DAY 1: Translational Bioinformatics: Thousands of Public Data Analysis

          8월 24일(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 Encyclopedia of DNA Elements (ENCODE) and Human Genome Research
- ENCODE Overview
- New Insights into the Human Genome
- Gencode project and UCSC Genome Browser

 홍경원 박사
(질병관리본부)

10:50 ~ 12:10

실 습 I: Explore ENCODE Data at UCSC Genome Browser
          Identify Transcription Factor Binding Loci from ChIP-seq Data
          Detection of Regulatory SNPs

윤선민

12:10 ~ 13:10

  중  식

13:10 ~ 14:00

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)

14:10 ~ 15:30

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

김기태

15:40 ~ 16:30

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

이계화 박사
(서울의대)

16:40 ~ 18:00

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

서희원

DAY 2: Methodology and Application for Next Generation Sequencing

           8월 25일(화)

시간

  주  제

강 사

8:30 ~ 9:30

9:30 ~ 9:50

Methodology and Application for Next Generation Sequencing

 김주한 교수

9:50 ~ 10:40

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

김지훈 박사
(랩지노믹스)

10:50 ~ 12:10

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

서희원

12:10 ~ 13:10

  중  식

13:10 ~ 14:00

Genome 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: Genome Sequencing Alignment
          SNP and INDEL Identification
          Variation Filtering

박찬희

15:40 ~ 16:30

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

정제균 박사
(삼성유전체연구소)

16:40 ~ 18:00

실 습 III: Read alignment with TopHat
            Expression Quantification with Cufflinks
            Alternative Splicing Identification

서희원

DAY 3: Exome Sequencing and Cancer Genome Bioinformatics

          8월 26일(수)

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

박유미

12:10 ~ 13:10

  중  식

13:10 ~ 14:00

Cancer Genome Bioinformatics
- Cancer Genome Analysis
- Identifying Genomic Rearrangement
- 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

15:40 ~ 16:30

Copy Number and Genomic Rearrangement
- CNV Identification in Cancer Genome
- Copy Number Data Processing
- Genomic Rearrangement

김봉조 박사
(국립보건연구원)

16:40 ~ 18:00

실 습 III: Cancer Genomic Rearrangement
          Identification of CNV regions
          CNV Database

김기태

DAY 4: NGS-based Rare and Common Disease Variant Analysis

          8월 27일(목)

시간

  주  제

강 사

8:30 ~ 9:30

9:30 ~ 9:50

김주한 교수

9:50 ~ 10:40

Functional Annotation of Sequence Variants
- Coding, Noncoding Variant Analysis
- Rare variants filtering based on Allele Frequency
- Identification of Pathogenic Variant as Diagnostic Marker

이수연 박사
(삼성SDS)

10:50 ~ 12:10

실 습 I: Functional Effects of variant (SIFT, PolyPhen2, CADD, RegulomeDB)
          GENCODE and Ensembl Biomart
          Genetic Association Database, OMIM, Cancer Gene Census (COSMIC)

김기태

12:10 ~ 13:10

  중  식

13:10 ~ 14:00

Rare and common and disease variant analysis using NGS
- Variant prioritization strategy
- Interpretation of deleterious variants in genes with known roles
- Gene-centric approaches

김주한 교수
(서울의대)

14:10 ~ 15:30

실 습 II: Identification of rare variants using public database (dbSNP, ALFRED)
           A variant burden test
           Resources for Personal Genome Interpretation (ClinVar, HGMD, PheGeni, SNPedia, PhenoDB)

윤선민

15:40 ~ 16:30

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

이계화 박사
(서울의대)

16:40 ~ 18:00

실 습 III: Genetic Risk Prediction methods
           ACMG recommended genes annotation
           

박지혜

DAY 5: Advanced Microarray and RNA-seq Data Analysis

          8월 28일(금)

시간

  주  제

강 사

8:30 ~ 9:30

9:30 ~ 9:50

김주한 교수

9:50 ~ 10:40

Gene Expression Analysis
- Normalization
- Differential Expression Analysis
- Classification Analysis

김주한 교수
(서울의대)

10:50 ~ 12:10

실 습 I: Bioconductor
          t-test, SAM, ANOVA, FDR
          LDA, DTs, SVM
          KNN, SOM, HC, PCA

김주연

12:10 ~ 13:10

  중  식

13:10 ~ 14:00

Sequence-level Transcriptome Analysis
- RNA-seq Expression Profile Analysis
- Novel Transcript Discovery
- RNA-editing Analysis

박지연 박사
(서울의대)

14:10 ~ 15:30

실 습 II: RNA-Seq Gene Expression Analysis
           RNA Editing Site Annotation
           RNA-DNA Difference (RDD) Analysis

박지혜

15:40 ~ 16:30

Non-coding RNAs in RNA-Seq Data
- miRNA Expression Profiling
- miRNA Target Gene Prediction
- Non-coding RNA Characterization

  남진우 교수
(한양대)

16:40 ~ 18:00

실 습 III: miRNA Sequencing Data Process
           miRNA Expression Profiling
           non-coding RNA Resources

임영균