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Developing a Tissue Resource to Characterize the Genome of Pancreatic Cancer

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Abstract

With recent advances in DNA sequencing technology, medicine is entering an era in which a personalized genomic approach to diagnosis and treatment of disease is feasible. However, discovering the role of altered DNA sequences in various disease states will be a challenging task. The genomic approach offers great promise for diseases, such as pancreatic cancer, in which the effect of current diagnostic and treatment modalities is disappointing. To facilitate the characterization of the genome of pancreatic cancer, high-quality and well-annotated tissue repositories are needed. This article summarizes the basic principles that guide the creation of such a repository, including sample processing and preservation techniques, sample size and composition, and collection of clinical data elements.

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References

  1. Jemal A, Tiwari RC, Murray T et al (2004) Cancer statistics, 2004. CA Cancer J Clin 54:8–29

    Article  PubMed  Google Scholar 

  2. Kleeff J, Michalski C, Friess H et al (2006) Pancreatic cancer: from bench to 5-year survival. Pancreas 33:111–118

    Article  PubMed  CAS  Google Scholar 

  3. International Consortium completes Human Genome Project [National Human Genome Research Institute website]. http://www.genome.gov. Accessed 14 April 2003

  4. Wheeler DA, Srinivasan M, Egholm M et al (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature 452:872–876

    Article  PubMed  CAS  Google Scholar 

  5. Blow N (2007) Genomics: the personal side of genomics. Nature 449:627–630

    Article  PubMed  CAS  Google Scholar 

  6. Cancer Sequencing Projects (CSPs) [National Human Genome Research Institute website]. http://www.genome.gov. Accessed April 2008

  7. Collins FS, Barker AD (2007) Mapping the cancer genome. Pinpointing the genes involved in cancer will help chart a new course across the complex landscape of human malignancies. Sci Am 296:50–57

    Article  PubMed  CAS  Google Scholar 

  8. Weir BA, Woo MS, Getz G et al (2007) Characterizing the cancer genome of lung adenocarcinoma. Nature 450:893–898

    Article  PubMed  CAS  Google Scholar 

  9. Morente MM, de Alava E, Fernandez PL (2007) Tumour banking: the Spanish design. Pathobiology 74:245–250

    Article  PubMed  CAS  Google Scholar 

  10. Knox K, Kerr DJ (2004) Establishing a national tissue bank for surgically harvested cancer tissue. Br J Surg 91:134–136

    Article  PubMed  CAS  Google Scholar 

  11. Asslaber M, Abuja PM, Stark K et al (2007) The Genome Austria Tissue Bank (GATiB). Pathobiology 74:251–258

    Article  PubMed  CAS  Google Scholar 

  12. Tilstone C (2006) Further plans announced for national biobanks. Lancet Oncol 7:195–196

    Article  PubMed  Google Scholar 

  13. Riegman PH, Dinjens WN, Oomen MH et al (2006) TuBaFrost 1: uniting local frozen tumour banks into a European network: an overview. Eur J Cancer 42:2678–2683

    Article  PubMed  CAS  Google Scholar 

  14. Schmitt M, Mengele K, Schueren E et al (2007) European Organisation for Research and Treatment of Cancer (EORTC) Pathobiology Group Standard operating procedure for the preparation of human tumour tissue extracts suited for the quantitative analysis of tissue-associated biomarkers. Eur J Cancer 43:835–844

    Article  PubMed  CAS  Google Scholar 

  15. Melamed J, Datta MW, Becich MJ et al (2004) The cooperative prostate cancer tissue resource: a specimen and data resource for cancer researchers. Clin Cancer Res 10:4614–4621

    Article  PubMed  Google Scholar 

  16. Sandusky GE, Teheny KH, Esterman M et al (2007) Quality control of human tissues: experience from the Indiana University Cancer Center-Lilly Research Labs human tissue bank. Cell Tissue Bank 8:287–295

    Article  PubMed  Google Scholar 

  17. Mohanty SK, Mistry AT, Amin W et al (2008) The development and deployment of Common Data Elements for tissue banks for translational research in cancer: an emerging standard based approach for the Mesothelioma Virtual Tissue Bank. BMC Cancer 8:91

    Article  PubMed  Google Scholar 

  18. Ponzoni M, Kwee I, Mazzucchelli L et al (2007) A virtual tissue bank for primary central nervous system lymphomas in immunocompetent individuals. Pathobiology 74:264–269

