Biospecimen Reporting for Improved Study Quality (BRISQ)

Journal of Proteome Research

Volumn 10, Issue 8, 2011, Pages 3429-3438

  Moore, Helen M ^a   Kelly, Andrea B ^b   Jewell, Scott D ^c   McShane, Lisa M ^a   Clark, Douglas P ^d   Greenspan, Renata ^e   Hayes, Daniel F ^f   Hainaut, Pierre ^g   Kim, Paula ^h   Mansfield, Elizabeth ⁱ   Potapova, Olga ^j   Riegman, Peter ^k   Rubinstein, Yaffa ^l   Seijo, Edward ^m   Somiari, Stella ⁿ   Watson, Peter ^o   Weier, Heinz Ulrich ^p   Zhu, Claire ^a   Vaught, Jim ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b Rose Li and Associates Inc   (United States)

^c VAN ANDEL RESEARCH INSTITUTE   (United States)

^d JOHNS HOPKINS HOSPITAL   (United States)

^e US Military Cancer Institute   (United States)

^f UNIVERSITY OF MICHIGAN COMPREHENSIVE CANCER CENTER   (United States)

^g INTERNATIONAL AGENCY FOR RESEARCH ON CANCER   (France)

^h Translating Research Across Communities Green   (United States)

ⁱ CENTER FOR DRUG EVALUATION AND RESEARCH   (United States)

^j Cureline Inc   (United States)

^k ERASMUS MEDICAL CENTER   (Netherlands)

^l NATIONAL INSTITUTES OF HEALTH   (United States)

^m H LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE   (United States)

ⁿ WINDBER RESEARCH INSTITUTE   (United States)

^o BRITISH COLUMBIA CANCER AGENCY   (Canada)

^p LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

more..

Author keywords

biospecimen; BRISQ; collection; handling; preanalytical; processing; reporting; sample; specimen; storage

Indexed keywords

ACCURACY; ARTICLE; BIOSPECIMEN; EVIDENCE BASED MEDICINE; EXPERIMENTAL STUDY; HUMAN; OUTCOME ASSESSMENT; PRACTICE GUIDELINE; PRIORITY JOURNAL; PUBLICATION; QUALITY CONTROL; SCIENTIFIC LITERATURE; STANDARDIZATION; TISSUE SECTION;

HUMANS; QUALITY CONTROL; RESEARCH; SPECIMEN HANDLING;

EID: 79961224436     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr200021n     Document Type: Article

References (85)

