National Lung Screening Trial (NLST): Post-Trial Data and Image Exploration with an Open Source Query Tool

Transcription

1 National Lung Screening Trial (NLST): Post-Trial Data and Image Exploration with an Open Source Query Tool Ken Clark 1, Paul Commean 1, Josh Rathmell 2, Tom Riley 2, Gordon Jones 2, Guillermo Marquez 3, Fred Prior 1 1 Washington University in Saint Louis 2 Information Management Services, Inc. 3 National Cancer Institute May 20-22, 2013 Society for Clinical Trials

2 Acknowledgement & Disclaimer The authors thank the National Cancer Institute (NCI) for access to NCI's data collected by the National Lung Screening Trial. The statements contained herein are solely those of the authors and do not represent or imply concurrence or endorsement by the National Cancer Institute. May 20-22, 2013 Society for Clinical Trials

3 National Lung Screening Trial == AIMS == Does image-screening reduce lung-cancer mortality in subjects with heavy smoking histories? YES! Is image-screening with low-dose spiral computed tomography (SCT) superior to chest X-ray? YES! May 20-22, 2013 Society for Clinical Trials

4 National Lung Screening Trial == TIME - LINE == : 53,454 subjects randomized to SCT and X-ray groups : Subjects received 3 imaging screens at annual intervals : Non-image data collection and follow-up. 2011: Results published May 20-22, 2013 Society for Clinical Trials

5 NLST Data & Image Repositories Non-Image Data: Information Management Services (Rockville, Maryland) 450 variables for 53,454 subjects SCT Images: Washington University (Saint Louis, Missouri) 73,000+ SCT studies = 21,000,000+ images X-rays: ( Remain at NLST screening sites ) May 20-22, 2013 Society for Clinical Trials

6 Challenge Monday s opening lecture (Dr. Butte) and invited session Public Use Datasets discussed the NIH requirements and expectations for creating public use datasets and sharing data and the challenges for doing so. In that spirit How to make NLST data and images available to the public?? May 20-22, 2013 Society for Clinical Trials

7 Our Solution Build a Query Tool that empowers investigators is easy to use is open source May 20-22, 2013 Society for Clinical Trials

8 Query Tool Model for non-image Data PostgreSQL DB NLST data From IMS Query Tool NLST Data Users May 20-22, 2013 Society for Clinical Trials

9 What is to query? == Definition == Retrieve a subset of the database. == Example (NLST database) == Retrieve the heights and weights of 57-year-old men who smoked cigars and a pipe. May 20-22, 2013 Society for Clinical Trials

10 How to Query in 5 Easy Steps 1 From tables, click to select variables 2 Click to set variable conditions 3 Click Run Query 4 Adjust the query & re-run OR save results 5 Download associated images (optional) Structured Query Language (SQL) knowledge NOT required!! May 20-22, 2013 Society for Clinical Trials

11 Query Tool Interface May 20-22, 2013 Society for Clinical Trials

12 5 Selections, Conditions, Results Run Query button Tri-Function Window 1 2 Choose variables to condition Select variables from tables 3a 3b View query results View and set condition limits View selections made Result count May 20-22, 2013 Society for Clinical Trials c 6 4 SQL statement Progress bar

13 May 20-22, 2013 Society for Clinical Trials

14 Smoking History Table A few Smoking History Table variables May 20-22, 2013 Society for Clinical Trials

15 Decoding Variable Names Hover over variable shows tooltip May 20-22, 2013 Society for Clinical Trials

16 Set Numerical Variable Conditions Buttons: = < > Between < <= > >= In For table Demographics and variable Age, condition with In ( Age = 49 or 52 or 56 ) May 20-22, 2013 Society for Clinical Trials

17 Click to Run the Query Results appear in a scrollable window; total count 525 is given below. May 20-22, 2013 Society for Clinical Trials

18 Saving Results Text File All Data for Query May 20-22, 2013 Society for Clinical Trials

19 Image Servicing May 20-22, 2013 Society for Clinical Trials

20 The Cancer Imaging Archive (TCIA) Washington University in Saint Louis The Cancer Imaging Archive (TCIA) 21 million images 4 million images NLST SCT Images Image Download Manager Non-NLST Cancer Image Collections Software NBIA Image Download Manager Public TCIA Users Anatomical Sites Brain Breast Chest Head-Neck Kidney Lung Ovary Prostate May 20-22, 2013 Society for Clinical Trials

21 Access to NLST Data and Images Washington University in Saint Louis The Cancer Imaging Archive (TCIA) PostgreSQL DB NLST data From IMS NLST SCT Images Non-NLST Cancer Image Collections Query Tool Link Pose queries Data Returned NLST Users Software NBIA Image Download Manager Images Returned TCIA Users May 20-22, 2013 Society for Clinical Trials

22 Obtaining Images for Query Results == Two Options == 1. Download images immediately. 2. Save Pointers in a Shared List : Download images later. Collaborators may access same images. May 20-22, 2013 Society for Clinical Trials

23 Downloading the Images User specifies storage location 2 1 Start 3 4 Download Progress May 20-22, 2013 Society for Clinical Trials

24 Query Tool Menu Bar Queries of general interest Direct links to NLST publications Save, recall, or delete my own queries May 20-22, 2013 Society for Clinical Trials

25 Query Tool Menu Bar -- Help May 20-22, 2013 Society for Clinical Trials

26 Open Source Query Tool PostgreSQL NBIA Application ( National Biomedical Imaging Archive ) May 20-22, 2013 Society for Clinical Trials

27 Conclusion The open source Query Tool facilitates the exploration and mining of large-scale clinical trial data, including radiology images. ( more ) May 20-22, 2013 Society for Clinical Trials

28 Conclusion Though applied to NLST data, the Query Tool was designed to be trial independent and should, therefore, be attractive to investigators wanting to quickly harvest data and perform exploratory data analysis. May 20-22, 2013 Society for Clinical Trials

29 Accessing NLST Data & Images The Cancer Imaging Archive Query Tool Contacts Paul Commean: ( 314 ) commeanp@mir.wustl.edu Ken Clark: ( 314 ) clarkk@mir.wustl.edu May 20-22, 2013 Society for Clinical Trials