Biomedical Informatics for Anatomic Pathology

  • Waqas Amin
  • Uma Chandran
  • Anil V. Parwani
  • Michael J. Becich


Biomedical informatics has made a deep impact in the overall workflow of the surgical pathology practice and has provided a variety of software tools that accelerate the overall turnaround time, cost effectiveness, and accuracy of information. Laboratory Information System functions as a single comprehensive piece of software managing laboratory workflow, reporting, and billing. Related technologies, such as digital imaging, whole slide imaging, voice recognition, telepathology, synoptic reporting, and use of the Internet, are also important in surgical pathology and will also be discussed in this chapter, because of their relevance to the development of biomedical informatics systems, and these important tools are evolving in parallel with these emerging technologies. These technologies are increasingly been used with the LIS workflow, particularly digital imaging tools. In this chapter, we will talk briefly about the software tools that have been adopted in surgical pathology practice over the last two decades.


Surgical pathology workflow Synoptic reporting Imaging Molecular data analysis and management 

Suggested Reading

  1. .
    Alizadeh AA, Eisen MB, Davis RE, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000;403:503–511.PubMedCrossRefGoogle Scholar
  2. .
    Aller R, Carey K. Anatomic pathology computer systems. CAP Today 1999;13:70–72, 74, 76 passim.Google Scholar
  3. .
    Aller RD. Linking software making gains and foraying into new domains. CAP Today 2005;19:29–30, 32–34, 36–38 passim.Google Scholar
  4. .
    Allison DB, Cui X, Page GP, Sabripour M. Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet 2006;7:55–65.PubMedCrossRefGoogle Scholar
  5. .
    Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. J Mol Biol 1990;215:403–410.Google Scholar
  6. .
    Amin MB, Srigley JR, Grignon DJ, et al. Updated protocol for the ­examination of specimens from patients with carcinoma of the urinary bladder, ureter, and renal pelvis. Arch Pathol Lab Med 2003;127:1263–1279.PubMedGoogle Scholar
  7. .
    Amin W, Parwani AV, Schmandt L, et al. National Mesothelioma Virtual Bank: a standard based biospecimen and clinical data resource to enhance translational research. BMC Cancer 2008;8:236.PubMedCrossRefGoogle Scholar
  8. .
    Barbareschi M, Demichelis F, Forti S, et al. Science Fiction? Int J Surg Pathol 2000;8:261–263PubMedCrossRefGoogle Scholar
  9. .
    Becich MJ, Gilbertson JR, Gupta D, et al. Pathology and patient safety: the critical role of pathology informatics in error reduction and quality initiatives. Clin Lab Med 2004;24:913–943,VI.Google Scholar
  10. .
    Becich MJ. Information management: moving from test results to clinical information. Clin Leadersh Manag Rev 2000;14:296–300.PubMedGoogle Scholar
  11. .
    Bhattacharyya AK, Davis JR, Halliday BE, et al. Case triage model for the practice of telepathology. Telemed J 1995;1:9–17.PubMedCrossRefGoogle Scholar
  12. .
    Brauchli K, Christen H, Haroske G, et al. Telemicroscopy by the Internet revisited. J Pathol 2002;196:238–243.PubMedCrossRefGoogle Scholar
  13. .
    Demichelis F, Barbareschi M, Dalla Palma P, et al. The virtual case: a new method to completely digitize cytological and histological slides. Virchows Arch 2002;441:159–164.PubMedCrossRefGoogle Scholar
  14. .
    Dupuy A, Simon RM. Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting. J Natl Cancer Inst 2007;99:147–157.PubMedCrossRefGoogle Scholar
  15. .
    Eisen MB, Spellman PT, Brown PO, et al. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 1998;95:14863–14868.PubMedCrossRefGoogle Scholar
