Next Generation Sequencing Course - Center - Center for Computational Biology and Bioinformatics

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Next Generation Sequencing Course - Center

MGEN-G788 (INFO-I590) Introduction to Next Generation Sequencing

Time: 3PM-6PM, Fridays

Location: HS 1110 (Map)

Registration:

School of Medicine (MGEN-G788): http://registrar.iupui.edu/enrollment/4118/classes/MGEN/MGEN-G788.html
School of Informatics (INFO-I590): http://registrar.iupui.edu/enrollment/4118/classes/INFO/INFO-I590.html

Goal:

Understanding the basic principles of next generation sequencing technology. This includes basic biological applications, basics in data processing, statistical and informatics theories in data analysis, advantages, limitations, and assumptions of different methodologies, and biological interpretation of the results.

Expected outcomes:

For School of Informatics students: know how to do the analysis

Understand the basics of biological questions
Implement different analysis tools (such as alignment, alternative splicing, variant call, ...)
Fully understand the standard data structure; capable of retrieving relevant information through basic programming
Understand statistical/computational models to solve different biological questions

For School of Medicine students: know how to interpret the results, and know how to creatively design an experiment using NGS technology

Understand the basics of informatics theories
Understand the standard data structure (what information is included in each file)
Appreciate the advantages, limitations, and assumptions of standard statistical/bioinformatics methods
Interpret the analysis results
Creatively design an experiment for solving the problem of your own research interest

For faculty and staff sitting in the class: due to the expected heterogeneous nature of the class, some of the lectures may provide more informatics/statisitics details than you need. If you have any suggestions on the class contents, please feel free to contact me at yunliu@iupui.edu.

If you want to officially audit the class, please read and follow the IUPUI audit policy on the IUPUI Office of Registrar. If no credit is needed, please just drop me a message indicating you are interested in auditing.

Syllabus:

*** Lab tour to the Center for Medical Genomics will be separately arranged

Week	Date	Lecture
1	26-Aug-11	Overview of next generation sequencing technology What is NGS? Biological applications Platform overview Basic concepts Recent scientific breakthroughs using NGS technology Class overview
2	2-Sep-11	Data processing Analysis workflow Sequence quality evaluation Alignment theories Data formats Data visualization Cloud computing
3	9-Sep-11	DNA-seq I What is genetic variations? States of the genetic research for complex disease prior to high throughput sequencing NGS and genetics of complex disease (etiology) NGS and personal genome sequencing Experimental considerations Whole genome sequencing Target sequencing Pool sequencing
4	16-Sep-11 @BRTC	Guest Lecture - Drs. Howard Edenberg and Xiaoling Xuei Basics of library preparation protocols for SOLiD platform Tour of the Center for Medical Genomics sequencing facility
5	23-Sep-11	DNA-seq II – Bioinformatics topics for DNA-seq data analysis Sequencing mappability Refined alignment Quality recalibration Variants identification for Diploid genome Pooled DNA sequencing Cancer genome Pair-ends – identifying structure variants Copy number variations
6	30-Sep-11	Guest lecture – Dr. Tatiana Foroud Exome sequencing in FIA and PD DNA-seq III Prioritizing genetic variants Non-synonymous variants (SIFT, PolyPhen) Synonymous variants Regulatory variants Statistical methods on rare variants
7	7-Oct-11	RNA-seq I Biological theories on RNA-seq experiments Experimental considerations Published examples Major scientific advance using RNA-seq Alignment Gene expression analysis Differential expression analysis
8	14-Oct-11	RNA-seq II Splicing and alternative splicing Variants identification Estimation for the allele specific expression RNA-seq experimental design, sample size justification, sequencing depth evaluation Non-coding RNA analysis
9	21-Oct-11	RNA-seq III Guest lecture (biological application) Pair-ends/mate pairs – identify gene fusion smRNA
10	28-Oct-11	Guest lecture – Dr. Bill Muir (Purdue University) Power analysis of experiments in general Whole genome comparison between populations Detection of variants within individuals ChIP-seq I Biological theories on ChIP-seq analysis Published studies Experimental considerations
11	4-Nov-11	ChIP-seq II - Bioinformatics topics in ChIP-seq analysis Standard ChIP-seq data processing DNA fragment evaluation Peak identification Two condition comparison Saturation analysis Integrative data analysis Motif finding and related theories Integrate transcription factor binding data with RNA-seq experiment Identify miRNA promoters using ChIP-seq data Genetic variation in ChIP-seq-identified regions RNA binding protein data analysis
12	11-Nov-11	ChIP-seq III: Epigenetics DNA methylation Experimental considerations Statistical considerations Bioinformatics tools Histone modification Experimental approaches Statistical considerations Hidden Markov model annotating histone marks
13	18-Nov-11	Other topics Genome assembly Metagenomics Third generation and beyond
14	25-Nov-11	Thanksgiving recess
15	2-Dec-11	Student presentation
16	9-Dec-11	Final exam