Digital pathology and image analysis augment biospecimen annotation and biobank quality assurance harmonization

Clinical Biochemistry

Volumn 47, Issue 4-5, 2014, Pages 274-279

  Wei, Bih Rong ^a   Simpson, R Mark ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Biological specimen bank; Biomarkers; Computer assisted diagnosis; Isolation and purification; Morphometry; Pattern recognition image analysis; Quantitative pathology; Standards

Indexed keywords

ALGORITHM; ARTICLE; AUTOMATED PATTERN RECOGNITION; COMPUTER ASSISTED DIAGNOSIS; CRYOPRESERVATION; DATA MINING; DIGITAL IMAGING; FREEZING; HEALTH CARE FACILITY; HISTOPATHOLOGY; HUMAN; IMAGE ANALYSIS; MACROMOLECULE; PATHOLOGIST; PATHOLOGY; PRIORITY JOURNAL; QUALITY CONTROL; REPRODUCIBILITY; TISSUE SECTION;

BIOLOGICAL SPECIMEN BANK; BIOMARKERS; COMPUTER-ASSISTED DIAGNOSIS; ISOLATION AND PURIFICATION; MORPHOMETRY; PATTERN RECOGNITION IMAGE ANALYSIS; QUANTITATIVE PATHOLOGY; STANDARDS;

BIOLOGICAL SPECIMEN BANKS; DIAGNOSIS, COMPUTER-ASSISTED; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; PATTERN RECOGNITION, AUTOMATED; QUALITY CONTROL; REPRODUCIBILITY OF RESULTS; SPECIMEN HANDLING; TRANSLATIONAL MEDICAL RESEARCH;

EID: 84896054257     PISSN: 00099120     EISSN: 18732933     Source Type: Journal    
DOI: 10.1016/j.clinbiochem.2013.12.008     Document Type: Article

References (55)

