KR102476915B1 - 생물학적 서열의 자동화된 주석달기 및 스크리닝을 위한 시스템 및 방법 - Google Patents

생물학적 서열의 자동화된 주석달기 및 스크리닝을 위한 시스템 및 방법 Download PDF

Info

Publication number
KR102476915B1
KR102476915B1 KR1020197000811A KR20197000811A KR102476915B1 KR 102476915 B1 KR102476915 B1 KR 102476915B1 KR 1020197000811 A KR1020197000811 A KR 1020197000811A KR 20197000811 A KR20197000811 A KR 20197000811A KR 102476915 B1 KR102476915 B1 KR 102476915B1
Authority
KR
South Korea
Prior art keywords
sequence
biological
sequences
deleterious
combined
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.)
Active
Application number
KR1020197000811A
Other languages
English (en)
Korean (ko)
Other versions
KR20190017932A (ko
Inventor
제임스 디갠스
Original Assignee
트위스트 바이오사이언스 코포레이션
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
Application filed by 트위스트 바이오사이언스 코포레이션 filed Critical 트위스트 바이오사이언스 코포레이션
Publication of KR20190017932A publication Critical patent/KR20190017932A/ko
Application granted granted Critical
Publication of KR102476915B1 publication Critical patent/KR102476915B1/ko
Active legal-status Critical Current
Anticipated expiration legal-status Critical

Links

Images

Classifications

    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10Sequence alignment; Homology search
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/10Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034Isolating an individual clone by screening libraries
    • C12N15/1068Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/10Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034Isolating an individual clone by screening libraries
    • C12N15/1089Design, preparation, screening or analysis of libraries using computer algorithms
    • GPHYSICS
    • G05CONTROLLING; REGULATING
    • G05BCONTROL OR REGULATING SYSTEMS IN GENERAL; FUNCTIONAL ELEMENTS OF SUCH SYSTEMS; MONITORING OR TESTING ARRANGEMENTS FOR SUCH SYSTEMS OR ELEMENTS
    • G05B15/00Systems controlled by a computer
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/20Sequence assembly
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B35/00ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B50/00ICT programming tools or database systems specially adapted for bioinformatics
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B50/00ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/30Data warehousing; Computing architectures
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B99/00Subject matter not provided for in other groups of this subclass
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/10Processes for the isolation, preparation or purification of DNA or RNA

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Chemical & Material Sciences (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Theoretical Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • General Engineering & Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Biomedical Technology (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Organic Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Plant Pathology (AREA)
  • Microbiology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Bioethics (AREA)
  • Databases & Information Systems (AREA)
  • Library & Information Science (AREA)
  • General Physics & Mathematics (AREA)
  • Automation & Control Theory (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)
KR1020197000811A 2016-06-10 2017-06-09 생물학적 서열의 자동화된 주석달기 및 스크리닝을 위한 시스템 및 방법 Active KR102476915B1 (ko)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201662348786P 2016-06-10 2016-06-10
US62/348,786 2016-06-10
US201662375858P 2016-08-16 2016-08-16
US62/375,858 2016-08-16
PCT/US2017/036868 WO2017214574A1 (en) 2016-06-10 2017-06-09 Systems and methods for automated annotation and screening of biological sequences

Publications (2)

Publication Number Publication Date
KR20190017932A KR20190017932A (ko) 2019-02-20
KR102476915B1 true KR102476915B1 (ko) 2022-12-12

Family

ID=60574009

Family Applications (1)

Application Number Title Priority Date Filing Date
KR1020197000811A Active KR102476915B1 (ko) 2016-06-10 2017-06-09 생물학적 서열의 자동화된 주석달기 및 스크리닝을 위한 시스템 및 방법

Country Status (8)

Country Link
US (1) US20170357752A1 (enExample)
EP (1) EP3469499A4 (enExample)
JP (2) JP2019523940A (enExample)
KR (1) KR102476915B1 (enExample)
CN (1) CN109564769A (enExample)
CA (1) CA3027127A1 (enExample)
SG (1) SG11201811025VA (enExample)
WO (1) WO2017214574A1 (enExample)

