JP7689737B2 - シングルセルRNA-Seq解析のカウントデータセットの補正方法、シングルセルRNA-Seqの解析方法、細胞種の構成比率の解析方法、並びにこれらの方法を実行するための装置及びコンピュータプログラム - Google Patents

シングルセルRNA-Seq解析のカウントデータセットの補正方法、シングルセルRNA-Seqの解析方法、細胞種の構成比率の解析方法、並びにこれらの方法を実行するための装置及びコンピュータプログラム Download PDF

Info

Publication number
JP7689737B2
JP7689737B2 JP2021576209A JP2021576209A JP7689737B2 JP 7689737 B2 JP7689737 B2 JP 7689737B2 JP 2021576209 A JP2021576209 A JP 2021576209A JP 2021576209 A JP2021576209 A JP 2021576209A JP 7689737 B2 JP7689737 B2 JP 7689737B2
Authority
JP
Japan
Prior art keywords
cell
rna
analysis
seq
count data
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
JP2021576209A
Other languages
English (en)
Japanese (ja)
Other versions
JPWO2021157739A1 (https=
Inventor
匠徳 佐藤
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.)
Karydo TherapeutiX Inc
Original Assignee
Karydo TherapeutiX 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
Application filed by Karydo TherapeutiX Inc filed Critical Karydo TherapeutiX Inc
Publication of JPWO2021157739A1 publication Critical patent/JPWO2021157739A1/ja
Application granted granted Critical
Publication of JP7689737B2 publication Critical patent/JP7689737B2/ja
Active legal-status Critical Current
Anticipated expiration legal-status Critical

Links

Images

Classifications

    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6809Methods for determination or identification of nucleic acids involving differential detection
    • 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
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869Methods for sequencing
    • 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
    • G16B25/00ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • 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
    • G16B40/00ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • 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
    • G16B40/00ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20Supervised data analysis

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Chemical & Material Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Medical Informatics (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Evolutionary Biology (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Organic Chemistry (AREA)
  • Molecular Biology (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Data Mining & Analysis (AREA)
  • Bioethics (AREA)
  • Artificial Intelligence (AREA)
  • Software Systems (AREA)
  • Evolutionary Computation (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Public Health (AREA)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
JP2021576209A 2020-02-06 2021-02-06 シングルセルRNA-Seq解析のカウントデータセットの補正方法、シングルセルRNA-Seqの解析方法、細胞種の構成比率の解析方法、並びにこれらの方法を実行するための装置及びコンピュータプログラム Active JP7689737B2 (ja)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
JP2020018989 2020-02-06
JP2020018989 2020-02-06
PCT/JP2021/004470 WO2021157739A1 (ja) 2020-02-06 2021-02-06 シングルセルRNA-Seq解析のカウントデータセットの補正方法、シングルセルRNA-Seqの解析方法、細胞種の構成比率の解析方法、並びにこれらの方法を実行するための装置及びコンピュータプログラム

Publications (2)

Publication Number Publication Date
JPWO2021157739A1 JPWO2021157739A1 (https=) 2021-08-12
JP7689737B2 true JP7689737B2 (ja) 2025-06-09

Family

ID=77199636

Family Applications (1)

Application Number Title Priority Date Filing Date
JP2021576209A Active JP7689737B2 (ja) 2020-02-06 2021-02-06 シングルセルRNA-Seq解析のカウントデータセットの補正方法、シングルセルRNA-Seqの解析方法、細胞種の構成比率の解析方法、並びにこれらの方法を実行するための装置及びコンピュータプログラム

Country Status (6)

Country Link
US (1) US20230074644A1 (https=)
EP (1) EP4101933A4 (https=)
JP (1) JP7689737B2 (https=)
CA (1) CA3170368A1 (https=)
IL (1) IL295227A (https=)
WO (1) WO2021157739A1 (https=)

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2019018684A1 (en) 2017-07-21 2019-01-24 The Board Of Trustees Of The Leland Stanford Junior University SYSTEMS AND METHODS FOR ANALYZING MIXED CELL POPULATIONS