1. Hullsiek K.H., George M., Brown S.K. Designing and managing a flexible and dynamic biorepository system: a 15-year perspective from the CPCRA, ESPRIT, and INSIGHT clinical trial networks. Curr Opin HIV AIDS Nov 2010, 5(6):538-544. [PubMed PMID: 20978398. Pubmed Central PMCID: PMC3039520. Epub 2010/10/28. eng].
2. Grizzle W.E., Bell W.C., Sexton K.C. Issues in collecting, processing and storing human tissues and associated information to support biomedical research. Cancer Biomark 2010, 9(1-6):531-549. [PubMed PMID: 22112494. Pubmed Central PMCID: PMC3445033. Epub 2011/11/25. eng].
3. Gaffney E.F., Madden D., Thomas G.A. The human side of cancer biobanking. Methods Mol Biol 2012, 823:59-77. [PubMed PMID: 22081339. Epub 2011/11/15. eng].
4. Vaught J., Lockhart N.C. The evolution of biobanking best practices. Clin Chim Acta Oct 9 2012, 413(19-20):1569-1575. [PubMed PMID: 22579478. Pubmed Central PMCID: PMC3409343. Epub 2012/05/15. eng].
5. Hveem K. Creation of a new prospective research biobank: the example of HUNT3. Methods Mol Biol 2011, 675:231-239. [PubMed PMID: 20949393. Epub 2010/10/16. eng].
6. Hewitt R.E. Biobanking: the foundation of personalized medicine. Curr Opin Oncol Jan 2011, 23(1):112-119. [PubMed PMID: 21076300. Epub 2010/11/16. eng].
7. Spruessel A., Steimann G., Jung M., Lee S.A., Carr T., Fentz A.K., et al. Tissue ischemia time affects gene and protein expression patterns within minutes following surgical tumor excision. Biotechniques Jun 2004, 36(6):1030-1037. [PubMed PMID: 15211754. eng].
8. Botling J., Micke P. Biobanking of fresh frozen tissue from clinical surgical specimens: transport logistics, sample selection, and histologic characterization. Methods Mol Biol 2011, 675:299-306. [PubMed PMID: 20949397].
9. Kang H.J., Jeon S.Y., Park J.S., Yun J.Y., Kil H.N., Hong W.K., et al. Identification of clinical biomarkers for pre-analytical quality control of blood samples. Biopreserv Biobank Apr 2013, 11(2):94-100. [PubMed PMID: 23634248. Pubmed Central PMCID: PMC3629782. Epub 2013/05/02. Eng].
10. Yin P., Peter A., Franken H., Zhao X., Neukamm S.S., Rosenbaum L., et al. Preanalytical aspects and sample quality assessment in metabolomics studies of human blood. Clin Chem May 2013, 59(5):833-845. [PubMed PMID: 23386698. Epub 2013/02/07. eng].
11. Betsou F., Barnes R., Burke T., Coppola D., Desouza Y., Eliason J., et al. Human biospecimen research: experimental protocol and quality control tools. Cancer Epidemiol Biomarkers Prev Apr 2009, 18(4):1017-1025. [PubMed PMID: 19336543. Epub 2009/04/02. eng].
12. Palmirotta R., De Marchis M.L., Ludovici G., Leone B., Savonarola A., Ialongo C., et al. Impact of preanalytical handling and timing for peripheral blood mononuclear cells isolation and RNA studies: the experience of the Interinstitutional Multidisciplinary BioBank (BioBIM). Int J Biol Markers Apr-Jun 2012, 27(2):e90-e98. [PubMed PMID: 22562396. Epub 2012/05/09. eng].
13. Mee B.C., Carroll P., Donatello S., Connolly E., Griffin M., Dunne B., et al. Maintaining breast cancer specimen integrity and individual or simultaneous extraction of quality DNA, RNA, and proteins from allprotect-stabilized and nonstabilized tissue samples. Biopreserv Biobank Dec 2011, 9(4):389-398. [PubMed PMID: 23386926. Pubmed Central PMCID: PMC3558729. Epub 2011/12/01. Eng].
14. Moore H.M., Kelly A., Jewell S.D., McShane L.M., Clark D.P., Greenspan R., et al. Biospecimen reporting for improved study quality. Biopreserv Biobank Apr 2011, 9(1):57-70. [PubMed PMID: 21826252. Pubmed Central PMCID: PMC3142856. ENG].
15. Nanni U., Spila A., Riondino S., Valente M.G., Somma P., Iacoboni M., et al. RFID as a new ICT tool to monitor specimen life cycle and quality control in a biobank. Int J Biol Markers Apr-Jun 2011, 26(2):129-135. [PubMed PMID: 21574153. Epub 2011/05/17. eng].
16. Hallmans G., Vaught J.B. Best practices for establishing a biobank. Methods Mol Biol 2011, 675:241-260. [PubMed PMID: 20949394. Epub 2010/10/16. eng].
17. Peakman T., Elliott P. Current standards for the storage of human samples in biobanks. Genome Med 2010, 2(10):72. [PubMed PMID: 20923579. Pubmed Central PMCID: PMC2988449. Epub 2010/10/07. eng].
