EP4107256A4 - Using machine learning to optimize assays for single cell targeted sequencing - Google Patents
Using machine learning to optimize assays for single cell targeted sequencing Download PDFInfo
- Publication number
- EP4107256A4 EP4107256A4 EP21756618.1A EP21756618A EP4107256A4 EP 4107256 A4 EP4107256 A4 EP 4107256A4 EP 21756618 A EP21756618 A EP 21756618A EP 4107256 A4 EP4107256 A4 EP 4107256A4
- Authority
- EP
- European Patent Office
- Prior art keywords
- machine learning
- single cell
- targeted sequencing
- cell targeted
- assays
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Pending
Links
- 238000003556 assay Methods 0.000 title 1
- 238000010801 machine learning Methods 0.000 title 1
- 238000012163 sequencing technique Methods 0.000 title 1
Classifications
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
- G16B40/20—Supervised data analysis
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
- C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B35/00—ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
- G16B35/10—Design of libraries
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/156—Polymorphic or mutational markers
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B35/00—ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
- G16B35/20—Screening of libraries
Landscapes
- Life Sciences & Earth Sciences (AREA)
- Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Physics & Mathematics (AREA)
- Chemical & Material Sciences (AREA)
- Medical Informatics (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- General Health & Medical Sciences (AREA)
- Biophysics (AREA)
- Biotechnology (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Evolutionary Biology (AREA)
- Theoretical Computer Science (AREA)
- Analytical Chemistry (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Organic Chemistry (AREA)
- Bioinformatics & Computational Biology (AREA)
- Wood Science & Technology (AREA)
- Zoology (AREA)
- Molecular Biology (AREA)
- Biochemistry (AREA)
- Genetics & Genomics (AREA)
- Data Mining & Analysis (AREA)
- Immunology (AREA)
- Library & Information Science (AREA)
- Pathology (AREA)
- Oncology (AREA)
- Artificial Intelligence (AREA)
- Evolutionary Computation (AREA)
- Hospice & Palliative Care (AREA)
- Microbiology (AREA)
- Bioethics (AREA)
- Computer Vision & Pattern Recognition (AREA)
- Databases & Information Systems (AREA)
- Epidemiology (AREA)
- Software Systems (AREA)
- General Engineering & Computer Science (AREA)
- Public Health (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Applications Claiming Priority (3)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US202062979840P | 2020-02-21 | 2020-02-21 | |
PCT/US2020/043154 WO2021016402A1 (en) | 2019-07-22 | 2020-07-22 | Using machine learning to optimize assays for single cell targeted dna sequencing |
PCT/US2021/018944 WO2021168383A1 (en) | 2020-02-21 | 2021-02-21 | Using machine learning to optimize assays for single cell targeted sequencing |
Publications (2)
Publication Number | Publication Date |
---|---|
EP4107256A1 EP4107256A1 (en) | 2022-12-28 |
EP4107256A4 true EP4107256A4 (en) | 2024-03-20 |
Family
ID=77391256
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
EP21756618.1A Pending EP4107256A4 (en) | 2020-02-21 | 2021-02-21 | Using machine learning to optimize assays for single cell targeted sequencing |
Country Status (2)
Country | Link |
---|---|
EP (1) | EP4107256A4 (en) |
WO (1) | WO2021168383A1 (en) |
Families Citing this family (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN113823356B (en) * | 2021-09-27 | 2024-05-28 | 电子科技大学长三角研究院(衢州) | Methylation site identification method and device |
CN115359840B (en) * | 2022-08-29 | 2023-04-21 | 西安交通大学 | Method for identifying key regulatory factors for branch point cell fate decisions in lineage trees |
