BioBank Resources and Links | Renaissance School of Medicine at Stony Brook University

Biobanking Links

Biobanking Literature

General
Sample Handling
Bioinformatics

Biobanking General Literature

1. Akervall J, Pruetz BL, Geddes TJ, Larson D, Felten DJ, Wilson GD. Beaumont Health System BioBank: A Multidisciplinary Biorepository and Translational Research Facility. Biopreserv Biobank . 2013 Aug [cited 2014 Apr 21];11(4):221–8. Available from: http://online.liebertpub.com/doi/abs/10.1089/bio.2013.0005

2. Auray-Blais C, Patenaude J. A biobank management model applicable to biomedical research. BMC Med Ethics . 2006 Jan [cited 2013 Aug 1];7:E4. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1475589&tool=pmcentrez&rendertype=abstract

3. Barbareschi M, Cotrupi S, Guarrera GM. Biobanks: instrumentation, personnel and cost analysis. Pathologica . 2008 Apr;100(2):139–48. Available from: http://www.ncbi.nlm.nih.gov/pubmed/18792526

4. Barnes RO, Parisien M, Murphy LC, Watson PH. Influence of evolution in tumor biobanking on the interpretation of translational research. Cancer Epidemiol Biomarkers Prev . 2008 Dec [cited 2013 Aug 1];17(12):3344–50. Available from: http://www.ncbi.nlm.nih.gov/pubmed/19064549

5. Bjugn R, Casati B. Stakeholder Analysis: A Useful Tool for Biobank Planning. Biopreserv Biobank . 2012 Jun [cited 2013 Aug 1];10(3):239–44. Available from: http://online.liebertpub.com/doi/abs/10.1089/bio.2011.0047

6. Boyer GJ, Whipple W, Cadigan RJ, Henderson GE. Biobanks in the United States: How to Identify an Undefined and Rapidly Evolving Population. Biopreserv Biobank . 2012 Dec [cited 2014 Apr 21];10(6):511–7. Available from: http://online.liebertpub.com/doi/abs/10.1089/bio.2012.0034

7. Cheah S, O’Donoghue S, Daudt H, Dee S, LeBlanc J, Braun L, et al. Permission to Contact (PTC)—A Strategy to Enhance Patient Engagement in Translational Research. Biopreserv Biobank . 2013 Aug [cited 2014 Apr 21];11(4):245–52. Available from: http://online.liebertpub.com/doi/abs/10.1089/bio.2013.0023

8. Corthals A, Desalle R. An application of tissue and DNA banking for genomics and conservation: the Ambrose Monell Cryo-Collection (AMCC). Syst Biol . 2005 Oct [cited 2012 Jan 23];54(5):819–23. Available from: http://www.ncbi.nlm.nih.gov/pubmed/16243765

9. Dörr D, Stracke F, Zimmermann H. Noninvasive Quality Control of Cryopreserved Samples. Biopreserv Biobank . 2012 Dec [cited 2013 Aug 1];10(6):529–31. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3698688&tool=pmcentrez&rendertype=abstract

10. Elliott P, Peakman TC. The UK Biobank sample handling and storage protocol for the collection, processing and archiving of human blood and urine. Int J Epidemiol . 2008 Apr [cited 2013 Aug 1];37(2):234–44. Available from: http://www.ncbi.nlm.nih.gov/pubmed/18381398

11. Evers K, Forsberg JS, Eliason JF. What Are Your Views on Commercialization of Tissues for Research? Biopreserv Biobank . 2012 Dec [cited 2013 Aug 1];10(6):476–8. Available from: http://online.liebertpub.com/doi/abs/10.1089/bio.2012.1062

12. Fahy GM. Cryoprotectant toxicity neutralization. Cryobiology . Elsevier Inc.; 2010 Jul [cited 2013 Aug 1];60(3 Suppl):S45–53. Available from: http://www.ncbi.nlm.nih.gov/pubmed/19501081