    Article  PubMed  Google Scholar 

  19. Figarella-Branger D, Colin C, Chinot O et al (2006) AP-HM tumour tissue bank: molecular signature of gliomas. Med Sci (Paris) 22:54–59

    Google Scholar 

  20. Prime W, Sobel ME, Herrington CS (2000) Utilization of human tissue in breast cancer research. Breast Cancer Res 2:237–240

    Article  PubMed  CAS  Google Scholar 

  21. Chu TY, Hwang KS, Yu MH et al (2002) A research-based tumor tissue bank of gynecologic oncology: characteristics of nucleic acids extracted from normal and tumor tissues from different sites. Int J Gynecol Cancer 12:171–176

    Article  PubMed  Google Scholar 

  22. Clausen KP, Grizzle WE, Livolsi V et al (1989) Special communication the cooperative human tissue network. Cancer 63:1452–1455

    Article  PubMed  CAS  Google Scholar 

  23. Human Cancer Biospecimen Core Resource (BCR) [The Tumor Gene Atlas website] http://cancergenome.nih.gov. Accessed April 2008

  24. International Society for Biological and Environmental Biorepositories. www.isber.org. Accessed April 2008

  25. BioBank Central. www.biobankcentral.org. Accessed April 2008

  26. Troyer D (2008) Biorepository standards and protocols for collecting, processing, and storing human tissues. Methods Mol Biol 441:193–220

    Article  PubMed  CAS  Google Scholar 

  27. NCI Best Practices for Biospecimen Resources. June 2007. Office of Biorepositories and Biospecimen Research [NCI website] http://biospecimens.cancer.gov. Accessed April 2008

  28. Grizzle WE, Fredenburgh J (2001) Avoiding biohazards in medical, veterinary and research laboratories. Biotech Histochem 76:183–206

    Article  PubMed  CAS  Google Scholar 

  29. CDC and NIH Biosafety in Microbiological and Biomedical Laboratories. http://bmbl.od.nih.gov. Accessed April 2008

  30. Morente MM, Mager R, Alonso S et al (2006) TuBaFrost 2: standardising tissue collection and quality control procedures for a European virtual frozen tissue bank network. Eur J Cancer 42:2684–2691

    Article  PubMed  CAS  Google Scholar 

  31. The Cancer Genome Atlas Biospecimen Selection Process. [The Cancer Tumor Atlas website] http://cancergenome.nih.gov. Accessed April 2008

  32. McGuire AL, Gibbs RA (2006) Genetics. No longer de-identified. Science 312:370–371

    Article  PubMed  CAS  Google Scholar 

  33. McGuire AL, Gibbs RA (2006) Currents in contemporary ethics: meeting the growing demands of genetic research. J Law Med Ethics 34:809–812

    Article  PubMed  Google Scholar 

  34. McGuire AL, Caulfield T, Cho MK (2007) Research ethics and the challenge of whole genome sequencing. Nat Rev Gen 9:152–156

    Google Scholar 

  35. Renegar G, Webster CJ, Stuerzebecker S et al (2006) Returning genetic research results to individuals: points to consider. Bioethics 20:24–36

    Article  PubMed  Google Scholar 

  36. Knoppers BM, Joly Y, Simard J et al (2006) The emergence of an ethical duty to disclose genetic research results: international perspectives. Eur. J. Human Gen 14:1170–1178

    Article  Google Scholar 

  37. MacNeil S, Fernandez C (2006) Informing research participants of research results: analysis of Canadian university based research ethics board policies. J Med Ethics 32:49–54

    Article  PubMed  CAS  Google Scholar 

  38. Kohane IS, Mandi KD, Taylor PL et al (2007) Reestablishing the researcher-patient compact. Science 316:836–837

    Article  PubMed  CAS  Google Scholar 

  39. Sjöblom T, Jones S, Wood LD, Parsons DW, Lin J et al (2006) The consensus coding sequences of human breast and colorectal cancers. Science 314:268–274

    Article  PubMed  CAS  Google Scholar 

  40. Getz G, Höfling H, Mesirov JP et al (2007) Comment on “The consensus coding sequences of human breast and colorectal cancers”. Science 317:1500

    Google Scholar 

  41. Grizzle WE, Aamodt R, Clausen K et al (1998) Providing human tissues for research: how to establish a program. Arch Pathol Lab Med 122:1065–1076

