Visualization of Group Related Differences in Histopatholgy Data

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Welcome to the site for the "Visualization of Group Related Differences in Histopathology Data" project group.

This page describes high-level project management details on the group, including purpose, milestones, attendees, and so on. We are part of the FDA/PhUSE Computational Sciences Nonclinical Working Group. Learn more about the larger working group at Non-Clinical Road-map and Impacts on Implementation.

Project Overview

Identified Need/Challenge

Histopathology data comprise a major component of toxicology studies and are typically presented in data tables (tabular format) in study reports. Can these data be graphically displayed in a visual format which provides a means for rapidly identifying and communicating treatment group differences, patterns in response, and/or changes in phenotypic expression ? Can cross-domain analyses (including organ weights, clinical pathology and histopathology data) be graphically displayed for analyses ? Can data from multiple studies be aggregated or graphically displayed for analysis ? How does incorporation of the SEND (Standard for Exchange of Nonclinical Data) standard enable this technology ?

Project Scope

To canvas opinion from toxicologists, pathologists, bioinformatics specialists and software designers on current methods of data visualization and how those might be improved or expanded to improve data analyses compared to currently used tabular (incidence) formats. To communicate points of discussion, ideas, case examples, etc. with key stake holders (the pharmaceutical industry, software developers/vendors, CROs, US FDA) via the wiki, poster presentations and publications.

Vision

To explore the use of various software applications for visually displaying histopathology data in novel ways to aid with data analysis and communication of findings, and to promote the use of the SEND standard for enabling this technology

Prior Project Plans

The working group completed its third year of activity (2017 to 2018). Project plans included the following.
1) Evaluate the use of the "sunburst" graphical display (termed HistoGraphic) and application for visualizing histopathology data from the IMI eTOX database
3) Explore use of the "sunburst" (HistoGraphic) application for simultaneously displaying microscopic findings and relevant biomarkers. As an example, initial efforts can focus on liver lesions and serum ALT, AST, ALKP and/or bilirubin changes
3) Collaborate with the Nonclinical Scripts working group for development and evaluation of novel software applications, such as HistoGraphic, for data visualization. The first two projects listed above are a component of this activity
4) Create mock SEND datasets of histopathology data for incorporation into various software applications to evaluate multi-study data displays

Future Plans

After 3 years of activity, the project has reached a natural conclusion with development of HistoGraphic for graphically displaying histopathology data from multiple toxicology studies which were obtained from the European Union's IMI eTOX database. Deliverables from the project team included 3 posters presented at FDA PhUSE CSS meetings and one publication. It is the project team's intent to place HistoGraphic on a publicly assessed site for downloading. A potential future plan includes developing a collaborative relationship with the EU's IMI eTRANSAFE initiative (Enhancing Translational Safety Assessment through Integrative Knowledge Management) eTRANSAFE

Milestones

March 2015 - March 2016 (completed)

1) Identify a panel of Toxicologists and Pathologists (2 weeks)
2) Supply of intended usage and a selection of 'use-cases' (6 weeks)
http://etransafe.eu/ 3) Gap analysis results (12 weeks)
4) Recommended visualisations (26 weeks)
5) Approach to fill gaps in SEND standard (52 weeks)
6) Communicate project results at 2016 FDA PhUSE Computational Sciences Symposium (52 weeks)

April 2016 - March 2017 (completed)

1) Prepare first draft of manuscript (July 2016) - completed
2) Prepare final draft of manuscript (October 2016) - completed
3) Submit to Regulatory Toxicology and Pharmacology (November 2016) - completed October 2016
4) Discuss cross-domain and cross-study graphical displays, including examples (by December 2016) - completed
5) Submit abstract for poster presentation for 2017 FDA PhUSE CSS (January 2017) - completed
6) Submit poster for 2017 FDA PhUSE CSS (February 2017) - completed
7) Poster presentation at 2017 FDA PhUSE CSS (March 2017) - completed

April 2017 - March 2018 (completed)

1) Obtain eTOX datasets and incorporate into HistoGraphic display tool (completed November 2017)
2) Submit abstract for poster presentation for 2018 FDA PhUSE CSS (completed January 2018)
3) Submit poster for 2018 FDA PhUSE CSS (completed February 2018)
4) Poster presentation at 2018 FDA PhUSE CSS - (completed March 2018)

Tasks

Upcoming milestones for 2018 FDA PhUSE Computational Sciences Symposium, 4-6 March 2018 in Silver Spring, Maryland, USA:

  • Prepare and submit abstract for poster presentation. Completed 5 Jan 2018.
  • Prepare and submit draft poster and copyright grant form. Due 2 Feb 2018.
  • Submit final poster. Due 16 Feb 2018.

