IP Library › Granted Patent US 12,223,651
Granted Patent B2
US 12,223,651 · App. 18/303,436 · Granted Feb 11, 2025

Identifying nucleotides by determining phasing

Inventors: Francisco Jose Garcia (San Diego, CA); Klaus Maisinger (Essex, GB); Stephen Tanner (San Diego, CA); John A. Moon (San Diego, CA); Tobias Mann (San Diego, CA); Michael Lawrence Parkinson (Reyrieux, FR); Anthony James Cox (Essex, GB); Haifang H. Ge (Essex, GB)
Assignee: Illumina, Inc.
G06T7/0014G06T7/0012G06T7/246G06T7/248G06T7/33G06T7/337G06T7/90G06T2207/10024G06T2207/30024G06T2207/30072
View Patent ↗
Loading inventors, assignments & file history…
Monitor This Case
Get email alerts when status or documents change.
Order Certified Copies
Most orders are placed with the USPTO same day — all within 24 business hours.
Order via The Patent Place →
Pre-filled with this patent's details
Quick Facts
Patent No.
US 12,223,651
App. No.
18/303,436
Granted
Feb 11, 2025
Kind
B2
Abstract

Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.

Claims (27)

1. A method for creating a template of nucleic acid cluster locations on a flow cell, comprising:

obtaining fluorescent emission signals from nucleic acid clusters on the flow cell, wherein a nucleic acid cluster comprises a plurality of nucleic acid molecules attached to the flow cell, and wherein the plurality of the nucleic acid molecules comprise fluorescently labeled nucleotides;

identifying a plurality of candidate cluster locations on the flowcell from the obtained fluorescent emission signals; and

determining whether to keep a candidate cluster location, discard a candidate cluster location, or merge a candidate cluster location with another location based on the obtained fluorescent emission signals, thereby generating a template of cluster locations on the flow cell.

2. The method of claim 1 , wherein said determination is based on clusters of fluorescent emission signals associated with neighboring candidate cluster locations of said candidate cluster location.

3. The method of claim 1 , wherein said determination comprises ordering said candidate cluster locations by their respective detection counts, wherein a detection count of a candidate cluster location is a number of times a fluorescent emission signal is detected within a predefined radius of the candidate cluster location during multiple sequencing cycles.

4. The method of claim 3 , wherein the predefined radius is adjusted based on a density of candidate cluster locations on the flow cell.

5. The method of claim 3 , wherein the predefined radius is measured from a center of the candidate cluster location, from an edge of the candidate cluster location, or from a point inside the candidate cluster location.

6. The method of claim 3 , wherein said plurality of candidate cluster locations are further ordered by their respective highest fluorescent emission signal intensities relative to highest fluorescent emission signal intensities associated with their neighboring candidate cluster locations.

7. The method of claim 1 , wherein said determination comprises ordering said plurality of candidate cluster locations by:

their respective highest fluorescent emission signal intensities,

their respective highest fluorescent emission signal intensities relative to a background intensity or a noise intensity, or

their respective highest fluorescent emission signal intensities relative to highest fluorescent emission signal intensities associated with their neighboring candidate cluster locations.

8. The method of claim 1 , wherein said determination comprises ordering said plurality of candidate cluster locations by distance to their respective nearest neighboring candidate cluster locations.

9. The method of claim 8 , wherein the distances are measured from a center of a candidate cluster location to a center of its nearest neighboring candidate cluster location, from an edge of a candidate cluster location to an edge of its nearest neighboring candidate cluster location, between the respective outer-most identifiable points of a candidate cluster location and its nearest neighboring candidate cluster location, or from a point inside a candidate cluster location to another point inside its nearest neighboring candidate cluster location.

10. The method of claim 1 , wherein said determination comprises ordering said plurality of candidate cluster locations by their respective chastities, wherein a chastity of a candidate cluster location in a template cycle relates to a comparison of the highest and the second highest fluorescent emission signals detected in the template cycle at the candidate cluster location by different detection channels having different wavelength ranges.

11. The method of claim 10 , wherein said determination is further based on preliminary base calls at said plurality of candidate cluster locations.