  16. .
    Friedman BA. Informatics as a separate section within a department of pathology. Am J Clin Pathol 1990;94:S2–S6.PubMedGoogle Scholar
  17. .
    Fujita K, Crowley RS. The Virtual Slide Set – a curriculum development system for digital microscopy. AMIA Annu Symp Proc 2003;846.Google Scholar
  18. .
    Gasch AP, Spellman PT, Kao CM, et al. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 2000;11:4241–4257.PubMedGoogle Scholar
  19. .
    Gilbertson JR, Petal A, Yagi Y. Clinical slide digitization – whole slide imaging in clinical practice. In: Gu J and Ogilvie RW, eds. Virtual Microscopy and Virtual Slides in Teaching, Diagnosis and Research. Boca Raton: Taylor and Francis; 2005.Google Scholar
  20. .
    Golub TR, Slonim DK, Tamayo P, et al. Molecular classification of ­cancer: class discovery and class prediction by gene expression monitoring. Science 1999;286:531–537.PubMedCrossRefGoogle Scholar
  21. .
    Gstaiger M, Aebersold R. Applying mass spectrometry-based ­proteomics to genetics, genomics and network biology. Nat Rev Genet 2009;10:617–627.PubMedCrossRefGoogle Scholar
  22. .
    Hastie T, Tibshirani R, Friedman J. The elements of statistical learning: data ­mining, inference, and prediction. NY: Springer; 2001.Google Scholar
  23. .
    Henricks WH, Roumina K, Skilton BE, et al. The utility and cost ­effectiveness of voice recognition technology in surgical pathology. Mod Pathol 2002;15:565–571.PubMedCrossRefGoogle Scholar
  24. .
    Kumar RK, Velan GM, Korell SO, et al. Virtual microscopy for learning and assessment in pathology. J Pathol 2004;204:613–618.PubMedCrossRefGoogle Scholar
  25. .
    LaFramboise T. Single nucleotide polymorphism arrays: a decade of ­biological, computational and technological advances. Nucleic Acids Res 2009;37:4181–4193.PubMedCrossRefGoogle Scholar
  26. .
    Lamb J, Crawford ED, Peck D, et al. The Connectivity Map: using ­gene-expression signatures to connect small molecules, genes, and ­disease. Science 2006;313:1929–1935.PubMedCrossRefGoogle Scholar
  27. .
    Lashkari DA, DeRisi JL, McCusker JH, et al. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc Natl Acad Sci U S A 1997;94:13057–13062.PubMedCrossRefGoogle Scholar
  28. .
    Leong AS. Synoptic/checklist reporting of breast biopsies: has the time come? Breast J 2001;7:271–274.PubMedCrossRefGoogle Scholar
  29. .
    Leslie KO, Rosai J. Standardization of the surgical pathology report: ­formats, templates, and synoptic reports. Semin Diagn Pathol 1994;11:253–257.PubMedGoogle Scholar
  30. .
    Liu CG, Calin GA, Meloon B, et al. An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc Natl Acad Sci U S A 2004;101:9740–9744.PubMedCrossRefGoogle Scholar
  31. .
    Markel SF, Hirsch SD. Synoptic surgical pathology reporting. Hum Pathol 1991;22:807–810.PubMedCrossRefGoogle Scholar
  32. .
    McDonald CJ, Huff SM, Suico JG, et al. LOINC, a universal standard for identifying laboratory observations: a 5-year update. Clin Chem 2003;49:624–633.PubMedCrossRefGoogle Scholar
  33. .
    Network TCGAR. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008;455:1061–1068.CrossRefGoogle Scholar
  34. .
    Oberholzer M, Christen H, Haroske G, et al. Modern telepathology: a distributed system with open standards. Curr Prob Dermatol 2003;32:102–114.CrossRefGoogle Scholar
  35. .
    Parmigiani G, Garrett, ES, Irizarry RA, et al. The analysis of gene expression data. NY: Springer; 2003.Google Scholar
  36. .
    Patel AA, Gilbertson JR, Parwani AV, et al. An informatics model for tissue banks – lessons learned from the Cooperative Prostate Cancer Tissue Resource. BMC Cancer 2006;6:120.PubMedCrossRefGoogle Scholar