Families Citing this family (34)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9409139B2 (en) 2013-08-05 2016-08-09 Twist Bioscience Corporation De novo synthesized gene libraries
CA2975852A1 (en) 2015-02-04 2016-08-11 Twist Bioscience Corporation Methods and devices for de novo oligonucleic acid assembly
WO2016172377A1 (en) 2015-04-21 2016-10-27 Twist Bioscience Corporation Devices and methods for oligonucleic acid library synthesis
AU2016324296A1 (en) 2015-09-18 2018-04-12 Twist Bioscience Corporation Oligonucleic acid variant libraries and synthesis thereof
CN108698012A (zh) 2015-09-22 2018-10-23 特韦斯特生物科学公司 用于核酸合成的柔性基底
CN108603307A (zh) 2015-12-01 2018-09-28 特韦斯特生物科学公司 功能化表面及其制备
CA3034769A1 (en) 2016-08-22 2018-03-01 Twist Bioscience Corporation De novo synthesized nucleic acid libraries
CN110248724B (zh) 2016-09-21 2022-11-18 特韦斯特生物科学公司 基于核酸的数据存储
CN110366613A (zh) 2016-12-16 2019-10-22 特韦斯特生物科学公司 免疫突触的变体文库及其合成
WO2018156792A1 (en) 2017-02-22 2018-08-30 Twist Bioscience Corporation Nucleic acid based data storage
CN110913865A (zh) 2017-03-15 2020-03-24 特韦斯特生物科学公司 免疫突触的变体文库及其合成
IL271205B2 (en) 2017-06-12 2025-02-01 Twist Bioscience Corp Methods for assembling continuous nucleic acids
WO2018231864A1 (en) 2017-06-12 2018-12-20 Twist Bioscience Corporation Methods for seamless nucleic acid assembly
US11407837B2 (en) 2017-09-11 2022-08-09 Twist Bioscience Corporation GPCR binding proteins and synthesis thereof
KR102637566B1 (ko) 2017-10-20 2024-02-16 트위스트 바이오사이언스 코포레이션 폴리뉴클레오타이드 합성을 위한 가열된 나노웰
CN112041438B (zh) 2018-01-04 2025-05-23 特韦斯特生物科学公司 基于dna的数字信息存储
CA3100739A1 (en) 2018-05-18 2019-11-21 Twist Bioscience Corporation Polynucleotides, reagents, and methods for nucleic acid hybridization
EP3891280A4 (en) * 2018-12-06 2022-08-10 Battelle Memorial Institute Technologies for nucleotide sequence screening
CA3124980A1 (en) 2018-12-26 2020-07-02 Twist Bioscience Corporation Highly accurate de novo polynucleotide synthesis
CN113785057A (zh) 2019-02-26 2021-12-10 特韦斯特生物科学公司 用于抗体优化的变异核酸文库
KR20210143766A (ko) 2019-02-26 2021-11-29 트위스트 바이오사이언스 코포레이션 Glp1 수용체에 대한 변이체 핵산 라이브러리
JP2022550497A (ja) 2019-06-21 2022-12-02 ツイスト バイオサイエンス コーポレーション バーコードに基づいた核酸配列アセンブリ
CA3155629A1 (en) 2019-09-23 2021-04-01 Twist Bioscience Corporation Variant nucleic acid libraries for crth2
AU2020355027A1 (en) 2019-09-23 2022-04-21 Twist Bioscience Corporation Antibodies that bind CD3 Epsilon
CA3177029A1 (en) 2020-04-27 2021-11-04 Aaron Sato Variant nucleic acid libraries for coronavirus
US12391762B2 (en) 2020-08-26 2025-08-19 Twist Bioscience Corporation Methods and compositions relating to GLP1R variants
US11970697B2 (en) 2020-10-19 2024-04-30 Twist Bioscience Corporation Methods of synthesizing oligonucleotides using tethered nucleotides
EP4002383A3 (en) * 2020-11-13 2022-08-03 Tokyo Institute of Technology Information processing device, information processing method, recording medium recording information processing program, and information processing system
EP4281112A4 (en) 2021-01-21 2025-01-15 Twist Bioscience Corporation METHODS AND COMPOSITIONS RELATING TO ADENOSINE RECEPTORS
US12258406B2 (en) 2021-03-24 2025-03-25 Twist Bioscience Corporation Antibodies that bind CD3 Epsilon
WO2022271884A2 (en) 2021-06-22 2022-12-29 Twist Bioscience Corporation Methods and compositions relating to covid antibody epitopes
WO2023069985A1 (en) * 2021-10-19 2023-04-27 Battelle Memorial Institute Technologies for genetic engineering detection
AU2022390457A1 (en) 2021-11-18 2024-06-20 Twist Bioscience Corporation Dickkopf-1 variant antibodies and methods of use
WO2023130123A2 (en) 2022-01-03 2023-07-06 Twist Bioscience Corporation Bispecific sars-cov-2 antibodies and methods of use

