Stony Brook University The Process for Joining TIES Project Team: PI Joel Saltz MD PhD Honest Broker David Cyrille MA Project Coordinator Elinor Schoenfeld PhD Pathology Kenneth Shroyer MD, Tianhou Zhao MD Pathology Imaging Tahsin Kurc PhD, Tammy DiPrima, NLP Niranjan Balasubramanian PhD, Le Hou, Veronica Lynn Cancer Center Mary Saltz MD Data Analytics Jonas Almeida PhD, Janos Hajagos PhD

ABOUT THE UNIVERSITY Stony Brook University Hospital started in 1980 603 beds regions only tertiary care center and level 1 trauma center Cancer Center Treats over 2600 cancer patients/year Designated lung cancer screening and treatment center One of 2 Medical Schools on LI 1 of 4 Public Universities within the NYS system One of top research institutions in US

https://bmi.stonybrookmedicine.edu/AboutBMI THE DEPARTMENT OF BIOMEDICAL INFORMATICS Started in 2013 dually housed in the School of Medicine and the College of Engineering and Applied Sciences Leadership Joel H Saltz MD PhD – Cherith Professor and Founding Chair Tahsin M Kurc PhD – Vice Chair Jonas Almeida PhD – Chief Technology Officer, Director BMI Graduate Program Graduate Program MS, PhD and advanced graduate certificate program 3 tracks – clinical informatics, translational bioinformatics, imaging informatics Areas of Research Integrative Multiscale Precision Medicine, Computational Systems Biology, Clinical Informatics, Translational Bioinformatics, Biomedical Data Science, Biomedical Informatics Infrastructure, Population Health Informatics, Computational Systems Biology https://bmi.stonybrookmedicine.edu/AboutBMI

SB TCRN Specific Aims join the TCRN to contribute de-identified cancer cases to the network and obtain cancer cases from the network to conduct molecular characterization of human tumors evaluate and share with the TIES TCRN network institutions a system that links features described in the TIES text-based pathology reports with features derived from automatic image analysis of the corresponding specimen slides. utilize the developed systems with the TCRN network’s available de-identified data to expand the Stony Brook team’s research in pathology features evaluation for rare/unique cancer types only available via this pooled data increase the power of studies that associate combined imaging feature and text extracted phenotype to outcomes and treatment response

Dual Server Deployment SB PHASE 1 - INTERNAL DEPLOYMENT Dual Server Deployment Application Server Windows Server 2012 R2 X64 6 Cores 12 Gb Ram 200 GB Storage Database Server Red Hat Enterprise Linux 7 16 GB Ram 500 GB Storage

Application Server Windows Server 2012 R2 X64 SB PHASE 2 (PUBLIC) – CONSORTIUM VM (DMZ) Application Server Windows Server 2012 R2 X64 6 Cores 12 Gb Ram 200 GB Storage Firewall rule to allow access to internal MySQL 5.7 Public Database Active threat scanning

SB DEPLOYMENT

TIES Configuration at SB SB has configured two instances of TIES TCRN repository (TCRN TIES) For sharing of de-identified pathology reports and slide images with the network SB repository (SB TIES) To use as a sandbox for development of new processes and methods Both instances share the same pathology report and imaging data linked by the same de-identification ID

TIES SB Sandbox SB TIES has been developed as a sandbox to evaluate and test enhanced and new systems for extracting data from pathology reports and images Provide enhancements to an existing natural language processing (NLP) free text coding and indexing system for pathology reports within TIES develop a system that links features described in the TIES text-based pathology reports with features derived from automatic image analysis of the corresponding specimen slides.

IRB status Submitted separate applications to IRB for approvals for SB TIES and TCRN TIES Both applications have completed initial IRB review with request for clarifications Response to reviewers have been submitted to IRB and are awaiting final approvals

Pathology Department uses CoPath to process their reports Pathology Reports Pathology Department uses CoPath to process their reports These reports are sent to Cerner (our EMR) for access and storage A total of 617,966 surgical pathology reports are stored within CoPath (1980-2016)

Readiness to join the TCRN 4-6 Months Lead Time SBMIT Resources identified and positioned to support TIES Honest Broker Database Administrators Linux and Windows Infrastructure Teams Network Security Need alignment of Internal resources toward consortium guidelines Identify key quality assurance personnel Domain expert Replicate consortium guidelines toward personnel and internal policies