13. Gonzalez-Sanchez MB, Lopez-Valeiras E, Morente MM, Fernández Lago O. Cost Model for Biobanks. Biopreserv Biobank . 2013 Oct [cited 2014 Apr 21];11(5):272–7. Available from: http://online.liebertpub.com/doi/abs/10.1089/bio.2013.0021

14. Grizzle W, Bell W, Sexton K. Issues in collecting, processing and storing human tissues and associated information to support biomedical research. Cancer Biomarkers . 2011 [cited 2013 Aug 1];9:531–49. Available from: http://iospress.metapress.com/index/A02428V61625Q089.pdf

15. Hebels DG a J, Georgiadis P, Keun HC, Athersuch TJ, Vineis P, Vermeulen R, et al. Performance in omics analyses of blood samples in long-term storage: opportunities for the exploitation of existing biobanks in environmental health research. Environ Health Perspect . 2013 Apr;121(4):480–7. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3620742&tool=pmcentrez&rendertype=abstract

16. Liu A. Developing an institutional cancer biorepository for personalized medicine. Clin Biochem . The Canadian Society of Clinical Chemists; 2014 Mar [cited 2014 Apr 21];47(4-5):293–9. Available from: http://www.ncbi.nlm.nih.gov/pubmed/24373923

17. Marko-Varga G, Végvári Á, Welinder C, Lindberg H, Rezeli M, Edula G, et al. Standardization and utilization of biobank resources in clinical protein science with examples of emerging applications. J Proteome Res . 2012 Nov 2;11(11):5124–34. Available from: http://www.ncbi.nlm.nih.gov/pubmed/22607352

18. Master Z, Claudio JO, Rachul C, Wang JCY, Minden MD, Caulfield T. Cancer patient perceptions on the ethical and legal issues related to biobanking. BMC Med Genomics . BMC Medical Genomics; 2013 Jan [cited 2013 Aug 1];6(1):8. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3599691&tool=pmcentrez&rendertype=abstract

19. Mee BC, 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 . 2011 Dec [cited 2013 Aug 1];9(4):389–98. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3558729&tool=pmcentrez&rendertype=abstract

20. Mintzer JL, Kronenthal CJ, Kelly V, Seneca M, Butler G, Fecenko-Tacka K, et al. Preparedness for a Natural Disaster: How Coriell Planned for Hurricane Sandy. Biopreserv Biobank . 2013 Aug [cited 2014 Apr 21];11(4):216–20. Available from: http://online.liebertpub.com/doi/abs/10.1089/bio.2013.0035

21. Miranda LB, Wyatt K, Johnston I, Milljanic M, Chaffey J. “Proof of Concept” Pilot Study: Bioprocess Chain of Custody and Bioresource Sample Management Temperature Observations. Sample Level Temperature Trends and Stability Data Obtained Via Utilization of Bluechiip ® Temperature Tracking Technology. Biopreserv Biobank . 2013 Apr [cited 2014 Apr 21];11(2):115–21. Available from: http://online.liebertpub.com/doi/abs/10.1089/bio.2012.0059

22. Mucci NR, Moore HM, Brigham LE, Goldthwaite C a., Little a. R, Lockhart NC, et al. Meeting Research Needs with Postmortem Biospecimen Donation: Summary of Recommendations for Postmortem Recovery of Normal Human Biospecimens for Research. Biopreserv Biobank . 2013 Apr [cited 2013 Aug 1];11(2):77–82. Available from: http://online.liebertpub.com/doi/abs/10.1089/bio.2012.0063

23. Nietfeld JJ, Sugarman J, Litton J-E. The Bio-PIN: a concept to improve biobanking. Nat Rev Cancer . Nature Publishing Group; 2011 Apr [cited 2013 Aug 1];11(4):303–8. Available from: http://www.ncbi.nlm.nih.gov/pubmed/21412253

24. Posevitz-Fejfár A, Wiendl H. The neuroinflammation biobank in the department of neurology, university hospital muenster, Germany. Biopreserv Biobank . 2014 Feb [cited 2014 Apr 21];12(1):74–5. Available from: http://www.ncbi.nlm.nih.gov/pubmed/24620773