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2019018684A1 (en) 2017-07-21 2019-01-24 The Board Of Trustees Of The Leland Stanford Junior University SYSTEMS AND METHODS FOR ANALYZING MIXED CELL POPULATIONS

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
KANG K. et al.,CDSeq: A novel complete deconvolution method for dissecting heterogeneous samples using gene express,PLOS Computational Biology,2019年,Vol.15, No.12, e1007510
MONACO G. et al.,RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Ty,Cell Reports,2019年,Vol.26, p.1627-1640
TSOUCAS D. et al.,Accurate estimation of cell-type composition from gene expression data,NATURE COMMUNICATIONS,2019年,Vol.10, 2975

Also Published As

Publication number Publication date
US20230074644A1 (en) 2023-03-09
WO2021157739A1 (ja) 2021-08-12
CA3170368A1 (en) 2021-08-12
EP4101933A4 (en) 2024-02-28
EP4101933A1 (en) 2022-12-14
IL295227A (en) 2022-10-01
JPWO2021157739A1 (https=) 2021-08-12

Similar Documents

Publication Publication Date Title
US11676684B2 (en) Artificial intelligence model for predicting actions of test substance in humans
CN111653359B (zh) 一种出血性疾病的智能预测模型构建方法和预测系统
CN110782945B (zh) 一种利用间接与直接特征信息识别lncRNA与疾病关联的方法
US20220076832A1 (en) Prediction device based on inter-organ cross talk system
WO2021145434A1 (ja) 目的とする薬剤又はその等価物質の適応症の予測方法、予測装置、及び予測プログラム
CN116825178A (zh) 疾病相关可变剪接异构体预测模型建立及其预测方法
Prado et al. Genomic resources for Asian (Elephas maximus) and African savannah elephant (Loxodonta africana) conservation and health research
JP7689737B2 (ja) シングルセルRNA-Seq解析のカウントデータセットの補正方法、シングルセルRNA-Seqの解析方法、細胞種の構成比率の解析方法、並びにこれらの方法を実行するための装置及びコンピュータプログラム
Tabula Microcebus Consortium de Morree Antoine 8 9 De Vlaminck Iwijn 19 Shapiro Liza 25 Razafindrakoto Andriamahery 26 Ravelonjanahary Hajanirina Noëline 26 Wright Patricia 27 Yoder Anne D. 28 Williams Cathy V. 29 Schopler Robert 29 Radespiel Ute 30 Verdier Jean-Michel 31 Lautier Corinne 31 Kirk E. Christopher 25 Lewis Rebecca 25 Gillich Astrid 1 2 Zhao Zicheng 2 20 Godoy Elias 20 Terrien Jérémy 16 Epelbaum Jacques 16 32 Gratzinger Dita 33 Lucot Katherine 33 Montine Thomas 33 D’Addabbo Jessica 4 34 Bakerman Isaac 4 Nguyen Patricia 4 12 34 Kershner Aaron 1 14 Mrouj Karim 14 Beachy Philip 3 13 14 35 Ambrosi Thomas H. 14 Hoover Malachia 14 Alam Alina 14 Chan Charles 14 Jang SoRi 1 2 Veerakumar Avin 1 2 7 Li Peng 1 2 Yung Andrea R. 1 2 Duffy Connor V. 2 18 Ding Song-Lin 36 Lein Ed S. 36 Konermann Silvana 1 2 Luo Liqun 2 15 Bakken Trygve E. 36 Kebschull Justus M. 37 Hodge Rebecca D. 36 Isobe Taichi 38 Clarke Michael F. 14 Bilen Biter 8 Farup Jean 8 9 Urtasun Andoni 8 Kang Jengmin 8 Chen Ming 18 Li BaoXiang 39 Subramaniam Varun Ramanan 39 Mukherjee Shravani 39 Swarup Aditi 39 Kim Lily 18 Scott Bronwyn 39 Al-Moujahed Ahmad 39 Wu Albert Y. 39 Vollrath Douglas 18 Schaum Nicholas 8 Wiggenhorn Amanda L. 33 40 Wyss-Coray Tony 8 41 Long Jonathan Z. 33 42 Liu Yin 1 2 Nabhan Ahmad 1 2 Loeb Gabriel 43 Lin Shengda 44 Paine Honor 45 Burhan Deviana 45 Taychameekiatchai Aris 45 Wang Bruce 45 Espinoza F. Hernán 1 2 Kuo Christin 46 Metzger Ross 4 46 Qi Zhen 14 Culver Rebecca 18 