2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2016
Abstrakt

Jared T Simpson, Rachael Workman, Philip C Zuzarte, Matei David, Lewis Jonathan Dursi, Winston Timp. Detecting DNA Methylation using the Oxford Nanopore Technologies MinION sequencer. Technical Report 047142, bioRxiv, 2016.

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Download from publisher: http://dx.doi.org/10.1101/047142

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Bibliography entry: BibTeX

Abstract:

Nanopore sequencing instruments measure the change in electric current 
caused by DNA transiting through the pore. In experimental and prototype 
nanopore sequencing devices it has been shown that the electrolytic current 
signals are sensitive to base modifications, such as 5-methylcytosine. Here 
we quantify the strength of this effect for the Oxford Nanopore Technologies 
MinION sequencer. Using synthetically methylated DNA we are able to train a 
hidden Markov model to distinguish 5-methylcytosine from unmethylated 
cytosine in DNA. We demonstrate by sequencing natural human DNA, without any 
special library preparation, that global patterns of methylation can be 
detected from low-coverage sequencing and that the methylation status of CpG 
islands can be reliably predicted from single MinION reads. Our trained 
model and prediction software is open source and freely available to the 
community under the MIT license.