US 12,216,110 B2
Method and system of estimating a sequence of polymer units
Stuart William Reid, Oxford (GB); Gavin Harper, Sonning (GB); Clive Gavin Brown, Cambridge (GB); James Anthony Clarke, Kidlington (GB); and Andrew John Heron, Oxford (GB)
Assigned to Oxford Nanopore Technologies PLC, Oxford (GB)
Filed by Oxford Nanopore Technologies PLC, Oxford (GB)
Filed on Apr. 13, 2017, as Appl. No. 15/487,329.
Application 15/487,329 is a continuation of application No. 14/346,549, abandoned, previously published as PCT/GB2012/052343, filed on Sep. 21, 2012.
Claims priority of provisional application 61/617,880, filed on Mar. 30, 2012.
Claims priority of provisional application 61/538,721, filed on Sep. 23, 2011.
Prior Publication US 2017/0219557 A1, Aug. 3, 2017
Int. Cl. G01N 33/483 (2006.01); C12Q 1/6869 (2018.01); G01N 27/447 (2006.01); G01N 33/487 (2006.01); G06F 17/18 (2006.01); G06N 7/01 (2023.01); G16B 30/00 (2019.01); G16B 30/10 (2019.01); B82Y 15/00 (2011.01)
CPC G01N 33/48721 (2013.01) [C12Q 1/6869 (2013.01); G01N 27/44791 (2013.01); G01N 33/483 (2013.01); G06F 17/18 (2013.01); G06N 7/01 (2023.01); G16B 30/00 (2019.02); G16B 30/10 (2019.02); B82Y 15/00 (2013.01)] 18 Claims
 
1. A computer-implemented method of estimating a sequence of polymer units in a polymer, the method comprising:
controlling translocation of the polymer through a nanopore using an enzyme;
detecting, using a measurement circuit coupled to electrodes arranged on each side of the nanopore, a sequence of measurements of the polymer, each measurement being indicative of an ion current flowing through the nanopore during said translocation of the polymer through the nanopore;
using at least one processor, coupled to a memory, to perform:
accessing, in the memory, a probabilistic model comprising, for a set of possible k-mers, wherein a k-mer is a group of k polymer units where k is a positive integer:
transition weightings each representing a probability of transition from an origin k-mer to a destination k-mer immediately subsequent in a sequence representing the sequence of polymer units, and wherein, when k is greater than one, transitions to destination k-mers that have a sequence in which the first k-1 polymer units are the same as the last k-1 polymer units of associated origin k-mers have greater probabilities than other transitions; and
emission weightings each representing a probability of obtaining given values of ion current measurements for a respective k-mer of the set of possible k-mers;
determining likelihoods, for each ion current measurement in the detected sequence of measurements of the polymer, that the ion current measurement was produced by respective k-mers of the set of possible k-mers, by optimizing a sequence of states of the probabilistic model based on the detected sequence of ion current measurements, the transition weightings, and the emission weightings; and
determining an estimated sequence of polymer units in the polymer based on the likelihoods determined for each ion current measurement.