1. Srinivasan, M.; Sedmak, D.; Jewell, S. Effect of fixatives and tissue processing on the content and integrity of nucleic acids Am. J. Pathol. 2002, 161 (6) 1961-71 (Pubitemid 35434840)
2. Moore, H. M.; Compton, C. C.; Lim, M. D. Biospecimen Research Network Symposium: Advancing Cancer Research through Biospecimen Science Cancer Res. 2009, 69, 6770-6772
3. Apweiler, R.; Aslanidis, C.; Deufel, T. Approaching clinical proteomics: current state and future fields of application in cellular proteomics Cytometry A. 2009a, 75 (10) 816-32
4. Apweiler, R.; Aslanidis, C.; Deufel, T. Approaching clinical proteomics: current state and future fields of application in fluid proteomics Clin. Chem. Lab. Med. 2009b, 47 (6) 724-44
5. Espina, V.; Muelle, C.; Edmiston, K. Tissue is alive: New technologies are needed to address the problems of protein biomarker pre-analytical variability Proteomics Clin. Appl. 2009, 3, 874-82
6. Ransohoff, D. F.; Gourlay, M. L. Sources of Bias in Specimens for Research About Molecular Markers for Cancer J. Clin. Oncol. 2010, 28 (4) 698-704
7. Engel, K. B.; Moore, H. M. Effects of preanalytic variables on the detection of proteins by immunohistochemistry in formalin-fixed, paraffin-embedded tissue Arch. Pathol. Lab Med. 2011, 135 (5) 537-43
8. Ransohoff, D. F. Bias as a threat to the validity of cancer molecular-marker research Nat. Rev. Cancer 2005, 5, 142-9 (Pubitemid 40215862)
9. Wolff, A. C.; Hammond, M. E.; Schwartz, J. N.; Hagerty, K. L.; Allred, D. C.; Cote, R. J.; Dowsett, M.; Fitzgibbons, P. L.; Hanna, W. M.; Langer, A.; McShane, L. M.; Paik, S.; Pegram, M. D.; Perez, E. A.; Press, M. F.; Rhodes, A.; Sturgeon, C.; Taube, S. E.; Tubbs, R.; Vance, G. H.; van de Vijver, M.; Wheeler, T. M.; Hayes, D. F. American Society of Clinical Oncology; College of American Pathologists. American Society of Clinical Oncology/College of American Pathologists guideline recommendations for human epidermal growth factor receptor 2 testing in breast cancer J. Clin. Oncol. 2007, 25 (1) 118-45 (Pubitemid 350003059)
10. Hammond, M. E.; Hayes, D. F.; Dowsett, M.; Allred, D. C.; Hagerty, K. L.; Badve, S.; Fitzgibbons, P. L.; Francis, G.; Goldstein, N. S.; Hayes, M.; Hicks, D. G.; Lester, S.; Love, R.; Mangu, P. B.; McShane, L.; Miller, K.; Osborne, C. K.; Paik, S.; Perlmutter, J.; Rhodes, A.; Sasano, H; Schwartz, J. N.; Sweep, F. C.; Taube, S.; Torlakovic, E. E.; Valenstein, P.; Viale, G.; Visscher, D.; Wheeler, T.; Williams, R. B.; Wittliff, J. L.; Wolff, A. C. American Society of Clinical Oncology; College of American Pathologists. American Society of Clinical Oncology/College of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer (unabridged version) Arch. Pathol. Lab. Med. 2010, 134 (7) e48-72
11. Beatty, B. G.; Bryant, R.; Wang, W. HER-2/neu detection in fine-needle aspirates of breast cancer: fluorescence in situ hybridization and immunocytochemical analysis Am. J. Clin. Pathol. 2004, 122 (2) 246-55 (Pubitemid 38971358)
12. McShane, L. M.; Altman, D. G.; Sauerbrei, W. Statistics Subcommittee of the NCI-EORTC Working Group on Cancer Diagnostics. Reporting recommendations for tumor marker prognostic studies (REMARK) J. Natl. Cancer Inst. 2005, 97 (16) 1180-4
13. von Elm, E.; Altman, D. G.; Egger, M. STROBE Initiative. The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement: guidelines for reporting observational studies J. Clin. Epidemiol. 2008, 61 (4) 344-9 (Pubitemid 351289042)
14. Betsou, F.; Lehmann, S.; Ashton, G. Standard preanalytical coding for biospecimens: defining the sample PREanalytical code Cancer Epidemiol. Biomarkers Prev. 2010, 19 (4) 1004-11
