A novel cross-disciplinary multi-institute approach to translational cancer research: Lessons learned from Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC)

Cancer Informatics

Volumn 3, Issue , 2007, Pages 255-274

  Patel, Ashokkumar A ^a   Gilbertson, John R ^a   Showe, Louise C ^b   London, Jack W ^c   Ross, Eric ^d   Ochs, Michael F ^d   Carver, Joseph ^e   Lazarus, Andrea ^f   Parwani, Anil V ^a   Dhir, Rajiv ^a   Beck, J Robert ^d   Liebman, Michael ^g   Garcia, Fernando U ^h   Prichard, Jeff ⁱ   Wilkerson, Myra ^a   Herberman, Ronald B ^a   Becich, Michael J ^a   Whelan, Nancy ^a   Mathews, Lois ^a   Winters, Sharon ^a   Urda, Susan ^a   Gianella, Heidi ^a   Bisceglia, Michelle ^a   Gupta, Rajnish ^a   Singh, Harpreet ^a   Li, Songhui ^a   Nie, Yimin ^a   Chu, Vicky ^a   Mohanty, Sambit ^a   Mann, Dorothy ^a   Mignogna, Linda ^a   Monzon Bordonaba, Federico ^a   Katsur, Alice ^a   Kirkwood, John ^a   Brufsky, Adam ^a   Colecchia, Theresa ^a   Green, Carolyn ^a   Glick, John ^e   Tigges, Jesse ^e   Fenstermacher, David ^e   Rebbeck, Timothy R ^e   DeMichele, Angela ^e   Weber, Barbara ^e   Guerry, DuPont ^e   Poppert, Elizabeth ^e   Haney, Kate ^d   Brusstar, Steve ^d   Malick, John ^d   Capriotti, Arlene ^d   Balshem, Andrew ^d   Uzzo, Robert G ^d   Goldstein, Lori J ^d   Lessin, Stuart R ^d   Harsche, Pat ^d   London, W Thomas ^d   Davidson, Richard L ^c   DeBaca, Monica ^c   Orrico, Alejandra Ruiz ^c   Hannes, Adler ^c   Palazzo, Juan P ^c   Dicker, Adam ^c   Mastrangelo, Michael ^c   Chou, Katherine ^c   Loughran, Thomas ^f   Whayland, Pam ^f   Swetland, Pat ^f   Lazarus, Philip ^f   Harriet, Isom ^f   Beard, Dan ^f   Snyder, Alan J ^f   Rybka, Witold B ^f   Lorence, Daniel ^f   Lipton, Allan ^f   Harvey, Harold A ^f   Robertson, Gavin ^f   Claxton, David ^f   Rauscher, Richard ^f   Carlisle, Jenine ^b   Kaufman, Russel E ^b   Ewert, Donald ^b   O'Brien, Elizabeth ^b   Melnicoff, Meryle ^b   Blank, Kenneth ^h   Hailu, Tesfu ^h   Petushi, Sokol ^h   Steele Jr , Glenn D ⁱ   Buckley, Sandy ⁱ   Hunter, Nicole ⁱ   Yantus, Kim ^g   Hu, Hai ^g   Sheridan, Chris ^g   Rigby, Holly ^g   Jacobs, F Nicholas ^g   Bronder, Pat ^j   Palmer, David ^j   Glick, John H ^j   more..

^a UNIVERSITY OF PITTSBURGH CANCER INSTITUTE   (United States)

^b WISTAR INSTITUTE   (United States)

^c THOMAS JEFFERSON UNIVERSITY   (United States)

^d FOX CHASE CANCER CENTER   (United States)

^e UNIVERSITY OF PENNSYLVANIA   (United States)

^f PENN STATE MILTON S HERSHEY MEDICAL CENTER   (United States)

^g WINDBER RESEARCH INSTITUTE   (United States)

^h DREXEL UNIVERSITY COLLEGE OF MEDICINE   (United States)

ⁱ GEISINGER HEALTH SYSTEM   (United States)

^j University of Pittsburgh Cancer Institute ^*

more..

