Maintaining breast cancer specimen integrity and individual or simultaneous extraction of quality DNA, RNA, and proteins from allprotect-stabilized and nonstabilized tissue samples

Biopreservation and Biobanking

Volumn 9, Issue 4, 2011, Pages 389-398

  Mee, Blanaid C ^a   Carroll, Paul ^a   Donatello, Simona ^b   Connolly, Elizabeth ^a   Griffin, Mairead ^a   Dunne, Barbara ^a   Burke, Louise ^c   Flavin, Richard ^d   Rizkalla, Hala ^a   Ryan, Ciara ^a   Hayes, Brian ^a   D'Adhemar, Charles ^a   Banville, Niamh ^a   Faheem, Nazia ^a   Muldoon, Cian ^a   Gaffney, Eoin F ^a  

^a ST JAMES S HOSPITAL   (Ireland)

^b BEAUMONT HOSPITAL   (Ireland)

^c University College Cork and INFANT Centre   (Ireland)

^d UNIVERSITY HOSPITAL GALWAY   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BREAST CANCER; BREAST CARCINOMA; CANCER TISSUE; DNA EXTRACTION; FREEZE THAWING; FROZEN SECTION; HUMAN; HUMAN TISSUE; MORPHOLOGY; NUCLEIC ACID ANALYSIS; PRIORITY JOURNAL; PROTEIN ISOLATION; QUALITY CONTROL; QUANTITATIVE ANALYSIS; RNA EXTRACTION; RNA STABILITY; ROOM TEMPERATURE;

EID: 84855182930     PISSN: 19475535     EISSN: 19475543     Source Type: Journal    
DOI: 10.1089/bio.2011.0034     Document Type: Article

References (47)