18. International Society for Biological and Environmental Repositories 2012 best practices for repositories, collection, storage, retrieval, and distribution of biological materials for research. Biopreserv Biobank 2012, 10(2):79-161.
19. GTEx SOP Library [cited 2013 Nov. 26]. http://biospecimens.cancer.gov/resources/sops/library.asp.
20. Shevde L.A., Riker A.I. Current concepts in biobanking: development and implementation of a tissue repository. Front Biosci 2009, 1:188-193. [PubMed PMID: 19482694].
21. Schrohl A.S., Wurtz S., Kohn E., Banks R.E., Nielsen H.J., Sweep F.C., et al. Banking of biological fluids for studies of disease-associated protein biomarkers. Mol Cell Proteomics Oct 2008, 7(10):2061-2066. [PubMed PMID: 18676364. Pubmed Central PMCID: PMC2559931. Epub 2008/08/05. eng].
22. Malm J., Fehniger T.E., Danmyr P., Vegvari A., Welinder C., Lindberg H., et al. Developments in biobanking workflow standardization providing sample integrity and stability. J Proteomics Jul 13 2013, 95:38-45. [PubMed PMID: 23856607. Epub 2013/07/17. Eng].
23. Sandusky G., Dumaual C., Cheng L. Review paper: human tissues for discovery biomarker pharmaceutical research: the experience of the Indiana University Simon Cancer Center-Lilly Research Labs Tissue/Fluid BioBank. Vet Pathol Jan 2009, 46(1):2-9. [PubMed PMID: 19112109. eng].
24. TCGA tissue sample requirements: high quality requirements yield high quality data [cited 2013 Nov. 26]. http://cancergenome.nih.gov/cancersselected/biospeccriteria.
25. Clinical Proteomic Tumor Analysis Consortium [cited 2013 Nov. 26]. http://proteomics.cancer.gov/programs/cptacnetwork.
26. McDonald S.A. Principles of research tissue banking and specimen evaluation from the pathologist's perspective. Biopreserv Biobank Dec 2010, 8(4):197-201. [PubMed PMID: 23386923. Pubmed Central PMCID: PMC3562469. ENG].
27. Webster J.D., Simpson E.R., Michalowski A.M., Hoover S.B., Simpson R.M. Quantifying histological features of cancer biospecimens for biobanking quality assurance using automated morphometric pattern recognition image analysis algorithms. J Biomol Tech Sep 2011, 22(3):108-118. [PubMed PMID: 21966258. Pubmed Central PMCID: PMC3165860. eng].
28. Pfizer-CCOGC Biospecimen Repository (internet) cn, cited 2013 Oct. 1:Available from:. http://www.ccogc.net.
29. Thomas RSM, Simpson M, Mochizuki H, Williams C, Poorman K, Kennedy K, Mazcko C, Modiano JF, Breen M. Quality control and quality assurance of canine biological specimens available through the Pfizer-CCOGC, Inc. national biorepository for comparative oncology studies. (abstract). Am Assoc Cancer Res Translational Impact of Model Organisms in Cancer, San Diego, CA, November 6, 2013; unpublished data.
30. Simpson R.M., Bastian B.C., Michael H.T., Webster J.D., Prasad M.L., Conway C.M., et al. Sporadic naturally occurring melanoma in dogs as a preclinical model for human melanoma. Pigment Cell Melanoma Res Oct 15 2013, [PubMed PMID: 24128326]. 10.1111/pcmr.12185.
31. Webster J.D., Michalowski A.M., Dwyer J.E., Corps K.N., Wei B.R., Juopperi T., et al. Investigation into diagnostic agreement using automated computer-assisted histopathology pattern recognition image analysis. J Pathol Inform 2012, 3:18. [PubMed PMID: 22616030. Pubmed Central PMCID: PMC3352619. eng].
32. Jara-Lazaro A.R., Thamboo T.P., Teh M., Tan P.H. Digital pathology: exploring its applications in diagnostic surgical pathology practice. Pathology 2010, 42(6):512-518. [PubMed PMID: 20854068].
33. Al-Janabi S., Huisman A., Van Diest P.J. Digital pathology: current status and future perspectives. Histopathology Jul 2012, 61(1):1-9. [PubMed PMID: 21477260].
34. Mulrane L., Rexhepaj E., Penney S., Callanan J.J., Gallagher W.M. Automated image analysis in histopathology: a valuable tool in medical diagnostics. Expert Rev Mol Diagn Nov 2008, 8(6):707-725. [PubMed PMID: 18999923].
35. Stathonikos N., Veta M., Huisman A., van Diest P.J. Going fully digital: perspective of a Dutch academic pathology lab. J Pathol Inform 2013, 4:15. [PubMed PMID: 23858390. Pubmed Central PMCID: PMC3709427. Epub 2013/07/17. eng].
36. Al Habeeb A., Evans A., Ghazarian D. Virtual microscopy using whole-slide imaging as an enabler for teledermatopathology: a paired consultant validation study. J Pathol Inform 2012, 3:2. [PubMed PMID: 22439122. Pubmed Central PMCID: PMC3307226. Epub 2012/03/23. eng].
