IW-Scoring: an Integrative Weighted Scoring framework for annotating and prioritizing genetic variations in the noncoding genome

Cancer Research UK Centre of Excellence Award to Barts Cancer Centre [C16420/A18066]; Barts and The London Charity Grant [MGU0344]; D.U. is funded by Pancreatic Cancer Research Fund Tissue Bank Grant. Funding for open access charge: Charity Open Access Fund (COAF) award

The Pancreatic Expression Database: 2018 update.

The Pancreatic Expression Database (PED, http://www.pancreasexpression.org) continues to be a major resource for mining pancreatic -omics data a decade after its initial release. Here, we present recent updates to PED and describe its evolution into a comprehensive resource for extracting, analysing and integrating publicly available multi-omics datasets. A new analytical module has been implemented to run in parallel with the existing literature mining functions. This analytical module has been created using rich data content derived from pancreas-related specimens available through the major data repositories (GEO, ArrayExpress) and international initiatives (TCGA, GENIE, CCLE). Researchers have access to a host of functions to tailor analyses to meet their needs. Results are presented using interactive graphics that allow the molecular data to be visualized in a user-friendly manner. Furthermore, researchers are provided with the means to superimpose layers of molecular information to gain greater insight into alterations and the relationships between them. The literature-mining module has been improved with a redesigned web appearance, restructured query platforms and updated annotations. These updates to PED are in preparation for its integration with the Pancreatic Cancer Research Fund Tissue Bank (PCRFTB), a vital resource of pancreas cancer tissue for researchers to support and promote cutting-edge research.Pancreatic Cancer Research Fund [Tissue Bank grant]; Cancer Research UK [Grant A12008]; Breast Cancer Campaign [Tissue Bank Bioinformatics grant TB2016BIF]

Multimorbidity in patients living with and beyond cancer: protocol for a scoping review

INTRODUCTION: The number of people living with and beyond cancer is increasing rapidly. Many of them will experience ongoing physical or psychological sequelae as a result of their original cancer diagnosis or comorbidities arising from risk factors common to cancers and other long-term conditions. This poses the complex problem of managing cancer as a ‘chronic’ illness along with other existing comorbidities. This scoping review aims to map the literature available on multimorbidity in patients living with and beyond cancer, to explore, quantify and understand the impact of comorbid illnesses to inform work around cancer care in UK primary care settings. METHODS AND ANALYSIS: This review will be guided by Joanna Briggs Institute Reviewer’s manual for scoping reviews. A systematic literature search using Medical Subject Heading and text words related to cancer survivors and multimorbidity will be performed in MEDLINE, CINAHL, Embase and Web of Science, from 1990. Results will be described in a narrative style, reported in extraction tables and diagrams, and where appropriate in themes and text. ETHICS AND DISSEMINATION: The scoping review will undertake secondary analysis of published literature; therefore, ethics committee approval is not required. Results will be disseminated through a peer-reviewed scientific journal and presented in relevant conferences. The scoping review will inform understanding of the burden of multimorbidity for cancer survivors, thus allow families, practitioners, clinicians and researchers to take the steps necessary to improve patient-centred care

Derivative scores from site accessibility and ranking of miRNA target predictions

In the present study, we define derivative scoring functions from PITA and STarMir predictions. The scoring functions are evaluated for up to five selected miRNAs with a relatively large number of validated targets reported by TarBase and miRecords. The average ranking of validated targets returned by PITA and STarMir is compared to the average ranking produced by the new derivatives scores. We obtain an average improvement of 13.6% (STD∼5.7%) relative to the average ranking of validated targets produced by PITA and STarMir

Differentiating Ductal Adenocarcinoma of the Pancreas from Benign Conditions Using Routine Health Records: A Prospective Case-Control Study

The study aimed to develop a prediction model for differentiating suspected PDAC from benign conditions. We used a prospective cohort of patients with pancreatic disease (n = 762) enrolled at the Barts Pancreas Tissue Bank (2008-2021) and performed a case-control study examining the association of PDAC (n = 340) with predictor variables including demographics, comorbidities, lifestyle factors, presenting symptoms and commonly performed blood tests. Age (over 55), weight loss in hypertensive patients, recent symptoms of jaundice, high serum bilirubin, low serum creatinine, high serum alkaline phosphatase, low red blood cell count and low serum sodium were identified as the most important features. These predictors were then used for training several machine-learning-based risk-prediction models on 75% of the cohort. Models were assessed on the remaining 25%. A logistic regression-based model had the best overall performance in the validation cohort (area-under-the-curve = 0.90; Spiegelhalter’s z = −1·82, p = 0.07). Setting a probability threshold of 0.15 guided by the maximum F2-score of 0.855, 96.8% sensitivity was reached in the full cohort, which could lead to earlier detection of 84.7% of the PDAC patients. The prediction model has the potential to be applied in primary, secondary and emergency care settings for the early distinction of suspected PDAC patients and expedited referral to specialist hepato-pancreatico-biliary services

'Multi-omic' data analysis using O-miner

This project was funded by Cancer Research UK (Grant A12008: A.S.,A.Z.D.U., Barts Cancer Research UK Centre Award: J.W., A.N.) and EPSRC (DTP grant, J.M.). J.M. and A.Z.D.U. are currently funded by Pancreatic Cancer Research Fund (Tissue Bank Award). E.G. is funded by Breast Cancer Now (Tissue Bank Award). H.R.A is funded by Barts and the London Charity (grant 467/1690)