  37. .
    Potti A, Mukherjee S, Petersen R, et al. A genomic strategy to refine prognosis in early-stage non-small-cell lung cancer. N Engl J Med 2006;355:570–580.PubMedCrossRefGoogle Scholar
  38. .
    Quackenbush J. Computational analysis of microarray data. Nat Rev Genet 2001;2:418–427.PubMedCrossRefGoogle Scholar
  39. .
    Qualman SJ, Bowen J, Amin MB, et al. Protocol for the examination of specimens from patients with Wilms tumor (nephroblastoma) or other renal tumors of childhood. Arch Pathol Lab Med 2003;127:1280–1289.PubMedGoogle Scholar
  40. .
    Rashbass J. The impact of information technology on histopathology. Histopathology 2000;36:1–7.PubMedCrossRefGoogle Scholar
  41. .
    Rosai J. Standardized reporting of surgical pathology diagnoses for the major tumor types. A proposal. The Department of Pathology, Memorial Sloan-Kettering Cancer Center. Am J Clin Pathol 1993;100:240–255.PubMedGoogle Scholar
  42. .
    Sauter G, Simon R, Hillan K. Tissue microarrays in drug discovery. Nat Rev Drug Discov 2003;2:962–972.PubMedCrossRefGoogle Scholar
  43. .
    Sawyers CL. The cancer biomarker problem. Nature 2008;452:548–552.PubMedCrossRefGoogle Scholar
  44. .
    Schubert E, Gross W, Siderits RH, et al. A pathologist-designed imaging system for anatomic pathology signout, teaching, and research. Semin Diagn Pathol 1994;11:263–273.PubMedGoogle Scholar
  45. .
    Srigley JR, Amin MB, Bostwick DG, et al. Updated protocol for the examination of specimens from patients with carcinomas of the prostate gland: a basis for checklists. Cancer Committee. Arch Pathol Lab Med 2000;124:1034–1039.PubMedGoogle Scholar
  46. .
    Stoughton RB. Applications of DNA microarrays in biology. Annu Rev Biochem 2005;74:53–82.PubMedCrossRefGoogle Scholar
  47. .
    Tamayo P, Slonim D, Mesirov J, et al. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci U S A 1999;96:2907–2912.PubMedCrossRefGoogle Scholar
  48. .
    Thorne NMJ, Rakyan V, Ibrahim A, et al. DNA methylation arrays: Methods and analysis. In: Hardiman G, ed. Microarray Innovations: Technology and Experimentation in Drug Discovery and Biomedical Research. Boca Raton, FL: CRC Press; 2009:Ch 13.Google Scholar
  49. .
    Wang Y, Klijn JGM, Zhang Y, et al. Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. The Lancet 2005;365:671–679.Google Scholar
  50. .
    Weinstein RS, Descour MR, Liang C, et al. An array microscope for ultrarapid virtual slide processing and telepathology. Design, fabrication, and validation study. Hum Pathol 2004;35:1303–1314.PubMedCrossRefGoogle Scholar
  51. .
    Weinstein RS, Descour MR, Liang C, et al. Telepathology overview: from concept to implementation. Hum Pathol 2001;32:1283–1299.PubMedCrossRefGoogle Scholar
  52. .
    Weinstein RS. Innovations in medical imaging and virtual microscopy. Hum Pathol 2005;36:317–319.PubMedCrossRefGoogle Scholar
  53. .
    Weinstein RS. Static image telepathology in perspective. Hum Pathol 1996;27:99–101.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Waqas Amin
    • 1
  • Uma Chandran
    • 2
  • Anil V. Parwani
    • 3
  • Michael J. Becich
    • 4
  1. 1.Department of Biomedical InformaticsUniversity of PittsburghPittsburghUSA
  2. 2.Department of Biomedical Informatics, Cancer Informatics ServicesUniversity of Pittsburgh Cancer InstitutePittsburghUSA
  3. 3.Division Director, Pathology Informatics, Staff PathologistUniversity of Pittsburgh School of Medicine and Shadyside HospitalPittsburghUSA
  4. 4.Information Sciences and Telecommunications, Department of Biomedical InformaticsUniversity of Pittsburgh School of MedicinePittsburghUSA

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