    PubMed  CAS  Google Scholar 

  42. Blow N (2007) Tissue preparation: tissue issues. Nature 448:959–963

    Article  PubMed  CAS  Google Scholar 

  43. Ribeiro-Silva A, Zhang H, Jeffrey SS (2007) RNA extraction from ten year old formalin-fixed paraffin-embedded breast cancer samples: a comparison of column purification and magnetic bead-based technologies. BMC Mol Biol 8:118

    Article  PubMed  CAS  Google Scholar 

  44. Ferrer I, Armstrong J, Capellari S et al (2007) Effects of formalin fixation, paraffin embedding, and time of storage on DNA preservation in brain tissue: a BrainNet Europe study. Brain Pathol 17:297–303

    Article  PubMed  CAS  Google Scholar 

  45. van Maldegem F, de Wit M, Morsink F et al (2008) Effects of processing delay, formalin fixation, and immunohistochemistry on RNA recovery from formalin-fixed paraffin-embedded tissue sections. Diagn Mol Pathol 17:51–58

    PubMed  Google Scholar 

  46. Srinivasan M, Sedmak D, Jewell S (2002) Effect of fixatives and tissue processing on the content and integrity of nucleic acids. Am J Pathol 161:1961–1971

    PubMed  CAS  Google Scholar 

  47. Florell SR, Coffin CM, Holden JA et al (2001) Preservation of RNA for functional genomic studies: a multidisciplinary tumor bank protocol. Mod Pathol 14:116–128

    Article  PubMed  CAS  Google Scholar 

  48. Mutter GL, Zahrieh D, Liu C et al (2004) Comparison of frozen and RNALater solid tissue storage methods for use in RNA expression microarrays. BMC Genomics 5:88

    Article  PubMed  CAS  Google Scholar 

  49. Huang J, Qi R, Quackenbush J, Dauway E, Lazaridis E, Yeatman T et al (2001) Effects of ischemia on gene expression. J Surg Res 99:222–227

    Article  PubMed  CAS  Google Scholar 

  50. Blackhall FH, Pintilie M, Wigle DA et al (2004) Stability and heterogeneity of expression profiles in lung cancer specimens harvested following surgical resection. Neoplasia 6:761–767

    Article  PubMed  Google Scholar 

  51. Spruessel A, Steimann G, Jung M et al (2004) Tissue ischemia time affects gene and protein expression patterns within minutes following surgical tumor excision. Biotechniques 36:1030–1037

    PubMed  CAS  Google Scholar 

  52. Tada M, Omata M, Kawai S et al (1993) Detection of ras gene mutations in pancreatic juice and peripheral blood of patients with pancreatic adenocarcinoma. Cancer Res 53:2472–2474

    PubMed  CAS  Google Scholar 

  53. International Society for Biological and Environment Repositories. Best practices for repositories I collection, storage, and retrieval of human biological materials for research. http://www.isber.org. Accessed April 2008

  54. International Air Transport Association (IATA) Infectious Substances Shipping Guidelines 2006 http://www.iata.org. Accessed April 2008

  55. Occupation Safety and Health Administration (OSHA). Regulations on toxic and hazardous substances. http://www.osha.gov. Accessed April 2008

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Authors and Affiliations

  1. Michael E. DeBakey Department of Surgery, Baylor College of Medicine, 1709 Dryden, Suite 1500, Houston, TX, 77030, USA

    Georgios Voidonikolas, Marie-Claude Gingras, Sally Hodges, Changyi Chen, F. Charles Brunicardi & William E. Fisher

  2. The Elkins Pancreas Center, Houston, TX, USA

    Georgios Voidonikolas, Sally Hodges, F. Charles Brunicardi & William E. Fisher

  3. Department of Molecular and Human Genetics, Human Genome Sequencing Center, Houston, TX, USA

    Marie-Claude Gingras & Richard A. Gibbs

  4. The Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, USA

    Amy L. McGuire

Authors
  1. Georgios Voidonikolas
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  2. Marie-Claude Gingras
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  3. Sally Hodges
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  4. Amy L. McGuire
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  5. Changyi Chen
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  6. Richard A. Gibbs
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  7. F. Charles Brunicardi
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  8. William E. Fisher
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Corresponding author

Correspondence to William E. Fisher.

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Voidonikolas, G., Gingras, MC., Hodges, S. et al. Developing a Tissue Resource to Characterize the Genome of Pancreatic Cancer. World J Surg 33, 723–731 (2009). https://doi.org/10.1007/s00268-008-9877-1

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  • DOI: https://doi.org/10.1007/s00268-008-9877-1

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