Huang Kerwyn C. 6 7 47 Neuhöfer Patrick 1 11 12 Chang Charles A. 13 48 Hang Yan 13 48 Kim Seung K. 12 13 48 49 Weinstein Hannah NW 50 51 52 Allegakoen Paul 50 Huang Franklin W. 50 Sivakamasundari V 14 Lee Song Eun 8 41 Frank Hannah K. 33 53 Boyd Scott D. 33 Lu Wan-Jin 14 Baghel Ankit 15 Kong William 14 Israel Carly 6 Maynard Ashley 6 Tan Michelle 6 Ouadah Youcef 1 Baruni Jalal 1 2 15 54 Wu Timothy Ting-Hsuan 1 2 Jones Robert C. 8 Darmanis Spyros 6 Crasta Sheela 6 Yan Jia 6 Agrawal Aditi 6 Huynh Shelly 6 Yu Brian 6 Webber James 6 Tan Weilun 6 Nafees Saba 6 Li Zhengda 3 Wang Michael FZ 19 55 Dehghannasiri Roozbeh 1 56 Olivieri Julia 1 57 Salzman Julia 1 56 Guethlein Lisbeth A. 47 58 Parham Peter 47 58 Jing Qiuyu 21 Antony Jane 14 Stanley Geoff 7 Yang Jinxurong 21 Koh Winston 59 60 Wang Sheng 61 Agarwal Snigdha 6 Awayan Kyle 6 McGeever Erin 6 Vemuri Venkata NP 6 Lalgudi Pranav V. 1 18 et al. A molecular cell atlas of mouse lemur, an emerging model primate
Sandel et al. Primate behavior and the importance of comparative studies in biological anthropology
Nguyen et al. Efficient discretization approaches for machine learning techniques to improve disease classification on gut microbiome composition data
Xiong et al. Chord: identifying doublets in single-cell RNA sequencing data by an ensemble machine learning algorithm
CN117219167B (zh) 一种样本间差异的归因方法、装置、电子设备及存储介质
CN114678072B (zh) 一种基因表达数据处理方法及其相关设备
CN111192244A (zh) 一种基于关键点确定舌部特征的方法及系统
US20260074020A1 (en) Genetic data processing
Kelemen Modelling human complex traits with regression and neural-network based methods
e Cunha Neural Networks for 2D Representations of Cell Expression
Jethnani Statistical analysis of rare genetic variants in the first exon of the ataxin-2 gene in patients with neurodegenerative diseases
JP2025009997A (ja) 保険料算出システム及び保険料算出方法
Brown Gene Expression Normalization for Sparse Or Heterogenous MRNA Sequencing Data and Time-course Study of Embriological Developmental Timing in Chimeric Tissues
CN119905146A (zh) 基于深度学习的核酸细胞粒度反卷积方法及装置
WO2026035198A1 (en) Brain foundation models adapted to downstream tasks
HK40114901A (zh) 婴幼儿肠道菌群发育成熟度判别方法和装置
Fischer Statistical Methods and Analyses in Computational Genomics: Explorations of Eukaryotic Transcription

Legal Events

Date Code Title Description
A621 Written request for application examination

Free format text: JAPANESE INTERMEDIATE CODE: A621

Effective date: 20240117

A131 Notification of reasons for refusal

Free format text: JAPANESE INTERMEDIATE CODE: A131

Effective date: 20250107

A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20250306

TRDD Decision of grant or rejection written
A01 Written decision to grant a patent or to grant a registration (utility model)

Free format text: JAPANESE INTERMEDIATE CODE: A01

Effective date: 20250513

A61 First payment of annual fees (during grant procedure)

Free format text: JAPANESE INTERMEDIATE CODE: A61

Effective date: 20250521

R150 Certificate of patent or registration of utility model

Ref document number: 7689737

Country of ref document: JP

Free format text: JAPANESE INTERMEDIATE CODE: R150