BR112018003631A2 - sistemas e métodos para busca por variante de alta precisão - Google Patents

sistemas e métodos para busca por variante de alta precisão

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Publication number
BR112018003631A2
BR112018003631A2 BR112018003631A BR112018003631A BR112018003631A2 BR 112018003631 A2 BR112018003631 A2 BR 112018003631A2 BR 112018003631 A BR112018003631 A BR 112018003631A BR 112018003631 A BR112018003631 A BR 112018003631A BR 112018003631 A2 BR112018003631 A2 BR 112018003631A2
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BR
Brazil
Prior art keywords
systems
hla
methods
high precision
type
Prior art date
Application number
BR112018003631A
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English (en)
Inventor
Zachary Sanborn John
Original Assignee
Nantomics Llc
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Publication date
Application filed by Nantomics Llc filed Critical Nantomics Llc
Publication of BR112018003631A2 publication Critical patent/BR112018003631A2/pt

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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
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/40—Population genetics; Linkage disequilibrium
    • 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
    • G16B30/10—Sequence alignment; Homology search
    • 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
    • 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
    • G16B45/00—ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
    • 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
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
    • G16C20/60—In silico combinatorial chemistry

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  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Theoretical Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Chemical & Material Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Molecular Biology (AREA)
  • Genetics & Genomics (AREA)
  • Bioethics (AREA)
  • Data Mining & Analysis (AREA)
  • Databases & Information Systems (AREA)
  • Physiology (AREA)
  • Ecology (AREA)
  • Biochemistry (AREA)
  • Library & Information Science (AREA)
  • Medicinal Chemistry (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Computing Systems (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)

Abstract

são apresentados sistemas e métodos para predição in silico do tipo de hla de um paciente em que as leituras de sequência de paciente e uma sequência de referência com alelos de hla conhecidos e distintos são usadas em um gráfico de de bruijn. uma pontuação compatível de compósito é, então, usada para classificar alelos de hla, desse modo, fornecendo um primeiro tipo de hla. um segundo tipo de hla é identificado reclassificando-se uma pontuação compatível de compósito ajustada.
BR112018003631A 2015-08-25 2016-08-25 sistemas e métodos para busca por variante de alta precisão BR112018003631A2 (pt)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201562209858P 2015-08-25 2015-08-25
PCT/US2016/048768 WO2017035392A1 (en) 2015-08-25 2016-08-25 Systems and methods for high-accuracy variant calling

Publications (1)

Publication Number Publication Date
BR112018003631A2 true BR112018003631A2 (pt) 2018-09-25

Family

ID=58101056

Family Applications (1)

Application Number Title Priority Date Filing Date
BR112018003631A BR112018003631A2 (pt) 2015-08-25 2016-08-25 sistemas e métodos para busca por variante de alta precisão

Country Status (13)

Country Link
US (2) US11393557B2 (pt)
EP (1) EP3341877B1 (pt)
JP (2) JP6533011B2 (pt)
KR (2) KR102211461B1 (pt)
CN (1) CN108351917B (pt)
AU (2) AU2016311444B2 (pt)
BR (1) BR112018003631A2 (pt)
CA (1) CA2996702C (pt)
HK (1) HK1257052A1 (pt)
IL (2) IL257724B (pt)
MX (1) MX2018002293A (pt)
RU (1) RU2018106934A (pt)
WO (1) WO2017035392A1 (pt)

