# US 2019/0169688 A1 · Methods and apparatus that increase sequencing-by-binding efficiency > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2019/0169688 A1 - Document ID: US20190169688A1 - Status: Published application - Kind: A1 - Application number: 16/154,598 - Filed: 2018-10-08 - Published: 2019-06-06 - Earliest claimed: 2017-04-25 - Assignees: Omniome, Inc. - Applicants: Omniome, Inc. - Inventors: Sean STROMBERG; John VIECELI; Kandaswamy VIJAYAN; Arnold OLIPHANT - Web page: https://patentgrep.com/patent/US20190169688A1 ## CPC - C12Q 1/6874: involving nucleic acid arrays, e.g. sequencing by hybridisation - C12Q 1/6832: Enhancement of hybridisation reaction - C12Q 1/6853: using modified primers or templates - C12Q 1/6869: Methods for sequencing - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES ## Abstract A method of determining a nucleic acid sequence that includes steps of: (a) contacting a primed template nucleic acid with a series of mixtures for forming ternary complexes, wherein each of the mixtures includes a polymerase and nucleotide cognates for at least two different base types suspected of being present at the next template position of the template nucleic acid; (b) monitoring the next template position for ternary complexes formed by the series of mixtures, wherein a signal state indicates presence or absence of ternary complex formed at the next template position by each individual mixture, thereby determining a series of signal states that encodes a base call for the next template position; and (c) decoding the series of signal states to distinguish a correct base call for the next template position from an error in the base call. ## Claims ### Claim 1 A method of determining a nucleic acid sequence, comprising: (a) contacting a primed template nucleic acid with a series of mixtures for forming stabilized ternary complexes, wherein each of the mixtures comprises a polymerase and nucleotide cognates for at least two different base types suspected of being present at the next template position of the template nucleic acid; wherein the mixtures differ by the presence or absence of at least one type of nucleotide cognate; wherein the stabilized ternary complexes are prevented from covalently incorporating nucleotides from the mixtures into the primed template nucleic acid; (b) monitoring the next template position for stabilized ternary complexes formed by the series of mixtures, wherein a signal state indicates presence or absence of a stabilized ternary complex formed at the next template position by each of the mixtures within said series of mixtures, thereby determining a series of signal states that encodes a base call for the next template position; and (c) decoding the series of signal states to distinguish a correct base call for the next template position from an erroneous base call for the next template position. ### Claim 2 (depends on 1) The method of claim 1, wherein the series of signal states comprises an error correcting code. ### Claim 3 (canceled) ### Claim 4 (depends on 2) The method of claim 2, wherein the error correcting code comprises a repetition code. ### Claim 5 (canceled) ### Claim 6 (canceled) ### Claim 7 (depends on 2) The method of claim 2, wherein the error correcting code comprises a Hamming code. ### Claim 8 (canceled) ### Claim 9 (canceled) ### Claim 10 (canceled) ### Claim 11 (canceled) ### Claim 12 (depends on 1) The method of claim 1, wherein the decoding of the series of signal states identifies the base call as being an erroneous base call. ### Claim 13 (depends on 12) The method of claim 12, further comprising correcting the erroneous base call to make a valid base call for the next template position. ### Claim 14 (canceled) ### Claim 15 (canceled) ### Claim 16 (canceled) ### Claim 17 (depends on 1) The method of claim 1, wherein the series of signal states comprises a parity code. ### Claim 18 (depends on 1) The method of claim 1, wherein each of the signal states is represented by a binary digit. ### Claim 19 (depends on 18) The method of claim 18, wherein the binary digit comprises (i) symbols for presence and absence of a signal; (ii) symbols for signals emitted at two different wavelengths; (iii) symbols for signals having two different intensities; or (iv) symbols for signals resulting from excitation at two different wavelengths. ### Claim 20 (depends on 1) The method of claim 1, wherein each of the signal states is represented by a ternary digit. ### Claim 21 (depends on 20) The method of claim 20, wherein the ternary digit comprises (i) symbols for signals emitted at three different wavelengths; (ii) symbols for signals having three different intensities; or (iii) symbols for signals resulting from excitation at three different wavelengths. ### Claim 22 (depends on 1) The method of claim 1, wherein each of the mixtures within said series of mixtures comprises nucleotide cognates for at least two and no more than three of four different base types suspected of being in the primed template nucleic acid. ### Claim 23 (depends on 1) The method of claim 1, wherein each of the mixtures within said series of mixtures comprises nucleotide cognates for at least two and no more than two of four different base types suspected of being in the primed template nucleic acid. ### Claim 24 (depends on 1) The method of claim 1, wherein the mixtures differ by the presence of a nucleotide cognate for a first base type in a first mixture of the series of mixtures and absence of the nucleotide cognate for the first base type in a second mixture of the series of mixtures. ### Claim 25 (depends on 1) The method of claim 1, wherein the mixtures differ by the number or type of label attached to at least one type of nucleotide cognate. ### Claim 26 (depends on 1) The method of claim 1, further comprising: (d) adding a next correct nucleotide to the primer of the primed template nucleic acid after step (b), thereby producing an extended primer. ### Claim 27 (depends on 26) The method of claim 26, further comprising repeating steps (a) through (d) for the primed template nucleic acid that comprises the extended primer. ### Claim 28 (depends on 26) The method of claim 26, wherein the next correct nucleotide that is added to the primer is a reversibly terminated nucleotide. ### Claim 29 (depends on 28) The method of claim 28, further comprising repeating steps (a) through (d) for the primed template nucleic acid that comprises the extended, reversibly terminated primer. ### Claim 30 (depends on 29) The method of claim 29, further comprising (e) removing the reversible terminator moiety from the extended, reversibly terminated primer after steps (a) through (d) are repeated. ### Claim at position 31 31-32. (canceled) ### Claim 33 (depends on 1) The method of claim 1, wherein the mixtures differ by a first type of exogenous label being attached to a nucleotide cognate for a first base type in a first mixture of the series of mixtures and absence of the first type of exogenous label from nucleotide cognates for the first base type in a second mixture of the series of mixtures. ### Claim 34 (depends on 1) The method of claim 1, wherein each of the mixtures within said series of mixtures comprises nucleotide cognates for four different base types suspected of being present at the next template position of the template nucleic acid. ### Claim 35 (depends on 34) The method of claim 34, wherein the mixtures differ by the type of label attached to a nucleotide cognate for a first base type in different mixtures of the series of mixtures. ### Claim 36 A method of determining a series of signal states for a series of nucleotide cognate mixtures, comprising: (a) sequentially contacting a primed template nucleic acid with a series of mixtures, wherein each of the mixtures within said series of mixtures comprise a polymerase and nucleotide cognates for at least two different base types, and each of the mixtures within said series of mixtures differ by the presence or absence of at least one type of nucleotide cognate; and (b) detecting the presence or absence of a stabilized ternary complex formed at the next template position for each of the mixtures within said series of mixtures, thereby determining a series of signal states for said series of mixtures, wherein the stabilized ternary complex is prevented from covalently incorporating nucleotides from the mixtures into the primed template nucleic. ### Claim 37 (depends on 1) The method of claim 1 further comprising decoding the series of signal states, thereby identifying the next correct nucleotide for the primed template nucleic acid. ### Claim 38 (depends on 1) The method of claim 1 further comprising decoding the series of signal states to distinguish a correct base call for the next template position from an erroneous base call for the next template position.