Developing a Tissue Resource to Characterize the Genome of Pancreatic Cancer

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.

[1]  Francis S. Collins,et al.  Mapping the cancer genome , 2007 .

[2]  J. Lupski,et al.  The complete genome of an individual by massively parallel DNA sequencing , 2008, Nature.

[3]  N. Blow.  Tissue preparation: Tissue issues , 2007, Nature.

[4]  Nadine Cohen,et al.  Returning genetic research results to individuals: points-to-consider. , 2006, Bioethics.

[5]  A. Jemal,et al.  Cancer Statistics, 2004 , 2004, CA: a cancer journal for clinicians.

[6]  S. Jewell,et al.  Copyright © American Society for Investigative Pathology Review Effect of Fixatives and Tissue Processing on the Content and Integrity of Nucleic Acids , 2022 .

[7]  H. Lai,et al.  A research-based tumor tissue bank of gynecologic oncology: characteristics of nucleic acids extracted from normal and tumor tissues from different sites , 2001, International Journal of Gynecologic Cancer.

[8]  I. Jurisica,et al.  Stability and heterogeneity of expression profiles in lung cancer specimens harvested following surgical resection. , 2004, Neoplasia.

[9]  D. Troyer,et al.  Biorepository standards and protocols for collecting, processing, and storing human tissues. , 2008, Methods in molecular biology.

[10]  Virgilia Macias,et al.  The Cooperative Prostate Cancer Tissue Resource , 2004, Clinical Cancer Research.

[11]  Richard A. Gibbs,et al.  No Longer De-Identified , 2006, Science.

[12]  David A Jones,et al.  Preservation of RNA for Functional Genomic Studies: A Multidisciplinary Tumor Bank Protocol , 2001, Modern Pathology.

[13]  E. de Álava,et al.  Tumour Banking: The Spanish Design , 2007, Pathobiology.

[14]  A. McGuire,et al.  Research ethics and the challenge of whole-genome sequencing , 2008, Nature Reviews Genetics.

[15]  G. Parmigiani,et al.  The Consensus Coding Sequences of Human Breast and Colorectal Cancers , 2006, Science.

[16]  Richard A. Gibbs,et al.  Currents in Contemporary Ethics: Meeting the Growing Demands of Genetic Research , 2006, Journal of Law, Medicine & Ethics.

[17]  H. Saisho,et al.  Detection of ras gene mutations in pancreatic juice and peripheral blood of patients with pancreatic adenocarcinoma. , 1993, Cancer research.

[18]  R. Tibshirani,et al.  Comment on "The Consensus Coding Sequences of Human Breast and Colorectal Cancers" , 2007, Science.

[19]  N. Blow.  Genomics: The personal side of genomics , 2007, Nature.

[20]  M M Morente,et al.  TuBaFrost 2: Standardising tissue collection and quality control procedures for a European virtual frozen tissue bank network. , 2006, European journal of cancer.

[21]  H. Juhl,et al.  Tissue ischemia time affects gene and protein expression patterns within minutes following surgical tumor excision. , 2004, BioTechniques.

[22]  A Berghold,et al.  The Genome Austria Tissue Bank (GATiB) , 2007, Pathobiology.

[23]  B. Knoppers,et al.  The emergence of an ethical duty to disclose genetic research results: international perspectives , 2006, European Journal of Human Genetics.

[24]  Rajiv Dhir,et al.  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 , 2008, BMC Cancer.

[25]  H. Budka,et al.  Effects of Formalin Fixation, Paraffin Embedding, and Time of Storage on DNA Preservation in Brain Tissue: A BrainNet Europe Study , 2007, Brain pathology.

[26]  Donna Neuberg,et al.  Comparison of frozen and RNALater solid tissue storage methods for use in RNA expression microarrays , 2004, BMC Genomics.

[27]  W. Grizzle,et al.  Avoiding biohazards in medical, veterinary and research laboratories , 2001, Biotechnic & histochemistry : official publication of the Biological Stain Commission.

[28]  C. V. van Noesel,et al.  Effects of Processing Delay, Formalin Fixation, and Immunohistochemistry on RNA Recovery From Formalin-fixed Paraffin-embedded Tissue Sections , 2008, Diagnostic molecular pathology : the American journal of surgical pathology, part B.

[29]  G. Sandusky,et al.  Quality control of human tissues-experience from the Indiana University Cancer Center-Lilly Research Labs human tissue bank , 2007, Cell and Tissue Banking.

[30]  William E. Grizzle,et al.  Special communication. The cooperative human tissue network , 1989 .

[31]  Derek Y. Chiang,et al.  Characterizing the cancer genome in lung adenocarcinoma , 2007, Nature.

[32]  Christoph Michalski,et al.  Pancreatic Cancer: From Bench to 5-Year Survival , 2006, Pancreas.

[33]  Kenneth D. Mandl,et al.  Reestablishing the Researcher-Patient Compact , 2007, Science.

[34]  Stefanie S Jeffrey,et al.  Bmc Molecular Biology Rna Extraction from Ten Year Old Formalin-fixed Paraffin-embedded Breast Cancer Samples: a Comparison of Column Purification and Magnetic Bead-based Technologies , 2022 .

[35]  F. Cavalli,et al.  A Virtual Tissue Bank for Primary Central Nervous System Lymphomas in Immunocompetent Individuals , 2007, Pathobiology.

[36]  Jim Vaught,et al.  Best practices for repositories I: Collection, storage, and retrieval of human biological materials for research , 2005 .

[37]  Amy L McGuire,et al.  Genetics. No longer de-identified. , 2006, Science.

[38]  K Knox,et al.  Establishing a national tissue bank for surgically harvested cancer tissue , 2004, The British journal of surgery.

[39]  J Quackenbush,et al.  Effects of ischemia on gene expression. , 2001, The Journal of surgical research.

[40]  M M Morente,et al.  TuBaFrost 1: Uniting local frozen tumour banks into a European network: an overview. , 2006, European journal of cancer.

[41]  T. Pretlow,et al.  Providing human tissues for research: how to establish a program. , 1998, Archives of pathology & laboratory medicine.

[42]  C. Fernandez,et al.  Informing research participants of research results: analysis of Canadian university based research ethics board policies , 2005, Journal of Medical Ethics.

[43]  Francis S Collins,et al.  Mapping the cancer genome. Pinpointing the genes involved in cancer will help chart a new course across the complex landscape of human malignancies. , 2007, Scientific American.

[44]  N. Brünner,et al.  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. , 2007, European journal of cancer.