15. Secko, D. M.; Preto, N.; Niemeyer, S. Informed consent in biobank research: a deliberative approach to the debate Soc. Sci. Med. 2009, 68 (4) 781-9
16. Di Nunno, N.; Costantinides, F.; Cina, S. J. What is the best sample for determining the early postmortem period by on-the-spot flow cytometry analysis? Am. J. Forensic Med. Pathol. 2002, 23 (2) 173-80 (Pubitemid 34579330)
17. Humphreys-Beher, M. G.; King, F. K.; Bunnel, B. Isolation of biologically active RNA from human autopsy for the study of cystic fibrosis Biotechnol. Appl. Biochem. 1986, 8 (5) 392-403
18. Barton, R. H.; Nicholson, J. K.; Elliott, P. High-throughput 1H NMR-based metabolic analysis of human serum and urine for large-scale epidemiological studies: validation study Int. J. Epidemiol. 2008, 37 (Suppl 1) i31-40
19. Centeno, B. A.; Enkemann, S. A.; Coppola, D. Classification of human tumors using gene expression profiles obtained after microarray analysis of fine-needle aspiration biopsy samples Cancer 2005, 105 (2) 101-9 (Pubitemid 40604944)
20. Hoff-Olsen, P.; Jacobsen, S.; Mevåg, B. Microsatellite stability in human post-mortem tissues Forensic Sci. Int. 2001, 119 (3) 273-8 (Pubitemid 32487718)
21. Yang, Z. W.; Yang, S. H.; Chen, L. Comparison of blood counts in venous, fingertip and arterial blood and their measurement variation Clin. Lab. Haematol. 2001, 23 (3) 155-9 (Pubitemid 34204407)
22. Heinrich, M.; Matt, K.; Lutz-Bonengel, S. Successful RNA extraction from various human postmortem tissues Int. J. Legal Med. 2007, 121 (2) 136-42 (Pubitemid 46233194)
23. Weis, S.; Llenos, I. C.; Dulay, J. R. Quality control for microarray analysis of human brain samples: The impact of postmortem factors, RNA characteristics, and histopathology J. Neurosci. Methods 2007, 165 (2) 198-209 (Pubitemid 47212459)
24. Tantipaiboonwong, P.; Sinchaikul, S.; Sriyam, S. Different techniques for urinary protein analysis of normal and lung cancer patients Proteomics 2005, 5 (4) 1140-9 (Pubitemid 40469041)
25. He, S.; Wang, Q.; He, J. Proteomic analysis and comparison of the biopsy and autopsy specimen of human brain temporal lobe Proteomics 2006, 6 (18) 4987-96 (Pubitemid 44483894)
26. Jones, R. F.; Sunheimer, R.; Friedman, H. Comparison of ante- and post-mortem PSA levels for epidemiological studies Anticancer Res. 2005, 25 (2B) 1263-7 (Pubitemid 40546800)
27. Pinder, S. E.; Provenzano, E.; Earl, H.; Ellis, I. O. Laboratory handling and histology reporting of breast specimens from patients who have received neoadjuvant chemotherapy Histopathology 2007, 50 (4) 409-17 (Pubitemid 46328171)
28. Tomita, H.; Vawter, M. P.; Walsh, D. M. Effect of agonal and postmortem factors on gene expression profile: quality control in microarray analyses of postmortem human brain Biol. Psychiatry 2004, 55 (4) 346-52 (Pubitemid 38199983)
29. Preece, P.; Virley, D. J.; Costandi, M. An optimistic view for quantifying mRNA in post-mortem human brain Brain Res. Mol. Brain Res. 2003, 116 (1-2) 7-16 (Pubitemid 36993692)
30. Johnston, N. L.; Cervenak, J.; Shore, A. D. Multivariate analysis of RNA levels from postmortem human brains as measured by three different methods of RT-PCR. Stanley Neuropathology Consortium J. Neurosci. Methods 1997, 77 (1) 83-92 (Pubitemid 27488092)
31. Webster, M. J. Tissue preparation and banking Prog. Brain Res. 2006, 158, 3-14
32. Ellis, M.; Davis, N.; Coop, A. Development and validation of a method for using breast core needle biopsies for gene expression microarray analyses Clin. Cancer Res. 2002, 8 (5) 1155-66 (Pubitemid 34517653)
