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Integrating Specimen Data in an i2b2 Research Data Mart

Jack London, PhD Jack.london@jefferson.edu

Cancer Center Informatics Summit February 21, 2013

Use case

A project requiring frozen breast tissue is proposed to study the survival of “triple negative” African American infiltrating breast cancer patients who were treated with taxanes. How many such patients treated at Jefferson have frozen specimens available to researchers?

Current biobanking at Jefferson

167,620 patients 409,004 paraffin

block specimens } TJUH clinica l paraffin block archive

2,597 patients 6,469 fixed,

8,674 frozen, 671 other specimens } Path Dept tumor bank

(KCC member P. McCue, PI)

889 patients 1,463 fixed, 2,982 frozen, 1,580 fluid , 2,642 serum,

443 other specimens } Pancreatic tumor bank (KCC member C. Yeo,

PI) 907 patients

1,685 fixed, 3,730 frozen,

83 other specimens } Breast tumor bank (KCC member J. Palazzo, PI)

499 patients 777 fixed,

1,693 frozen specimens } ENT (thyroid) tumor

bank (KCC member W. Keane,PI)

97 patients 1,052 frozen specimens } Brain tumor bank (KCC

member D. Andrews, PI)

135 patients 134 plasma,

363 serum specimens } Liver tumor bank (KCC member V. Navarro, PI)

Jefferson-KCC Integrated Research Specimen bank

(caTissue):

170,402 patients 443,445 specimens

} 73,046 cancer patients

Cancer patients having comprehensive annotation from the

Tumor Registry, AND having banked specimens:

23,312 patients*

144,127 specimens

*NOTE: About 1 /3 of KCC cancer patients have specimens available for research;

These constitute about 1 /3 of al l research specimens.

via i2b2 RDM

KCC Tumor

Registry

Above slide from last CCSG submission. Current totals are: 801,901 specimens from 221,596 patients. Of the 86,228 Tumor Registry patients, 40,765 have specimens.

Current i2b2 Research Data Mart (RDM) •  Integrates

–  clinical data from hospital clinical data warehouse o  demographics, diagnoses, procedures, labs, medications, hospitalizations, vitals

–  specimen data from caTissue o  class, type, pathology

–  tumor registry data from vendor system o  primary dx, histology, stage,grade, survival, recurrence, treatment, site specific factors

•  RDM data are de-identidentified. Re-identification possible via honest broker.

•  Currently > 28M observations on > 350,000 patients. Data refreshed monthly.

•  Built on “informatics for integrating biology and the bedside” (i2b2) framework from NIH-funded National Center for Biomedical Computing based at Partners HealthCare System.

Drag-and-drop i2b2 query tool

How many patients are ER-PR-Her2 negative, with infiltrating breast cancer, and African-American?

How many patients are ER-PR-Her2 negative, with infiltrating breast cancer, African-American, and have frozen tissue available for researchers?

How many patients are ER-PR-Her2 negative, with infiltrating breast cancer, African-American, have frozen tissue available for researchers, treated with taxanes, and > 1 year survival?

Honest broker has tool to re-identify data.