title: Cancer Digital Slide Archive: an informatics resource to support integrated in silico analysis of TCGA pathology data.
abstract: BACKGROUND
  The integration and visualization of multimodal datasets is a common challenge in biomedical informatics. Several recent studies of The Cancer Genome Atlas (TCGA) data have illustrated important relationships between morphology observed in whole-slide images, outcome, and genetic events. The pairing of genomics and rich clinical descriptions with whole-slide imaging provided by TCGA presents a unique opportunity to perform these correlative studies. However, better tools are needed to integrate the vast and disparate data types.
  
  
  OBJECTIVE
  To build an integrated web-based platform supporting whole-slide pathology image visualization and data integration.
  
  
  METHODS
  All images and genomic data were directly obtained from the TCGA and National Cancer Institute (NCI) websites.
  
  
  RESULTS
  The Cancer Digital Slide Archive (CDSA) produced is accessible to the public (http://cancer.digitalslidearchive.net) and currently hosts more than 20,000 whole-slide images from 22 cancer types.
  
  
  CONCLUSIONS
  The capabilities of CDSA are demonstrated using TCGA datasets to integrate pathology imaging with associated clinical, genomic and MRI measurements in glioblastomas and can be extended to other tumor types. CDSA also allows URL-based sharing of whole-slide images, and has preliminary support for directly sharing regions of interest and other annotations. Images can also be selected on the basis of other metadata, such as mutational profile, patient age, and other relevant characteristics.
  
  
  CONCLUSIONS
  With the increasing availability of whole-slide scanners, analysis of digitized pathology images will become increasingly important in linking morphologic observations with genomic and clinical endpoints.
authors.affiliation: Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, Georgia, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Gutman
authors.forename: Jake
authors.initials: J
authors.lastname: Cobb
authors.forename: Dhananjaya
authors.initials: D
authors.lastname: Somanna
authors.forename: Yuna
authors.initials: Y
authors.lastname: Park
authors.forename: Fusheng
authors.initials: F
authors.lastname: Wang
authors.forename: Tahsin
authors.initials: T
authors.lastname: Kurc
authors.forename: Joel H
authors.initials: JH
authors.lastname: Saltz
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Brat
authors.forename: Lee A D
authors.initials: LA
authors.lastname: Cooper
mesh_terms: D001271:Atlases as Topic; D003198:Computer Simulation; D016208:Databases, Factual; D015894:Genome, Human; D006801:Humans; D020407:Internet; D009369:Neoplasms / Q000473:pathology*; D010338:Pathology, Clinical / Q000379:methods*; D018511:Systems Integration
keywords: Cancer; Cell Morphology; Computer-Assisted Image Analysis; Digital Pathology; Image Cytometry; TCGA
references.citation: Comput Methods Programs Biomed. 2007 Sep;87(3):181-8
references.pmid: 17618703
references.citation: Am J Pathol. 2012 May;180(5):2108-19
references.pmid: 22440258
references.citation: Proc AMIA Symp. 1998;:912-6
references.pmid: 9929351
references.citation: IEEE Trans Biomed Eng. 2011 Dec;58(12):3469-74
references.pmid: 21947516
references.citation: Nat Rev Drug Discov. 2011 Aug 31;10(9):643-4
references.pmid: 21878966
references.citation: Proc SPIE Int Soc Opt Eng. 2012 Feb 16;8319:
references.pmid: 22844574
references.citation: BMC Bioinformatics. 2011 Dec 20;12:484
references.pmid: 22185703
references.citation: IEEE Trans Inf Technol Biomed. 2003 Dec;7(4):230-48
references.pmid: 15000350
references.citation: Sci Transl Med. 2011 Nov 9;3(108):108ra113
references.pmid: 22072638
references.citation: Arch Pathol Lab Med. 2002 May;126(5):533-9
references.pmid: 11958657
references.citation: J Am Med Inform Assoc. 2012 Mar-Apr;19(2):317-23
references.pmid: 22278382
references.citation: Histopathology. 2012 Jul;61(1):132-4
references.pmid: 22551421
references.citation: Stud Health Technol Inform. 2007;129(Pt 1):434-8
references.pmid: 17911754
references.citation: J Pathol Inform. 2011;2:23
references.pmid: 21633489
references.citation: Hum Pathol. 2000 Jul;31(7):779-80
references.pmid: 10923911
references.citation: Nature. 2010 Jan 21;463(7279):318-25
references.pmid: 20032975
references.citation: IEEE Trans Inf Technol Biomed. 2009 Jul;13(4):636-44
references.pmid: 19369162
references.citation: Proc SPIE Int Soc Opt Eng. 2010 Jan 1;7628(2010):762805
references.pmid: 21218167
references.citation: J Struct Biol. 1999 Apr-May;125(2-3):235-45
references.pmid: 10222280
references.citation: J Pathol Inform. 2011;2:32
references.pmid: 21845230
references.citation: Am J Pathol. 2012 May;180(5):1768-71
references.pmid: 22449951