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20090170802A1 (en) 1999-02-19 2009-07-02 Febit Holding Gmbh Method for producing polymers
US20100292102A1 (en) 2009-05-14 2010-11-18 Ali Nouri System and Method For Preventing Synthesis of Dangerous Biological Sequences
US20110172127A1 (en) 2008-08-27 2011-07-14 Westemd Asset Clearinghouse Company, LLC Methods and Devices for High Fidelity Polynucleotide Synthesis
US20150120265A1 (en) * 2011-09-01 2015-04-30 Genome Compiler Corporation System for polynucleotide construct design, visualization and transactions to manufacture the same
US20160096160A1 (en) 2013-08-05 2016-04-07 Twist Bioscience Corporation De novo synthesized gene libraries

Family Cites Families (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5701256A (en) * 1995-05-31 1997-12-23 Cold Spring Harbor Laboratory Method and apparatus for biological sequence comparison
EP1789786A4 (en) * 2004-08-18 2008-02-13 Abbott Molecular Inc DETERMINING DATA QUALITY AND / OR SEGMENTAL ANEUMS USING A COMPUTER SYSTEM
EP2718862B1 (en) * 2011-06-06 2018-10-31 Koninklijke Philips N.V. Method for assembly of nucleic acid sequence data
CN104871164B (zh) * 2012-10-24 2019-02-05 南托米克斯有限责任公司 处理和呈现基因组序列数据中核苷酸变化的基因组浏览器系统

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20090170802A1 (en) 1999-02-19 2009-07-02 Febit Holding Gmbh Method for producing polymers
US20110172127A1 (en) 2008-08-27 2011-07-14 Westemd Asset Clearinghouse Company, LLC Methods and Devices for High Fidelity Polynucleotide Synthesis
US20100292102A1 (en) 2009-05-14 2010-11-18 Ali Nouri System and Method For Preventing Synthesis of Dangerous Biological Sequences
US20150120265A1 (en) * 2011-09-01 2015-04-30 Genome Compiler Corporation System for polynucleotide construct design, visualization and transactions to manufacture the same
US20160096160A1 (en) 2013-08-05 2016-04-07 Twist Bioscience Corporation De novo synthesized gene libraries

Also Published As

Publication number Publication date
SG11201811025VA (en) 2019-01-30
JP2022181213A (ja) 2022-12-07
CA3027127A1 (en) 2017-12-14
KR20190017932A (ko) 2019-02-20
US20170357752A1 (en) 2017-12-14
JP2019523940A (ja) 2019-08-29
EP3469499A1 (en) 2019-04-17
CN109564769A (zh) 2019-04-02
EP3469499A4 (en) 2020-10-21
WO2017214574A1 (en) 2017-12-14

