Statstical Genetics Summer School 2023
http://www.sg.med.osaka-u.ac.jp/school_2023.html
Aug 25-27th 2023, Osaka University, The University of Tokyo, RIKENm, Japan
This document provides an overview of comparative genomics. It defines comparative genomics as combining genomic data and evolutionary biology to study genome structure, evolution and function. It discusses three levels of genome comparison: bulk properties like chromosome size and number, whole genome sequence similarity and organization, and functional genome features. The history of experimental comparative genomics is reviewed, noting that practical comparisons predated widespread genome sequencing.
Statstical Genetics Summer School 2023
http://www.sg.med.osaka-u.ac.jp/school_2023.html
Aug 25-27th 2023, Osaka University, The University of Tokyo, RIKENm, Japan
Tokyo Medical and Dental University (TMDU) bioresouroce center (BRC) seminor slide by Yukinori Okada on Dec 10, 2013.
http://plaza.umin.ac.jp/~yokada/
http://plaza.umin.ac.jp/~yokada/datasource/software.htm
Part 4 of RNA-seq for DE analysis: Extracting count table and QCJoachim Jacob
Fourth part of the training session 'RNA-seq for Differential expression analysis'. We explain how we get a count table from a mapping result. We show how to do quality control on the count table. Interested in following this session? Please contact http://www.jakonix.be/contact.html
Part 1 of RNA-seq for DE analysis: Defining the goalJoachim Jacob
First part of the training session 'RNA-seq for Differential expression' analysis. We explain how we can detect differential expression based on RNA-seq data. Interested in following this session? Please contact http://www.jakonix.be/contact.html
This document discusses the use of single-cell RNA sequencing (scRNA-seq) to study brain tumors. It compares different scRNA-seq approaches and discusses challenges of working with clinical tumor samples. The document outlines how scRNA-seq can be used to answer questions about tumor cell subtypes and immune cell profiles in brain tumors. Specifically, it describes a study that used scRNA-seq to identify gene signatures that distinguish tumor-associated macrophages by their origin in glioma samples.
This document provides an overview of comparative genomics. It defines comparative genomics as combining genomic data and evolutionary biology to study genome structure, evolution and function. It discusses three levels of genome comparison: bulk properties like chromosome size and number, whole genome sequence similarity and organization, and functional genome features. The history of experimental comparative genomics is reviewed, noting that practical comparisons predated widespread genome sequencing.
Statstical Genetics Summer School 2023
http://www.sg.med.osaka-u.ac.jp/school_2023.html
Aug 25-27th 2023, Osaka University, The University of Tokyo, RIKENm, Japan
Tokyo Medical and Dental University (TMDU) bioresouroce center (BRC) seminor slide by Yukinori Okada on Dec 10, 2013.
http://plaza.umin.ac.jp/~yokada/
http://plaza.umin.ac.jp/~yokada/datasource/software.htm
Part 4 of RNA-seq for DE analysis: Extracting count table and QCJoachim Jacob
Fourth part of the training session 'RNA-seq for Differential expression analysis'. We explain how we get a count table from a mapping result. We show how to do quality control on the count table. Interested in following this session? Please contact http://www.jakonix.be/contact.html
Part 1 of RNA-seq for DE analysis: Defining the goalJoachim Jacob
First part of the training session 'RNA-seq for Differential expression' analysis. We explain how we can detect differential expression based on RNA-seq data. Interested in following this session? Please contact http://www.jakonix.be/contact.html
This document discusses the use of single-cell RNA sequencing (scRNA-seq) to study brain tumors. It compares different scRNA-seq approaches and discusses challenges of working with clinical tumor samples. The document outlines how scRNA-seq can be used to answer questions about tumor cell subtypes and immune cell profiles in brain tumors. Specifically, it describes a study that used scRNA-seq to identify gene signatures that distinguish tumor-associated macrophages by their origin in glioma samples.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.3- Introduction to NGS Variant Calling Analysis.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
RNA-seq for DE analysis: detecting differential expression - part 5BITS
Part 5 of the training sesson 'RNA-seq for differential expression analysis' considers the algorithm used for detecting differential expression between conditions. See http://www.bits.vib.be
Abstract: The focus in this session will be put on the differences between standard DNA mapping and RNAseq-specific transcript mapping: identifying splice variants and isoforms. The issue of transcript quantification and genomic variants that can be identified from RNAseq data will be discussed.