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; TUMOR MARKER;

ARTICLE; AUTOMATION; BIOINFORMATICS; BLOOD SAMPLING; BREAST CANCER; CANCER LOCALIZATION; CANCER PATIENT; CANCER REGISTRY; CANCER RESEARCH; COMMUNITY; DATA BASE; GENOMICS; HEALTH CARE SYSTEM; HUMAN; HUMAN TISSUE; INFORMATION PROCESSING; LEARNING; MAJOR CLINICAL STUDY; MEDICAL RESEARCH; MEDICAL SOCIETY; MELANOMA; ORGANIZATION AND MANAGEMENT; PROSTATE CANCER; PROTEOMICS; UNITED STATES;

EID: 42549107938     PISSN: 11769351     EISSN: 11769351     Source Type: Journal    
DOI: None     Document Type: Article

References (47)

1. Becich MJ: 2000. The role of the pathologist as tissue refiner and data miner: the impact of functional genomics on the modern pathology laboratory and the critical roles of pathology informatics and bioinformatics. Mol. Diagn., 5(4):287-299.
2. Eiseman, E., Rand Corporation.: Case studies of existing human tissue repositories: "best practices" for a biospecimen resource for the genomic and proteomic era (http://www.rand.org/publications/MG/MG120/). Santa Monica, CA: RAND; 2003.
3. Patel, A.A., Gilbertson, J.R., Parwani, A.V., Dhir, R., Datta, M.W., Gupta, R., Berman, J.J., Melamed, J., Kajdacsy-Balla, A., Orenstein J. et al: 2006. An informatics model for tissue banks - Lessons learned from the Cooperative Prostate Cancer Tissue Resource. B.M.C. Cancer, 6(1):120.
4. Gilbertson, J.R., Gupta, R., Nie, Y., Patel, A.A., Becich, M.J.: 2004. Automated clinical annotation of tissue bank specimens. Medinfo 11(Pt 1):607-610.
5. Master Settlement Agreement [http://www.attorneygeneral.gov/ uploadedFiles/Consumers/msa.pdf]
6. Pennsylvania's Act 77 of 2001, the Tobacco Settlement Act [http://www.legis.state.pa.us/WU01/LI/BI/BT/2001/0/HB0002P2378. HTM]
7. Pennsylvania's Health Research and CURE program [http://www.dsf.health. state.pa.us/health/cwp/browse.asp?A=175&BMDRN=2000&BCOB=0&C=38811]
8. Technology Transfer: Administration of the Bayh-Dole Act by Research Universities [http://www.gao.gov/archive/1998/rc98126.pdf]
9. Patel, A.A., Kajdacsy-Balla, A., Berman, J.J., Bosland, M., Datta, M.W., Dhir, R., Gilbertson, J., Melamed, J., Orenstein, J., Tai, K.F. et al. 2005. The development of common data elements for a multi-institute prostate cancer tissue bank: the Cooperative Prostate Cancer Tissue Resource (CPCTR) experience. B.M.C. Cancer, 5:108.
10. Melamed, J., Datta, M.W., Becich, M.J., Orenstein, J.M., Dhir, R., Silver, S., Fidelia-Lambert, M., Kadjacsy-Balla, A., Macias, V., Patel, A. et al: 2004. The cooperative prostate cancer tissue resource: a specimen and data resource for cancer researchers. Clin. Cancer, Res., 10(14):4614-4621.
11. Greene, F.L., American Joint Committee on Cancer., American Cancer Society.: AJCC cancer staging manual, 6th edn. New York: Springer-Verlag; 2002.
12. NAACCR Data Standards for Cancer Registries [http://www.naaccr.org/index. asp?Col_SectionKey=7&Col_ContentID=122
13. The CAP Cancer protocols: Checklist for prostate gland [http://www.cap.org/apps/docs/cancer_protocols/prostate04_pw.pdf
14. The NCICB's Cancer Data Standards Repository (caDSR) [http://ncicb.nci. nih.gov/NCICB/infrastructure/cacore_overview/cadsr]
15. Winget, M.D., Baron, J.A., Spitz, M.R., Brenner, D.E., Warzel, D., Kincaid, H., Thornquist, M., Feng, Z. 2003. Development of common data elements: the experience of and recommendations from the early detection research network. Int. J. Med. Inform., 70(1):41-48.
16. Department of Health and Human Services. 45 CFR (Code of Federal Regulations), 164.514(6)(2)(i). Standards for Privacy of Individually Identifiable Health Information (final) [http://www.hhs.gov/ocr/regtext.html]
17. Health Insurance Portability and Accountability Act of 1996 [http://aspe.hhs.gov/admnsimp/pl104191.htm]
18. Dhir, R., Patel, A.A., Winters, S., Grzybicki, D., Bisceglia, M., Swanson, D., Aamodt, R., Becich, M.J. 2006. A multi-disciplinary approach to honest broker services for tissue banks and clinical data: a pragmatic and practical model. (In submission). CLin. Canc. Research.
