World Endometriosis Research Foundation Endometriosis Phenome and Biobanking Harmonisation Project: IV. Tissue collection, processing, and storage in endometriosis research

Fertility and Sterility

Volumn 102, Issue 5, 2014, Pages 1244-1253

  Fassbender, Amelie ^a   Rahmioglu, Nilufer ^b   Vitonis, Allison F ^c   Viganò, Paola ^d   Giudice, Linda C ^e,f   D'Hooghe, Thomas M ^a   Hummelshoj, Lone ^f   David Adamson, G ^f,g   Becker, Christian M ^h,i   Missmer, Stacey A ^c,j   Zondervan, Krina T ^b,h,i  

^a UNIVERSITY OF LEUVEN   (Belgium)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c BRIGHAM AND WOMEN S HOSPITAL   (United States)

^d SAN RAFFAELE HOSPITAL   (Italy)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f World Endometriosis Research Foundation (WERF)   (United Kingdom)

^g PALO ALTO MEDICAL FOUNDATION   (United States)

^h UNIVERSITY OF OXFORD   (United Kingdom)

ⁱ UNIVERSITY OF OXFORD   (United Kingdom)

^j HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

more..

Author keywords

Endometriosis; EPHect; Standard operating procedures; Standardization; Tissue

Indexed keywords

CONSENSUS; CONSULTATION; DATA COLLECTION METHOD; DATA PROCESSING; ENDOMETRIOSIS; ENDOMETRIUM; EVIDENCE BASED PRACTICE; FEMALE; HUMAN; HUMAN TISSUE; INFORMATION PROCESSING; MEDICAL RESEARCH; MYOMETRIUM; PILOT STUDY; PRACTICE GUIDELINE; PRIORITY JOURNAL; RELIABILITY; REVIEW; RNA ANALYSIS; STANDARD; STANDARDIZATION; TISSUE PRESERVATION; VALIDITY; WORKSHOP; BLOOD; BLOOD SAMPLING; HEALTH CARE FACILITY; INTERNATIONAL COOPERATION; LABORATORY DIAGNOSIS; PATHOLOGY; STANDARDS;

BLOOD SPECIMEN COLLECTION; ENDOMETRIOSIS; FEMALE; HUMANS; INTERNATIONALITY; PRACTICE GUIDELINES AS TOPIC; SPECIMEN HANDLING; TISSUE BANKS;

EID: 84922057971     PISSN: 00150282     EISSN: 15565653     Source Type: Journal    
DOI: 10.1016/j.fertnstert.2014.07.1209     Document Type: Review

References (80)

1. Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A 2001;98:10869-74.
2. Welsh JB, Zarrinkar PP, Sapinoso LM, Kern SG, Behling CA, Monk BJ, et al. Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer. Proc Natl Acad Sci U S A 2001;98:1176-81.
3. Baird RD, Caldas C. Genetic heterogeneity in breast cancer: the road to personalized medicine? BMC Med 2013;11:151.
4. Lehmann BD, Pietenpol JA. Identification and use of biomarkers in treatment strategies for triple-negative breast cancer subtypes. J Pathol 2014;232:142-50.
5. Stopeck AT, Brown-Glaberman U, Wong HY, Park BH, Barnato SE, Gradishar WJ, et al. The role of targeted therapy and biomarkers in breast cancer treatment. Clin Exp Metastasis 2012;29:807-19.
6. Ogino S, Fuchs CS, Giovannucci E. How many molecular subtypes? Implications of the unique tumor principle in personalized medicine. Expert Rev Mol Diagn 2012;12:621-8.
7. Ogino S, Chan AT, Fuchs CS, Giovannucci E. Molecular pathological epidemiology of colorectal neoplasia: an emerging transdisciplinary and interdisciplinary field. Gut 2011;60:397-411.
8. Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature 2012;490:61-70.
9. Chadwick LH. The NIH Roadmap Epigenomics Program data resource. Epigenomics 2012;4:317-24.
10. Consortium GT. The Genotype-Tissue Expression (GTEx) project. Nat Genet 2013;45:580-5.
11. Altmae S, Esteban FJ, Stavreus-Evers A, Simon C, Giudice L, Lessey BA, et al. Guidelines for the design, analysis and interpretation of "omics" data: focus on human endometrium. Hum Reprod Update 2014;20:12-28.
12. Sheldon E, Vo KC, McIntire RA, Aghajanova L, Zelenko Z, Irwin JC, et al. Biobanking human endometrial tissue and blood specimens: standard operating procedure and importance to reproductive biology research and diagnostic development. Fertil Steril 2011;95:2120-2.e1-12.
13. Becker CM, Laufer MR, Stratton P, Hummelshoj L, Missmer SM, Zondervan KT, et al. World Endometriosis Research Foundation Endometriosis Phenome and Biobanking Harmonization Project: I. Surgical phenotype data collection in endometriosis research. Fertil Steril 2014;102:1213-22.
14. Vitonis AF, Vincent K, Rahmioglu N, Fassbender A, Buck Louis GM, Hummelshoj L, et al. World Endometriosis Research Foundation Endometriosis Phenome and Biobanking Harmonization: II. Clinical and covariate phenotype data collection in endometriosis research. Fertil Steril 2014;102:1223-32.
15. Fassbender A, Vodolazkaia A, Saunders P, Lebovic D, Waelkens E, de Moor B, et al. Biomarkers of endometriosis. Fertil Steril 2013;99:1135-45.
16. Gion M, Fabricio AS. New frontiers in tumor marker studies: from biobanking to collaboration in translational research. Int J Biol Markers 2011;26:73-4.
17. May KE, Villar J, Kirtley S, Kennedy SH, Becker CM. Endometrial alterations in endometriosis: a systematic review of putative biomarkers. Hum Reprod Update 2011;17:637-53.
18. Rogers PA, d'Hooghe TM, Fazleabas A, Gargett CE, Giudice LC, Montgomery GW, et al. Priorities for endometriosis research: recommendations from an international consensus workshop. Reprod Sci 2009;16:335-46.
19. Rogers PA, d'Hooghe TM, Fazleabas A, Giudice LC, Montgomery GW, Petraglia F, et al. Defining future directions for endometriosis research: workshop report from the 2011 World Congress of Endometriosis In Montpellier, France. Reprod Sci 2013;20:483-99.
20. Rahmioglu N, Fassbender A, Vitonis AF, Tworoger S, Hummelshoj L, d'Hooghe TM, et al. World Endometriosis Research Foundation Endometriosis Phenome and Biobanking Harmonisation Project: III. Fluid biospecimen collection, processing, and storage in endometriosis research. Fertil Steril 2014;102:1233-43.
21. Williams AR, Brechin S, Porter AJ, Warner P, Critchley HO. Factors affecting adequacy of Pipelle and Tao brush endometrial sampling. BJOG 2008;115:1028-36.
