title: Specificity of methylation assays in cancer research: a guideline for designing primers and probes.
abstract: DNA methylation is an epigenetic regulation mechanism of genomic function, and aberrant methylation pattern has been found to be a common event in many diseases and human cancers. A large number of cancer studies have been focused on identification of methylation changes as biomarkers (i.e., breast cancer). However, still clinical use of them is very limited because of lack of specificity and sensitivity for diagnostic test. This highlights the critical need for specific primer and probe design to avoid false-positive detection of methylation profiling. The guideline and online web tools that are introduced in this paper might help to perform a successful experiment and to develop specific diagnosis biomarkers by designing right primer pair and probe prior to experimental step.
authors.affiliation: Laboratory for Gynecological Oncology, Women's Hospital and Department of Biomedicine, University of Basel, Basel 4031, Switzerland.
authors.forename: Zeinab
authors.initials: Z
authors.lastname: Barekati
authors.forename: Ramin
authors.initials: R
authors.lastname: Radpour
authors.forename: Corina
authors.initials: C
authors.lastname: Kohler
authors.forename: Xiao Yan
authors.initials: XY
authors.lastname: Zhong
references.citation: Clin Chem. 2007 Dec;53(12):2119-27
references.pmid: 17962364
references.citation: Development. 1987 Mar;99(3):371-82
references.pmid: 3653008
references.citation: Biotechniques. 2003 Jul;35(1):152-6
references.pmid: 12866415
references.citation: J Urol. 2002 Apr;167(4):1854-8
references.pmid: 11912447
references.citation: Nucleic Acids Res. 2000 Apr 15;28(8):E32
references.pmid: 10734209
references.citation: Mol Cancer Res. 2008 Nov;6(11):1702-9
references.pmid: 19010818
references.citation: Clin Chem. 2009 Aug;55(8):1471-83
references.pmid: 19520761
references.citation: Cancer Res. 1999 Jan 1;59(1):67-70
references.pmid: 9892187
references.citation: Cancer Res. 2004 Jul 1;64(13):4442-52
references.pmid: 15231653
references.citation: Methods. 2001 Dec;25(4):456-62
references.pmid: 11846615
references.citation: Nucleic Acids Res. 2002 Mar 15;30(6):e25
references.pmid: 11884644
references.citation: Nucleic Acids Res. 2008 Apr;36(7):e42
references.pmid: 18344521
references.citation: Nat Rev Genet. 2002 Jun;3(6):415-28
references.pmid: 12042769
references.citation: Methods Mol Biol. 2009;507:207-27
references.pmid: 18987817
references.citation: EXS. 1993;64:358-84
references.pmid: 7678203
references.citation: Clin Chem. 2001;47(7):1183-9
references.pmid: 11427447
references.citation: Mod Pathol. 2010 May;23(5):763-72
references.pmid: 20081803
references.citation: Cancer Res. 1999 Aug 15;59(16):3899-903
references.pmid: 10463578
references.citation: Nucleic Acids Res. 2004 Jan 13;32(1):e10
references.pmid: 14722226
references.citation: J Biol Chem. 1997 Aug 29;272(35):22322-9
references.pmid: 9268383
references.citation: Nucleic Acids Res. 1997 Jun 15;25(12):2529-31
references.pmid: 9171109
references.citation: Biochemistry. 1970 Jul 7;9(14):2858-65
references.pmid: 5459538
references.citation: Proc Natl Acad Sci U S A. 2002 Mar 19;99(6):3740-5
references.pmid: 11891299
references.citation: J Biochem Biophys Methods. 2006 Mar 31;66(1-3):33-43
references.pmid: 16442635
references.citation: Cancer Res. 2000 Feb 1;60(3):702-6
references.pmid: 10676656
references.citation: Mol Carcinog. 2001 Sep;32(1):19-27
references.pmid: 11568972
references.citation: Proc Natl Acad Sci U S A. 1996 Sep 3;93(18):9821-6
references.pmid: 8790415
references.citation: Hum Mol Genet. 2010 Aug 1;19(15):2936-46
references.pmid: 20466735
references.citation: Proc Natl Acad Sci U S A. 1992 Mar 1;89(5):1827-31
references.pmid: 1542678
references.citation: N Engl J Med. 2008 Mar 13;358(11):1148-59
references.pmid: 18337604
references.citation: Development. 2007 Nov;134(22):3959-65
references.pmid: 17928417
references.citation: Expert Rev Mol Diagn. 2007 Sep;7(5):519-31
references.pmid: 17892361
references.citation: Nucleic Acids Res. 1997 Jun 15;25(12):2532-4
references.pmid: 9171110
references.citation: Nat Rev Cancer. 2003 Apr;3(4):253-66
references.pmid: 12671664
references.citation: Biotechniques. 2003 Jul;35(1):146-50
references.pmid: 12866414
references.citation: Genet Test Mol Biomarkers. 2009 Oct;13(5):565-71
references.pmid: 19814613
references.citation: Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15785-90
references.pmid: 16243968
references.citation: Biotechnol Lett. 2004 Aug;26(16):1289-93
references.pmid: 15483389
references.citation: Epigenetics Chromatin. 2008 Nov 03;1(1):7
references.pmid: 19014416
references.citation: Curr Opin Clin Nutr Metab Care. 2007 Sep;10(5):576-81
references.pmid: 17693740
references.citation: Oncogene. 2002 Aug 12;21(35):5462-82
references.pmid: 12154408
references.citation: Gastroenterology. 2009 Feb;136(2):640-51.e1
references.pmid: 19084528
references.citation: Lab Invest. 2001 Apr;81(4):635-8
references.pmid: 11304583
references.citation: Eur J Haematol. 2006 Jan;76(1):23-32
references.pmid: 16343268
references.citation: Oncogene. 2009 Aug 20;28(33):2969-78
references.pmid: 19503099
references.citation: Anal Biochem. 2003 Jun 15;317(2):259-65
references.pmid: 12758266
references.citation: Biosens Bioelectron. 2008 Apr 15;23(9):1333-9
references.pmid: 18215791
references.citation: Nucleic Acids Res. 1994 Aug 11;22(15):2990-7
references.pmid: 8065911
references.citation: Genes Dev. 2002 Jan 1;16(1):6-21
references.pmid: 11782440
references.citation: J Pathol. 2002 Jan;196(1):1-7
references.pmid: 11748635
references.citation: Biochem Biophys Res Commun. 1970 Aug 24;40(4):839-43
references.pmid: 5495733