25. Sapre N, Hong MKH, Huang JG, Pedersen J, Ryan A, Anderson P, et al. Bladder Cancer Biorepositories in the “-Omics” Era: Integrating Quality Tissue Specimens with Comprehensive Clinical Annotation. Biopreserv Biobank . 2013 Jun [cited 2014 Apr 21];11(3):166–72. Available from: http://online.liebertpub.com/doi/abs/10.1089/bio.2012.0062

26. Scicchitano MS, Dalmas D a, Bertiaux M a, Anderson SM, Turner LR, Thomas R a, et al. Preliminary comparison of quantity, quality, and microarray performance of RNA extracted from formalin-fixed, paraffin-embedded, and unfixed frozen tissue samples. J Histochem Cytochem . 2006 Nov [cited 2014 Apr 13];54(11):1229–37. Available from: http://www.ncbi.nlm.nih.gov/pubmed/16864893

27. Shabihkhani M, Lucey GM, Wei B, Mareninov S, Lou JJ, Vinters H V, et al. The procurement, storage, and quality assurance of frozen blood and tissue biospecimens in pathology, biorepository, and biobank settings. Clin Biochem . The Canadian Society of Clinical Chemists; 2014 Mar [cited 2014 Mar 23];47(4-5):258–66. Available from: http://www.ncbi.nlm.nih.gov/pubmed/24424103

28. Sheldon E, Vo K, McIntire R, Aghajanova L, Zelenko Z, Irwin J, et al. Biobanking Human Endometrial Tissue and Subject Blood Specimens: Standard Operating Procedure and Importance to Reproductive Biology Research and Diagnostic Development. Fertil Steril . 2011 [cited 2013 Aug 1];95(6):2120–2. Available from: http://www.sciencedirect.com/science/article/pii/S0015028211002433

29. Teunissen CE, Tumani H, Engelborghs S, Mollenhauer B. Biobanking of CSF: International standardization to optimize biomarker development. Clin Biochem . The Canadian Society of Clinical Chemists; 2014 Mar [cited 2014 Apr 21];47(4-5):288–92. Available from: http://www.ncbi.nlm.nih.gov/pubmed/24389077

30. Tworoger SS, Hankinson SE. Collection, processing, and storage of biological samples in epidemiologic studies: sex hormones, carotenoids, inflammatory markers, and proteomics as examples. Cancer Epidemiol Biomarkers Prev . 2006 Sep [cited 2013 Aug 1];15(9):1578–81. Available from: http://www.ncbi.nlm.nih.gov/pubmed/16985015

31. Unhale S, Skubitz A. Stabilization of Tissue Specimens for Pathological Examination and Biomedical Research. Biopreserv Biobank . 2012 [cited 2014 Apr 21];10(6). Available from: http://online.liebertpub.com/doi/abs/10.1089/bio.2012.0031

32. Wahlberg K, Huggett J, Sanders R, Whale AS, Bushell C, Elaswarapu R, et al. Quality Assessment of Biobanked Nucleic Acid Extracts for Downstream Molecular Analysis. Biopreserv Biobank . 2012 Jun [cited 2013 Aug 1];10(3):266–75. Available from: http://online.liebertpub.com/doi/abs/10.1089/bio.2012.0004

33. Watson PH, Wilson-McManus JE, Barnes RO, Giesz SC, Png A, Hegele RG, et al. Evolutionary concepts in biobanking - the BC BioLibrary. J Transl Med . 2009 Jan [cited 2013 Aug 1];7:95. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2785772&tool=pmcentrez&rendertype=abstract

Biobanking Specimen Handling

1. Ahmann GJ, Chng WJ, Henderson KJ, Price-Troska TL, DeGoey RW, Timm MM, et al. Effect of tissue shipping on plasma cell isolation, viability, and RNA integrity in the context of a centralized good laboratory practice-certified tissue banking facility. Cancer Epidemiol Biomarkers Prev . 2008 Mar [cited 2014 Apr 7];17(3):666–73. Available from: http://www.ncbi.nlm.nih.gov/pubmed/18349285

