfully shared with all programs. The majority of trainees achieved overall technical (EUS, 82%; ERCP, 60%) and cognitive (EUS, 76%; ERCP, 100%) competence at conclusion of training. CONCLUSIONS: These results demonstrate the feasibility of establishing a centralized database to report individualized learning curves and confirm the substantial variability in time to achieve competence among AETs in EUS and ERCP. ClinicalTrials.gov: NCT02509416.

Low Yield and High Cost of Gastric and Duodenal Biopsies for Investigation of Symptoms of Abdominal Pain During Routine Esophagogastroduodenoscopy.

BACKGROUND: Esophagogastroduodenoscopy (EGD) referrals for symptoms of abdominal pain are common. Current guidelines for dyspepsia recommend biopsies of gastric mucosa for Helicobacter pylori in all patients referred for EGD. Our study aimed to determine the clinical yield and cost-effectiveness of gastric and duodenal biopsy in EGDs performed for abdominal pain. METHODS: Three hundred and ninety-one outpatient EGDs performed at a single academic tertiary care center were studied. For each procedure, endoscopic as well as pathologic findings from the stomach and duodenum were then recorded. Charge of biopsy was calculated using the increased charges for professional fees, forceps, and pathology fees when a biopsy was performed. RESULTS: Gastric biopsies were obtained on 304 EGDs performed with 13 (4.2%) patients diagnosed with H. pylori. In patients with abnormal gastric mucosa on EGD, 11 of 167 (6.5%) were positive for H. pylori compared to 2 of 137 (1.4%) with normal appearing mucosa (p = 0.02). Charge per diagnosis of H. pylori for normal mucosa was calculated to be $43,073. Duodenal biopsies were performed in 263 cases. Celiac disease was diagnosed in 4 of 263 cases (1.5%). Of patients with abnormal duodenal mucosa on EGD, 1 of 36 (2.7%) were positive for celiac disease compared to 3 of 227 (1.3%) with normal mucosa (p = 0.57). Charge per diagnosis of celiac disease for normal mucosa was calculated to be $47,580. CONCLUSION: Routine biopsy during EGD for symptoms of abdominal pain has low yield with high costs. Practice of routine biopsies of normal appearing tissue and the present guidelines should be reconsidered in the investigation of abdominal pain with EGD.

Impact and outcomes of research sponsored by the American Society for Gastrointestinal Endoscopy.

BACKGROUND AND AIMS: Since 1985, the American Society for Gastrointestinal Endoscopy (ASGE) has awarded grants for endoscopic-related research. The goals of this study were to examine trends in ASGE grant funding and to assess productivity of previous recipients of the ASGE grant awards. METHODS: This was a retrospective cohort analysis of all research grants awarded by the ASGE through 2009. Measures of academic productivity and self-assessment of the ASGE awards' impact on the recipients' careers were defined by using publicly available resources (eg, National Library of Medicine-PubMed) and administration of an electronic survey to award recipients. RESULTS: The ASGE awarded 304 grants totaling $12.5 million to 214 unique awardees. Funding increased 7.5-fold between 1985 and 1989 (mean $102,000/year) and between 2005 and 2009 (mean $771,000/year). The majority of awardees were men (83%), were at or below the level of assistant professor (82%), with a median of 3 years of postfellowship experience at the time of the award, and derived from a broad spectrum of institutions as measured by National Institutes of Health funding rank (median 26, interquartile range [IQR] 12-64). Nineteen percent had a master's degree in a research-related field. Awardees' median publications per year increased from 3.5 (IQR 1.2-9.0) before funding to 5.7 (IQR 1.8-9.5) since funding; P = .04, and median h-index scores increased from 3 (IQR 1-8) to 17 (IQR 8-26); P < .001. Multivariate analysis found that the presence of a second advanced degree (eg, masters or doctorate) was independently predictive of high productivity (odds ratio [OR] 2.92; 95% confidence interval [CI], 1.09-7.81). Among 212 unique grant recipients, 82 (40%) completed the online survey. Of the respondents, median peer-reviewed publications per year increased from 3.4 (IQR 1.9-5.5) to 4.5 (IQR 2.0-9.5); P = .17. Ninety-one percent reported that the ASGE grant had a positive or very positive impact on their careers, and 85% of respondents are currently practicing in an academic environment. Most of the grants resulted in at least 1 peer-reviewed publication (67% per Internet-based search and 81% per survey). CONCLUSIONS: The ASGE research program has grown considerably since 1985, with the majority of grants resulting in at least 1 grant-related publication. Overall academic productivity increased after the award, and the majority of awardees report a positive or very positive impact of the award on their careers. Medical professional societies are an important sponsor of clinical research.

