The use of multiple displacement amplified DNA as a control for mMethylation specific PCR, pyrosequencing, bisulfite sequencing and methylation-sensitive restriction enzyme PCR

BMC Molecular Biology

Volumn 8, Issue , 2007, Pages

  Hughes, Simon ^a   Jones, J Louise ^a  

^a QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BRCA1 PROTEIN; INTERSTITIAL COLLAGENASE; DNA; HYDROGEN SULFITE; RESTRICTION ENDONUCLEASE; SULFITE; UNCLASSIFIED DRUG;

ANALYTIC METHOD; ARTICLE; BISULFITE SEQUENCING; CONTROLLED STUDY; CPG ISLAND; DNA EXTRACTION; DNA METHYLATION; GENE AMPLIFICATION; GENE EXPRESSION; HUMAN; HUMAN TISSUE; METHYLATION SENSITIVE RESTRICTION ENZYME POLYMERASE CHAIN REACTION; METHYLATION SPECIFIC POLYMERASE CHAIN REACTION; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PYROSEQUENCING; ALGORITHM; CELL CULTURE; DNA SEQUENCE; EVALUATION; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; QUALITY CONTROL; STANDARD;

ALGORITHMS; BASE SEQUENCE; CELLS, CULTURED; DNA; DNA METHYLATION; DNA RESTRICTION ENZYMES; HUMANS; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; QUALITY CONTROL; REFERENCE STANDARDS; SEQUENCE ANALYSIS, DNA; SULFITES;

EID: 37849031757     PISSN: None     EISSN: 14712199     Source Type: Journal    
DOI: 10.1186/1471-2199-8-91     Document Type: Article

References (20)

1. Yang E Kang HJ Koh KH Rhee H Kim NK Kim H Frequent inactivation of SPARC by promoter hypermethylation in colon cancers Int J Cancer 2007, 121(3):567-575. 10.1002/ijc.22706 17397030
2. Pulukuri SM Patibandla S Patel J Estes N Rao JS Epigenetic inactivation of the tissue inhibitor of metalloproteinase-2 (TIMP-2) gene in human prostate tumors Oncogene 2007. 17325663
3. Esteller M Corn PG Baylin SB Herman JG A gene hypermethylation profile of human cancer Cancer Res 2001, 61:3225-3229. 11309270
4. Okino ST Pookot D Majid S Zhao H Li LC Place RF Dahiya R Chromatin changes on the GSTP1 promoter associated with its inactivation in prostate cancer Mol Carcinog 2007. 17415778
5. Sato N Fukushima N Matsubayashi H Goggins M Identification of maspin and S100P as novel hypomethylation targets in pancreatic cancer using global gene expression profiling Oncogene 2004, 23:1531-1538. 10.1038/ sj.onc.1207269 14716296
6. Shukeir N Pakneshan P Chen G Szyf M Rabbani SA Alteration of the methylation status of tumor-promoting genes decreases prostate cancer cell invasiveness and tumorigenesis in vitro and in vivo Cancer Res 2006, 66:9202-9210. 10.1158/0008-5472.CAN-06-1954 16982764
7. Herman JG Graff JR Myohanen S Nelkin BD Baylin SB Methylation-specific PCR: A novel PCR assay for methylation status of CpG islands Proc Natl Acad Sci U S A 1996, 93:9821-9826. 38513 8790415 10.1073/pnas.93.18.9821
8. Roach HI Yamada N Cheung KS Tilley S Clarke NM Oreffo RO Kokubun S Bronner F Association between the abnormal expression of matrix-degrading enzymes by human osteoarthritic chondrocytes and demethylation of specific CpG sites in the promoter regions Arthritis Rheum 2005, 52:3110-3124. 10.1002/art.21300 16200590
9. Melnikov AA Gartenhaus RB Levenson AS Motchoulskaia NA Levenson Chernokhvostov VV MSRE-PCR for analysis of gene-specific DNA methylation Nucleic Acids Res 2005, 33:e93. 1145194 15944447 10.1093/nar/gni092
10. Weisenberger DJ Campan M Long TI Kim M Woods C Fiala E Ehrlich M Laird PW Analysis of repetitive element DNA methylation by MethyLight Nucleic Acids Res 2005, 33:6823-6836. 1301596 16326863 10.1093/nar/gki987
11. Dean FB Hosono S Fang L Wu X Faruqi AF Bray-Ward P Sun Z Zong Q Du Y Du J Driscoll M Song W Kingsmore SF Egholm M Lasken RS Comprehensive human genome amplification using multiple displacement amplification Proc Natl Acad Sci U S A 2002, 99:5261-5266. 122757 11959976 10.1073/pnas.082089499
12. Dean FB Nelson JR Giesler TL Lasken RS Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification Genome Res 2001, 11:1095-1099. 311129 11381035 10.1101/gr.180501
13. Paez JG Lin M Beroukhim R Lee JC Zhao X Richter DJ Gabriel S Herman P Sasaki H Altshuler D Li C Meyerson M Sellers WR Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification Nucleic Acids Res 2004, 32:e71. 419624 15150323 10.1093/nar/gnh069
14. Nelson JR Cai YC Giesler TL Farchaus JW Sundaram ST Ortiz-Rivera M Hosta LP Hewitt PL Mamone JA Palaniappan C Fuller CW TempliPhi, phi29 DNA polymerase based rolling circle amplification of templates for DNA sequencing Biotechniques 2002, Suppl:44-47. 12083397
15. Lage JM Leamon JH Pejovic T Hamann S Lacey M Dillon D Segraves R Vossbrinck B Gonzalez A Pinkel D Albertson DG Costa J Lizardi PM Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH Genome Res 2003, 13:294-307. 420367 12566408 10.1101/gr.377203
16. Matsuo K Silke J Gramatikoff K Schaffner W The CpG-specific methylase SssI has topoisomerase activity in the presence of Mg2+ Nucleic Acids Res 1994, 22:5354-5359. 332082 7816625 10.1093/nar/22.24.5354
17. Ronaghi M Pettersson B Uhlen M Nyren P PCR-introduced loop structure as primer in DNA sequencing Biotechniques 1998 25 876 8, 880-2, 884. 9821590
18. Ronaghi M Karamohamed S Pettersson B Uhlen M Nyren P Real-time DNA sequencing using detection of pyrophosphate release Anal Biochem 1996, 242:84-89. 10.1006/abio.1996.0432 8923969
19. Ronaghi M Pyrosequencing sheds light on DNA sequencing Genome Res 2001, 11:3-11. 10.1101/gr.11.1.3 11156611
20. Birgisdottir V Stefansson OA Bodvarsdottir SK Hilmarsdottir H Jonasson JG Eyfjord JE Epigenetic silencing and deletion of the BRCA1 gene in sporadic breast cancer Breast Cancer Res 2006, 8:R38. 1779478 16846527 10.1186/bcr1522