Penn Ties update November 2016 FTF

Penn Team Michael Feldman, Assoc Prof Path & Lab Med – Site PI Joellen Weaver – Director SOM Biobank – Regulatory and Admin Nate Digiorgio – Sys Admin and DBA – Kevin Lux – Interface Tara McSherry – End user training and support, QA Fred Valdivieso – Tissue bank manager – honest broker

Database Latest code set running 5.6 Records coded ~940K Active coding pipeline via daily data load from Medview (home grown web portal for lab results) Catching all Surg path cases from 3 hospitals downtown hospitals at Penn Medicine (65K/yr)

Roll out Roll Out SOM Biobank as honest broker 35 Active users on the system Expanding to more cancer center investigators Monthly training Working with new Cancer Center CIO SOM Biobank as honest broker

Value TIES study in prep to research Query – Find all pancreas cancer cases where we have the primary tumor along with metastatic tumor Results – 41 cases of primary and mets Exomes, RNAseq and Immune Neoantigen scores 500K Supplement to our Cancer Center P30 grant to study these pairs to look for drivers in metastatic progression

Value TIES study in prep to research Query – Find all triple negative breast cancer cases where we have the primary tumor along with metastatic tumor Results – 73 cases of primary and mets Pulling cases to start new Basser Center Study Exomes, RNAseq and Immune Neoantigen scores Other Cancer specific groups are interested GI – Colon, esophagus

Value Clinical Assay Development Retrospective cohort study Find cases in neuropathology that look infectious but for which no organism has been found Test set to look at new tools to discover infectious agents DNA and RNA seq to look for agents Pathochip to look for agents

Research study Rosai Dorfman Disease Rosai Dorfman disease is an idiopathic reactive condition characterized by exuberant macrophage reaction in lymph nodes or soft tissue Etiology is unknown but some studies have implicated a virus, Herpes virus 6 in some cases Pathochip is a microarray technology All known pathogenic virus and bacteria and fungi arrayed Allows FFPE to be probed for infectious signature in lesional tissue compared to normal controls

“Breast Papilloma study” Find all breast needle cores with diagnosis of a papilloma but nothing worse at the time of or before the core biopsy who then went on to a subsequent resection In the resection after the papilloma core biopsy, what is the frequency of finding either in situ or invasive carcinoma Compare the carcinoma rate to carcinoma in a random core biopsy population with BIRADS4

Structured + NLP How can we link structured data with TIES? Pathology Biobank – LIMS is labvantage, same at RPCI Oncology – tumor registry Metriq similar to Pitt and RPCI

Virtual slides at Penn Need to get our vslides coded for use in TIES We have ~40K slides in spectrum, some subset is usable with TIES

How can TIES be expanded (more corpuses) Radiology Oncology Diagnosis Response Criteria (RECIST) – Lesion changes, Lymph node size, bone lesion, PET… Heterogeneity – structural (CT and MRI) and genomic (PET) Integrated process research – precision medicine