Epiallele Quantification Using Molecular Inversion Probes

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SELECTBIO

DNA Methylation has been implicated in the onset and progression of cancer. The position and density of cytosine methylation within a genome is emerging as a potential biomarker for cancer diagnosis. However, it is currently very difficult to comprehensively detect and quantify different methylated epialleles of a gene or promoter. In an attempt to address this problem a versatile and reproducible assay to quantify several different methylation epialleles in bisulphite treated genomic DNA was developed. The assay combines the specificity and sensitivity of molecular inversion probes with the speed of flow cytometry to enable the elucidation and quantification of multiple different methylated epialleles using a suspension of multiplexable microbead DNA biosensors. The assay can be used to ‘fingerprint’ the methylation status of CpG dinucleotides at high resolution using only minute amounts (picograms) of bisulphite treated DNA. It can also be used to measure small amounts of CpG methylation in a 600 fold excess of unmethylated DNA. The assay can be readily customized to quantify multiple suspected methylation sites which may provide an insight into the methylation fingerprint of CpG sites and cancer.