37. Brennan D.J., Brandstedt J., Rexhepaj E., Foley M., Ponten F., Uhlen M., et al. Tumour-specific HMG-CoAR is an independent predictor of recurrence free survival in epithelial ovarian cancer. BMC Cancer 2010, 10:125. [PubMed PMID: 20359358. Pubmed Central PMCID: 3087316].
38. Brachtel E., Yagi Y. Digital imaging in pathology-current applications and challenges. J Biophotonics Apr 2012, 5(4):327-335. [PubMed PMID: 22213680. Epub 2012/01/04. eng].
39. Cornish T.C., Swapp R.E., Kaplan K.J. Whole-slide imaging: routine pathologic diagnosis. Adv Anat Pathol May 2012, 19(3):152-159. [PubMed PMID: 22498580. Epub 2012/04/14. eng].
40. Krenacs T., Zsakovics I., Micsik T., Fonyad L., Varga S.V., Ficsor L., et al. Digital microscopy the upcoming revolution in histopathology teaching, diagnostics, research and quality assurance. Microscopy: science, technology, applications and education 2010, 2:965-977. Formatex Research Center, Badajoz. A. Méndez-Vilas, J.D. Álvarez (Eds.).
41. Pantanowitz L., Szymas J., Yagi Y., Wilbur D. Whole slide imaging for educational purposes. J Pathol Inform 2012, 3:46. [PubMed PMID: 23372987. Pubmed Central PMCID: PMC3551531. Epub 2013/02/02. eng].
42. Teodorovic I., Isabelle M., Carbone A., Passioukov A., Lejeune S., Jamine D., et al. TuBaFrost 6: virtual microscopy in virtual tumour banking. Eur J Cancer Dec 2006, 42(18):3110-3116. [PubMed PMID: 17027253. Epub 2006/10/10. eng].
43. Isse K., Lesniak A., Grama K., Roysam B., Minervini M.I., Demetris A.J. Digital transplantation pathology: combining whole slide imaging, multiplex staining and automated image analysis. Am J Transplant Jan 2012, 12(1):27-37. [PubMed PMID: 22053785. Pubmed Central PMCID: PMC3627485. Epub 2011/11/08. eng].
44. CaHub, The Cancer Human Biobank cited 2013 Nov. 30:available from:. http://cahub.cancer.gov/.
45. Angeletti C., Harvey N.R., Khomitch V., Fischer A.H., Levenson R.M., Rimm D.L. Detection of malignancy in cytology specimens using spectral-spatial analysis. Lab Investig Dec 2005, 85(12):1555-1564. [PubMed PMID: 16200074].
46. Espina V., Heiby M., Pierobon M., Liotta L.A. Laser capture microdissection technology. Expert Rev Mol Diagn Sep 2007, 7(5):647-657. [PubMed PMID: 17892370].
47. Annotating digitally scanned microscope slides (PR-0002-W1 v1.0.0) [cited 2013 Nov. 26]. http://biospecimens.cancer.gov/resources/sops/GTEx_SOPs/V/A/Annotating%20Digitally%20Scanned%20Microscope%20Slides%20(PR-0002-W1%20v1.0.0).pdf.
48. Webster J.D., Yuzbasiyan-Gurkan V., Miller R.A., Kaneene J.B., Kiupel M. Cellular proliferation in canine cutaneous mast cell tumors: associations with c-KIT and its role in prognostication. Vet Pathol May 2007, 44(3):298-308. [PubMed PMID: 17491070. eng].
49. Letard S., Yang Y., Hanssens K., Palmerini F., Leventhal P.S., Guery S., et al. Gain-of-function mutations in the extracellular domain of KIT are common in canine mast cell tumors. Mol Cancer Res Jul 2008, 6(7):1137-1145. [PubMed PMID: 18644978].
50. Sandusky G.E., Teheny K.H., Esterman M., Hanson J., Williams S.D. Quality control of human tissues-experience from the Indiana University Cancer Center-Lilly Research Labs human tissue bank. Cell Tissue Bank 2007, 8(4):287-295. [PubMed PMID: 17387635. Epub 2007/03/28. eng].
51. NCI Center for Biomedical Informatics and Information Technology (internet) cnngnb-i-ra, cited 2013 Oct. 1:Available from:. http://cbiit.nci.nih.gov/ncip/biomedical-informatics-resources/applications.
52. Potts S.J., Young G.D., Voelker F.A. The role and impact of quantitative discovery pathology. Drug Discov Today Nov 2010, 15(21-22):943-950. [PubMed PMID: 20946967].
53. Henderson G.E., Cadigan R.J., Edwards T.P., Conlon I., Nelson A.G., Evans J.P., et al. Characterizing biobank organizations in the U.S.: results from a national survey. Genome Med Jan 25 2013, 5(1):3. [PubMed PMID: 23351549. Pubmed Central PMCID: PMC3706795. Epub 2013/01/29. Eng].
54. Riegman P.H., Dinjens W.N., Oosterhuis J.W. Biobanking for interdisciplinary clinical research. Pathobiology 2007, 74(4):239-244. [PubMed PMID: 17709966. eng].
55. GENetic Imagery Exploitation, operated by Los Alamos National Security, LLC for the U.S. Department of Energy's NNSA cited 2013 Oct. 1:Available from:. http://genie.lanl.gov/.