Method and system of estimating a sequence of polymer units

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United States of America

PATENT NO 12216110
APP PUB NO 20170219557A1
SERIAL NO

15487329

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Abstract

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A sequence of polymer units in a polymer (3), eg. DNA, is estimated from at least one series of measurements related to the polymer, eg. ion current as a function of translocation through a nanopore (1), wherein the value of each measurement is dependent on a k-mer being a group of k polymer units (4). A probabilistic model, especially a hidden Markov model (HMM), is provided, comprising, for a set of possible k-mers: transition weightings representing the chances of transitions from origin k-mers to destination k-mers; and emission weightings in respect of each k-mer that represent the chances of observing given values of measurements for that k-mer. The series of measurements is analysed using an analytical technique, eg. Viterbi decoding, that refers to the model and estimates at least one estimated sequence of polymer units in the polymer based on the likelihood predicted by the model of the series of measurements being produced by sequences of polymer units. In a further embodiment, different voltages are applied across the nanopore during translocation in order to improve the resolution of polymer units.

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Patent Owner(s)

  • OXFORD NANOPORE TECHNOLOGIES PLC

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Inventor(s)

Inventor Name Address # of filed Patents Total Citations
Brown, Clive Gavin Cambridge, GB 73 1223
Clarke, James Anthony Kidlington, GB 75 1512
Harper, Gavin Sonning, GB 19 253
Heron, Andrew John Oxford, GB 95 1812
Reid, Stuart William Oxford, GB 24 414

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