Method and system for detecting tissue-specific differentially methylated region (tDMR)

Abstract

The invention discloses a method and a system for detecting a tissue-specific differentially methylated region (tDMR). The method comprises the following steps: obtaining single-point methylation information on a complete genome by genome-wide sequencing; determining a seed tDMR on the complete genome under a pre-selection condition according to the single-point methylation information on the complete genome; extending the seed tDMR along two sides, and obtaining candidate tDMRs based on an extension terminal condition; and filtering the candidate tDMRs based on a filtering condition to obtain the tDMR result. By means of the method and the system provided by the invention, the methylation state of each site on the complete genome can be defined so as to determine the tDMR within the range of the complete genome, thus greatly improving the detection efficiency and lowering the cost. Subsequent validation shows that the found tDMR has high accuracy rate up to 85%; and validation in a plurality of species (not only limited to mammals) shows that the method has higher accuracy and higher sensitivity compared with other methods such as vardhman Rakyan and the like.

Description

technical field [0001] The present invention relates to the fields of genomics and bioinformatics, and in particular to a tissue-specific differentially methylated region (tissue-specific differentially methylated region, tDMR) detection method and system. Background technique [0002] In mammals, DNA methylation is required for genome function. Many existing genome-wide studies have shown that mammalian DNA methylation profiles (translated into maps) are tissue-specific. tDMR (Reference [1]) is an important method to realize the differential function between tissues, and finding tDMR between different tissues is of great significance to the study of genome function. [0003] Conventional methods usually examine methylation on individual genes or partial regions of the genome. The existing experimental method for detecting tDMR based on chip technology is complex in operation, low in success rate and high in cost. At present, gene chip technology can only study the regula...

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Problems solved by technology

The existing experimental method for detecting tDMR based on chip technology is complicated to operate, with low success rate and high cost

At present, gene chip technology can only study the regulatory regions of known individual genes, but cannot analyze the methylation of a large number of genes, especially unknown genes, and the chip production and detection processes such as target gene and probe preparation are complicated, and the experiment is successful low rate, high cost

The research method of Vardhman Rakyan et al. [1] shows that if the region of interest is found with a chip, if the average methylation rate in one tissue is above 60%, while the other tissue is below 40%, it is defined as tDMR, the threshold The selection is relatively arbitrary, the positive predictive value (positive predictive value) and sensitivity (sensitivity) of tDMR are 78% and 61%, respectively, and the error is large

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