Laparoscopic-assisted ERCP and EUS in patients with prior Roux-en-Y gastric bypass surgery: a dual-center case series experience.

BACKGROUND: Patients with Roux-en-Y gastric bypass (RYGB) develop pancreatobiliary issues after surgery. Endoscopic management via the conventional route with endoscopic retrograde cholangiopancreatography (ERCP) and endoscopic ultrasound (EUS) is quite limited due to the altered anatomy. Laparoscopic-assisted ERCP (LA-ERCP) via the excluded stomach has been highly successful. Reported use of laparoscopic-assisted EUS (LA-EUS) is extremely rare. METHODS: A retrospective review was conducted at two tertiary referral centers for cases that involved laparoscopic-assisted ERCP and EUS. Patient demographic data were collected along with data regarding procedure, indication, complications and length of stay. RESULTS: A total of 16 cases involving 15 patients were identified: 11 cases of LA-ERCP and five cases of combined LA-EUS plus LA-ERCP were performed. Four patients had previously undergone failed endoscopy via the conventional route (27 %). There was a 100 % biliary/pancreatic cannulation and intervention rate. There were no endoscopic-related complications. Therapeutic interventions included laparoscopic cholecystectomy, lysis of adhesions, biliary and pancreatic sphincterotomy, biliary and pancreatic stent placement, stone removal including mechanical lithotripsy and EUS biopsy and diagnosis of pancreatic cancer. Average discharge was on postoperative day 3.4. However, 50 % were discharged after 1 day. CONCLUSIONS: LA-ERCP and combined LA-EUS plus LA-ERCP are safe and highly successful diagnostic and therapeutic modalities for a wide variety of pancreatobiliary ailments in RYGB patients.

Variation in Aptitude of Trainees in Endoscopic Ultrasonography, Based on Cumulative Sum Analysis.

BACKGROUND & AIMS: Studies have reported substantial variation in the competency of advanced endoscopy trainees, indicating a need for more supervised training in endoscopic ultrasound (EUS). We used a standardized, validated, data collection tool to evaluate learning curves and measure competency in EUS among trainees at multiple centers. METHODS: In a prospective study performed at 15 centers, 17 trainees with no prior EUS experience were evaluated by experienced attending endosonographers at the 25th and then every 10th upper EUS examination, over a 12-month training period. A standardized data collection form was used (using a 5-point scoring system) to grade the EUS examination. Cumulative sum analysis was applied to produce a learning curve for each trainee; it tracked the overall performance based on median scores at different stations and also at each station. Competency was defined by a median score of 1, with acceptable and unacceptable failure rates of 10% and 20%, respectively. RESULTS: Twelve trainees were included in the final analysis. Each of the trainees performed 265 to 540 EUS examinations (total, 4257 examinations). There was a large amount of variation in their learning curves: 2 trainees crossed the threshold for acceptable performance (at cases 225 and 245), 2 trainees had a trend toward acceptable performance (after 289 and 355 cases) but required continued observation, and 8 trainees needed additional training and observation. Similar results were observed at individual stations. CONCLUSIONS: A specific case load does not ensure competency in EUS; 225 cases should be considered the minimum caseload for training because we found that no trainee achieved competency before this point. Ongoing training should be provided for trainees until competency is confirmed using objective measures.