This document provides an overview of genomics and related fields. It discusses the historical discoveries that laid the foundations of genomics. It then defines key genomics terms and describes different areas of genomics research like comparative genomics, metagenomics, structural genomics, functional genomics, transcriptomics, proteomics and metabolomics. The document also discusses genome sequencing techniques, genome organization of different organisms like bacteria, plants and humans. It concludes with an overview of genome mapping methods.
Statstical Genetics Summer School 2023
http://www.sg.med.osaka-u.ac.jp/school_2023.html
Aug 25-27th 2023, Osaka University, The University of Tokyo, RIKENm, Japan
Role of Pangenomics for crop ImprovementPatelSupriya
It describes about the role of pangenomics in the crop improvement.It includes pangenome,superpangenome,databases,tools used in pangenomics,utilisation in crop improvement
BITS - Comparative genomics on the genome levelBITS
This is the third presentation of the BITS training on 'Comparative genomics'.
It reviews the basic concepts of sequence homology on the gene
Thanks to Klaas Vandepoele of the PSB department.
This document provides an overview of essential bioinformatics resources for designing PCR primers and oligos for various applications. It begins by outlining general rules for PCR primer design, including recommendations for primer length, melting temperature, specificity, secondary structures, and other factors. It then describes several online tools and databases for designing primers for general purpose PCR, real-time qPCR, methylation studies, and other applications. These resources include Primer3, Primer3Plus, PrimerZ, and Vector NTI. Databases like NCBI Probe and RTPrimerDB provide validated primer sequences. The document emphasizes considering multiple design tools and validation of primers.
The ClinGen Sequence Variant Interpretation Working Group: Refining Criteria ...Human Variome Project
The ClinGen Sequence Variant Interpretation Working Group aims to refine criteria for classifying genetic variants by standardizing how different types of evidence are integrated. In the short term, it will refine and modify current American College of Medical Genetics guidelines. It will work with disease-specific groups to evaluate criteria like population frequency thresholds and computational methods. The long term goal is to develop a quantitative Bayesian framework to classify variants. The working group will analyze ClinVar to identify disease genes with many reported variants to help evaluate criteria.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.3- Introduction to NGS Variant Calling Analysis.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
RNA-seq for DE analysis: detecting differential expression - part 5BITS
Part 5 of the training sesson 'RNA-seq for differential expression analysis' considers the algorithm used for detecting differential expression between conditions. See http://www.bits.vib.be
Abstract: The focus in this session will be put on the differences between standard DNA mapping and RNAseq-specific transcript mapping: identifying splice variants and isoforms. The issue of transcript quantification and genomic variants that can be identified from RNAseq data will be discussed.
This document provides an overview of genomics and related fields. It discusses the historical discoveries that laid the foundations of genomics. It then defines key genomics terms and describes different areas of genomics research like comparative genomics, metagenomics, structural genomics, functional genomics, transcriptomics, proteomics and metabolomics. The document also discusses genome sequencing techniques, genome organization of different organisms like bacteria, plants and humans. It concludes with an overview of genome mapping methods.
Statstical Genetics Summer School 2023
http://www.sg.med.osaka-u.ac.jp/school_2023.html
Aug 25-27th 2023, Osaka University, The University of Tokyo, RIKENm, Japan
Role of Pangenomics for crop ImprovementPatelSupriya
It describes about the role of pangenomics in the crop improvement.It includes pangenome,superpangenome,databases,tools used in pangenomics,utilisation in crop improvement
BITS - Comparative genomics on the genome levelBITS
This is the third presentation of the BITS training on 'Comparative genomics'.
It reviews the basic concepts of sequence homology on the gene
Thanks to Klaas Vandepoele of the PSB department.