1. Florell SR, Coffin CM, Holden JA, et al. Preservation of RNA for functional genomic studies: a multidisciplinary tumor bank protocol. Mod Pathol 2001;14:116-128. (Pubitemid 32173395)
2. Foster CS, Gosden CM, Ke YQ. Primer: tissue fixation and preservation for optimal molecular analysis of urologic tissues. Nat Clin Pract Urol 2006;3:268-278. (Pubitemid 43738869)
3. Weedon-Fekjaer H, Lindqvist BH, Vatten LJ, et al. Breast cancer tumor growth estimated through mammography screening data. Breast Cancer Res 2008;10:R41.
4. Ravaioli A, Foca F, Colamartini A, et al. Incidence, detection, and tumor stage of breast cancer in a cohort of Italian women with negative screening mammography report recommending early (short-interval) rescreen. BMC Med 2010;8:11.
5. Zabicki K, Colbert JA, Dominguez FJ, et al. Breast cancer diagnosis in women 〈 or = 40 versus 50 to 60 years: increasing size and stage disparity compared with older women over time. Ann Surg Oncol 2006;13:1072-1077. (Pubitemid 44337966)
6. Fleige S, Pfaffl MW. RNA integrity and the effect on the real-time qRT-PCR performance. Mol Aspects Med 2006;27:126-139.
7. Jewell SD, Srinivasan M, McCart LM, et al. Analysis of the molecular quality of human tissues: an experience from the Cooperative Human Tissue Network. Am J Clin Pathol 2002;118:733-741. (Pubitemid 37046318)
8. Micke P, Ohshima M, Tahmasebpoor S, et al. Biobanking of fresh frozen tissue: RNA is stable in nonfixed surgical specimens. Lab Invest 2006;86:202-211. (Pubitemid 43117599)
9. Imbeaud S, Graudens E, Boulanger V, et al. Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces. Nucleic Acids Res 2005;33:e56.
10. Ohashi Y, Creek KE, Pirisi L, et al. RNA degradation in human breast tissue after surgical removal: a time-course study. Exp Mol Pathol 2004;77:98-103. (Pubitemid 39209291)
11. Malik KJ, Chen CD, Olsen TW. Stability of RNA from the retina and retinal pigment epithelium in a porcine model simulating human eye bank conditions. Invest Ophthalmol Vis Sci 2003;44:2730-2735. (Pubitemid 36618437)
12. Chowdary DL, Skelton J, Curtin K, et al. Prognostic gene signatures can be measured in tissues collected in RNAlater preservative. J Mol Diagn 2005;8:31-39. (Pubitemid 43257432)
13. Grotzer MA, Patti R, Geoerger B, et al. Biological stability of RNA isolated from RNAlater-treated brain tumor and neuroblastoma xenografts. Med Pediatr Oncol 2000;34:438-442. (Pubitemid 30346413)
14. Ellis M, Davis N, Coop A, et al. Development and validation of a method for using breast core needle biopsies for gene expression microarray analyses. Clin Cancer Res 2002;8:1155-1166. (Pubitemid 34517653)
15. Strand C, Enell J, Hedenfalk I, et al. RNA quality in frozen breast cancer samples and the influence on gene expression analysis-a comparison of three evaluation methods using microcapillary electrophoresis traces. BMC Mol Biol 2007;8:38.
16. Morrow JK. Quality makes a difference in RNA prep. Genet Eng Biotechnol News 2009;29:38-39.
17. Xu C, Houck JR, Fan W, et al. Simultaneous isolation of DNA and RNA from the same cell population obtained by laser capture microdissection for genome and transcriptome profiling. J Mol Diagn 2008;10:129-134. (Pubitemid 351428394)
18. Becker C, Hammerle-Fickinger A, Riedmaier I, et al. mRNA and microRNA quality control for RT-qPCR analysis. Method 2010; 50:237-243.
19. Ibberson D, Benes V, Muckenthaler MU, et al. RNA degradation compromises the reliability of microRNA expression profiling. BMC Biotechnol 2009;9:102.
20. Copois V, Bibeau F, Bascoul-Mollevi C, et al. Impact of RNA degradation on gene expression profiles: assessment of different methods to reliably determine RNA quality. J Biotechnol 2007;12: 549-559. (Pubitemid 44959110)
21. Perez-Novo CA, Claeys C, Speleman F, et al. Impact of RNA quality on reference gene expression stability. Biotechniques 2005;39:52, 54, 56.
22. Santella RM. Approaches to DNA/RNA extraction and whole genome amplification. Cancer Epidemiol Biomarkers Prev 2006; 15:1585-1587. (Pubitemid 44497091)
23. Thompson KL, Pine PS, Rosenzweig BA, et al. Characterization of the effect of sample quality on high density oligonucleotide microarray data using progressively degraded rat liver RNA. BMC Biotechnol 2007;7:57.
24. ISBER. Best practices for repositories collection, storage, retrieval and distribution of biological materials for research. Cell Preserv Technol 2008;6:1-110.
25. OBBR. NCI Best Practices for Biospecimen Resources. 2010. http://biospecimens.cancer.gov/practices/2010bp.asp.
26. Wales Cancer Bank. www.walescancerbank.com/.
27. Spanish Tumour Bank. www.cnio.es/ing/grupos/plantillas/presentacion.asp? pag = 529.
28. Canadian Tumour Repository Network. www.ctrnet.ca.
29. Hainaut PC, Caboux E, Bevilacqua G, et al. Pathology as the cornerstone of human tissue banking: European consensus expert group report. Biopreserv Biobank 2010;7:157-160.
30. Morrogh M, Olvera N, Bogomolniy F, et al. Tissue preparation for laser capture microdissection and RNA extraction from fresh frozen breast tissue. Biotechniques 2007;43:41-42.
31. Kendall A, Anderson H, Dunbier AK, et al. Impact of estrogen deprivation on gene expression profiles of normal postmenopausal breast tissue in vivo. Cancer Epidemiol Biomarkers Prev 2008;17:855-863. (Pubitemid 351536416)
32. Sun C, Southard C, Witonsky DB, et al. Allelic imbalance (AI) identifies novel tissue-specific cis-regulatory variation for human UGT2B15. Hum Mutat 2010;31:99-107.
33. Nemunaitis J, Senzer N, Khalil I, et al. Proof concept for clinical justification of network mapping for personalized cancer therapeutics. Cancer Gene Ther 2007;14:686-695. (Pubitemid 47080360)
34. Radpour R, Sikora M, Grussenmeyer T, et al. Simultaneous isolation of DNA, RNA, and proteins for genetic, epigenetic, transcriptomic, and proteomic analysis. J Proteome Res 2009;8: 5264-5274.
35. Gross V, Carlson G, Kwan AT, et al. Tissue fractionation by hydrostatic pressure cycling technology: the unified sample preparation technique for systems biology studies. J Biomol Tech 2008;19:189-199.
36. AllPrep-DNA/RNA/Protein Mini Handbook. For simultaneous purification of genomic DNA, total RNA, and total protein from the same cell or tissue sample. Qiagen 2010:18. www .qiagen.com.
37. Ennis DP, Pidgeon GP, Millar N, et al. Building a bioresource for esophageal research: lessons from the early experience of an academic medical center. Dis Esophagus 2010;23:1-7.
38. De Cecco L, Musella V, Veneroni S, et al. Impact of biospecimens handling on biomarker research in breast cancer. BMC Cancer 2009;9:409.
39. Riedmaier I, Bergmaier M, Pfaffl MW. Comparison of two available platforms for determination of RNA quality. Biotechnol Biotechnol Eq 2010;24:2154-2159.
40. Pfaffl MW, Fleige S, Riedmaier I. Validation of lab-on-chip capillary electrophoresis systems for total RNA quality and quantity control. Biotechnol Biotechnol Eq 2008;22:829-834.
41. Compton C. Getting to personalized cancer medicine: taking out the garbage. Cancer 2007;110:1641-1643. (Pubitemid 47557286)
42. Park A. 10 Ideas Changing the World Right Now. Time Magazine 2009, March 23rd:44.
43. Asslaber M, Zatloukal K. Biobanks: transnational, European and global networks. Brief Funct Genomic Proteomics 2007;6:193-201. (Pubitemid 351863876)
44. Yuille M, van Ommen GJ, Brechot C, et al. Biobanking for Europe. Brief Bioinform 2008;9:14-24.
45. Hirtzlin I, Dubreuil C, Preaubert N, et al. An empirical survey on biobanking of human genetic material and data in six EU countries. Eur J Hum Genet 2003;11:475-488. (Pubitemid 36722268)
46. Salvaterra E, Lecchi L, Giovanelli S, et al. Banking together. A unified model of informed consent for biobanking. EMBO Rep 2008;9:307-313.
47. Gaskell G. Biobanks need publicity. Nature 2011;471:159-160.