DAY 1: Translational Bioinformatics: Public Bio Big Data

          8월 21일(월)

시간

  주  제

강 사

8:30 ~ 9:30

9:30 ~ 9:50

Translational Bioinformatics: Thousands of Public Data Analysis

 김주한 교수

9:50 ~ 10:40

The Cancer Genome Atlas (TCGA) Project and Cancer Genome Research
- TCGA Introduction
- TCGA Data and Scientific Findings
- Impact of TCGA and Future

 김태민 교수
(카톨릭의대)

10:50 ~ 12:10

실 습 I: TCGA Somatic Mutation Landscape
          Find Significantly Mutated Genes
          Identify Driver Groups of Mutations

이우승, 임영균

12:10 ~ 13:10

  중  식

13:10 ~ 14:00

The 1000 Genomes Project and Human Genome Diversity
- 1000 Genome Samples and Populations
- Mutation Frequencies in Diverse Populations
- 1KP Transcriptomes and Functional Variation

이계화 교수
(서울대병원)

14:10 ~ 15:30

실 습 II: The 1000 Genomes Project Browser
          Allele Frequency and Genotypic Frequency Calculation
          Identification of Rare and Deleterious Mutations

박유미, 김주연

15:40 ~ 16:30

The Dominant Regulatory microRNAs and Epigenetic Modulators
- Translational Research
- Oncogenomics
- Epigenetic Regulation

남석우 교수
(카톨릭의대)

16:40 ~ 18:00

실 습 III: ENCODE Data at UCSC Genome Browser
           DNA Mutations in Genome Level
           Functional Methylation/Histone Modification in Epigenetic Level
           Epigenetic Regulation of Gene Expression 

윤선민, 김기태

DAY 2: Methodology and Application for Next Generation Sequencing

           8월 22일(화)

시간

  주  제

강 사

8:30 ~ 9:30

9:30 ~ 9:50

김주한 교수

9:50 ~ 10:40

NGS Platforms and Applications
- Current NGS Platforms
- NGS Data Formats
- NGS Data Analysis Technologies
- NGS Applications

김지훈 박사
(어큐진)

10:50 ~ 12:10

실 습 I: NGS Data Processing
          NGS Data Format Converting
          NGS Visualization Tools

박유미, 류영재

12:10 ~ 13:10

  중  식

13:10 ~ 14:00

NGS Data Analysis
- Sequence Alignment Algorithms
- Whole Genome and Exome Data Analysis
- Variation Detection and Reference Genome

최무림 교수
(서울의대)

14:10 ~ 15:30

실 습 II: Exome Sequencing Alignment
           SNP and Indel Identification
           Variation Filtering

박찬희, 유경훈

15:40 ~ 16:30

Advanced NGS Data Analysis
- Different types of variation in cancer
- Matched normal and tumor pair data analysis
- Cancer clonality and sequencing depth
- Visualizaing cancer genomics data

 김상우 교수
(연세의대)

16:40 ~ 18:00

실 습 III: Somatic mutation/CNV detection
           Read depth, quailty and coverage
           Mutual exclusivity and coverage
           Lollipop and CIRCOS plot for visualization

김기태, 임영균

DAY 3: NGS-based Rare and Common Disease Variant Analysis

          8월 23일(수)

시간

  주  제

강 사

8:30 ~ 9:30

9:30 ~ 9:50

NGS-based Rare and Common Disease Variant Analysis

 김주한 교수

9:50 ~ 10:40

Rare and common disease variant analysis using NGS
- CVCD vs. RVCD: synthetic association
- Variant prioritization strategy
- Interpretation of deleterious variants
- Gene-centric approaches

김주한 교수
(서울의대)

10:50 ~ 12:10

실 습 I: Functional effects of variant (CADD, SIFT, PolyPhen2)
          Gene-wise analysis using gene scoring system (RVIS, GDI)

박유미, 류영재

12:10 ~ 13:10

  중  식

13:10 ~ 14:00

Advanced methods and algorithms for genetic association analysis
- Statistical methods for genomic association tests
- HLA imputation and fine-mapping
- Analysis of clinical geterogeneity and pleiotropy