12. The method of claim 1 , further comprising processing the cluster of fluorescent emission signals associated with each of said plurality of candidate cluster locations to produce a clump of processed fluorescent emission signals associated with each of said plurality of candidate cluster locations.

13. The method of claim 12 , wherein determining whether to keep a candidate cluster location, discard a candidate cluster location, or merge a candidate cluster location with another location is based on the associated clump of processed fluorescent emission signals.

14. The method of claim 12 , wherein processing the cluster of fluorescent emission signals associated with each of said plurality of candidate cluster locations comprises discarding fluorescent emission signals among the cluster of fluorescent emission signals that are not within an expected size measure.

15. The method of claim 12 , wherein processing the cluster of fluorescent emission signals associated with each of said plurality of candidate cluster locations comprises selecting the fluorescent emission signal among the cluster of fluorescent emission signals that has the highest intensity.

16. A system for determining nucleotide sequences of nucleic acid clusters in a flow cell, the system comprising:

an optical system for detecting fluorescent emissions;

a non-transitory memory configured to store executable instructions; and

a hardware processor in communication with the optical system and the non-transitory memory, the hardware processor programmed by the executable instructions to perform the process of claim 2 .

17. The system of claim 16 , wherein the nucleic acid sequencer is configured to acquire images of the flow cell.

18. The system of claim 16 , wherein the hardware processor is configured to control the nucleic acid sequencer to perform sequencing reactions on the nucleic acid clusters to determine the nucleotide sequences in each cluster.

Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jul 13, 2023
From: GARCIA, FRANCISCO J.; TANNER, STEPHEN; MOON, JOHN A.; MANN, TOBIAS; MAISINGER, KLAUS; PARKINSON, MICHAEL; COX, ANTHONY JAMES; GE, HAIFANG H.
To: ILLUMINA, INC.
Reel/Frame 064245/0909 →
Continuity (9)
Continuation 17445994 · Aug 26, 2021
Continuation 17157622 · Jan 25, 2021
Continuation 16378894 · Apr 9, 2019
Continuation 15354540 · Nov 17, 2016
Continuation 14608471 · Jan 29, 2015
Continuation 13006206 · Jan 13, 2011
Provisional Application 61321029 · Apr 5, 2010
Provisional Application 61294811 · Jan 13, 2010
Related Publication 20230351598A1 · Nov 2, 2023
References Cited (151)
US 6006170A · Marcantonio et al. · 1999 [cited by applicant]
US 6438496B1 · Yoshida et al. · 2002 [cited by applicant]
US 6839454B1 · Park et al. · 2005 [cited by applicant]
US 6969589B2 · Patil et al. · 2005 [cited by applicant]
US 6973053B1 · Passman et al. · 2005 [cited by applicant]
US 7033754B2 · Chee et al. · 2006 [cited by applicant]
US 7035740B2 · Kermani et al. · 2006 [cited by applicant]
US 7060431B2 · Chee et al. · 2006 [cited by applicant]
US 7115884B1 · Walt et al. · 2006 [cited by applicant]
US 7226734B2 · Chee et al. · 2007 [cited by applicant]
US 7285384B2 · Fan et al. · 2007 [cited by applicant]
US 7348181B2 · Walt et al. · 2008 [cited by applicant]
US 7455971B2 · Chee et al. · 2008 [cited by applicant]
US 7668697B2 · Volkov et al. · 2010 [cited by applicant]
US 8339586B2 · Zahniser · 2012 [cited by applicant]
US 8407012B2 · Erlich et al. · 2013 [cited by applicant]
US 8965076B2 · Garcia et al. · 2015 [cited by applicant]
US 9388462B1 · Eltoukhy et al. · 2016 [cited by applicant]
US 9530207B2 · Garcia et al. · 2016 [cited by applicant]
US 10192024B2 · Chen et al. · 2019 [cited by applicant]
US 10304189B2 · Garcia et al. · 2019 [cited by applicant]
US 11605165B2 · Garcia et al. · 2023 [cited by applicant]
US 11676275B2 · Garcia et al. · 2023 [cited by applicant]
US 20020150909A1 · Stuelpnagel et al. · 2002 [cited by applicant]
US 20030053097A1 · Ohga et al. · 2003 [cited by applicant]
US 20030196695A1 · O'Connor et al. · 2003 [cited by applicant]
US 20040101191A1 · Seul et al. · 2004 [cited by applicant]
US 20040218793A1 · Corson et al. · 2004 [cited by applicant]
US 20050069189A1 · Bartell et al. · 2005 [cited by applicant]
US 20050129329A1 · Kudo · 2005 [cited by applicant]
US 20050214825A1 · Stuelpnagel · 2005 [cited by applicant]
US 20050256673A1 · Hikida · 2005 [cited by applicant]
US 20050272086A1 · Patil et al. · 2005 [cited by applicant]
US 20060041384A1 · Kermani et al. · 2006 [cited by applicant]
US 20060083428A1 · Ghosh et al. · 2006 [cited by applicant]
US 20060120584A1 · Hillman et al. · 2006 [cited by applicant]
US 20060222226A1 · Xia et al. · 2006 [cited by applicant]
US 20070091174A1 · Kochi et al. · 2007 [cited by applicant]
US 20070250274A1 · Volkov et al. · 2007 [cited by applicant]
US 20070274243A1 · Yamaguchi · 2007 [cited by applicant]
US 20080026367A9 · Cox et al. · 2008 [cited by applicant]
US 20080075380A1 · Dube et al. · 2008 [cited by applicant]
US 20080182757A1 · Heiner et al. · 2008 [cited by applicant]
US 20080231876A1 · Harada · 2008 [cited by applicant]
US 20080273793A1 · Oishi · 2008 [cited by applicant]
US 20090010535A1 · Koishi · 2009 [cited by applicant]
US 20090041349A1 · Suzuki et al. · 2009 [cited by applicant]
US 20100088255A1 · Mann et al. · 2010 [cited by applicant]
US 20100138385A1 · Palermiti · 2010 [cited by applicant]
US 20100246925A1 · Nagatsuka et al. · 2010 [cited by applicant]
US 20100272334A1 · Yamada et al. · 2010 [cited by applicant]
US 20110091065A1 · Chandrashekar et al. · 2011 [cited by applicant]
US 20110211098A1 · Bosco · 2011 [cited by applicant]
US 20110304659A1 · Lee · 2011 [cited by applicant]
US 20120020537A1 · Garcia et al. · 2012 [cited by applicant]
US 20120191678A1 · Liu · 2012 [cited by applicant]
US 20120262703A1 · Zahniser · 2012 [cited by applicant]