33. Reyna, R.; Traynor, K. D.; Hines, G. Repeated freezing and thawing does not generally alter assay results for several commonly studied reproductive hormones Fertil. Steril. 2001, 76, 823-5 (Pubitemid 32928413)
34. Papale, M.; Pedicillo, M. C.; Thatcher, B. J. Urine profiling by SELDI-TOF/MS: monitoring of the critical steps in sample collection, handling and analysis J. Chromatogr., B: Analyt. Technol. Biomed. Life Sci. 2007, 856 (1-2) 205-13 (Pubitemid 47307442)
35. Barnes, R. O.; Parisien, M.; Murphy, L. C. Influence of evolution in tumor biobanking on the interpretation of translational research Cancer Epidemiol. Biomarkers Prev. 2008, 17 (12) 3344-50
36. McIntosh, M.; Anderson, G.; Drescher, C. Ovarian cancer early detection claims are biased Clin. Cancer Res. 2008, 14 (22) 7574
37. Sidiropoulos, N.; Dumont, L. J.; Golding, A. C. Quality improvement by standardization of procurement and processing of thyroid fine-needle aspirates in the absence of on-site cytological evaluation Thyroid 2009, 19 (10) 1049-52
38. Thorpe, J. D.; Duan, X.; Forrest, R. Effects of blood collection conditions on ovarian cancer serum markers PLoS One 2007, 2 (12) e1281
39. Karsan, A.; Eigl, B. J.; Flibotte, S. Analytical and preanalytical biases in serum proteomic pattern analysis for breast cancer diagnosis Clin. Chem. 2005, 51 (8) 1525-8 (Pubitemid 41060893)
40. Sung, M. T.; Lin, H.; Koch, M. O. Radial distance of extraprostatic extension measured by ocular micrometer is an independent predictor of prostate-specific antigen recurrence: A new proposal for the substaging of pT3a prostate cancer Am. J. Surg. Pathol. 2007, 31 (2) 311-8 (Pubitemid 46175034)
41. Morrison, C.; Palatini, J.; Riggenbach, J. Fine-needle aspiration biopsy of non-Hodgkin lymphoma for use in expression microarray analysis Cancer 2006, 108 (5) 311-8 (Pubitemid 44583710)
42. Schaub, S.; Wilkins, J.; Weiler, T. Urine protein profiling with surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry Kidney Int. 2004, 65 (1) 323-32 (Pubitemid 38037520)
43. Smith, J. L.; Pillay, S. P.; de Jersey, J. Effect of ischaemia on the activities of human hepatic acyl-CoA:cholesterol acyltransferase and other microsomal enzymes Clin. Chim. Acta 1989, 184 (3) 259-68 (Pubitemid 19251161)
44. Visvikis, S.; Schlenck, A.; Maurice, M. DNA extraction and stability for epidemiological studies Clin. Chem. Lab. Med. 1998, 36 (8) 551-5 (Pubitemid 28468303)
45. Micke, P.; Ohshima, M.; Tahmasebpoor, S. Biobanking of fresh frozen tissue: RNA is stable in nonfixed surgical specimens Lab. Invest. 2006, 86 (2) 202-11 (Pubitemid 43117599)
46. Burke, W. J.; O'Malley, K. L.; Chung, H. D. Effect of pre- and postmortem variables on specific mRNA levels in human brain Brain Res. Mol. Brain Res. 1991, 11 (1) 37
47. Spruessel, A.; Steimann, G.; Jung, M. Tissue ischemia time affects gene and protein expression patterns within minutes following surgical tumor excision Biotechniques 2004, 36 (6) 1030-7 (Pubitemid 38747367)
48. Espina, V.; Edmiston, K. H.; Heiby, M. A portrait of tissue phosphoprotein stability in the clinical tissue procurement process Mol. Cell. Proteomics 2008, 7 (10) 1998-2018
49. van Maldegem, F.; de Wit, M.; Morsink, F. Effects of processing delay, formalin fixation, and immunohistochemistry on RNA Recovery From Formalin-fixed Paraffin-embedded Tissue Sections Diagn. Mol. Pathol. 2008, 17 (1) 51-8
50. Langebrake, C.; Günther, K.; Lauber, J. Preanalytical mRNA stabilization of whole bone marrow samples Clin. Chem. 2007, 53 (4) 87-93
