pVACview: an interactive visualization tool for efficient neoantigen prioritization and selection.

Background: Neoantigen-targeting therapies including personalized vaccines have shown promise in the treatment of cancers, particularly when used in combination with checkpoint blockade therapy. At least 100 clinical trials involving these therapies have been initiated globally. Accurate identification and prioritization of neoantigens is crucial for designing these trials, predicting treatment response, and understanding mechanisms of resistance.

pVACview: an interactive visualization tool for efficient neoantigen prioritization and selection.

Background: Neoantigen targeting therapies including personalized vaccines have shown promise in the treatment of cancers, particularly when used in combination with checkpoint blockade therapy. At least 100 clinical trials involving these therapies are underway globally. Accurate identification and prioritization of neoantigens is highly relevant to designing these trials, predicting treatment response, and understanding mechanisms of resistance.

Natural history and growth prediction model of pancreatic serous cystic neoplasms.

Objective: Serous cystic neoplasms (SCN) are benign pancreatic cystic neoplasms that may require resection based on local complications and rate of growth. We aimed to develop a predictive model for the growth curve of SCNs to aid in the clinical decision making of determining need for surgical resection.

Methods: Utilizing a prospectively maintained pancreatic cyst database from a single institution, patients with SCNs were identified.

Comparative Effectiveness of Virtual Versus In-person Visits for Abdominal Pain During the COVID-19 Pandemic.

Background And Aims: The COVID-19 pandemic has highlighted the importance of telemedicine in improving healthcare access and reducing costs. This study aimed to assess order compliance in the virtual versus in-person setting for the initial evaluation of abdominal pain (AP) prior to and during the pandemic.

Methods: A retrospective evaluation of virtual and in-person outpatient gastroenterology visits for AP were identified through natural language processing from January 2019 through September 2021 at the Cleveland Clinic main campus and regional hospitals in Ohio.

DGIdb 5.0: rebuilding the drug-gene interaction database for precision medicine and drug discovery platforms.

The Drug-Gene Interaction Database (DGIdb, https://dgidb.org) is a publicly accessible resource that aggregates genes or gene products, drugs and drug-gene interaction records to drive hypothesis generation and discovery for clinicians and researchers. DGIdb 5.

Challenges in and Opportunities for Electronic Health Record-Based Data Analysis and Interpretation.

Electronic health records (EHRs) have been increasingly adopted in clinical practices across the United States, providing a primary source of data for clinical research, particularly observational cohort studies. EHRs are a high-yield, low-maintenance source of longitudinal real-world data for large patient populations and provide a wealth of information and clinical contexts that are useful for clinical research and translation into practice. Despite these strengths, it is important to recognize the multiple limitations and challenges related to the use of EHR data in clinical research.

Impact of Clinical and Endoscopic Features on the Development of Metachronous Colorectal Advanced Serrated Lesions.

Background And Aims: High-risk adenomas predict metachronous advanced adenomatous neoplasia. Limited data exist on predictors of metachronous advanced serrated lesions (mASLs). We analyzed clinical and endoscopic predictors of mASLs.

Neoplastic Progression of Barrett's Esophagus Among Organ Transplant Recipients: a Retrospective Cohort Study.

Background: Several small studies reported high risk of progression to high-grade dysplasia (HGD) and esophageal adenocarcinoma (EAC) in Barrett's esophagus (BE) patients who undergo solid organ transplantation (SOT) and implied that this may be due to immunosuppressant use. However, the major shortcoming of these studies was the lack of a control population. Therefore, we aimed to determine the rates of neoplastic progression in BE patients who underwent SOT and compare to that in controls and identify the predictors of progression.

Evaluating approaches to diagnosis and management of idiopathic acute pancreatitis.

Introduction: Idiopathic acute pancreatitis (IAP) is a diagnosis of exclusion; systematic work-up is challenging but essential. Recent advances suggest IAP results from micro-choledocholithiasis, and that laparoscopic cholecystectomy (LC) or endoscopic sphincterotomy (ES) may prevent recurrence.

Methods: Patients diagnosed with IAP from 2015-21 were identified from discharge billing records.

Computational prediction of MHC anchor locations guides neoantigen identification and prioritization.

Neoantigens are tumor-specific peptide sequences resulting from sources such as somatic DNA mutations. Upon loading onto major histocompatibility complex (MHC) molecules, they can trigger recognition by T cells. Accurate neoantigen identification is thus critical for both designing cancer vaccines and predicting response to immunotherapies.