2. Baust JM, Vogel MJ, Snyder KK, Van Buskirk RG, Baust JG. Activation of Mitochondrial-Associated Apoptosis Contributes to Cryopreservation Failure. Cell Preserv Technol . 2007 Sep [cited 2013 Aug 1];5(3):155–64. Available from: http://www.liebertonline.com/doi/abs/10.1089/cpt.2007.9990

3. Bellare JR, Davis HT, Scriven LE, Talmon Y. Controlled environment vitrification system: an improved sample preparation technique. J Electron Microsc Tech . 1988 Sep;10(1):87–111. Available from: http://www.ncbi.nlm.nih.gov/pubmed/3193246

4. Braun M, Menon R, Nikolov P, Kirsten R, Petersen K, Schilling D, et al. The HOPE fixation technique--a promising alternative to common prostate cancer biobanking approaches. BMC Cancer . BioMed Central Ltd; 2011 Jan [cited 2013 Aug 1];11(1):511. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3248383&tool=pmcentrez&rendertype=abstract

5. Campbell LH, Taylor MJ, Brockbank KGM. Development of Pancreas Storage Solutions : Initial Screening of Cytoprotective Supplements for b -Cell Survival and Metabolic Status after Hypothermic Storage. 2013;11(1):12–9.

6. Condelli V, Lettini G, Patitucci G, D’Auria F, D’Amico M, Vita G, et al. Validation of vacuum-based refrigerated system for biobanking tissue preservation: analysis of cellular morphology, protein stability, and RNA quality. Biopreserv Biobank . 2014 Feb [cited 2014 Apr 21];12(1):35–45. Available from: http://www.ncbi.nlm.nih.gov/pubmed/24620768

7. Cox ML, Schray CL, Luster CN, Stewart ZS, Korytko PJ, M Khan KN, et al. Assessment of fixatives, fixation, and tissue processing on morphology and RNA integrity. Exp Mol Pathol . 2006 Apr [cited 2014 Apr 13];80(2):183–91. Available from: http://www.ncbi.nlm.nih.gov/pubmed/16332367

8. Ellis HJ, Venturini DS. Demonstration of a Frozen Sample Aliquotter to Prepare Plasma and Serum Aliquots Without Thawing Frozen Parent Samples. Biopreserv Biobank . 2013 Jun [cited 2014 Apr 21];11(3):153–60. Available from: http://online.liebertpub.com/doi/abs/10.1089/bio.2012.0049

9. Fahy GM, Wowk B, Wu J, Paynter S. Improved vitrification solutions based on the predictability of vitrification solution toxicity. Cryobiology . 2004 Feb [cited 2013 Aug 1];48(1):22–35. Available from: http://www.ncbi.nlm.nih.gov/pubmed/14969679

10. Hatzis C, Sun H, Yao H, Hubbard RE, Meric-Bernstam F, Babiera G V, et al. Effects of tissue handling on RNA integrity and microarray measurements from resected breast cancers. J Natl Cancer Inst . 2011 Dec 21;103(24):1871–83. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3243675&tool=pmcentrez&rendertype=abstract

11. Huber AJT, Brockbank KGM, Aberle T, Schleicher M, Chen ZZ, Greene ED, et al. Development of a Simplified Ice-Free Cryopreservation Method for Heart Valves Employing VS83, an 83% Cryoprotectant Formulation. Biopreserv Biobank . 2012 Dec [cited 2013 Aug 1];10(6):479–84. Available from: http://online.liebertpub.com/doi/abs/10.1089/bio.2012.0006