This document provides an overview of essential bioinformatics resources for designing PCR primers and oligos for various applications. It begins by outlining general rules for PCR primer design, including recommendations for primer length, melting temperature, specificity, secondary structures, and other factors. It then describes several online tools and databases for designing primers for general purpose PCR, real-time qPCR, methylation studies, and other applications. These resources include Primer3, Primer3Plus, PrimerZ, and Vector NTI. Databases like NCBI Probe and RTPrimerDB provide validated primer sequences. The document emphasizes considering multiple design tools and validation of primers.
The ClinGen Sequence Variant Interpretation Working Group: Refining Criteria ...Human Variome Project
The ClinGen Sequence Variant Interpretation Working Group aims to refine criteria for classifying genetic variants by standardizing how different types of evidence are integrated. In the short term, it will refine and modify current American College of Medical Genetics guidelines. It will work with disease-specific groups to evaluate criteria like population frequency thresholds and computational methods. The long term goal is to develop a quantitative Bayesian framework to classify variants. The working group will analyze ClinVar to identify disease genes with many reported variants to help evaluate criteria.
Statstical Genetics Summer School 2023
http://www.sg.med.osaka-u.ac.jp/school_2023.html
Aug 25-27th 2023, Osaka University, The University of Tokyo, RIKENm, Japan
Similar to StatGenSummerSchool2023_GenomeDataAnalysis5.pdf (8)
Statstical Genetics Summer School 2023
http://www.sg.med.osaka-u.ac.jp/school_2023.html
Aug 25-27th 2023, Osaka University, The University of Tokyo, RIKENm, Japan
Statstical Genetics Summer School 2023
http://www.sg.med.osaka-u.ac.jp/school_2023.html
Aug 25-27th 2023, Osaka University, The University of Tokyo, RIKENm, Japan
Statstical Genetics Summer School 2023
http://www.sg.med.osaka-u.ac.jp/school_2023.html
Aug 25-27th 2023, Osaka University, The University of Tokyo, RIKENm, Japan
Statstical Genetics Summer School 2023
http://www.sg.med.osaka-u.ac.jp/school_2023.html
Aug 25-27th 2023, Osaka University, The University of Tokyo, RIKENm, Japan
Statstical Genetics Summer School 2023
http://www.sg.med.osaka-u.ac.jp/school_2023.html
Aug 25-27th 2023, Osaka University, The University of Tokyo, RIKENm, Japan
Statstical Genetics Summer School 2023
http://www.sg.med.osaka-u.ac.jp/school_2023.html
Aug 25-27th 2023, Osaka University, The University of Tokyo, RIKENm, Japan
http://www.sg.med.osaka-u.ac.jp/school_2023.html
Statstical Genetics Summer School 2023
Poster
Aug 25-27th 2023, Osaka University, The University of Tokyo, RIKENm, Japan
25. (PRS taskforce in ICDA. Nat Med 2021)
Long way to return
Near way to predict
PRSを個人に還元するまでの「遠い」道のり
・PRSによる疾患発症予測精度向上のための課題整備が進められています。
・一方、「得られたPRSをどのように個人に還元するか」については、未だ具体的
な道筋が得られていない状況です。
・医療機関・アカデミア・ベンチャーの密な連携を通じてゲノム個別化医療社会
実装に取り組んでいく時代が到来しています。 25
① Polygenic risk score(PRS)とゲノム個別化医療
26. (Hao L et al. Nat Med 2022)
Veterans Affairs Genomic MedicineにおけるPRS還元の取り組み
・実際にPRSを臨床現場に還元する枠組みも、少しずつ始まっているようです。
26
① Polygenic risk score(PRS)とゲノム個別化医療
27. 27
(Turley P et al. NEJM 2021, Forzano F et al. Eur J Hum Genet 2021, Kozlov Nature 2022, Kumar A et al. Nat Med 2022)
出生前診断におけるPRS活用を巡る懸念
・出生前診断で複数胚由来のゲノム情報からPRSを推定し、特定形質における
推定値に基づき胚を選択する医療行為について、懸念が提唱されています。
① Polygenic risk score(PRS)とゲノム個別化医療