US 20120262704A1 · Zahniser · 2012 [cited by applicant]
US 20120262705A1 · Zahniser et al. · 2012 [cited by applicant]
US 20150125053A1 · Vieceli · 2015 [cited by applicant]
US 20160018520A1 · Hirai et al. · 2016 [cited by applicant]
US 20200074630A1 · Garcia et al. · 2020 [cited by applicant]
CA 2873146A1 · 2013 [cited by examiner]
FR 2766496A1 · 1999 [cited by examiner]
WO WO199908233 · 1999 [cited by applicant]
WO WO2008119046 · 2008 [cited by applicant]
WO WO2010062913 · 2010 [cited by applicant]
Cortes J et al., “New Nucleic Acid Sequences Encoding Enzymes Involved In Macrolide Biosynthesis”, FR 2766496 A1, published on 2000 (Year: 2000). [cited by examiner]
Chen et al. “System and Method for Generation and Use of Optimal Nucleotide Flow Orders”, CA 2873146 A1, published on 2013 (Year: 2013). [cited by examiner]
Adjeroh, et al., “On denoising and compression of DNA microarray images”, Pattern Recognition, 39(12), 2006, 2478-2493. [cited by applicant]
Elser, et al., “Searching with iterated maps”, PNAS 104, 2007, 418-423. [cited by applicant]
Eltoukhy, et al., “Modeling and base-calling for Dna Sequencing-by-Synthesis”, Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings. 2006 IEEE International Conference, May 2006, II-II. [cited by applicant]
Ewing, et al., “Base-calling of automated sequencer traces using phred. II. Error probabilities”, Genome Research, 8, 1998, 186-194. [cited by applicant]
Herranz, et al., “Filtering techniques for the detection of Sunyaev-Zel'dovich clusters in multifrequency maps”, Monthly Notices of the Royal Astronomical Society, 336, 2002, 10571068. [cited by applicant]
Herranz, et al., “Scale-adaptive filters for the detection/separation of compact sources”, The Astrophysical Journal, 580, 2002, 610. [cited by applicant]
HiSeq 2000 obtained from PolITiGenomics, http://www.politigenomics.com/2010/01/hiseq-2000.html on Oct. 20, 2011, Jan. 12, 2010, 8 pages. [cited by applicant]
Hobson, et al., “A Bayesian Approach to discrete object detection in astronomical datasets”. [cited by applicant]
Hua, Jianping et al., “Microarray BASICA: Background adjustment, segmentation, image compression and analysis of microarray images”, Eurasip Journal on Applied Signal Processing, 2004(1), 2004, 92-107. [cited by applicant]
Illumina Sequencing,, “Reversing the Trend: More Bases with Less Computing”, May 5, 2009, 2 pages. [cited by applicant]
Illumina Systems and Software,, “Complete Secondary Analysis Workflow for the Genome Analyzer”, Technical Note, Oct. 19, 2009, 8 pages. [cited by applicant]
Illumina,, “Draft—Genome Analyzer Operations Guide”. [cited by applicant]
Illumina,, “Genome Analyzer IIx Operations Guide”, Apr. 2009. [cited by applicant]
Illumina,, “Genome Analyzer Operations Guide”, Apr. 2009. [cited by applicant]
Illumina,, “Genome Analyzer Operations Guide”, Aug. 2009. [cited by applicant]
Illumina,, “Genome Analyzer Operations Guide”, Nov. 2009. [cited by applicant]
Illumina,, “RTA 1.4.15 update Release Notes”, 2010. [cited by applicant]
Illumina,, “RTA Theory of Operation”, Jun. 12, 2009. [cited by applicant]
Illumina,, “SCS 2.4 and RTA 1.4.6 Release Notes”, Apr. 2010. [cited by applicant]
Illumina,, “SCS 2.5. and RTA 1.5. Release Notes”, Sep. 2010. [cited by applicant]
Illumina,, “SCS 2.6 and RTA 1.6 Release Notes”, Jan. 2011. [cited by applicant]
Irwin,, “Detectors and Data Analysis Techniques for Wide Filed Optical Imaging”. [cited by applicant]
Kao, et al., “BayesCall: A model-based basecalling algorithm for high-throughput short-read sequencing”, Genome Research, 19, 2009, 1884-1895. [cited by applicant]
Li, et al., “An estimate of the cross-talk matrix in four-dye fluorescence-based DNA sequencing”, Electrophoresis, 20(7), 1999, 1433. [cited by applicant]
Lopez-Caniego, et al., “Filter design for the detection of compact sources based on the Neyman-Pearson detector”. [cited by applicant]
Luo, et al., “Storage and transmission of microarray images”, Drug Discovery Today, vol. 10 (No. 23/24), 2005, 1689-1695. [cited by applicant]