19. Solbrig, H.R. 2000. Metadata and the reintegration of clinical information: ISO 11179. MD., Comput, 17(3):25-28.
20. The ISO/IEC 11179 specification developed by the National Institute of Standards and Technology (NIST) [http://isotc.iso.ch/livelink/livelink/fetch/ 2000/2489/Ittf_Home/PubliclyAvailableStandards.htm]
21. The NCI's Cancer Biomedical Informatics Grid (caBIG) [http://cabig.nci. nih.gov/]
22. NCI Thesaurus [http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do]
23. Berman, J.J., Datta, M., Kajdacsy-Balla, A., Melamed, J., Orenstein, J., Dobbin, K., Patel, A., Dhir, R. and Becich, M.J. 2004. The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource. BMC Bioinformatics, 5(1):19.
24. Li, S., Becich, M. and Gilbertson, J. 2004. Microarray Data Mining Using Gene Ontology. Medinfo. 778-782.
25. Yu, Y.P., Landsittel, D., Jing, L., Nelson, J., Ren, B., Liu, L., McDonald, C., Thomas, R., Dhir, R., Finkelstein, S. et al. 2004. Gene Expression Alterations in Prostate Cancer Predicting Tumor Aggression and Preceding Development of Malignancy. J. Clin. Oncol., 22(14): 2790-2799.
26. Patel, A.A., Gupta, D., Seligson, D., Hattab, E.M., Balis, U.J., Ulbright, T.M., Kohane, I.S., Berman, J.J., Gilbertson, J.R., Dry S. et al. 2007. Availability and quality of paraffin blocks identified in pathology archives: a multi-institutional study by the Shared Pathology Informatics Network (SPIN). B.M.C., Cancer, 7:37.
27. The U.K. Biobank Project [http://www.biobank.ac.uk]
28. Swedish National Biobank Program [www.biobanks.se]
29. ATIP03.042. 2003. The Biobank Japan Project (http://www.atip.org/public/ atip.reports.03/atip03.042.pdf). In: Asian Technology Information Program,.
30. McCaffrey P. 2003. Iceland's database tussle http://www.bio-itworld.com/ news/040103_report2255.html. Bio-IT World.
31. Australasian Biospecimen Network (ABN) [http://www.abrn.net/]
32. Thorn, H.C.D., Devereux, L., MacCallum, P. and Zeps N: 2005. A more auspicious start for the Australasian Biospecimen Network [Letter to the Editor]. J. Clin. Invest.
33. The Singapore Tissue Network [http://www.stn.org]
34. Spinney, L. 2003. U.K. launches tumor bank to match maligned Biobank. Nat. Med., 9(5):491.
35. The National Biospecimen Network (NBN) blueprint [http://biospecimens. cancer.gov/nbn/blueprint.asp]
36. VonEschenbach, A.C., Buetow K. 2006. Cancer Informatics Vision: caBIG. Cancer Informatics, 2:22-24.
37. Summary of Key Points in the Master Settlement Agreement [http://www.attorneygeneral.gov/consumers.aspx?id=683]
38. CURE Awarded Grants: Health Research Nonformula Grant Awards for SFY 2001-02 [http://www.dsf.health.state.pa.us/health/lib/health/cure/ 2001_nonformula_grants_sfy_01-02.pdf]
39. The Pittsburgh Life Sciences Greenhouse [http://www. pittsburghlifesciences.com]
40. George J. 2006. Study details tobacco settlement's boon to Pennsylvania. In: Philadelphia Business Journal.
41. National Cancer Advisory Board meeting minutes, November 2004 [http://deainfo.nci.nih.gov/advisory/ncab/132_1104/30nov04mins.pdf]
42. National Cancer Institute's Board of Scientific Advisors meeting minutes, November 2004 [http://deainfo.nci.nih.gov/advisory/bsa/bsa1104/08nov04mins.htm]
43. Cooperative Prostate Cancer Tissue Resource [http://www.prostatetissues. org]
44. The Cooperative Breast Cancer Tissue Resource [http://www-cbctr.ims.nci. nih.gov/]
45. Cooperative prostate cancer tissue resource: Release Date April 29,1999, RFA CA-99-012, National Cancer Institute [http://grants1.nih.gov/grants/guide/ rfa-files/RFA-CA-99-012.html]
46. Cooperative human tissue network: Release Date March 12, 2000. RFA CA-01-009, National Cancer Institute [http://grants.nih.gov/grants/guide/rfa- files/RFA-CA-01-009.html]
47. Cooperative breast cancer tissue registry: Release Date February 19,1993, RFA CA-93-19, National Cancer Institute [http://grants2.nih.gov/grants/guide/ rfa-files/RFA-CA-93-019.html]