Citations (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
EP2101275A1 (en) * | 2008-03-10 | 2009-09-16 | Koninklijke Philips Electronics N.V. | Method for polynucleotide design and selection |
US20190309365A1 (en) * | 2010-05-18 | 2019-10-10 | Natera, Inc. | Methods for simultaneous amplification of target loci |
Family Cites Families (7)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US7970718B2 (en) * | 2001-05-18 | 2011-06-28 | Health Discovery Corporation | Method for feature selection and for evaluating features identified as significant for classifying data |
US20040110227A1 (en) * | 2002-03-19 | 2004-06-10 | Erez Levanon | Methods and systems for identifying putative fusion transcripts, polypeptides encoded therefrom and polynucleotide sequences related thereto and methods and kits utilizing same |
US9047559B2 (en) * | 2011-07-22 | 2015-06-02 | Sas Institute Inc. | Computer-implemented systems and methods for testing large scale automatic forecast combinations |
US20160019339A1 (en) * | 2014-07-06 | 2016-01-21 | Mercator BioLogic Incorporated | Bioinformatics tools, systems and methods for sequence assembly |
WO2017075294A1 (en) * | 2015-10-28 | 2017-05-04 | The Board Institute Inc. | Assays for massively combinatorial perturbation profiling and cellular circuit reconstruction |
US20210238592A1 (en) * | 2018-04-16 | 2021-08-05 | Baylor College Of Medicine | Chimeric rna-driven genomic rearrangement in mammalian cells |
CN113811617A (en) * | 2019-04-02 | 2021-12-17 | 使命生物公司 | Methods and systems for proteomic profiling and characterization |
-
2021
- 2021-02-21 EP EP21756618.1A patent/EP4107256A4/en active Pending
- 2021-02-21 WO PCT/US2021/018944 patent/WO2021168383A1/en unknown
Patent Citations (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
EP2101275A1 (en) * | 2008-03-10 | 2009-09-16 | Koninklijke Philips Electronics N.V. | Method for polynucleotide design and selection |
US20190309365A1 (en) * | 2010-05-18 | 2019-10-10 | Natera, Inc. | Methods for simultaneous amplification of target loci |
Non-Patent Citations (3)
Title |
---|
BROWN J T ET AL: "Establishment of a standardized multiplex assay with the analytical performance required for quantitative measurement of BCR-ABL1 on the international reporting scale", BLOOD CANCER JOURNAL, vol. 1, no. 3, 25 March 2011 (2011-03-25), GB, pages e13 - e13, XP093127668, ISSN: 2044-5385, Retrieved from the Internet <URL:http://www.nature.com/articles/bcj201110> [retrieved on 20240206], DOI: 10.1038/bcj.2011.10 * |
See also references of WO2021168383A1 * |
WILLIAMS HANNAH L ET AL: "Validation of the Oncomine(TM)focus panel for next-generation sequencing of clinical tumour samples", VIRCHOWS ARCHIV, SPRINGER BERLIN HEIDELBERG, BERLIN/HEIDELBERG, vol. 473, no. 4, 13 August 2018 (2018-08-13), pages 489 - 503, XP036603112, ISSN: 0945-6317, [retrieved on 20180813], DOI: 10.1007/S00428-018-2411-4 * |
Also Published As
Publication number | Publication date |
---|---|
WO2021168383A1 (en) | 2021-08-26 |
EP4107256A1 (en) | 2022-12-28 |
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Effective date: 20220913 |
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DAX | Request for extension of the european patent (deleted) | ||
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A4 | Supplementary search report drawn up and despatched |
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RIC1 | Information provided on ipc code assigned before grant |
Ipc: G16B 40/20 20190101ALI20240214BHEP Ipc: G16B 35/10 20190101ALI20240214BHEP Ipc: G16B 30/00 20190101ALI20240214BHEP Ipc: C12Q 1/6886 20180101ALI20240214BHEP Ipc: C12Q 1/6827 20180101ALI20240214BHEP Ipc: C12N 15/86 20060101ALI20240214BHEP Ipc: C12N 15/113 20100101ALI20240214BHEP Ipc: C12N 5/10 20060101AFI20240214BHEP |