Improved amplification efficiency on stool samples by addition of spermidine and its use for non-invasive detection of colorectal cancer
KAUST DepartmentBioscience Core Lab
Computational Bioscience Research Center (CBRC)
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Online Publication Date2015-05-29
Print Publication Date2015-12
Permanent link to this recordhttp://hdl.handle.net/10754/556146
MetadataShow full item record
AbstractBackground Using quantitative methylation-specific PCR (QM-MSP) is a promising method for colorectal cancer (CRC) diagnosis from stool samples. Difficulty in eliminating PCR inhibitors of this body fluid has been extensively reported. Here, spermidine is presented as PCR facilitator for the detection of stool DNA methylation biomarkers using QM-MSP. We examined its effectiveness with NPY, PENK and WIF1, three biomarkers which we have previously shown to be of relevance to CRC. Results We determined an optimal window for the amplification of the albumin (Alb) gene (100 ng of bisulfite-treated stool DNA added of 1 mM spermidine) at which we report that spermidine acts as a PCR facilitator (AE = 1680%) for SG RT-PCR. We show that the amplification of methylated PENK, NPY and WIF1 is considerably facilitated by QM-MSP as measured by an increase of CMI (Cumulative Methylation Index, i.e. the sum of the three methylation values) by a factor of 1.5 to 23 fold in individual samples, and of 10 fold in a pool of five samples. Conclusions We contend that spermidine greatly reduces the problems of PCR inhibition in stool samples. This observed feature, after validation on a larger sampling, could be used in the development of stool-based CRC diagnosis tests.
CitationImproved amplification efficiency on stool samples by addition of spermidine and its use for non-invasive detection of colorectal cancer 2015, 15 (1) BMC Biotechnology
PubMed Central IDPMC4446959
- Aberrant methylation of NPY, PENK, and WIF1 as a promising marker for blood-based diagnosis of colorectal cancer.
- Authors: Roperch JP, Incitti R, Forbin S, Bard F, Mansour H, Mesli F, Baumgaertner I, Brunetti F, Sobhani I
- Issue date: 2013 Dec 1
- Comparative detection of aberrantly methylated DNA in preoperative and postoperative stool from patients with colorectal cancers.
- Authors: Nishioka Y, Ueki T, Hokazono K, Nagayoshi K, Tanaka M
- Issue date: 2015 Jan-Mar
- Feasibility of quantifying <i>SDC2</i> methylation in stool DNA for early detection of colorectal cancer.
- Authors: Oh TJ, Oh HI, Seo YY, Jeong D, Kim C, Kang HW, Han YD, Chung HC, Kim NK, An S
- Issue date: 2017
- A panel of genes methylated with high frequency in colorectal cancer.
- Authors: Mitchell SM, Ross JP, Drew HR, Ho T, Brown GS, Saunders NF, Duesing KR, Buckley MJ, Dunne R, Beetson I, Rand KN, McEvoy A, Thomas ML, Baker RT, Wattchow DA, Young GP, Lockett TJ, Pedersen SK, Lapointe LC, Molloy PL
- Issue date: 2014 Jan 31
- Stool DNA methylation assays in colorectal cancer screening.
- Authors: Kadiyska T, Nossikoff A
- Issue date: 2015 Sep 21