Margulies, et al., “Genome sequencing in microfabricated high-density picolitre reactors”, Nature, vol. 437, 2005, 376-380 and Supplemental Materials. [cited by applicant]
Margulies, et al., “Supplemental Material 3”, Nature, 437, 2005, 1-34. [cited by applicant]
Rahnenfuhrer, et al., “Hybrid clustering for microarray image analysis combining intensity and shape features”, BMC Bioinformatics, 5, article 47, 2004. [cited by applicant]
Sanz, et al., “Optimal detection of sources on a homogeneous and isotropic background”, The Astrophysical Journal 552, 2001, 484. [cited by applicant]
Shendure, et al., “Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome”, Science, 309(5741), Sep. 9, 2005, 1728-1732. [cited by applicant]
41J Blog, Apr. 19, 2012, The Solexa Pipeline, 14 pp. [cited by applicant]
Bentley et al., Nov. 6, 2008, Accurate whole human genome sequencing using reversible terminator chemistry, Nature, 456:53-59 and Supplementary Information. [cited by applicant]
Bravo et al., Sep. 2010, Model-Based Quality Assessment and Base-Calling for Second- Generation Sequencing Data, Biometrics, 66:665-674. [cited by applicant]
Das et al., 2012, OnlineCall: fast online parameter estimation and base calling for illumina's next- generation sequencing, Bioinformatics, 28(13):1677-1683. [cited by applicant]
Das et al., 2013, Base calling for high-throughput short-read sequencing: dynamic programming solutions, BMC Bioinformatics, 14:129, 10 pp. [cited by applicant]
Erlich et al., Aug. 2008, Alta-Cyclic: a self-optimizing base caller for next-generation sequencing, Nat Methods, 5(8):679-682 with supplementary figures and text. [cited by applicant]
Gilks et al., Sep. 1, 2008, A base-calling statistical model for Illumina next-generation sequencing, University of Leeds and Rothamsted Research, Wellcome Trust Sanger Institute, 13 pp. [cited by applicant]
Illumina, Inc., 2008, Genome Analyzer Pipeline Software v03. User Guide, Part # 1003381, 108 pp. [cited by applicant]
Ji et al., 2012, BM-BC: a Bayesian method of base calling for Solexa sequence data, BMC Bioinformatics, 13(Suppl 13):S6. [cited by applicant]
Kao et al., 2009, BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing, Genome Research, 19:supplementary material. [cited by applicant]
Kircher et al., 2009, Improved base calling for the Illumina Genome Analyzer using machine learning strategies, Genome Biology, 10:R83 and supplementary information. [cited by applicant]
Kriseman et al., 2010, BING: Biomedical informatics pipeline for Next Generation Sequencing, Journal of Biomedical Informatics, 43:428-434. [cited by applicant]
Massingham et al., 2012, All Your Base: a fast and accurate probabilistic approach to base calling, Genome Biology, 13:R13, 15 pp. with additional material. [cited by applicant]
Menges et al., 2011, TotalReCaller: improved accuracy and performance via integrated alignment and base-calling, Bioinformatics, 27(17):2330-2337. [cited by applicant]
Preston, Jul. 2009, The New Genome Analyzer: Delivering more data, faster, and easier than ever before, Illumina®, PowerPoint presentation, 23 pp. [cited by applicant]
Renaud et al., Mar. 6, 2013, freelbis: an efficient basecaller with calibrated quality scores for Illumina sequencers, Bioinformatics Advance Access, 3 pp. [cited by applicant]
Rougemont et al., 2008, Probabilistic base calling of Solexa sequencing data, BMC Bioinformatics, 9:431, 12 pp. [cited by applicant]
Shen et al., 2012, ParticleCall: A particle filter for base calling in next-generation sequencing systems, BMC Bioinformatics, 13:160, 10 pp. [cited by applicant]
Whiteford et al., 2009, Swift: primary data analysis for the Illumina Solexa sequencing platform, Bioinformatics, 24(17):2194-2199. [cited by applicant]
Whiteford et al., 2009, Swift: primary data analysis for the Illumina Solexa sequencing Platform, Bioinformatics, 25(17):2194-2199. [cited by applicant]
