An efficient protocol for genomic DNA extraction from formalin-fixed paraffin-embedded tissues

Research in Veterinary Science

Volumn 86, Issue 3, 2009, Pages 421-426

  Santos, Sara ^a   Sá, Daniela ^a   Bastos, Estela ^a   Guedes Pinto, Henrique ^a   Gut, Ivo ^b   Gärtner, Fátima ^c   Chaves, Raquel ^a  

^a UNIVERSITY OF TRÁS OS MONTES AND ALTO DOURO   (Portugal)

^b DIF   (France)

^c UNIVERSITY OF PORTO   (Portugal)

Author keywords

Cat mammary tumours; DNA extraction; Formalin fixed paraffin embedded tissues; PCR amplification; Sequencing

Indexed keywords

DNA FRAGMENT; FORMALDEHYDE; GENOMIC DNA; PARAFFIN;

ANIMAL TISSUE; ARTICLE; BREAST TUMOR; CANCER INCIDENCE; CAT; CONTROLLED STUDY; DNA EXTRACTION; DNA SEQUENCE; GENE AMPLIFICATION; GENOMICS; NONHUMAN; POLYMERASE CHAIN REACTION; TISSUE FIXATION; VETERINARY MEDICINE;

ANIMALS; CAT DISEASES; CATS; DNA; DNA, NEOPLASM; FEMALE; FORMALDEHYDE; GENOME; MAMMARY NEOPLASMS, ANIMAL; MOLECULAR WEIGHT; NUCLEIC ACID AMPLIFICATION TECHNIQUES; PARAFFIN EMBEDDING;

EID: 64449083018     PISSN: 00345288     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.rvsc.2008.08.007     Document Type: Article

References (39)

