1. Penn Ties update
November 2016 FTF

2. 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

3. 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)

4. 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

5. 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

6. 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

7. 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

8. 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

9. “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

10. 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

11. 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

12. 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