Visual evaluation of the larynx and hypopharynx during esophagogastroduodenoscopy: a safety and feasibility study.

BACKGROUND: The larynx and hypopharynx are common sites for head and neck cancer, which shares many risk factors with upper digestive tract disease. Patient survival with malignancies depends on stage at the time of diagnosis. Endoscopic screening of the hypopharynx is neither routinely performed in clinical practice nor has it been evaluated in a formal study. METHODS: This is a prospective pilot study of patients undergoing routine EGD. Demographic data were collected from patients prior to the procedure. All patients in the study underwent an EGD and prior to performing the standard portion of the EGD procedure, the endoscopist evaluated the larynx and hypopharynx with both white light endoscopy (WLE) and narrow band imaging (NBI). Details of the procedure, including ability to see all anatomic structures, time spent, complications, and findings, were recorded. RESULTS: A total of 111 patients were included in the study. The exam of the laryngopharynx was completed in 87% of patients (97/111). Reasons for incomplete exam included intubated patients (2/14), inadequate sedation (9/14), and inability to see the entire hypopharynx (3/14). The mean time of the WLE was 20.2 s, while the NBI evaluation took 15.6 s for a mean and 35.8 s for the entire exam of the larynx and hypopharynx. Minor procedural complications occurred in 3/11 (2.7%) of the patients and included hypotension, tachycardia, and hypoxia. There were 6 patients who had hypopharyngeal abnormalities seen on both WLE and NBI (5.4%) and were subsequently referred to otolaryngology. Of the six referrals, one patient had a vocal cord biopsy showing leukoplakia, while the others were deemed normal anatomic variants. CONCLUSIONS: Evaluation of the hypopharynx can be accomplished by gastrointestinal endoscopists at the time of EGD in the vast majority of patients in a safe manner while adding only about 35 s to the overall exam time.

Influence of previous night call and sleep deprivation on screening colonoscopy quality.

OBJECTIVES: There are few studies evaluating the influence of sleep deprivation on endoscopic outcomes. To evaluate the effect of a previous night call on the quality of screening colonoscopies performed the following day. METHODS: Average-risk patients undergoing screening colonoscopies were included. Quality metrics were retrospectively compared between two groups of post-call colonoscopies and colonoscopies performed by the same individuals not on call the night before: those performed by gastroenterologists who were only on call the night prior and those performed by gastroenterologists who performed emergent on-call procedures the night prior. RESULTS: Between 1 July 2010 and 31 March 2012, 447 colonoscopies were performed by gastroenterologists who were on call only the night prior, 126 colonoscopies were performed by gastroenterologists who had completed on-call emergent procedures the night prior, and 8,734 control colonoscopies were completed. There was a lower percent of patients who were screened with adenomas detected in procedures performed by endoscopists who had performed emergent on-call procedures the night prior compared with the controls (30 vs. 39%, respectively; P=0.043). The mean withdrawal time for these colonoscopies was significantly longer than that for the control procedures (15.5 vs. 14.0 min; P=0.025). For the colonoscopies performed by endoscopists who were on call only the night prior, there was no significant difference in the percent of patients screened with adenomas detected compared with controls (42 vs. 39%, respectively; P=0.136). CONCLUSIONS: (1) Despite longer withdrawal times, being on call the night prior and performing an emergent procedure lead to a significant 24% decrease in the adenoma detection rates. (2) It is imperative for screening physicians to be aware of the influence of sleep deprivation on procedural outcomes and to consider altering their practice accordingly.

Devices for the endoscopic treatment of hemorrhoids.

Multiple endoscopic methods are available to treat symptomatic internal hemorrhoids. Because of its low cost, ease of use, low rate of adverse events, and relative effectiveness, RBL is currently the most widely used technique.