Oncology

Infectious Diseases

Informatics

Navigating the Landscape of Open Source Tools for Applications in Molecular Pathology

Program Committee Moderator(s)

• 

  Heather Blankenship, PhD

  Genomics Technical Director
  Michigan Department of Health and Human Services
  Lansing, Michigan, United States

Co-Moderator (Early Career)(s)

• 

  Wesley Goar, PhD (he/him/his)

  Senior Bioinformatics Scientist
  Nationwide Children's Hospital
  Westerville, Ohio, United States

Session

Description: In this breakout session, we will delve into the dynamic realm of open source and open access tools, exploring their pivotal role in advancing precision medicine within the context of molecular pathology. The speakers will highlight cutting-edge tools for clinical interpretation of cancer variants and identification of microorganisms from diagnostic samples. We will describe approaches and lessons learned in creating bioinformatics tools, featuring resources like CIViCdb for somatic variant interpretation and pVACtools for personalized neoantigen vaccine design. Additionally, we will explore the lifecycle of open source bioinformatic pipelines and tools for infectious diseases, discussing concepts such as reproducibility, portability, and accessibility, and their linkage to package and workflow managers.

If this session topic is of interest to you, please consider looking at the following course on AMP EDucation (AMPED™ Online)

Title: AMP 2020 Annual Meeting: SHORT COURSE: Next-generation Sequencing Assay development and validation
Click here to learn more.

Presentations:

• 10:15 AM – 11:00 AM PST

  Developing Open-Source Bioinformatics Pipelines and Packages for Molecular Pathology
  

  Breakout Speaker: Malachi Griffith, PhD (he/him/his) – Washington University
• 11:00 AM – 11:45 AM PST

  Open-Source Bioinformatics Pipelines and Packages for Infectious Diseases
  

  Breakout Speaker: Robert A. Petit, III, PhD – State of Wyoming