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CPTR 2017 Workshop: Summaries, Slides, and Videos — Day 3

Welcoming Remarks

Jim Gallarda (Bill & Melinda Gates Foundation)

Jim Gallarda opened the day’s agenda by reminding participants of the importance of collaboration and that silos often act as the largest impediments to progress in global health.

Video

 

 

Keynote Address: Learning from the Impact of the Drug-Diagnostic Development Strategy in Oncology

Jan Trost Jorgensen (Dx-Rx Institute)

Jan Trost Jorgensen addressed the similarities and differences in drug and diagnostic development strategies between cancer and tuberculosis. The heterogeneity of the disease must inform the approaches to tools development. Jorgensen noted that the successes of drug development in oncology are strongly related to development and use of companion diagnostics. Additionally, such coordination reduces the overall cost of drug development as it leads to less failure and increased speed and efficiency. This model is highly applicable to the challenges facing TB drug and diagnostic development and deployment.

Video

Video (Question and Answer)

Presentation

 

Roundtable Discussion on Patient Centric Solutions – In-Country Perspectives

Ethics Considerations in the Development and Implementation of TB Diagnostics

Diego Silva (Simon Fraser University)

Diego Silva stressed that the existence of diagnostics is alone insufficient. They must be used properly, and further, even when used properly, they must lead patients to available and effective care. Silva articulated the differences between clinical health and public heath goals as they relate to diagnosis – there is no direct health benefit to accurate diagnosis if that person can’t be cured. This serves as a reminder to approach product development with the end, and end-user, in mind.

 

From tools to patient-centric solutions

Madhukar Pai (McGill University)

Madhukar Pai presented a detailed map of patient care, showing how patients struggle to access new tools. Pai reiterated that health systems are not equipped and prepared to effectively diagnose TB outside the National Treatment Programs. The cascade of care in TB in India reveals where people drop off and lose access to care; diagnosis is the biggest problem. Pai presented a similar analysis for MDR-TB patients in South Africa. Many opportunities to fall off the path to care exist, so solutions are required across the entire spectrum of care. Pai noted that it is encouraging that use of GeneXpert is trending in the right direction, yet countries still seem to be under-utilizing tools they have bought into and invested in.

Video

Presentation

 

Panel Discussion

Moderator: Madhukar Pai (McGill University)

Video

 

Collaborations for Advancing Drug Susceptibility Test Development

Session Introduction

Tim Rodwell (FIND)

Video

 

Prediction of Drug Resistance Using Genotypic Data: An Argument for Machine Learning

Maha Farhat (Harvard University)

Maha Farhat began by summarizing the genetic basis of drug resistance, as well as presenting a construct to understand the molecular diagnostic gap. Farhat presented a prediction model using a random forest classifier to attempt to associate genotype to phenotype, accounting for potential gene-gene interaction. The model identifies the minimum set of mutations predictive of drug resistance. Farhat presented data on the predictive performance of the model, noting areas for improvement, indicating larger datasets as opportunities to further refine and train the model.

Video

Presentation

 

A Standardized System for Grading Mutations in Mycobacterium tuberculosis for Association with Drug Resistance

Paolo Miotto (San Raffaele Scientific Institute)

Paolo Miotto’s presentation shined light on the issue that there are no standardized measures to interpret data on TB mutation, and therefore conclude what those mutations mean in terms of detecting or predicting resistance. Miotto laid a system to standardize the grading of mutation data to predict resistance, based on extensive literature review, which covers more than 300 mutations.

Video

Presentation

 

What are we trying to say here? Standardizing Next Generation Sequencing Reports for TB

Jeff Tornheim (Johns Hopkins University)

Jeff Tornheim’s presentation focused on a lack of standardization and consistency of what data is recorded and reported to health systems and providers when DST tests are performed. While there are huge amounts of data that could be reported – what information do clinicians and epidemiologists want from DST test reports? How do we balance technical info with simplified data enabling quick and accurate decisions about treatment? How is that data organized and presented? These are all questions discussed by Tornheim.

Video

Presentation

 

The Genomic Epidemiology Ontology and Proof Sheet Application

Damion Dooley (University of British Columbia)

Damion Dooley presented on ontology which addresses inconsistencies between different public health databases in the vocabulary used to refer to the same kinds of data/measures. Dooley presented an open-source web-based system that helps group and associate like terms, synonyms, etc. – similar to the process by which dictionaries are created. Such efforts can provide immense value by bringing research together and clarifying trends and findings.

Video

Presentation

 

Panel Discussion

Moderator: Tim Rodwell (FIND)

Video

 

Innovative Partnerships to Advance Data Sharing Across Databases

Session Introduction

Marco Schito (Critical Path Institute)

Video

 

Brief Updates on Database Efforts (10 minute presentations)

Maha Farhat (Harvard University)

Maha Farhat presented on an interface for the analysis of genomics data – genTB. A short demo was given.

Video

 

Raja Mazumder (George Washington University)

Raja Mazumder presented on High Performance Integrated Virtual Environment (HIVE), showing a set of community tools and the importance of a biocomputer-ready pipeline.

Video

Presentation

 

Damion Dooley (University of British Columbia)

Damion Dooley presented on GenEpiO and BC Centre for disease control TB data projects.

Video

Presentation

 

Alison Yao (National Institute of Allergy and Infectious Diseases)

Alison Yao presented on NIAID bioinformatics resources for infectious diseases. The bioinformatics resource centers were started four years ago. There are four centers, each focusing on a specific pathogen, making use of the machine learning approach.

 

Patrick Phillips (UK Medical Research Council)

Patrick Phillips presented on PanACEA and associated opportunities for data sharing. With data from completed Phase 2 and 3 studies already included in databases, the coming years mark opportunities to expand data sharing with studies currently ongoing. Phillips stressed that there is a plan to share that data through open repository, though cautioned that there are great complexities involved in doing so.

 

Panel Discussion

Moderator: Marco Schito (Critical Path Institute)

Video

 

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