# US 12,119,087 B2 · Methods and systems for sequence calling > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 12,119,087 B2 - Document ID: US12119087B2 - Status: Granted - Kind: B2 - Application number: 17/574,260 - Filed: 2022-01-12 - Published: 2022-06-23 - Granted: 2024-10-15 - Earliest claimed: 2017-10-26 - Assignees: Ultima Genomics, Inc. - Applicants: Ultima Genomics, Inc. - Inventors: Mark Pratt; Gilad Almogy; Avishai Bartov - Web page: https://patentgrep.com/patent/US12119087B2 ## CPC - G16B 40/10: Signal processing, e.g. from mass spectrometry [MS] or from PCR - C12Q 1/6806: Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay (C12Q1/6804 takes precedence) - C12Q 1/6869: Methods for sequencing - G16B 30/10: Sequence alignment; Homology search - G16B 45/00: ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks - G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY - 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 The present disclosure provides methods and systems for accurate and efficient context-aware base calling of sequences. In an aspect, disclosed herein is a method for sequencing a nucleic acid molecule, comprising: (a) sequencing the nucleic acid molecule to generate a plurality of sequence signals; and (b) determining base calls of the nucleic acid molecule based at least in part on (i) the plurality of sequence signals and (ii) quantified context dependency for at least a portion of the plurality of sequence signals. ## Claims ### Claim 1 A system for processing a plurality of sequence signals, comprising: a database that stores said plurality of sequence signals, said plurality of sequence signals generated upon sequencing of a nucleic acid; and one or more computer processors coupled to said database, wherein said one or more computer processors are individually or collectively programmed to: (a) align said plurality of sequence signals to a reference genome in a reference signal database, wherein the reference genome comprises reference signals; (b) identify a reference locus comprising a homopolymer sequence based at least on said aligned sequence signals; and (c) generate a consensus sequence from said plurality of sequence signals aligned to said reference signal, which consensus sequence comprises a homopolymer sequence of N bases, based at least on said identified reference locus, a length of said homopolymer sequence of said reference locus, and said reference signal. ### Claim 2 (depends on 1) The system of claim 1, wherein said one or more computer processors are individually or collectively programmed to calculate a length of estimation error of said homopolymer sequence, wherein said length of estimation error is calculated based at least in part on a distribution of signals or imputed homopolymer lengths of said plurality of aligned sequence signals. ### Claim 3 (depends on 1) The system of claim 1, wherein said one or more computer processors are individually or collectively programmed to pre-process said plurality of sequence signals to remove systematic error. ### Claim 4 (depends on 1) The system of claim 1, wherein said plurality of sequence signals are generated upon sequencing a nucleic acid molecule of a subject, and wherein said reference genome is a species of said subject. ### Claim 5 (depends on 4) The system of claim 4, wherein a number of lengths computed or classified is restricted based in part on a ploidy of said species of said subject. ### Claim 6 (depends on 1) The system of claim 1, wherein said plurality of sequence signals is generated at least in part by massively parallel array sequencing. ### Claim 7 (depends on 1) The system of claim 1, wherein said plurality of sequence signals is generated at least in part by flow sequencing. ### Claim 8 (depends on 1) The system of claim 1, wherein said reference signal comprises an analog reference signal, and wherein said one or more computer processors align said plurality of sequence signals by performing analog signal sequencing. ### Claim 9 (depends on 1) The system of claim 1, wherein said nucleic acid comprises a deoxyribonucleic acid (DNA). ### Claim 10 (depends on 1) The system of claim 1, wherein said nucleic acid comprises a ribonucleic acid (RNA). ### Claim 11 A system for quantifying context dependency of a plurality of sequence signals, comprising: a database that stores said plurality of sequence signals; and one or more computer processors coupled to said database, wherein said one or more computer processors are individually or collectively programmed to: (a) align said plurality of sequence signals to a reference genome in a reference signal database, wherein the reference genome comprises reference signals; and (b) quantify said context dependency in said plurality of sequence read signals aligned to said reference signal, based at least on a known sequence associated with said plurality of sequence signals. ### Claim 12 (depends on 11) The system of claim 11, wherein said reference signal comprises an analog reference signal, and wherein said one or more computer processors align said plurality of sequence signals by performing analog signal processing. ### Claim 13 (depends on 11) The system of claim 11, wherein said database stores a second plurality of sequence signals. ### Claim 14 (depends on 13) The system of claim 13, wherein said one or more computer processors are further individually or collectively programmed to: (a) align said second plurality of sequence signals to said reference signal, said second plurality of sequence signals generated upon sequencing a test nucleic acid sequence; and (b) determine homopolymer lengths of said second set of sequence molecules based at least on said plurality of sequence signals aligned to said reference signal and said quantified context dependency. ### Claim 15 (depends on 11) The system of claim 11, wherein said plurality of sequence signals are generated upon sequencing a nucleic acid. ### Claim 16 (depends on 15) The system of claim 15, wherein said nucleic acid comprises deoxyribonucleic acid (DNA). ### Claim 17 (depends on 15) The system of claim 15, wherein said nucleic acid comprises ribonucleic acid (RNA). ### Claim 18 (depends on 11) The system of claim 11, wherein said plurality of sequence signals is generated at least in part by massively parallel array sequencing, at least in part by flow sequencing, or at least in part by a combination thereof. ### Claim 19 (depends on 11) The system of claim 11, wherein said one or more computer processors establish a context-specific mapping between signal amplitudes and homopolymer lengths for each locus of a plurality of loci to quantify said context dependency. ### Claim 20 (depends on 11) The system of claim 11, wherein said one or more computer processors are further individually or collectively programmed to, for each plurality of loci in said reference signal, determine an expected signal for said locus based at least in part on said aligned sequence signals and said pre-determined sequence.