# US 2019/0170684 A1 · Methods and Systems for Variant Detection > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2019/0170684 A1 - Document ID: US20190170684A1 - Status: Published application - Kind: A1 - Application number: 16/265,806 - Filed: 2019-02-01 - Published: 2019-06-06 - Earliest claimed: 2015-04-15 - Assignees: Life Technologies Corporation - Applicants: Life Technologies Corporation - Inventors: David DENNY; David WOO; Manjula ALIMINATI; Siva Kumar SAMSANI; Stephanie SCHNEIDER; Yoke Peng LIM; Sylvia CHANG - Web page: https://patentgrep.com/patent/US20190170684A1 ## CPC - G01N 27/44717: {Arrangements for investigating the separated zones, e.g. localising zones} - G16B 30/00: ICT specially adapted for sequence analysis involving nucleotides or amino acids - G16B 30/10: Sequence alignment; Homology search - G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q) - G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY ## Abstract In one exemplary embodiment, a method for detecting variants in electropherogram data is provided. The method includes receiving electropherogram data from an instrument and analyzing the electropherogram data to identify mixed bases in the electropherogram data. The method further includes validating the identified mixed bases. Then the method includes determining variants in the electropherogram data based on the validated mixed bases. ## Claims ### Claim 1 A method for detecting nucleic acid sequence variants in electropherogram data, the method comprising: receiving electropherogram data comprising one or more nucleic acid sequences from a Sanger sequencing instrument; analyzing the electropherogram data, the analysis comprising identifying mixed bases in the electropherogram data based on an orientation of each of the one or more nucleic acid sequences; validating the identified mixed bases by extracting peak location data for each of four electropherogram channels from the analyzed electropherogram data; and determining one or more variants in the electropherogram data based on the extracted peak location data. ### Claim 2 (depends on 1) The method of claim 1, wherein analyzing the electropherogram data to identify mixed bases includes determining a mixed-base alignment. ### Claim 3 (depends on 1) The method of claim 1, wherein validating the identified mixed bases comprises: detecting peaks in the electropherogram data; detecting intersections in the electropherogram data; and detecting stutter peaks in the electropherogram data. ### Claim 4 (depends on 3) The method of claim 3, wherein validating the identified mixed bases further comprises: mapping the detected peaks. ### Claim 5 (depends on 3) The method of claim 3, wherein validating the identified mixed bases further comprises: merging the peaks based on the detected peaks, the detected intersections, and the detected stutter peaks. ### Claim 6 (depends on 1) The method of claim 1, further comprising: validating the determined variants based on generating a score based on the identified features. ### Claim 7 A system for detecting variants in electropherogram data comprising one or more nucleic acid sequences, the system comprising: an input module configured to receive electropherogram data from a Sanger sequencing instrument; a mixed base variant validator module to identify mixed bases in the electropherogram data by detecting an orientation of each of the one or more nucleic acid sequences, and validate the identified mixed bases by extracting peak location data for each of four electropherogram channels from the electropherogram data; and a variant caller configured to determine variants in the electropherogram data based on the extracted peak location of the validated mixed bases. ### Claim 8 (depends on 7) The system of claim 7, further comprising: an alignment module configured to analyze the electropherogram data to determine a mixed-base alignment. ### Claim 9 (depends on 7) The system of claim 7, further comprising: a stutter and peak detector configured to identify features within the electropherogram data indicative of errors. ### Claim 10 (depends on 7) The system of claim 7, further comprising: a variant score generator configured to validate variants in the electropherogram data. ### Claim 11 A computer-readable storage medium encoded with processor executable instructions for detecting variants in electropherogram data comprising one or more nucleic acid sequences, the instructions comprising instructions for: receiving electropherogram data from an Sanger sequence instrument; analyzing the electropherogram data to identify mixed bases in the electropherogram data by detecting an orientation of each of the one or more nucleic acid sequences; validating the identified mixed bases by extracting peak location data for each of four electropherogram channels; and determining variants in the electropherogram data based on the extracted peak location data of the validated mixed bases. ### Claim 12 (depends on 11) The method of claim 11, wherein analyzing the electropherogram data to identify mixed bases includes determining a mixed-base alignment. ### Claim 13 (depends on 11) The method of claim 11, wherein validating the identified mixed bases comprises: detecting peaks in the electropherogram data; detecting intersections in the electropherogram data; and detecting stutter peaks in the electropherogram data. ### Claim 14 (depends on 13) The computer-readable storage medium of claim 13, wherein the instructions for validating the identified mixed bases further comprises instructions for: mapping the detected peaks. ### Claim 15 (depends on 13) The computer-readable storage medium of claim 13, wherein the instructions for validating the identified mixed bases further comprises instructions for: merging the peaks based on the detected peaks, the detected intersections, and the detected stutter peaks. ### Claim 16 (depends on 11) The computer-readable storage medium of claim 11, further comprising instructions for: validating the determined variants based on generating a score based on the identified features.