Comparison of Formalin-Fixed and Snap-Frozen Samples Analyzed by Multiplex Ligation-Dependent Probe Amplification for Prognostic Testing in Uveal Melanoma

Investigative Ophthalmology and Visual Science

Volumn 53, Issue 6, 2012, Pages 2647-2652

  Lake, Sarah L ^a   Kalirai, Helen ^a   Dopierała, Justyna ^a   Damato, Bertil E ^b   Coupland, Sarah E ^b  

^a UNIVERSITY OF LIVERPOOL   (United Kingdom)

^b ROYAL LIVERPOOL UNIVERSITY HOSPITAL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

FORMALDEHYDE; PARAFFIN;

ADULT; AGED; ARTICLE; CHROMOSOME 1P; CHROMOSOME 3P; CHROMOSOME 3Q; CHROMOSOME 6P; CHROMOSOME 6Q; CHROMOSOME 8Q; CHROMOSOME ADDITION; CHROMOSOME LOSS; CLINICAL ARTICLE; COMPARATIVE STUDY; COPY NUMBER VARIATION; DISOMY; DNA EXTRACTION; FEMALE; FROZEN SECTION; GENETIC SCREENING; HUMAN; HUMAN TISSUE; MALE; MULTIPLEX LIGATION DEPENDENT PROBE AMPLIFICATION; PRIORITY JOURNAL; TISSUE FIXATION; UVEA MELANOMA;

ADULT; AGED; AGED, 80 AND OVER; CHROMOSOME ABERRATIONS; CHROMOSOMES, HUMAN, PAIR 3; CHROMOSOMES, HUMAN, PAIR 6; CYTOGENETIC ANALYSIS; DNA COPY NUMBER VARIATIONS; DNA, NEOPLASM; EYE ENUCLEATION; FEMALE; FIXATIVES; FORMALDEHYDE; FROZEN SECTIONS; HUMANS; MALE; MELANOMA; MIDDLE AGED; MOLECULAR PROBE TECHNIQUES; NUCLEIC ACID AMPLIFICATION TECHNIQUES; PARAFFIN EMBEDDING; PROGNOSIS; TISSUE FIXATION; UVEAL NEOPLASMS;

EID: 84860618749     PISSN: 01460404     EISSN: 15525783     Source Type: Journal    
DOI: 10.1167/iovs.12-9584     Document Type: Article

References (35)