1. Aviel-Ronen S., Zhu C.Q., Coe B.P., Liu N., Watson S.K., Lam W.L., and Tsao M.S. Large fragment Bst DNA polymerase for whole genome amplification of DNA from formalin-fixed paraffin-embedded tissues. BMC Genomics 7 (2006) 312
2. Benavides J., Garcia-Pariente C., Gelmetti D., Fuertes M., Ferreras M.C., García-Marín J.F., and Pérez V. Effects of fixative type and fixation time on the detection of Maedi Visna virus by PCR and immunohistochemistry in paraffin-embedded ovine lung samples. Journal of Virological Methods 137 (2006) 317-324
3. De Maria R., Olivero M., Iussich S., Nakaichi M., Murata T., Biolatti B., and Di Renzo M.F. Spontaneous feline mammary carcinoma is a model of HER2 overexpressing poor prognosis human breast cancer. Cancer Research 65 (2005) 907-912
4. Dubeau L., Chandler L.A., Gralow J.R., Nichols P.W., and Jones P.A. Southern blot analysis of DNA extracted from formalin fixed pathology specimens. Cancer Research 46 (1986) 2964-2969
5. Fang S.G., Wan Q.H., and Fujihara N. Formalin removal from archival tissues by Critical Point Drying. Biotechniques 33 (2002) 604-611
6. Gilbert M.T.P., Sanchez J.J., Haselkorn T., Jewell L.D., Lucas S.B., van Marck E., Børsting C., Morling N., and Worobey M. Multiplex PCR with minisequencing as an effective higher-throughput SNP typing method for formalin fixed tissue. Electrophoresis 28 (2007) 2361-2367
7. Gilbert M.T.P., Haselkorn T., Bunce M., Sanchez J.J., Lucas S.B., Jewell L.D., van Marck E., and Worobey M. The isolation of nucleic acids from fixed, paraffin-embedded tissues - which methods are useful when?. PLoS ONE 2 6 (2007) e537 10.1371/journal.pone.0000537
8. Gillio-Tos A., De Marco L., Fiano V., Garcia-Bragado F., Dikshit R., Boffetta P., and Merletti F. Efficient DNA extraction from 25-year-old paraffin-embedded tissues: study of 365 samples. Pathology 39 (2007) 345-348
9. Gjerdrum L.M., Sorensen B.S., Kjeldsen E., Sorensen F.B., Nexo E., and Hamilton-Dutoit S. Real-time quantitative PCR of microdissected paraffin-embedded breast carcinoma. An alternative method for HER-2/neu analysis. Journal of Molecular Diagnostics 6 (2004) 42-51
10. Greer C.E., Peterson S.K., Kiviat N.B., and Manos M.M. PCR amplification from paraffin-embedded tissues. Effects of fixative and fixation time. American Journal of Clinical Pathology 95 (1991) 117-124
11. Hansen K., and Khanna C. Spontaneous and genetically engineered animal models: use in preclinical cancer drug development. European Journal of Cancer 40 (2004) 858-880
12. Jackson D.P., Lewis F.A., Taylor G.R., Boylston A.W., and Quirke P. Tissue extraction of DNA and RNA and analysis by the polymerase chain reaction. Journal of Clinical Pathology 43 (1990) 499-504
13. Jacobs S., Thompson E.R., Nannya Y., Yamamoto G., Pillai R., Ogawa S., Bailey D.K., and Campbell I.G. Genome-wide, high-resolution detection of copy number, loss of heterozygosity, and genotypes from formalin-fixed, paraffin-embedded tumor tissue using microarrays. Cancer Research 67 (2007) 2544-2551
14. Kidney B.A., Haines D.M., Ellis J.A., Burnham M.L., and Jackson M.L. Evaluation of formalin-fixed paraffin-embedded tissues from feline vaccine site-associated sarcomas for feline foamy virus DNA. American Journal of Veterinary Research 63 (2002) 60-63
15. Leers M.P.G., Schutte B., Theunissen P.H.M.H., Ramaekers F.C.S., and Nap M. Heat pretreatment increases resolution in DNA flow cytometry of paraffin-embedded tumor tissue. Cytometry 35 (1999) 260-266
16. MacEwen E.G. Spontaneous tumors in dogs and cats: models for the study of cancer biology and treatment. Cancer and Metastasis Reviews 9 (1990) 125-136
17. Mayr B., Reifinger M., Alton K., and Schaffner G. Novel p53 tumour suppressor mutations in cases of spindle cell sarcoma, pleomorphic sarcoma and fibrosarcoma in cats. Journal Veterinary Research Communications 22 (1998) 249-255
18. Meehan M., Melvin A., Gallagher E., Smith J., Mc Goldrick A., Moss C., Goossens S., Harrison M., Kay E., Fitzpatrick J., Dervan P., and Mc Cann A. Alpha-T-Catenin (CTNNA3) Displays tumour specific monoallelic expression in urothelial carcinoma of the bladder. Genes. Chromosomes and Cancer 46 (2007) 587-593
19. Miething F., Hering S., Hanschke B., and Dressler J. Effect of fixation to the degradation of nuclear and mitochondrial DNA in different tissues. Journal of Histochemistry and Cytochemistry 54 (2006) 371-374
