NGS course (G788/I590) - Yunlong Liu Lab - Center for Computational Biology and Bioinformatics

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NGS course (G788/I590) - Yunlong Liu Lab

The video collections for the 2011 lectures are now available at Youtube and Youku. The slides can also be downloaded.

Please address all the feedback to: yunliu@iupui.edu.

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

Time: 3PM-6PM, Fridays (Fall 2013 Semester)

Location: HS 1110 (Map)

Course materials:

Course materials are available in the oncourse system. If you need access, please email the course TA (Haoyu Cheng: haoychen@iupui.edu) for access. If you do NOT have an IU university ID, please acquire an IU guest user ID following instruction: https://kb.iu.edu/data/alqu.html.
Podcast of the lectures is now available in the oncourse system.

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 retrieve relevant information throug 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 stantistical/bioinformatics methods
Interpret the analysis results
Creativly design an experiement 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	Aug 23	Overview of next generation sequencing technology What is NGS? Platform overview Biological applications Basic concepts Recent scientific breakthroughs using NGS technology Class overview
2	Aug 30	Data processing Analysis workflow Sequence quality evaluation Alignment theories Data formats Data visualization
3	Sep 6	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	Sep 13	DNA-seq II – Bioinformatics topics for DNA-seq data analysis Sequencing mappability Refined alignment Base quality recalibration Variants identification for Diploid genome Pooled DNA sequencing Cancer genome Variation recalibration Pair-ends – identifying structure variants
5	Sep 20 @BRTC	Guest Lecture - Drs. Howard Edenberg and Xiaoling Xuei Basics of library preparation protocols for SOLiD platform Tour to the Center for Medical Genomics sequencing facility
6	Sep 27	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	Oct 4	RNA-seq I Biological theories on RNA-seq experiments Experimental considerations Published examples Major scientific advance using RNA-seq Alignment Gene expression analysis
8	Oct 11	Guest lecture - Dr. Sarath Janga Cloud computing RNA-seq II Differential expression analysis Alternative splicing
9	Oct 18	RNA-seq III Transcript variation Allele-specific expression RNA editing Non-coding RNA Pair-ends/mate pairs - identify gene fusion smRNA
10	Oct 25	ChIP-seq I Biological theories on ChIP-seq analysis Published studies Experimental considerations DNA frament evaluation Peak identification Two condition comparison Saturation analysis
11	Nov 1	Guest lecture - Dr. Milan Radovich Next generation sequencing in cancer research Guest lecture - Dr. Matteo Vatta Clinical sequencing
12	Nov 8	ChIP-seq II - Bioinformatics topics in ChIP-seq 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
13	Nov 15	ChIP-seq III: Epigenetics DNA methylation Experimental considerations Statistical considerations Bioinformatics tools Histone modification Experimental approaches Statistical considerations Hidden Markov model annotating histone marks
14	Nov 22	Student presentation
15	Nov 29	Thanksgiviing recess
16	Dec 6	final exam