Whiteford, Apr. 11, 2008, The Solexa Pipeline, 22 pp. [cited by applicant]
Illumina, Inc., Jun. 2008, Genome Analyzer Pipeline Software Version 1.0, User Guide, Part # 1004759 Rev. A, 136 pp. [cited by applicant]
Illumina, Inc., Jul. 2008, Integrated Primary Analysis and Reporting User Guide, Part # 1004159 Rev. A., 24 pp. [cited by applicant]
Maisinger, 2005, Main program for image analysis module in the Solexa data analysis pipeline, v1.0.0, 13 pp. [cited by applicant]
Illumina, Inc., Nov. 2008, Sequencing User Guide for Single-Read and Paired-End Sequencing, Part #1006747, Rev. A., 66 pp. [cited by applicant]
Illumina, Inc., Feb. 2009, Procedure, IPAR Assembly, Part # 1004414, Rev. D, 22 p. [cited by applicant]
Illumina, Inc., Nov. 2008, Cluster Station Operations Guide, Part # 1006745 Rev. A, 62 pp. [cited by applicant]
Illumina, Inc., Nov. 2008, Gemone Analyser II Operations Guide for Genome Analyzer II, Paired- end Module, and IPAR, Part # 1006746 Rev. A, 156 pp. [cited by applicant]
Maisinger, 2005, Main program for image analysis module in the Genome Analyzer data analysis pipeline, v1.3.0, 16 pp. [cited by applicant]
Maisinger, 2003, Main object used for the image image processing tasks in the Solexa software pipeline, v.1.3.0, 15 pp. [cited by applicant]
Illumina, Inc., Dec. 2008, Integrated Primary Analysis and Reporting User Guide, Part # 15000420 Rev. A, 32 pp. [cited by applicant]
Illumina, Inc., Dec. 2008, SCS 2.3 and IPAR 1.3 Release Notes, 7 pp. [cited by applicant]
Illumina, Inc., Jan. 2009, SCS2.3/IPAR1.3 Integrated Installer, 7 pp. [cited by applicant]
Illumina, Inc., Apr. 2009, Using Genome Analyzer Sequencing Control Software Version 2.4, Part # 15003831 Rev. A, 36 pp. [cited by applicant]
Maisinger, 2003, Main object used for the image image processing tasks in the Solexa Software pipeline, v1.4.0, 14 pp. [cited by applicant]
Maisinger, 2005, Main program for image analysis module in the Genome Analyzer data analysis pipeline, v.1.4.0, 12 pp. [cited by applicant]
Mclachlan, 2008, Implementation of the BuildTemplate interface using Pipeline default analysis, v1.4.0, 4 pp. [cited by applicant]
Illumina Inc., Sep. 2009, SCS 2.5 and RTA 1.5 Integrated Installer, 6 pp. [cited by applicant]
Mclachlan, 2008, Implementation of the BuildTemplate interface using Pipeline default analysis, v1.5.0, 4 pp. [cited by applicant]
Illumina, Inc., Aug. 2009, Genome Analyzer User Guide: Single-Read, Paired-End, and Multiplexed Sequencing, Part # 15005237 Rev. A, 118 pp. [cited by applicant]
Maisinger, 2005, Main program for image analysis module in the Genome Analyzer data analysis pipeline, v1.5.0, 12 pp. [cited by applicant]
Maisinger, 2003, Main object used for the image image processing tasks in the Solexa software pipeline, v1.5.0, 14 pp. [cited by applicant]
Illumina, Inc., Aug. 2009, Using Genome Analyzer Sequencing Control Software Version 2.5, Part # 15005901 Rev. A, 38 pp. [cited by applicant]
Mclachlan, 2008, Implementation of the BuildTemplate interface using Pipeline default analysis, 2008, v1.6.0, 8 pp. [cited by applicant]
Illumina, Inc., 2010, Genome Analyzer lle User Guide, Part # 15012075 Rev. A, 214 pp. [cited by applicant]
Maisinger, 2005, Main program for image analysis module in the Genome Analyzer data analysis pipeline, v1.6.0, 12 pp. [cited by applicant]
Maisinger, 2003, Main object used for the image image processing tasks in the Solexa software pipeline, v1.6.0, 14 pp. [cited by applicant]
Illumina, Inc., Dec. 2009, SCS 2.6 and RTA 1.6 Release Notes, 9 pp. [cited by applicant]
Illumina, Inc., Feb. 2010, SCS 2.6.26 and RTA 1.6.47.1 (with enhanced quality tables) Release Notes, 10 pp. [cited by applicant]
Illumina, Inc., Dec. 2009, SCS 2.6 and RTA 1.6 Integrated Installer, 6 pp. [cited by applicant]
Illumina, Inc., Oct. 2009, RTA 1.6 On-Instrument Primary Analysis for Genome Analyzer, Theory of Operation, Revision A, 20 pp. [cited by applicant]
Cited By (1)
US 12,620,098