Communications

1) Group communication via email: approximately every 3 weeks
2) Web conferences: approximately every 3-4 weeks
3) PhUSE Wiki: ad hoc

Deliverables For 2015 Project Year

Deliverables for 2016 Project Year

Publication in Regulatory Toxicology and Pharmacology

Poster presented at 2017 FDA PhUSE Computational Sciences Symposium

Deliverables for 2017 Project Year

Data Visualizations: Examples

Participation Needs

The team was established at the PhUSE CSS March 2015 and extended at the PhUSE CSS March 2016.

Call for participation!

What is the commitment?

  • Time (minimum of 1 hour every 2-3 weeks for team meetings, up to 3 hours / month)
  • Expected to contribute, not just be a spectator
  • Contribution of viewpoints and content
  • Wiki - creating/reviewing page content

If you would like to participate, please contact the co-leads for this group:

Work Group Participants

Participants:

  • Phil Drew, PDS Consultants (Project Leader)
  • Alan P. Brown, Novartis (Co-Lead)
  • Sree Rayavarapu, FDA
  • Brian Knight, Boehringer Ingelheim (Core Team)
  • Sean Troth, Merck (Core Team)
  • Anisa Scott, SAS
  • Montserrat Cases, Synapse
  • Steven Polley, GlaxoSmithKline
  • Elyse Hoffman, Boehringer Ingelheim
  • Bill Varady, Boehringer Ingelheim
  • Laura Kaufman, Eagle Pharmaceuticals
  • Linda Hunt, Merck
  • Benjamin Sefing, Merck
  • Suresh Madhavan, PointCross Life Sciences
  • Joyce Zandee, INDS
  • Karen Porter, PointCross Life Sciences
  • Philippe Marc, Novartis
  • Brian Johnson, Boehringer Ingelheim
  • Bettina Lawrenz, Bayer Pharma AG
  • Kevin Snyder, FDA
  • Belinda Hayes, FDA
  • Kuno Wuersch, Novartis
  • Dan Potenta, PDS Life Sciences
  • Jacquice Davis, PointCross Life Sciences
  • Robert Stull, Novartis
  • Jean-Pierre Kieffer, Roche
  • Mark Carfagna, Eli-Lilly
  • Matthew Hayes, Genentech
  • Patrick Villiger, Roche
  • Nidhi Khurana Nalawade, Gilead
  • Raja Ramesh, PointCross Life Sciences

Conference Calls and Minutes

24 April 2015 Meeting Minutes
22 May 2015 Meeting Minutes
5 June 2015 Meeting Minutes
10 July 2015 Meeting Minutes
24 July 2015 Meeting Minutes
14 August 2015 Meeting Minutes
28 August 2015 Meeting Minutes
11 September 2015 Meeting Minutes
13 November 2015 Meeting Minutes
4 December 2015 Meeting Minutes
8 January 2016 Meeting Minutes
29 January 2016 Meeting Minutes
1 April 2016 Meeting Minutes
29 April 2016 Meeting Minutes
3 June 2016 Meeting Minutes
1 July 2016 Meeting Minutes
22 July 2016 Meeting Minutes
9 September 2016 Meeting Minutes
30 September 2016 Meeting Minutes
28 October 2016 Meeting Minutes
6 January 2017 Meeting Minutes
19 January 2017 Meeting Minutes
3 February 2017 Meeting Minutes
3 March 2017 Meeting Minutes
12 April 2017 Meeting Minutes
26 May 2017 Meeting Minutes
23 June 2017 Meeting Minutes
3 August 2017 Meeting Minutes
1 December 2017 Meeting Minutes
8 December 2017 Meeting Minutes
15 December 2017 Meeting Minutes
5 January 2018 Meeting Minutes
12 January 2018 Meeting Minutes
16 March 2018 Meeting Minutes
13 April 2018 Meeting Minutes