Methods and Apparatuses for Estimating Parameters in a Predictive Model for Use in Sequencing-by-Synthesis

Abstract

A method of estimating a parameter related to sequencing of a sample nucleic acid template includes: receiving signal data relating to nucleotide incorporation events resulting from a series of flows of nucleotides onto an array of wells including (i) a first well containing the sample nucleic acid template and (ii) a plurality of other sample-containing wells; determining sequence information for the sample nucleic acid template using signal data from the first well; and constructing a phase-state model for a set of nucleotide flows that contributed at least in part to the sequence information, wherein the model includes a signal correction parameter that is determined using signal data from the plurality of other sample-containing wells.

What is claimed is: 
     
         1 . A system for estimating a parameter related to sequencing of a sample nucleic acid template, comprising:
 a machine-readable memory; and   a processor configured to execute machine-readable instructions, which are configured to, when executed by the processor, cause the system to perform steps, comprising:   (a) measuring signal data relating to nucleotide incorporation events resulting from a series of flows of nucleotides onto a sensor array comprising a plurality of regions of wells, at least one of the regions of wells comprising: (i) a first set of wells including a first well containing the sample nucleic acid template and (ii) a second set of wells including a plurality of other sample-containing wells,   (b) determining sequence information for the sample nucleic acid template using signal data from the first well containing the sample nucleic acid template;   (c) constructing a phase-state model for a set of nucleotide flows that contributed at least in part to the sequence information, wherein the model includes a signal correction parameter that is determined using signal data from the plurality of other sample-containing wells, and wherein the model is stored in a machine-readable memory;   (d) calculating, using the phase-state model, predicted signals for the plurality of other sample-containing wells resulting from the set of nucleotide flows;   (e) comparing the predicted signals to the signal data from the plurality of other sample-containing wells;   (f) fitting the signal correction parameter of the phase-state model based on the comparison of the predicted signals to the signal data from the plurality of other sample-containing wells; and   (g) storing the fitted signal correction parameter in the memory.   
     
     
         2 . The system of  claim 1 , wherein the signal correction parameter is obtained using signal data obtained from at least a portion of the plurality of other sample-containing wells and without using signal data obtained from the first well. 
     
     
         3 . The system of  claim 1 , wherein the signal correction parameter is obtained using signal data obtained from at least a portion of the plurality of other sample-containing wells and signal data obtained from the first well. 
     
     
         4 . The system of  claim 1 , further comprising:
 performing steps (b) through (g) for each of the obtained signal data from each or some of the plurality of other sample-containing wells to obtain multiple fitted signal correction parameters, wherein each of the multiple fitted signal correction parameters is determined for a given well without using signal data from that given well.   
     
     
         5 . The system of  claim 4 , wherein the comparing step comprises calculating a fitting metric that measures the fit between the predicted signals and the signal data. 
     
     
         6 . The system of  claim 1 , wherein the phase-state model includes two or more signal correction parameters, including a carry forward rate and an incomplete extension rate. 
     
     
         7 . The system of  claim 1 , wherein the comparing step comprises calculating a fitting metric that measures a fit between the predicted signals and the signal data. 
     
     
         8 . The system of  claim 7 , wherein the fitting step comprises determining a value of the signal correction parameter that optimizes the fitting metric. 
     
     
         9 . The system of  claim 7 , wherein the fitting step comprises determining a value of the signal correction parameter using Nelder-Mead optimization. 
     
     
         10 . The system of  claim 8 , wherein the fitting metric is calculated using only nucleotide flows that result in nucleotide non-incorporation or single nucleotide incorporations. 
     
     
         11 . The system of  claim 1 , further comprising performing a base calling analysis of the signal data using the fitted signal correction parameter. 
     
     
         12 . The system of  claim 1 , wherein the set of nucleotide flows is a first set of nucleotide flows and the sequence information is a first sequence information, the steps further comprising:
 applying the phase-state model using the fitted signal correction parameter,   calculating, using the phase-state model and the fitted signal correction parameter obtained using signal data from the plurality of other sample-containing wells, predicted signals for the first well resulting from a second set of nucleotide flows that includes nucleotide flows that are not in the first set of nucleotide flows,   making base calls by comparing the signal data from the first well to the predicted signals for the first well, and   obtaining a second sequence information about the sample nucleic acid template, wherein the second sequence information includes sequence information not contained in the first sequence information.   
     
     
         13 . The system of  claim 12 , further comprising repeating steps (d) through (g) using the second sequence information to obtain a further fitted signal correction parameter. 
     
     
         14 . A system for sequencing a sample nucleic acid template, comprising:
 a machine-readable memory; and   a processor configured to execute machine-readable instructions, which are configured to, when executed by the processor, cause the system to perform steps, comprising:   (a) measuring signal data relating to nucleotide incorporation events resulting from a series of flows of nucleotides onto an array of wells including (i) a first well containing the sample nucleic acid template and (ii) a plurality of other sample-containing wells, wherein the array includes a sensor array for detecting the signal data related to the chemical reactions resulting from the flow of nucleotides, wherein the signal data are received from the sensor array;   (b) determining preliminary sequence information for the sample nucleic acid template using the signal data from the first well,   (c) constructing a phase-state model for a first set of nucleotide flows that contributed at least in part to the sequence information, wherein the model includes a signal correction parameter fitted by comparing signal data from the plurality of other sample-containing wells to predicted signals for the plurality of other sample-containing wells resulting from the first set of nucleotide flows, and wherein the model is stored in a machine-readable memory,   (d) determining revised sequence information for the sample nucleic acid template by performing a base calling analysis of the signal data from the first well using the signal correction parameter fitted based on signal data from the plurality of other sample-containing wells,   wherein the first well containing the sample nucleic acid template is part of a first set of wells in a first region of the array, the plurality of other sample-containing wells are part of a second set of wells in the first region of the array, and   wherein the array further includes additional regions of the array that have additional respective first and second sets of wells that are distinguishable from one another within each of the additional regions of the array.   
     
     
         15 . The system of  claim 14 , wherein the first set of wells and the second set of wells in each of the first region of the array and the additional regions of the array are distinguishable from one another within each respective region of the array by inclusion in the defined spatial arrangement that is an alternating arrangement wherein the positions of the wells of the first set of wells alternate with the positions of wells of the second set of wells in each of the first region and the additional regions. 
     
     
         16 . The system of  claim 14 , further comprising:
 performing steps (c) and (d) for the signal data from each or some of the plurality of other sample-containing wells to obtain multiple signal correction parameters, wherein each of the multiple signal correction parameters is determined for a given well without using signal data from that given well.   
     
     
         17 . The system of  claim 14 , wherein the phase-state model includes two or more signal correction parameters, including a carry forward rate and an incomplete extension rate. 
     
     
         18 . The system of  claim 14 , the steps further comprising:
 calculating, using the phase-state model, the predicted signals for the plurality of other sample-containing wells resulting from the set of nucleotide flows,   comparing the predicted signals to the signal data from the plurality of other sample-containing wells, and   fitting the signal correction parameter of the phase-state model based on the comparison of the predicted signals to the signal data from the plurality of other sample-containing wells.   
     
     
         19 . The system of  claim 18 , wherein the comparing step comprises calculating a fitting metric that measures a fit between the predicted signals and the signal data. 
     
     
         20 . The system of  claim 19 , wherein the fitting step comprises determining a value of the signal correction parameter that optimizes the fitting metric.