Investigation of MGMT and DAPK1 methylation patterns in diffuse large B-cell lymphoma using allelic MSP-pyrosequencing

The tumor suppressor genes MGMT and DAPK1 become methylated in several cancers including diffuse large B-cell lymphoma (DLBCL). However, allelic methylation patterns have not been investigated in DLBCL. We developed a fast and cost-efficient method for the analysis of allelic methylation based on pyrosequencing of methylation specific PCR (MSP) products including a SNP. Allelic methylation patterns were reliably analyzed in standards of known allelic methylation status even when diluted in unmethylated DNA to below 1% methylation. When studying 148 DLBCL patients MGMT and DAPK1 methylation was observed in 19% and 89%, respectively, and among methylated and heterozygous patients 29% and 55%, respectively, were biallelically methylated. An association between the T-allele of the rs16906252 SNP and MGMT methylation was observed (p-value = 0.04), and DAPK1 methylation of the A-allele was associated with shorter overall survival (p-value = 0.006). In future cancer research allelic MSP-pyrosequencing may be used to study a wide range of other loci

Competitive amplification of differentially melting amplicons (CADMA) improves <it>KRAS</it> hotspot mutation testing in colorectal cancer

<p>Abstract</p> <p>Background</p> <p>Cancer is an extremely heterogeneous group of diseases traditionally categorized according to tissue of origin. However, even among patients with the same cancer subtype the cellular alterations at the molecular level are often very different. Several new therapies targeting specific molecular changes found in individual patients have initiated the era of personalized therapy and significantly improved patient care. In metastatic colorectal cancer (mCRC) a selected group of patients with wild-type <it>KRAS</it> respond to antibodies against the epidermal growth factor receptor (EGFR). Testing for <it>KRAS</it> mutations is now required prior to anti-EGFR treatment, however, less sensitive methods based on conventional PCR regularly fail to detect <it>KRAS</it> mutations in clinical samples.</p> <p>Methods</p> <p>We have developed sensitive and specific assays for detection of the seven most common <it>KRAS</it> mutations based on a novel methodology named Competitive Amplification of Differentially Melting Amplicons (CADMA). The clinical applicability of these assays was assessed by analyzing 100 colorectal cancer samples, for which <it>KRAS</it> mutation status has been evaluated by the commercially available TheraScreen® KRAS mutation kit.</p> <p>Results</p> <p>The CADMA assays were sensitive to at least 0.5% mutant alleles in a wild-type background when using 50 nanograms of DNA in the reactions. Consensus between CADMA and the TheraScreen kit was observed in 96% of the colorectal cancer samples. In cases where disagreement was observed the CADMA result could be confirmed by a previously published assay based on TaqMan probes and by <it>fast</it> COLD-PCR followed by Sanger sequencing.</p> <p>Conclusions</p> <p>The high analytical sensitivity and specificity of CADMA may increase diagnostic sensitivity and specificity of <it>KRAS</it> mutation testing in mCRC patients.</p