한 범 교수
(울산의대)

14:10 ~ 15:30

실 습 II: Statistical tests for association (Chi-square, Fisher's exact test and Odds ratio)
           Rare variant association tests (Burden tests, SKAT, SKAT-O)

이정훈, 윤선민

15:40 ~ 16:30

NGS Applications of Clinical Genetics and Genomics
- Understanding genetic risk prediction
- Genetic counseling
- Incidental findings from genomic sequencing data

이계화 교수
(서울대병원)

16:40 ~ 18:00

실 습 III: Genetic Risk Prediction methods
           ACMG recommended genes annotation
           Resources for personal genome interpretation(ClinVar, HGMD, PheGeni, SNPedia, PhenoDB)

윤선민, 류영재

DAY 4: Exome Sequencing and Cancer Genome Bioinformatics

          8월 24일(목)

시간

  주  제

강 사

8:30 ~ 9:30

9:30 ~ 9:50

Exome Sequencing and Cancer Genome Bioinformatics

 김주한 교수

9:50 ~ 10:40

Exome Sequencing Analysis in Clinical Research
- Exome Sequencing Data
- Study Design and Workflow
- Exome Sequencing of Familial Disease

김남신 박사
(생명공학연구원)

10:50 ~ 12:10

실 습 I: Trio-Exome-Sequencing Data Analysis
         Known Variant Filtering
         Detection of Disease-causing Variations
         Disease Gene Prioritization

송유림, 이정훈

12:10 ~ 13:10

  중  식

13:10 ~ 14:00

Cancer Genome Bioinformatics
- Cancer Genome Analysis
- Identifying Genomic Rearrangement and Copy Number
- Gene Fusion Analysis
- Survival Analysis

송영수 교수
(한양의대)

14:10 ~ 15:30

실 습 II: Fusion Gene Analysis from RNA-seq
          Network and Survival Analysis
          Resources for Cancer Research:
          cBioPortal, COSMIC, CCLE, OncoMap

임영균, 이정훈

15:40 ~ 16:30

Pathway and Network Analysis of Cancer Genomes
- Characteristics of Biological Network
- Cancer Gene Network Construction and Clustering
- Identification of Aberrant Pathway in Cancers

한현욱 교수
(아주의대)

16:40 ~ 18:00

실 습 III: Pathway analysis of TCGA using PARADIGM methods
           Network Visualization in Cancers

김기태, 송유림

DAY 5: Advanced Microarray and RNA-seq Data Analysis

          8월 25일(금)

시간

  주  제

강 사

8:30 ~ 9:30

9:30 ~ 9:50

Advanced Microarray and RNA-seq Data Analysis

 김주한 교수

9:50 ~ 10:40

RNA-Seq Data Analysis
- Read Alignment Methods
- Expression Quantification Strategy
- Differentially Expressed Genes Identification

강근수 교수
(단국대)

10:50 ~ 12:10

실 습 I: Read alignment with TopHat,
          Expression Quantification with Cufflinks
          RNA-Seq Gene Expression Analysis

이우승, 이정훈

12:10 ~ 13:10

  중  식

13:10 ~ 14:00

Biological Interpretation of Transcriptome Data
- Gene Ontology & Pathway Analysis
- Gene Set Enrichment Analysis
- Prognostic Subgroup Prediction

김주한 교수
(서울의대)

14:10 ~ 15:30

실 습 II: Gene Set Enrichment Analysis
           Cox-PH, Log Rank Test
           David, ArrayXPath

김주연, 임영균

15:40 ~ 16:30

Sequence-level Transcriptome Analysis
- Alternative Splicing Events
- Alternative Polyadenylation Analysis
- RNA Editing Analysis
- Non-coding RNA Characterization

정제균 박사
(삼성유전체연구소)

16:40 ~ 18:00

실 습 III: Alternative Splicing Identification
          RNA-DNA Difference (RDD) Analysis
          RNA Editing Site Annotation

류영재, 송유림