20. Moller K., Rinke J., Ross A., Buddle G., and Brimacombe R. The use of formaldehyde in RNA-protein cross-linking studies with ribosomal subunits from Escherichia coli. European Journal of Biochemistry 76 (1977) 175-187
21. Morris J.S., Nixon C., Bruck A., Nasir L., Morgan I.M., and Philbey A.W. Immunohistochemical expression of TopBP1 in feline mammary neoplasia in relation to histological grade, Ki67, ERa and p53. The Veterinary Journal 175 (2008) 218-226
22. Murakami Y., Tateyama S., Rungsipipat A., Uchida K., and Yamaguchi R. Immunohistochemical analysis of cyclin A, cyclin D1 and p53 in mammary tumors, squamous cell carcinomas and basal cell tumors of dogs and cats. Journal of Veterinary Medical Science 62 (2000) 743-750
23. Nasir L., Krasner H., Argyle D.J., and Williams A. Immunocytochemical analysis of the tumour suppressor protein (p53) in feline neoplasia. Cancer Letters 155 (2000) 1-7
24. Oosting J., Lips E.H., van Eijk R., Eilers P.H.C., Szuhai K., Wijmenga C., Morreau H., and van Wezel T. High-resolution copy number analysis of paraffin-embedded archival tissue using SNP Bead Arrays. Genome Research 17 (2007) 368-376
25. Poljak, M., Seme, K., Gale, N., 2000 Rapid Extraction of DNA From Archival Clinical Specimens: Our Experiences. Pflügers Archiv 439, R42-R44. Review.
26. Ribeiro C.N.M., Peres L.C., and Pina-Neto J.M. DNA extraction and quantification from touch and scrape preparations obtained from autopsy liver cells. Brazilian Journal of Medical and Biological Research 37 (2004) 635-642
27. Rogers B.B., Alpert L.C., Hine E.A.S., and Buffone G.J. Analysis of DNA in fresh and fixed tissue by the polymerase chain reaction. American Journal of Pathology 136 (1990) 541-548
28. Romero R., Juston A.C., Ballantyne J., and Henry B.E. The applicability of formalin-fixed and formalin-fixed paraffin embedded tissues in forensic DNA analysis. Journal of Forensic Sciences 42 (1997) 708-714
29. Seixas F., Pires M.A., and Lopes C.A. Complex carcinomas of the mammary gland in cats: pathological and immunohistochemical features. The Veterinary Journal 176 (2008) 210-215
30. Shi S.R., Datar R., Liu C., Wu L., Zhang Z., Cote R.J., and Taylor C.R. DNA extraction from archival formalin-fixed, paraffin-embedded tissues: heat-induced retrieval in alkaline solution. Histochemistry and Cell Biology 122 (2004) 211-218
31. Stanta G., and Schneider C. RNA extracted from paraffin-embedded human tissues is amenable to analysis by PCR amplification. Biotechniques 11 (1991) 304-308
32. Talaulikar D., Gray J.X., Shadbolt B., and McNiven M. A comparative study of the quality of DNA obtained from fresh frozen and formalin-fixed decalcified paraffin-embedded bone marrow trephine biopsies using two different methods. Journal of Clinical Pathology 61 (2008) 119-123
33. Vail D.M., and MacEwen E.G. Spontaneously occurring tumors of companion animals as models for human cancer. Cancer Investigation 18 (2000) 781-792
34. Vékony H., Ylstra B., Wilting S.M., Meijer G.A., van de Wiel M.A., Leemans C.R., van der Waal I., and Bloemena E. DNA Copy number gains at loci of growth factors and their receptors in salivary gland adenoid cystic carcinoma. Human Cancer Biology 13 (2007) 3133-3139
35. Wang L.T., Smith A., Iacopetta B., JWood D., Papadimitriou J.M., and Zheng M.H. Nested PCR-SSCP assay for the detection of p53 mutations in paraffin wax embedded bone tumours: improvement of sensitivity and fidelity. Journal of Clinical Pathology: Molecular Pathology 49 (1996) M176-M178
36. Winston J., Craft D.M., Scase T.J., and Bergman P.J. Immunohistochemical detection of HER-2/neu expression in spontaneous feline mammary tumours. Veterinary and Comparative Oncology 3 (2005) 8-15
37. Wu L., Patten N., Yamashiro C.T., and Chui B. Extraction and amplification of DNA from formalin-fixed, paraffin-embedded tissues. Applied Immunohistochemistry and Molecular Morphology 10 (2002) 269-274
38. Zappulli V., De Zan G., Cardazzo B., Bargelloni L., and Castagnaro M. Feline mammary tumours in comparative oncology. Journal of Dairy Research 72 (2005) 98-106
39. Zsikla V., Baumann M., and Cathomas G. Effect of buffered formalin on amplification of DNA from paraffin wax embedded small biopsies using real-time PCR. Journal of Clinical Pathology 57 (2004) 654-656