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RU2018106934A (ru) 2015-08-25 2019-09-26 Нантомикс, Ллс Системы и способы высокоточного определения вариантов
AU2016339022B2 (en) 2015-10-12 2020-09-10 Nantomics, Llc Iterative discovery of neoepitopes and adaptive immunotherapy and methods therefor
JP2018532736A (ja) 2015-10-12 2018-11-08 ナントミクス，エルエルシー チェックポイント阻害物質への感受性を予測するｍｓｉおよびネオエピトープの探索のための系、組成物、および方法
TW201739919A (zh) 2016-02-12 2017-11-16 南坦生物組學有限責任公司 患者特異性新抗原決定基之高通量識別以作為用於癌症免疫療法之治療劑
SG11201807770RA (en) 2016-03-24 2018-10-30 Nantcell Inc Sequence arrangements and sequences for neoepitope presentation
KR20210010678A (ko) 2016-06-30 2021-01-27 난트 홀딩스 아이피, 엘엘씨 난트 암 백신
US10319465B2 (en) * 2016-11-16 2019-06-11 Seven Bridges Genomics Inc. Systems and methods for aligning sequences to graph references
WO2018094309A2 (en) 2016-11-21 2018-05-24 Nant Holdings Ip, Llc Fractal combination therapy
CA3045811A1 (en) 2016-12-01 2018-06-07 Nantomics, Llc Tumor antigenicity processing and presentation
AU2018258119B2 (en) 2017-04-24 2021-04-01 Nantcell, Inc. Targeted neoepitope vectors and methods therefor
EP3933408A1 (en) 2017-05-30 2022-01-05 Nant Holdings IP LLC Circulating tumor cell enrichment using neoepitopes
US11646103B2 (en) * 2017-09-06 2023-05-09 Nant Holdings Ip, Llc HLA tissue matching and methods therefor
US11823773B2 (en) 2018-04-13 2023-11-21 Nant Holdings Ip, Llc Nant cancer vaccine strategies
US11564980B2 (en) 2018-04-23 2023-01-31 Nantcell, Inc. Tumor treatment method with an individualized peptide vaccine
TW202345890A (zh) 2018-04-23 2023-12-01 美商南特細胞公司 新抗原表位疫苗及免疫刺激組合物及方法
US20220108768A1 (en) * 2019-03-08 2022-04-07 Nantomics, Llc System and method for variant calling
CN112885406B (zh) * 2020-04-16 2023-01-31 深圳裕策生物科技有限公司 检测hla杂合性缺失的方法及***
CN112289376B (zh) * 2020-10-26 2021-07-06 北京吉因加医学检验实验室有限公司 一种检测体细胞突变的方法及装置
CN114496077B (zh) * 2022-04-15 2022-06-21 北京贝瑞和康生物技术有限公司 用于检测单核苷酸变异和***缺失的方法、设备和介质
KR20240072026A (ko) * 2022-11-16 2024-05-23 주식회사 세니젠 기준 서열 데이터와 타겟 및 비-타겟종의 교차검증을 활용한, PCR을 위한 K-mer 유전자 데이터 프로세싱 방법 및 그 장치

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JP7060324B2 (ja) 2013-12-20 2022-04-26 ザ・ブロード・インスティテュート・インコーポレイテッド ネオ抗原ワクチンによる併用療法
US20190099475A1 (en) 2015-04-08 2019-04-04 Nantomics, Llc Cancer neoepitopes
RU2018106934A (ru) 2015-08-25 2019-09-26 Нантомикс, Ллс Системы и способы высокоточного определения вариантов
KR20180107257A (ko) 2016-02-19 2018-10-01 난트 홀딩스 아이피, 엘엘씨 면역원 조절 방법 (methods of immunogenic modulation)
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Also Published As

Publication number Publication date
JP2018533111A (ja) 2018-11-08
US20220319640A1 (en) 2022-10-06
CA2996702C (en) 2020-07-14
US20180237949A1 (en) 2018-08-23
US11393557B2 (en) 2022-07-19
JP6883180B2 (ja) 2021-06-09
CN108351917A (zh) 2018-07-31
EP3341877A4 (en) 2018-10-03
KR102011440B1 (ko) 2019-08-16
IL257724B (en) 2018-11-29
CN108351917B (zh) 2022-03-08
CA2996702A1 (en) 2017-03-02
AU2019201869A1 (en) 2019-04-11
EP3341877B1 (en) 2023-05-10
EP3341877A1 (en) 2018-07-04
KR102211461B1 (ko) 2021-02-03
AU2016311444A1 (en) 2018-03-15
WO2017035392A1 (en) 2017-03-02
IL263115B (en) 2020-06-30
AU2016311444B2 (en) 2019-02-07
RU2018106934A (ru) 2019-09-26
MX2018002293A (es) 2018-09-05
HK1257052A1 (zh) 2019-10-11
KR20180058718A (ko) 2018-06-01
JP6533011B2 (ja) 2019-06-19
RU2018106934A3 (pt) 2019-09-26
IL263115A (en) 2018-12-31
KR20190090022A (ko) 2019-07-31
JP2019169177A (ja) 2019-10-03

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