1. Damato BE, Dopierala J, Klaasen A, van Dijk M, Sibbring J, Coupland S. Multiplex ligation-dependent probe amplification of uveal melanoma: correlation with metastatic ceath. Invest Ophthalmol Vis Sci. 2009;50:3048-3055.
2. Damato BE, Dopierala JA, Coupland SE. Genotypic profiling of 452 choroidal melanomas with multiplex ligation-dependent probe amplification. Clin Cancer Res. 2010;16:6083-6092.
3. Onken MD, Worley LA, Person E, Char DH, Bowcock AM, Harbour JW. Loss of heterozygosity of chromosome 3 detected with single nucleotide polymorphisms is superior to monoso-my 3 for predicting metastasis in uveal melanoma. Clin Cancer Res. 2007;13:2923-2927.
4. Prescher G, Bornfeld N, Hirche H, Horsthemke B, Jöckel KH, Becher R. Prognostic implications of monosomy 3 in uveal melanoma. Lancet. 1996;347:1222-1225.
5. Coupland SE, Vorum H, Mandal N, et al. Proteomics of uveal melanomas suggests HSP-27 as a possible surrogate marker of chromosome 3 loss. Invest Ophthalmol Vis Sci. 2010;51:12-20.
6. Russo A, Coupland SE, O'Keefe M, Damato BE. Choroidal melanoma in a 7-year-old child treated by trans-scleral local resection. Graefes Arch Clin Exp Ophthalmol. 2010;248:747-749.
7. Suesskind D, Schatz A, Schnichels S, et al. GDF-15: a novel serum marker for metastases in uveal melanoma patients. [published online ahead of print September 1, 2011]. Graefes Arch Clin Exp Ophthalmol.
8. Bonaldi L, Midena E, Filippi B, et al. FISH analysis of chromosomes 3 and 6 on fine needle aspiration biopsy samples identifies distinct subgroups of uveal melanomas. J Cancer Res Clin Oncol. 2008;134:1123-1127.
9. Häusler T, Stang A, Anastassiou G, et al. Loss of heterozygosity of 1p in uveal melanomas with monosomy 3. Int J Cancer. 2005;116:909-913.
10. Kilic E, Naus NC, van Gils W, et al. Concurrent loss of chromosome arm 1p and chromosome 3 predicts a decreased disease-free survival in uveal melanoma patients. Invest Ophthalmol Vis Sci. 2005;46:2253-2257.
11. Kilic E, van Gils W, Lodder E, et al. Clinical and cytogenetic analyses in uveal melanoma. Invest Ophthalmol Vis Sci. 2006; 47:3703-3707.
12. Lake SL, Coupland SE, Taktak AF, Damato BE. Whole-genome microarray detects deletions and loss of heterozygosity of chromosome 3 occurring exclusively in metastasizing uveal melanoma. Invest Ophthalmol Vis Sci. 2010;51:4884-4891.
13. Brutlag D, Schlehuber C, Bonner J. Properties of formaldehyde-treated nucleohistone. Biochemistry. 1969;8:3214-3218.
14. Feldman MY. Reaction of formaldehyde with nucleotides and ribonucleic acid. Biochim Biophys Acta. 1967;149:20-34.
15. Feldman MY. Reactions of nucleic acids and nucleoproteins with formaldehyde. Prog Nucleic Acid Res Mol Biol. 1973;13: 1-49.
16. Ilyin YV, Georgiev GP. Heterogeneity of deoxynucleoprotein particles as evidencec by ultracentrifugation of cesium chloride density gradient. J Mol Biol. 1969;41:299-303.
17. Miething F, Hering S, Hanschke B, Dressler J. Effect of fixation to the degradation of nuclear and mitochondrial DNA in different tissues. J Histochem Cytochem. 2006;54:371-374.
18. Varshavsky AY, Ilyin YV, Kadyckov VI, Senchenkov EP. Collapse of extended deoxyribonucleoprotein molecules upon increase of the ionic strength of solution. Biochim Biophys Acta. 1971; 246:583-588.
19. Benavides J, Garcia-Pariente C, Gelmetti D, et al. Effects of fixative type and fixation time on the detection of Maedi Visna virus by PCR and immunohistochemistry in paraffin-embedded ovine lung samples. J Virol Methods. 2006;137:317-324.
20. Greer CE, Peterson SL, Kiviat NB, Manos MM. PCR amplification from paraffin-embedded tissues. Effects of fixative and fixation time. Am J Clin Pathol. 1991;95:117-124.
21. Okayama N, Nishioka M, Hazama S, et al. The importance of evaluation of DNA amplificability in KRAS mutation testing with dideoxy sequencing using formalin-fixed and paraffin-embedded colorectal cancer tissues. Jpn J Clin Oncol. 2011; 41:165-171.
22. Romero RL, Juston AC, Ballantyne J, Henry BE. The applicability of formalin-fixed and formalin fixed paraffin embedded tissues in forensic DNA analysis. J Forensic Sci. 1997;42:708-714.
23. Linton K, Hey Y, Dibben S, et al. Methods comparison for high-resolution transcriptional analysis of archival material on Affymetrix Plus 2.0 and Exon 1.0 microarrays. Biotechniques. 2009;47:587-596.
24. Linton KM, Hey Y, Saunders E, et al. Acquisition of biologically relevant gene expression data by Affymetrix microarray analysis of archival formalin-fixed paraffin-embedded tumours. Br J Cancer. 2008;98:1403-1414.
25. Quach N, Goodman MF, Shibata D. In vitro mutation artifacts after formalin fixation and error prone translesion synthesis during PCR. BMC Clin Pathol. 2004;4:1.
26. Takata M. Detection of copy number changes at multiple loci in DNA prepared from formalin-fixed, paraffin-embedded tissue by multiplex ligation-dependent probe amplification. Methods Mol Biol. 2008;439:101-108.
27. van Dijk MC, Rombout PD, Boots-Sprenger SH, et al. Multiplex ligation-dependent probe amplification for the detection of chromosomal gains and losses in formalin-fixed tissue. Diagn Mol Pathol. 2005;14:9-16.
28. Jeuken JW, Cornelissen SJ, Vriezen M, et al. MS-MLPA: an attractive alternative laboratory assay for robust, reliable, and semiquantitative detection of MGMT promoter hypermethyla-tion in gliomas. Lab Invest. 2007;87:1055-1065.
29. Moerland E, van Hezik RL, van der Aa TC, van Beek MW, van den Brule AJ. Detection of HER2 amplification in breast carcinomas: comparison of Multiplex Ligation-dependent Probe Amplification (MLPA) and Fluorescence In Situ Hybridization (FISH) combined with automated spot counting. Cell Oncol. 2006;28:151-159.
30. Buffart TE, van Grieken NC, Tijssen M, et al. High resolution analysis of DNA copy-number aberrations of chromosomes 8, 13, and 20 in gastric cancers. Virchows Arch. 2009;455:213-223.
31. Dopierala J, Damato BE, Lake SL, Taktak AF, Coupland SE. Genetic heterogeneity in uveal melanoma assessed by multiplex ligation-dependent probe amplification. Invest Ophthalmol Vis Sci. 2010;51:4898-4905.
32. Font RL Croxatto JO, Rao N. Tumors of the eye and ocular adnexa. In: AFIP Atlas of Tumor Pathology. Washington, DC: ARP Press, 2007: 4th series, fasc. 5.
33. van Dongen JJ, Langerak AW, Brüggemann M, et al. Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: report of the BIOMED-2 Concerted Action BMH4-CT98-3936. Leukemia. 2003;17: 2257-2317.
34. Damato B, Eleuteri A, Taktak AF, Coupland SE. Estimating prognosis for survival after treatment of choroidal melanoma. Prog Retin Eye Res. 2011;30:285-295.
35. Kivela T, Harbour WJ, Coupland SE, et al. Malignant melanoma of the uvea. In: Edge SB, Byrd DB, Compton CC, et al., eds. AJCC Cancer Staging Manual, 7th ed. New York: Springer Publishing Co.; 2010:chap 51:547-559.