Similar Documents

Publication Publication Date Title
KR102476915B1 (ko) 생물학적 서열의 자동화된 주석달기 및 스크리닝을 위한 시스템 및 방법
Sachdeva et al. Unraveling the role of cloud computing in health care system and biomedical sciences
Narzisi et al. Comparing de novo genome assembly: the long and short of it
US20210319907A1 (en) Multi-omic search engine for integrative analysis of cancer genomic and clinical data
Zhang et al. Recent methodological advances in federated learning for healthcare
Ruzicka et al. ZFIN, The zebrafish model organism database: Updates and new directions
Wegrzyn et al. TreeGenes: a forest tree genome database
US20190392928A1 (en) Personal data marketplace for genetic, fitness, and medical information including health trust management
CN113169957A (zh) 个人医疗数据安全共享和所有权去中心化的所有权系统
JP2017537365A (ja) 患者データに基づく健康診断および治療のためのベイジアン因果関係ネットワークモデル
Song et al. New whole-genome alignment tools are needed for tapping into plant diversity
WO2013150039A1 (en) Systems and methods for disease knowledge modeling and clinical decision support
Shah et al. Seasonal antigenic prediction of influenza A H3N2 using machine learning
Seth et al. Securing bioinformatics cloud for big data: Budding buzzword or a glance of the future
Berman et al. MutaGAN: A sequence-to-sequence GAN framework to predict mutations of evolving protein populations
US20180330061A1 (en) Treatment Recommendation System And Method
Xiao et al. Challenges, solutions, and quality metrics of personal genome assembly in advancing precision medicine
Chen et al. Running ahead of evolution—AI-based simulation for predicting future high-risk SARS-CoV-2 variants
Chen et al. Extension of SEIR compartmental models for constructive Lyapunov control of COVID-19 and analysis in terms of practical stability
Teodoro et al. A Scoping Review of Artificial Intelligence Applications in Clinical Trial Risk Assessment
US20200202987A1 (en) System and method for computerized synthesis of simulated health data
Lvovs et al. Balancing ethical data sharing and open science for reproducible research in biomedical data science
Schulte et al. HOGVAX: Exploiting epitope overlaps to maximize population coverage in vaccine design with application to SARS-CoV-2
Getz et al. A runtime alterable epidemic model with genetic drift, waning immunity and vaccinations
Etchings Strategies in biomedical data science: driving force for innovation

Legal Events

Date Code Title Description
PA0105 International application

Patent event date: 20190109

Patent event code: PA01051R01D

Comment text: International Patent Application

PG1501 Laying open of application
AMND Amendment
PA0201 Request for examination

Patent event code: PA02012R01D

Patent event date: 20200604

Comment text: Request for Examination of Application

E902 Notification of reason for refusal
PE0902 Notice of grounds for rejection

Comment text: Notification of reason for refusal

Patent event date: 20211111

Patent event code: PE09021S01D

AMND Amendment
E601 Decision to refuse application
PE0601 Decision on rejection of patent

Patent event date: 20220515

Comment text: Decision to Refuse Application

Patent event code: PE06012S01D

Patent event date: 20211111

Comment text: Notification of reason for refusal

Patent event code: PE06011S01I

AMND Amendment
PX0901 Re-examination

Patent event code: PX09011S01I

Patent event date: 20220515

Comment text: Decision to Refuse Application

Patent event code: PX09012R01I

Patent event date: 20220111

Comment text: Amendment to Specification, etc.

Patent event code: PX09012R01I

Patent event date: 20200604

Comment text: Amendment to Specification, etc.

PX0701 Decision of registration after re-examination

Patent event date: 20220908

Comment text: Decision to Grant Registration

Patent event code: PX07013S01D

Patent event date: 20220816

Comment text: Amendment to Specification, etc.

Patent event code: PX07012R01I

Patent event date: 20220515

Comment text: Decision to Refuse Application

Patent event code: PX07011S01I

Patent event date: 20220111

Comment text: Amendment to Specification, etc.

Patent event code: PX07012R01I

Patent event date: 20200604

Comment text: Amendment to Specification, etc.

Patent event code: PX07012R01I

X701 Decision to grant (after re-examination)
GRNT Written decision to grant
PR0701 Registration of establishment

Comment text: Registration of Establishment

Patent event date: 20221208

Patent event code: PR07011E01D

PR1002 Payment of registration fee

Payment date: 20221208

End annual number: 3

Start annual number: 1

PG1601 Publication of registration