Frequency of Use and Outcomes of Colonoscopy in Individuals Older Than 75 Years.

Importance: The benefits from colorectal cancer (CRC) screening may take 10 to 15 years to accrue. Therefore, screening is recommended for older adults who are in good health.

Objective: To determine the number of screening colonoscopies done in patients older than 75 years with a life expectancy of fewer than 10 years, diagnostic yield, and associated adverse events within 10 days and 30 days of the procedure.

Increased Risk of Hospitalization in Celiac Disease With COVID-19 Infection Is Mitigated by Vaccination.

Background: We sought to describe clinical characteristics of celiac disease (CD) patients infected with coronavirus disease 2019 (COVID-19) and estimate hospitalization risk, intensive care unit (ICU) requirement, mortality, and thrombosis, and the impact of vaccination on these outcomes.

Methods: We performed a single-center, retrospective cohort study comparing biopsy-proven CD patients with a matched sample of non-CD (referent) patients diagnosed with COVID-19 between March 2020 and January 2022. Matching ensured 2 referent patients for every 1 CD patient by age, sex, ethnicity, and COVID-19 diagnosis date.

Temporal trends and disparities in gastroenterology care use before, during, and after COVID-19 lockdown.

Socioeconomic disparities adversely affected healthcare use during COVID-19 lockdown. However, trends in these disparities post lockdown are unknown. Therefore, our aim was to study temporal trends and factors associated with gastroenterology healthcare access and disparities during and after COVID-19 lockdown.

Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer.

Pancreatic ductal adenocarcinoma is a lethal disease with limited treatment options and poor survival. We studied 83 spatial samples from 31 patients (11 treatment-naïve and 20 treated) using single-cell/nucleus RNA sequencing, bulk-proteogenomics, spatial transcriptomics and cellular imaging. Subpopulations of tumor cells exhibited signatures of proliferation, KRAS signaling, cell stress and epithelial-to-mesenchymal transition.

Long term assessment of antibiotic prophylaxis and biliary microbiome in pancreaticoduodenectomy.

Introduction: Surgical site infections (SSI) can represent a major complication of pancreaticoduodenectomy (PD). We summarize the outcomes of process improvement efforts to reduce the SSI rates in PD that includes replacing Cefazolin with Ceftriaxone-Metronidazole as antibiotic prophylaxis. Additional efforts included current assessment of biliary microbiome and potential prophylactic failures based on bile cultures and suspected antibiotic allergies.

Kaposi Sarcoma in Afghanistan: A Case Series from a Tertiary Referral Center.

Kaposi sarcoma is a vascular endothelial neoplasm caused by human herpesvirus 8. Although it is a well-studied disease, little is known about the specific characteristics or epidemiology of Kaposi sarcoma in Afghanistan. The data consist primarily of anecdotal reports and epidemiological studies extrapolated from neighboring countries.

A community approach to the cancer-variant-interpretation bottleneck.

As guidelines, therapies, and literature on cancer variants expand, the lack of consensus variant interpretations impedes clinical applications. CIViC is a public domain, crowd-sourced, and adaptable knowledgebase of evidence for the Clinical Interpretation of Variants in Cancer, designed to reduce barriers to knowledge sharing and alleviate the variant interpretation bottleneck.

The Natural History of Asymptomatic Gallstones: A Longitudinal Study and Prediction Model.

Background & Aims: Despite the high prevalence of asymptomatic gallstones (AGs), there are limited data on their natural history. We aimed to determine the rate of symptom development in a contemporary population, determine factors associated with progression to symptomatic gallstones (SGs), and develop a clinical prediction model.

Methods: We used a retrospective cohort design.

The Human Pangenome Project: a global resource to map genomic diversity.

The human reference genome is the most widely used resource in human genetics and is due for a major update. Its current structure is a linear composite of merged haplotypes from more than 20 people, with a single individual comprising most of the sequence. It contains biases and errors within a framework that does not represent global human genomic variation.

Venous Thromboembolism in Patients Admitted for IBD: An Enterprise-Wide Experience of 86,000 Hospital Encounters.

Background: Recommendations regarding venous thromboembolism prophylaxis in patients admitted to the hospital for IBD continue to evolve.

Objective: This study aimed to determine the 90-day rate and risk factors of deep venous thromboembolism and pulmonary embolism in cohorts of patients with IBD admitted to medical and surgical services.

Design: This was a retrospective review.