51. Yucel, A.; Karakus, R.; Cemalettin, A. Effect of blood collection tube types on the measurement of human epidermal growth factor J. Immunoassay Immunochem. 2007, 28 (1) 47-60 (Pubitemid 44844299)
52. Drake, S. K.; Bowen, R. A.; Remaley, A. T. Potential interferences from blood collection tubes in mass spectrometric analyses of serum polypeptides Clin. Chem. 2004, 50 (12) 2398-401 (Pubitemid 39552184)
53. Preissner, C. M.; Reilly, W. M.; Cyr, R. C. Plastic versus glass tubes: effects on analytical performance of selected serum and plasma hormone assays Clin. Chem. 2004, 50 (7) 1245-7 (Pubitemid 38824238)
54. Frank, M.; Döring, C.; Metzler, D. Global gene expression profiling of formalin-fixed paraffin-embedded tumor samples: a comparison to snap-frozen material using oligonucleotide microarrays Virchows Arch. 2007, 450 (6) 699-711 (Pubitemid 46986227)
55. Scicchitano, M. S.; Dalmas, D. A.; Bertiaux, M. A. 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, 54 (11) 1229-37 (Pubitemid 44623343)
56. Narayanan, S. Considerations in the application of selected molecular biology techniques in the clinical laboratory: preanalytical and analytical issues Rinsho Byori 1996, Suppl 103) 262-70
57. Greer, C. E.; Lund, J. K.; Manos, M. M. PCR amplification from paraffin-embedded tissues: recommendations on fixatives for long-term storage and prospective studies PCR Methods Appl. 1991, 1 (1) 46-50
58. Kouri, T.; Malminiemi, O.; Penders, J. Limits of preservation of samples for urine strip tests and particle counting Clin. Chem. Lab. Med. 2008, 46 (5) 703-13 (Pubitemid 351749104)
59. Zsikla, V.; Baumann, M.; Cathomas, G. Effect of buffered formalin on amplification of DNA from paraffin wax embedded small biopsies using real-time PCR J. Clin. Pathol. 2004, 57 (6) 654-6 (Pubitemid 38725772)
60. Ferry, J. D.; Collins, S.; Sykes, E. Effect of serum volume and time of exposure to gel barrier tubes on results for progesterone by Roche Diagnostics Elecsys 2010 Clin. Chem. 1999, 45 (9) 1574-5 (Pubitemid 29419017)
61. Macabeo-Ong, M.; Ginzinger, D. G.; Dekker, N. Effect of duration of fixation on quantitative reverse transcription polymerase chain reaction analyses Mod. Pathol. 2002, 15 (9) 979-87
62. Miething, F.; Hering, S.; Hanschke, B. Effect of fixation to the degradation of nuclear and mitochondrial DNA in different tissues J. Histochem. Cytochem. 2006, 54 (3) 371-4 (Pubitemid 43291282)
63. Gillio-Tos, A.; De Marco, L.; Fiano, V. Efficient DNA extraction from 25-year-old paraffin-embedded tissues: study of 365 samples Pathology 2007, 39 (3) 345-8 (Pubitemid 46897597)
64. Sigurdson, A. J.; Ha, M.; Cosentino, M. Long-term storage and recovery of buccal cell DNA from treated cards Cancer Epidemiol. Biomarkers Prev. 2006, 15 (2) 385-8 (Pubitemid 43342191)
65. Atkins, D.; Reiffen, K. A.; Tegtmeier, C. L. Immunohistochemical detection of EGFR in paraffin-embedded tumor tissues: variation in staining intensity due to choice of fixative and storage time of tissue sections J. Histochem. Cytochem. 2004, 52 (7) 893-901 (Pubitemid 38857154)
66. Zhou, H.; Yuen, P. S.; Pisitkun, T. Collection, storage, preservation, and normalization of human urinary exosomes for biomarker discovery Kidney Int. 2006, 69 (8) 1471-6
67. Ahmad, S.; Sundaramoorthy, E.; Arora, R. Progressive degradation of serum samples limits proteomic biomarker discovery Anal. Biochem. 2009, 394 (2) 237-42
68. Isaksson, H. S.; Nilsson, T. K. Preanalytical aspects of quantitative TaqMan real-time RT-PCR: applications for TF and VEGF mRNA quantification Clin Biochem. 2006, 39 (4) 373-7
