BR112018003631A2 - sistemas e métodos para busca por variante de alta precisão - Google Patents
sistemas e métodos para busca por variante de alta precisãoInfo
- 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
- Authority
- BR
- Brazil
- Prior art keywords
- systems
- hla
- methods
- high precision
- type
- Prior art date
Links
Classifications
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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
Landscapes
- 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.
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) |
Families Citing this family (21)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
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 |
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 |
Family Cites Families (19)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US20100261189A1 (en) * | 2008-10-03 | 2010-10-14 | Roche Molecular Systems, Inc. | System and method for detection of HLA Variants |
DK2511843T3 (en) * | 2009-04-29 | 2017-03-27 | Complete Genomics Inc | METHOD AND SYSTEM FOR DETERMINING VARIATIONS IN A SAMPLE POLYNUCLEOTIDE SEQUENCE IN TERMS OF A REFERENCE POLYNUCLEOTIDE SEQUENCE |
US20130267429A1 (en) | 2009-12-21 | 2013-10-10 | Lawrence Livermore National Security, Llc | Biological sample target classification, detection and selection methods, and related arrays and oligonucleotide probes |
US20140228223A1 (en) * | 2010-05-10 | 2014-08-14 | Andreas Gnirke | High throughput paired-end sequencing of large-insert clone libraries |
US20140114584A1 (en) | 2012-10-08 | 2014-04-24 | Spiral Genetics Inc. | Methods and systems for identifying, from read symbol sequences, variations with respect to a reference symbol sequence |
US9181583B2 (en) | 2012-10-23 | 2015-11-10 | Illumina, Inc. | HLA typing using selective amplification and sequencing |
EP2931042B1 (en) | 2012-12-13 | 2021-04-28 | CytRx Corporation | Anthracycline formulations |
US9562269B2 (en) | 2013-01-22 | 2017-02-07 | The Board Of Trustees Of The Leland Stanford Junior University | Haplotying of HLA loci with ultra-deep shotgun sequencing |
CN105307724A (zh) | 2013-06-05 | 2016-02-03 | 西特克斯公司 | 用于治疗癌症的细胞毒素剂 |
JP2015035212A (ja) | 2013-07-29 | 2015-02-19 | アジレント・テクノロジーズ・インクAgilent Technologies, Inc. | ターゲットシークエンシングパネルから変異を見つける方法 |
US10162933B2 (en) * | 2013-10-15 | 2018-12-25 | Regeneron Pharmaceuticals, Inc. | High resolution allele identification |
CN103699819B (zh) | 2013-12-10 | 2016-09-07 | 深圳先进技术研究院 | 基于多步双向De Bruijn图的变长kmer查询的顶点扩展方法 |
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) |
SG11201808058PA (en) | 2016-03-18 | 2018-10-30 | Nantcell Inc | Multimodal vector for dendritic cell infection |
KR20210010678A (ko) | 2016-06-30 | 2021-01-27 | 난트 홀딩스 아이피, 엘엘씨 | 난트 암 백신 |
US20200352972A1 (en) | 2017-09-06 | 2020-11-12 | Nantcell, Inc. | Aldoxorubicin combination treatments and methods |
-
2016
- 2016-08-25 RU RU2018106934A patent/RU2018106934A/ru not_active Application Discontinuation
- 2016-08-25 MX MX2018002293A patent/MX2018002293A/es unknown
- 2016-08-25 BR BR112018003631A patent/BR112018003631A2/pt not_active IP Right Cessation
- 2016-08-25 CA CA2996702A patent/CA2996702C/en active Active
- 2016-08-25 EP EP16840152.9A patent/EP3341877B1/en active Active
- 2016-08-25 KR KR1020197020554A patent/KR102211461B1/ko active IP Right Grant
- 2016-08-25 CN CN201680054282.0A patent/CN108351917B/zh active Active
- 2016-08-25 WO PCT/US2016/048768 patent/WO2017035392A1/en active Application Filing
- 2016-08-25 AU AU2016311444A patent/AU2016311444B2/en active Active
- 2016-08-25 KR KR1020187008056A patent/KR102011440B1/ko active IP Right Grant
- 2016-08-25 US US15/755,095 patent/US11393557B2/en active Active
- 2016-08-25 JP JP2018510056A patent/JP6533011B2/ja active Active
-
2018
- 2018-02-25 IL IL257724A patent/IL257724B/en active IP Right Grant
- 2018-11-19 IL IL263115A patent/IL263115B/en active IP Right Grant
- 2018-12-18 HK HK18116187.9A patent/HK1257052A1/zh unknown
-
2019
- 2019-03-18 AU AU2019201869A patent/AU2019201869A1/en not_active Abandoned
- 2019-05-22 JP JP2019095951A patent/JP6883180B2/ja active Active
-
2022
- 2022-06-16 US US17/842,519 patent/US20220319640A1/en active Pending
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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