Bisulfite-Based DNA Methylation Analysis from Recent and Archived Formalin-Fixed, Paraffin Embedded Colorectal Tissue Samples

Pathology and Oncology Research

Volumn 21, Issue 4, 2015, Pages 1149-1156

  Kalmár, Alexandra ^a,b   Péterfia, Bálint ^a,b   Hollósi, Péter ^a,b   Wichmann, Barnabás ^b   Bodor, András ^c   Patai, Árpád V ^a   Schöller, Andrea ^a   Krenács, Tibor ^a   Tulassay, Zsolt ^a,b   Molnár, Béla ^a,b  

^a SEMMELWEIS UNIVERSITY   (Hungary)

^b INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

^c EÖTVÖS LORÁND UNIVERSITY   (Hungary)

Author keywords

Colorectal cancer; DNA methylation; Genomic DNA isolation; Methylation sensitive high resolution melting analysis; Pyrosequencing

Indexed keywords

BISULFITE; SECRETED FRIZZLED RELATED PROTEIN 1; SECRETED FRIZZLED RELATED PROTEIN 2; DNA; FORMALDEHYDE; HYDROGEN SULFITE; PARAFFIN; SULFITE;

AMPLICON; ARTICLE; CLINICAL ARTICLE; COLORECTAL CANCER; COLORECTAL CARCINOMA; COMPARATIVE STUDY; CONTROLLED STUDY; DIAGNOSTIC KIT; DNA METHYLATION; DNA METHYLATION ASSAY; EPIGENETICS; GENE; GENETIC ANALYSIS; GENETIC PROCEDURES; HUMAN; HUMAN TISSUE; MAL GENE; PROMOTER REGION; RELIABILITY; REPRODUCIBILITY; SFRP1 GENE; SFRP2 GENE; TISSUE CULTURE TECHNIQUE; CHEMISTRY; COLORECTAL TUMOR; DNA SEQUENCE; GENETICS; PROCEDURES;

COLORECTAL NEOPLASMS; DNA; DNA METHYLATION; FORMALDEHYDE; HUMANS; PARAFFIN; PARAFFIN EMBEDDING; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; SULFITES;

EID: 84940451767     PISSN: 12194956     EISSN: 15322807     Source Type: Journal    
DOI: 10.1007/s12253-015-9945-4     Document Type: Article

References (20)

1. Krijgsman O, Israeli D, Haan JC et al (2012) CGH arrays compared for DNA isolated from formalin-fixed, paraffin-embedded material. Genes Chromosom Cancer 51(4):344–352. doi:10.1002/gcc.21920
2. Lyons-Weiler M, Hagenkord J, Sciulli C et al (2008) Optimization of the affymetrix GeneChip mapping 10K 2.0 assay for routine clinical use on formalin-fixed paraffin-embedded tissues. Diagn Mol Pathol Am J Sur Pathol Part B 17(1):3–13. doi:10.1097/PDM.0b013e31815aca30
3. Schweiger MR, Kerick M, Timmermann B et al (2009) Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutation-analysis. PLoS One 4(5):e5548. doi:10.1371/journal.pone.0005548
4. Kalmar A, Wichmann B, Galamb O et al (2013) Gene expression analysis of normal and colorectal cancer tissue samples from fresh frozen and matched formalin-fixed, paraffin-embedded (FFPE) specimens after manual and automated RNA isolation. Methods 59(1):S16–19. doi:10.1016/j.ymeth.2012.09.011
5. von Ahlfen S, Missel A, Bendrat K et al (2007) Determinants of RNA quality from FFPE samples. PLoS One 2(12):e1261. doi:10.1371/journal.pone.0001261
6. Macabeo-Ong M, Ginzinger DG, Dekker N et al (2002) Effect of duration of fixation on quantitative reverse transcription polymerase chain reaction analyses. Modern Pathol Off J US Canadian Acad Pathol Inc 15(9):979–987. doi:10.1097/01.MP.0000026054.62220.FC
7. Solassol J, Ramos J, Crapez E et al (2011) KRAS mutation detection in paired frozen and formalin-fixed paraffin-embedded (FFPE) colorectal cancer tissues. Int J Mol Sci 12(5):3191–3204. doi:10.3390/ijms12053191
8. Jemal A, v F, Center MM et al (2011) Global cancer statistics. CA Cancer J Clin 61(2):69–90. doi:10.3322/caac.20107
9. Cancer Genome Atlas N (2012) Comprehensive molecular characterization of human colon and rectal cancer. Nature 487(7407):330–337. doi:10.1038/nature11252
10. Caldwell GM, Jones C, Gensberg K et al (2004) The Wnt antagonist sFRP1 in colorectal tumorigenesis. Cancer Res 64(3):883–888
11. Oberwalder M, Zitt M, Wontner C et al (2008) SFRP2 methylation in fecal DNA–a marker for colorectal polyps. Int J Color Dis 23(1):15–19. doi:10.1007/s00384-007-0355-2
12. Wang DR, Tang D (2008) Hypermethylated SFRP2 gene in fecal DNA is a high potential biomarker for colorectal cancer noninvasive screening. World J Gastroenterol WJG 14(4):524–531
13. Takeda M, Nagasaka T, Dong-Sheng S et al (2011) Expansion of CpG methylation in the SFRP2 promoter region during colorectal tumorigenesis. Acta Med Okayama 65(3):169–177
14. Lind GE, Ahlquist T, Kolberg M et al (2008) Hypermethylated MAL gene - a silent marker of early colon tumorigenesis. J Transl Med 6:13. doi:10.1186/1479-5876-6-13
15. Wojdacz TK, Dobrovic A (2007) Methylation-sensitive high resolution melting (MS-HRM): a new approach for sensitive and high-throughput assessment of methylation. Nucleic Acids Res 35(6):e41. doi:10.1093/nar/gkm013
16. Kalmar A, Peterfia B, Wichmann B et al (2015) Comparison of automated and manual DNA isolation methods for DNA methylation analysis of biopsy, fresh frozen, and formalin-fixed paraffin-embedded colorectal cancer samples. Journal of laboratory automation. doi:10.1177/2211068214565903
17. Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J Mol Biol 147(1):195–197
18. Gotoh O (1982) An improved algorithm for matching biological sequences. J Mol Biol 162(3):705–708
19. Luo C, Tsementzi D, Kyrpides N et al (2012) Direct comparisons of illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS One 7(2):e30087. doi:10.1371/journal.pone.0030087
20. TCGA Research Network: http://cancergenome.nih.gov/