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 PDF

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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
Application number
EP21756618.1A
Other languages
German (de)
French (fr)
Other versions
EP4107256A1 (en
Inventor
Dongmyunghee KIM
Manimozhi MANIVANNAN
Saurabh GULATI
Shu Wang
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Mission Bio Inc
Original Assignee
Mission Bio Inc
Priority date (The priority date 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 date listed.)
Filing date
Publication date
Priority claimed from PCT/US2020/043154 external-priority patent/WO2021016402A1/en
Application filed by Mission Bio Inc filed Critical Mission Bio Inc
Publication of EP4107256A1 publication Critical patent/EP4107256A1/en
Publication of EP4107256A4 publication Critical patent/EP4107256A4/en
Pending legal-status Critical Current

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    • 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)
EP21756618.1A 2020-02-21 2021-02-21 Using machine learning to optimize assays for single cell targeted sequencing Pending EP4107256A4 (en)

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)

* Cited by examiner, † Cited by third party
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)

* Cited by examiner, † Cited by third party
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)

* Cited by examiner, † Cited by third party
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
WO2019204302A2 (en) * 2018-04-16 2019-10-24 Baylor College Of Medicine Chimeric rna-driven genomic rearrangement in mammalian cells
CN113795591A (en) * 2019-04-02 2021-12-14 使命生物公司 Methods and systems for characterizing tumors and identifying tumor heterogeneity

Patent Citations (2)

* Cited by examiner, † Cited by third party
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)

* Cited by examiner, † Cited by third party
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
EP4107256A1 (en) 2022-12-28
WO2021168383A1 (en) 2021-08-26

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