12. Huber AJT, Brockbank KGM, Aberle T, Schleicher M, Chen ZZ, Greene ED, et al. Development of a Simplified Ice-Free Cryopreservation Method for Heart Valves Employing VS83, an 83% Cryoprotectant Formulation. Biopreserv Biobank . 2012 Dec [cited 2014 Apr 21];10(6):479–84. Available from: http://online.liebertpub.com/doi/abs/10.1089/bio.2012.0006

13. Lee J-H, Jung D-H, Lee D-H, Park J-K, Lee S-K. Slow cooling rate with a shock cooling program can effectively cryopreserve pig hepatocytes. Transplant Proc . Elsevier Inc.; 2012 May [cited 2013 Aug 1];44(4):1002–4. Available from: http://www.ncbi.nlm.nih.gov/pubmed/22564609

14. Liu BL, McGrath J. Vitrification Solutions for the Cryopreservation of Tissue-Engineered Bone. Cell Preserv Technol . 2004 Jun;2(2):133–43. Available from: http://www.liebertonline.com/doi/abs/10.1089/153834404774101972

15. Martins WK. A useful procedure to isolate simultaneously DNA and RNA from a single tumor sample. Nat Outlook, Protoc Exch . Nature Publishing Group; 2009 Aug 17; Available from: http://dx.doi.org/10.1038/nprot.2009.163

16. Mathot L, Wallin M, Sjöblom T. Automated serial extraction of DNA and RNA from biobanked tissue specimens. BMC Biotechnol . 2013 Jan [cited 2014 Mar 24];13:66. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3751724&tool=pmcentrez&rendertype=abstract

17. Michaud CL, Foran DR. Simplified field preservation of tissues for subsequent DNA analyses. J Forensic Sci . 2011 Jul [cited 2014 Apr 11];56(4):846–52. Available from: http://www.ncbi.nlm.nih.gov/pubmed/21480896

18. Micke P, Ohshima M, Tahmasebpoor S, Ren Z-P, Ostman A, Pontén F, et al. Biobanking of fresh frozen tissue: RNA is stable in nonfixed surgical specimens. Lab Invest . 2006 Feb [cited 2014 Apr 21];86(2):202–11. Available from: http://www.ncbi.nlm.nih.gov/pubmed/16402036

19. Miranda LB, Wyatt K, Johnston I, Milljanic M, Chaffey J. “Proof of Concept” Pilot Study: Bioprocess Chain of Custody and Bioresource Sample Management Temperature Observations. Sample Level Temperature Trends and Stability Data Obtained Via Utilization of Bluechiip ® Temperature Tracking Technology. Biopreserv Biobank . 2013 Apr [cited 2014 Apr 21];11(2):115–21. Available from: http://online.liebertpub.com/doi/abs/10.1089/bio.2012.0059

20. Muyal JP, Muyal V, Kaistha BP, Seifart C, Fehrenbach H. Systematic comparison of RNA extraction techniques from frozen and fresh lung tissues: checkpoint towards gene expression studies. Diagn Pathol . 2009 Jan [cited 2014 Apr 21];4:9. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2669047&tool=pmcentrez&rendertype=abstract

21. Nagy ZT. A hands-on overview of tissue preservation methods for molecular genetic analyses. Org Divers Evol . 2010 Mar 9 [cited 2013 Aug 1];10(1):91–105. Available from: http://link.springer.com/10.1007/s13127-010-0012-4

22. Neyzen S, Van de Leur E, Borkham-Kamphorst E, Herrmann J, Hollweg G, Gressner AM, et al. Cryopreservation of hepatic stellate cells. J Hepatol . 2006 May [cited 2013 Aug 1];44(5):910–7. Available from: http://www.ncbi.nlm.nih.gov/pubmed/16169118

23. Olivieri EHR, de Andrade Franco L, Pereira RG, Carvalho Mota LD, Campos AHJFM, Carraro DM. Biobanking practice: RNA storage at low concentration affects integrity. Biopreserv Biobank . 2014 Feb [cited 2014 Apr 21];12(1):46–52. Available from: http://www.ncbi.nlm.nih.gov/pubmed/24620769