22. Tokushige N, Markham R, Russell P, Fraser IS. Different types of small nerve fibers in eutopic endometrium and myometrium in women with endometriosis. Fertil Steril 2007;88:795-803.
23. Brosens JJ, Barker FG. The role of myometrial needle biopsies in the diagnosis of adenomyosis. Fertil Steril 1995;63:1347-9.
24. Fassbender A, Overbergh L, Verdrengh E, Kyama CM, Vodolazakaia A, Bokor A, et al. How can macroscopically normal peritoneum contribute to the pathogenesis of endometriosis? Fertil Steril 2011;96:697-9.
25. Young VJ, Brown JK, Saunders PT, Horne AW. The role of the peritoneum in the pathogenesis of endometriosis. Hum Reprod Update 2013;19:558-69.
26. Peakman TC, Elliott P. The UK Biobank sample handling and storage validation studies. Int J Epidemiol 2008;37:i2-6.
27. de Cecco L, Dugo M, Canevari S, Daidone MG, Callari M. Measuring microRNA expression levels in oncology: from samples to data analysis. Crit Rev Oncog 2013;18:273-87.
28. Neubauer C, Kiesel L, Gotte M. MicroRNAs and the pathogenesis of endometriosis. J Endometr 2012;4:1-16.
29. Baker AF, Dragovich T, Ihle NT, Williams R, Fenoglio-Preiser C, Powis G. Stability of phosphoprotein as a biological marker of tumor signaling. Clin Cancer Res 2005;11:4338-40.
30. Spruessel A, Steimann G, Jung M, Lee SA, Carr T, Fentz AK, et al. Tissue ischemia time affects gene and protein expression patterns within minutes following surgical tumor excision. Biotechniques 2004;36:1030-7.
31. Dash A, Maine IP, Varambally S, Shen R, Chinnaiyan AM, Rubin MA. Changes in differential gene expression because of warm ischemia time of radical prostatectomy specimens. Am J Pathol 2002;161:1743-8.
32. Huang J, Qi R, Quackenbush J, Dauway E, Lazaridis E, Yeatman T. Effects of ischemia on gene expression. J Surg Res 2001;99:222-7.
33. Blackhall FH, Pintilie M, Wigle DA, Jurisica I, Liu N, Radulovich N, et al. Stability and heterogeneity of expression profiles in lung cancer specimens harvested following surgical resection. Neoplasia 2004;6:761-7.
34. de Cecco L, Musella V, Veneroni S, Cappelletti V, Bongarzone I, Callari M, et al. Impact of biospecimens handling on biomarker research in breast cancer. BMC Cancer 2009;9:409.
35. Popova T, Mennerich D, Weith A, Quast K. Effect of RNA quality on transcript intensity levels in microarray analysis of human post-mortem brain tissues. BMC Genomics 2008;9:91.
36. Wong V, Wang DY, Warren K, Kulkarni S, Boerner S, Done SJ, et al. The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers. BMC Cancer 2008;8:277.
37. Hankinson SE, London SJ, Chute CG, Barbieri RL, Jones L, Kaplan LA, et al. Effect of transport conditions on the stability of biochemical markers in blood. Clin Chem 1989;35:2313-6.
38. Townsend MK, Clish CB, Kraft P, Wu C, Souza AL, Deik AA, et al. Reproducibility of metabolomic profiles among men and women in 2 large cohort studies. Clin Chem 2013;59:1657-67.
39. Tuck MK, Chan DW, Chia D, Godwin AK, Grizzle WE, Krueger KE, et al. Standard operating procedures for serum and plasma collection: early detection research network consensus statement standard operating procedure integration working group. J Proteome Res 2009;8:113-7.
40. Matsuzaki S, Canis M, Mage G. Use of laser capture microdissection in studying hormone-dependent diseases: endometriosis. Methods Mol Biol 2009;590:295-306.
41. Emmert-Buck MR, Bonner RF, Smith PD, Chuaqui RF, Zhuang Z, Goldstein SR, et al. Laser capture microdissection. Science 1996;274:998-1001.
42. Burgemeister R. Nucleic acids extraction from laser microdissected FFPE tissue sections. Methods Mol Biol 2011;724:117-29.
43. Lin J, Kennedy SH, Svarovsky T, Rogers J, Kemnitz JW, Xu A, et al. High-quality genomic DNA extraction from formalin-fixed and paraffin-embedded samples deparaf finized using mineral oil. Anal Biochem 2009;395:265-7.