69. Kauppinen, T.; Martikainen, P.; Alafuzoff, I. Human postmortem brain tissue and 2-mm tissue microarrays Appl Immunohistochem. Mol. Morphol. 2006, 14 (3) 353-9 (Pubitemid 44319064)
70. Rosenling, T.; Slim, C. L.; Christin, C. The effect of preanalytical factors on stability of the proteome and selected metabolites in cerebrospinal fluid (CSF) J. Proteome Res. 2009, 8 (12) 5511-22
71. Paik, S; Kim, C. Y.; Song, Y. K.; Kim, W. S. Technology insight: Application of molecular techniques to formalin-fixed paraffin-embedded tissues from breast cancer Nat. Clin. Pract. Oncol. 2005, 2 (5) 246-54 (Pubitemid 40812455)
72. Guder, W. G. Preanalytical factors and their influence on analytical quality specifications Scand. J. Clin. Lab. Invest. 1999, 59 (7) 545-9 (Pubitemid 30056749)
73. Timms, J. F.; Arslan-Low, E.; Gentry-Maharaj, A. Preanalytic influence of sample handling on SELDI-TOF serum protein profiles Clin. Chem. 2007, 53 (4) 645-56 (Pubitemid 46580234)
74. Chan, K. C.; Yeung, S. W.; Lui, W. B. Effects of preanalytical factors on the molecular size of cell-free DNA in blood Clin. Chem. 2005, 51 (4) 781-4 (Pubitemid 40463932)
75. Fiedler, G. M.; Baumann, S.; Leichtle, A. Standardized peptidome profiling of human urine by magnetic bead separation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry Clin. Chem. 2007, 53 (3) 421-8 (Pubitemid 46447938)
76. Kirk, M. J.; Hayward, R. M.; Sproull, M. Non-patient related variables affecting levels of vascular endothelial growth factor in urine biospecimens J. Cell. Mol. Med. 2008, 12 (4) 1250-5
77. Kueltzo, L. A.; Wang, W.; Randolph, T. W. Effects of solution conditions, processing parameters, and container materials on aggregation of a monoclonal antibody during freeze-thawing J. Pharm. Sci. 2008, 97 (5) 1801-12
78. Ginocchio, C. C.; Wang, X. P.; Kaplan, M. H. Effects of specimen collection, processing, and storage conditions on stability of human immunodeficiency virus type 1 RNA levels in plasma J. Clin. Microbiol. 1997, 35 (11) 2886-93 (Pubitemid 27452429)
79. Braakhuis, B. J. M.; Tabor, M. P.; Kummer, J. A. A genetic explanation of slaughter's concept of field cancerization: evidence and clinical implications Cancer Res. 2003, 63 (8) 1727-30 (Pubitemid 36460827)
80. Deng, G.; Lu, Y.; Zlotnikov, G. Loss of heterozygosity in normal tissue adjacent to breast carcinomas Science 1996, 274 (5295) 2057-9 (Pubitemid 27020695)
81. Mojica, W. D.; Stein, L.; Hawthorn, L. An exfoliation and enrichment strategy results in improved transcriptional profiles when compared to matched formalin fixed samples BMC Clin. Pathol. 2007, 7, 7
82. Umar, A.; Dalebout, J. C.; Timmermans, A. M. Method optimization for peptide profiling of microdissected breast carcinoma tissue by matrix-assisted laser desorption/ionisation-time of flight and matrix-assisted laser desorption/ionisation-time of flight/time of flight-mass spectrometry Proteomics 2005, 5 (10) 2680-8 (Pubitemid 40966495)
83. Breit, S.; Nees, M.; Schaefer, U. Impact of pre-analytical handling on bone marrow mRNA gene expression Br. J. Hamaetol. 2004, 126 (2) 231-43 (Pubitemid 38961943)
84. Coudry, R. A.; Meireles, S. I.; Stoyanova, R. Successful application of microarray technology to microdissected formalin-fixed, paraffin-embedded tissue J. Mol. Diagn. 2007, 9 (1) 70-9 (Pubitemid 47322016)
85. Sanchez-Carbayo, M.; Saint, F.; Lozano, J. J. Comparison of gene expression profiles in laser-microdissected, nonembedded, and OCT-embedded tumor samples by oligonucleotide microarray analysis Clin. Chem. 2003, 49 (12) 2096-100 (Pubitemid 37449488)