24. Renzi S, Lombardo T, Dotti S, Dessì SS, De Blasio P, Ferrari M. Mesenchymal Stromal Cell Cryopreservation. Biopreserv Biobank . 2012 Jun [cited 2013 Aug 1];10(3):276–81. Available from: http://online.liebertpub.com/doi/abs/10.1089/bio.2012.0005

25. Ross-Rodriguez LU, Elliott J a W, McGann LE. Non-ideal Solution Thermodynamics of Cytoplasm. Biopreserv Biobank . 2012 Oct [cited 2013 Aug 1];10(5):462–71. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3698627&tool=pmcentrez&rendertype=abstract

26. Schrohl A, Würtz S, Kohn E. Banking of biological fluids for studies of disease-associated protein biomarkers. Mol Cell Proteomics . 2008 [cited 2014 Apr 21];7(10):2061–6. Available from: http://www.mcponline.org/content/7/10/2061.short

27. Unhale S, Skubitz A. Stabilization of Tissue Specimens for Pathological Examination and Biomedical Research. Biopreserv Biobank . 2012 [cited 2014 Apr 21];10(6). Available from: http://online.liebertpub.com/doi/abs/10.1089/bio.2012.0031

Biobanking and Bioinformatics

1. Casparie M, Tiebosch a TMG, Burger G, Blauwgeers H, van de Pol a, van Krieken JHJM, et al. Pathology databanking and biobanking in The Netherlands, a central role for PALGA, the nationwide histopathology and cytopathology data network and archive. Cell Oncol . 2007 Jan;29(1):19–24. Available from: http://www.ncbi.nlm.nih.gov/pubmed/17429138

2. Nadkarni PM, Kemp R, Parikh CR. Leveraging a clinical research information system to assist biospecimen data and workflow management: a hybrid approach. J Clin Bioinforma . BioMed Central Ltd; 2011 Jan [cited 2013 Aug 1];1(1):22. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3174108&tool=pmcentrez&rendertype=abstract

3. Norlin L, Fransson MN, Eriksson M, Merino-Martinez R, Anderberg M, Kurtovic S, et al. A Minimum Data Set for Sharing Biobank Samples, Information, and Data: MIABIS. Biopreserv Biobank . 2012 Aug [cited 2013 Aug 1];10(4):343–8. Available from: http://online.liebertpub.com/doi/abs/10.1089/bio.2012.0003

4. Norling M, Kihara A, Kemp S. Web-Based Biobank System Infrastructure Monitoring Using Python, Perl, and PHP. Biopreserv Biobank . 2013 Dec [cited 2014 Apr 21];11(6):355–8. Available from: http://online.liebertpub.com/doi/abs/10.1089/bio.2013.0048

5. Sapre N, Hong MKH, Huang JG, Pedersen J, Ryan A, Anderson P, et al. Bladder Cancer Biorepositories in the “-Omics” Era: Integrating Quality Tissue Specimens with Comprehensive Clinical Annotation. Biopreserv Biobank . 2013 Jun [cited 2014 Apr 21];11(3):166–72. Available from: http://online.liebertpub.com/doi/abs/10.1089/bio.2012.0062

6. Tukacs E, Korotij A, Maros-Szabo Z, Molnar AM, Hajdu A, Torok Z. Model requirements for Biobank Software Systems. Bioinformation . 2012 Jan;8(6):290–2. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3321242&tool=pmcentrez&rendertype=abstract

7. Wei B-R, Simpson RM. Digital pathology and image analysis augment biospecimen annotation and biobank quality assurance harmonization. Clin Biochem . Elsevier B.V.; 2014 Mar [cited 2014 Apr 5];47(4-5):274–9. Available from: http://www.ncbi.nlm.nih.gov/pubmed/24362266

8. Wylie JE, Mineau GP. Biomedical databases: protecting privacy and promoting research. Trends Biotechnol . 2003 Mar [cited 2013 Aug 1];21(3):113–6. Available from: http://www.ncbi.nlm.nih.gov/pubmed/12628367