44. Sah S, Chen L, Houghton J, Kemppainen J, Marko AC, Zeigler R, et al. Functional DNA quantification guides accurate next-generation sequencing mutation detection in formalin-fixed, paraffin-embedded tumor biopsies. Genome Med 2013;5:77.
45. Knapp M, Hofreiter M. Next generation sequencing of ancient DNA: requirements, strategies and perspectives. Genes 2010;1:227-43.
46. Grotzer MA, Patti R, Geoerger B, Eggert A, Chou TT, Phillips PC. Biological stability of RNA isolated from RNAlater-treated brain tumor and neuroblastoma xenografts. Med Pediatr Oncol 2000;34:438-42.
47. Ohashi Y, Creek KE, Pirisi L, Kalus R, Young SR. RNA degradation in human breast tissue after surgical removal: a time-course study. Exp Mol Pathol 2004;77:98-103.
48. Lee SM, Schelcher C, Gashi S, Schreiber S, Thasler RM, Jauch KW, et al. RNA stability in human liver: comparison of different processing times, temperatures and methods. Mol Biotechnol 2013;53:1-8.
49. Vincek V, Nassiri M, Nadji M, Morales AR. A tissue fixative that protects macromolecules (DNA, RNA, and protein) and histomorphology in clinical samples. Lab Invest 2003;83:1427-35.
50. Wang SS, Sherman ME, Rader JS, Carreon J, Schiffman M, Baker CC. Cervical tissue collection methods for RNA preservation: comparison of snap-frozen, ethanol-fixed, and RNAlater-fixation. Diagn Mol Pathol 2006;15:144-8.
51. Staff S, Kujala P, Karhu R, Rokman A, Ilvesaro J, Kares S, et al. Preservation of nucleic acids and tissue morphology in paraffin-embedded clinical samples: comparison of five molecular fixatives. J Clin Pathol 2013;66:807-10.
52. Paska C, Bogi K, Szilak L, Tokes A, Szabo E, Sziller I, et al. Effect of formalin, acetone, and RNAlater fixatives on tissue preservation and different size amplicons by real-time PCR from paraffin-embedded tissue. Diagn Mol Pathol 2004;13:234-40.
53. Hall GL, Kademani D, Risk JM, Shaw RJ. Tissue banking in head and neck cancer. Oral Oncol 2008;44:109-15.
54. Qiu J, Kulkarni S, Chandrasekhar R, Rees M, Hyde K, Wilding G, et al. Effect of delayed formalin fixation on estrogen and progesterone receptors in breast cancer: a study of three different clones. Am J Clin Pathol 2010;134:813-9.
55. Selvarajan S, Bay BH, Choo A, Chuah KL, Sivaswaren CR, Tien SL, et al. Effect of fixation period on HER2/neu gene amplification detected by fluorescence in situ hybridization in invasive breast carcinoma. J Histochem Cytochem 2002;50:1693-6.
56. Goldstein NS, Ferkowicz M, Odish E, Mani A, Hastah F. Minimum formalin fixation time for consistent estrogen receptor immunohistochemical staining of invasive breast carcinoma. Am J Clin Pathol 2003;120:86-92.
57. Arber DA. Effect of prolonged formalin fixation on the immunohistochemical reactivity of breast markers. Appl Immunohistochem Mol Morphol 2002;10:183-6.
58. Khoury T, Sait S, Hwang H, Chandrasekhar R, Wilding G, Tan D, et al. Delay to formalin fixation effect on breast biomarkers. Mod Pathol 2009;22:1457-67.
59. Pinhel IF, Macneill FA, Hills MJ, Salter J, Detre S, A'Hern R, et al. Extreme loss of immunoreactive p-Akt and p-Erk1/2 during routine fixation of primary breast cancer. Breast Cancer Res 2010;12:R76.
60. Holzer TR, Fulford AD, Arkins AM, Grondin JM, Mundy CW, Nasir A, et al. Ischemic time impacts biological integrity of phospho-proteins in PI3K/Akt, Erk/MAPK, and p38 MAPK signaling networks. Anticancer Res 2011;31:2073-81.
61. Apple S, Pucci R, Lowe AC, Shintaku I, Shapourifar-Tehrani S, Moatamed N. The effect of delay in fixation, different fixatives, and duration of fixation in estrogen and progesterone receptor results in breast carcinoma. Am J Clin Pathol 2011;135:592-8.
62. Srinivasan M, Sedmak D, Jewell S. Effect of fixatives and tissue processing on the content and integrity of nucleic acids. Am J Pathol 2002;161:1961-71.
63. Ralton LD, Murray GI. The use of formalin fixed wax embedded tissue for proteomic analysis. J Clin Pathol 2011;64:297-302.
64. Abbaraju NV, Cai Y, Rees BB. Protein recovery and identification from the gulf killifish, Fundulus grandis: comparing snap-frozen and RNAlater preserved tissues. Proteomics 2011;11:4257-61.
65. van Eijsden RG, Stassen C, Daenen L, Van Mulders SE, Bapat PM, Siewers V, et al. A universal fixation method based on quaternary ammonium salts (RNAlater) for omics-technologies: Saccharomyces cerevisiae as a case study. Biotechnol Lett 2013;35:891-900.
66. Su SC, Garbers S, Rieper TD, Toniolo P. Temperature variations in upright mechanical freezers. Cancer Epidemiol Biomarkers Prev 1996;5:139-40.
67. Rai AJ, Gelfand CA, Haywood BC, Warunek DJ, Yi J, Schuchard MD, et al. HUPO Plasma Proteome Project specimen collection and handling: toward the standardization of parameters for plasma proteome samples. Proteomics 2005;5:3262-77.
68. Olivieri EH, Franco Lde A, Pereira RG, Mota LD, Campos AH, Carraro DM. Biobanking practice: RNA storage at low concentration affects integrity. Biopreserv Biobank 2014;12:46-52.
69. Bao WG, Zhang X, Zhang JG, Zhou WJ, Bi TN, Wang JC, et al. Biobanking of fresh-frozen human colon tissues: impact of tissue ex-vivo ischemia times and storage periods on RNA quality. Ann Surg Oncol 2013;20:1737-44.
70. Shabihkhani M, Lucey GM, Wei B, Mareninov S, Lou JJ, Vinters HV, et al. The procurement, storage, and quality assurance of frozen blood and tissue biospecimens in pathology, biorepository, and biobank settings. Clin Biochem 2014;47:258-66.
71. Aghajanova L, Giudice LC. Molecular evidence for differences in endometrium in severe versus mild endometriosis. Reprod Sci 2011;18:229-51.
72. Burney RO, Talbi S, Hamilton AE, Vo KC, Nyegaard M, Nezhat CR, et al. Gene expression analysis of endometrium reveals progesterone resistance and candidate susceptibility genes in women with endometriosis. Endocrinology 2007;148:3814-26.
73. Kao LC, Germeyer A, Tulac S, Lobo S, Yang JP, Taylor RN, et al. Expression profiling of endometrium from women with endometriosis reveals candidate genes for disease-based implantation failure and infertility. Endocrinology 2003;144:2870-81.
74. Talbi S, Hamilton AE, Vo KC, Tulac S, Overgaard MT, Dosiou C, et al. Molecular phenotyping of human endometrium distinguishes menstrual cycle phases and underlying biological processes in normo-ovulatory women. Endocrinology 2006;147:1097-121.
75. Fassbender A, Verbeeck N, Bornigen D, Kyama CM, Bokor A, Vodolazkaia A, et al. Combined mRNA microarray and proteomic analysis of eutopic endometrium of women with and without endometriosis. Hum Reprod 2012;27:2020-9.
76. Baird DD, McConnaughey DR, Weinberg CR, Musey PI, Collins DC, Kesner JS, et al. Application of a method for estimating day of ovulation using urinary estrogen and progesterone metabolites. Epidemiology 1995;6:547-50.
77. Waller K, Swan SH, Windham GC, Fenster L, Elkin EP, Lasley BL. Use of urine biomarkers to evaluate menstrual function in healthy premenopausal women. Am J Epidemiol 1998;147:1071-80.
78. Shah DK, Correia KF, Vitonis AF, Missmer SA. Body size and endometriosis: results from 20 years of follow-up within the Nurses' Health Study II prospective cohort. Hum Reprod 2013;28:1783-92.
79. McDowell MA, Fryar CD, Ogden CL. Anthropometric reference data for children and adults: United States, 1988-1994. Vital and health statistics series 11, data from the national health survey. Hyattsville, Maryland: U.S Department of Health and Human Services; 2009.
80. Centers for Disease Control. National Health and Nutrition Examination Survey III: body measurements (anthropometry). Atlanta: Centers for Disease Control. Rockville, Maryland: Westat Inc.; 1988.