Short Course on NGS

Next-generation sequencing technology is impacting almost all aspects of biomedical research. This technology generates an unprecedented wealth of data that demands novel analysis strategies. While IT infrastructure and bioinformatics developments are obviously required to enable sound information extraction, sophisticated statistical methodologies and algorithms are also essential for interpreting the data. In this regard, we are organizing a NHGRI funded four-day short course, calling statisticians, genetic epidemiologists, bioinformaticians, and genome biologists, to discuss the statistical challenges and opportunities in next-generation sequencing data analysis. We believe that this course will provide a venue for exchanging of cutting-edge information and ideas, and fostering collaborations among methodologists, analysts, and biomedical investigators.

Schedule of Events: Agenda

Mon 12/12/16 – UAB in Birmingham, AL

Time	Topic	Speaker	Video
08:00 – 09:15 AM	Registration- Continental Breakfast	Wanda Skipwith/Mary Ann Rice
09:15- 09:30 AM	Introductory Remarks	Hemant Tiwari  PhD
09:30 – 10:30 AM	Technical Overview of NGS (Platforms; chemistry; library construction)	Shawn Levy PhD
10:30 – 10:45 AM	Discussion	Shawn Levy PhD
10:45 – 11:00 AM	BREAK
11:00 – 12:00 PM	Next Generation Sequencing in Methylation Studies	Devin Absher, PhD
12:00 – 12:15 PM	Discussion	Devin Absher, PhD
12:15 – 01:30 PM	Lunch Break
01:30 – 02:30 PM	Variant Calling & Assembly NGS Data	David Crossman, PhD
02:30 – 02:45PM	Discussion	David Crossman, PhD
02:45 – 03:00PM	BREAK
03:00 – 04:00 PM	Introduction to Virtual Machine	Jelai Wang
04:00- 05:00 PM	Software Demonstration & Hands-on Computing (R & Bioinformatics File Formats)	Xiangqin Cui, PhD

Tue 12/13/16 – UAB in Birmingham, AL

Time	Topic	Speaker	Video
	Continental Breakfast
09:00 – 10:00 AM	Decoding the regulatory genome through functional genomics and high-throughput assays	Dan Savic, PhD
10:00 – 10:15 AM	Discussion	Dan Savic, PhD
10:15 – 10:30 AM	BREAK
10:30 – 11:30 PM	Predicting Causal Variation	Greg Cooper PhD
11:30 – 11:45 AM	Discussion	Greg Cooper PhD
11:45 – 01:15 PM	Lunch Break
01:15- 02:15 PM	Rare Variants Analysis	Michael Wu, PhD
02:15- 02:30 PM	Discussion	Michael Wu, PhD
02:30 – 02:45 PM	BREAK
02:45- 05:00 PM	Software Demonstration & Hands-on Computing (Exome & Whole Genome NGS)	Michael Wu, PhD, David Crossman, PhD
06:00- 08:00 PM	Social Dinner @ Hill Student Center (Ball Room B) 1400 University Blvd.	Participants & Faculty

Wed 12/14/16 – UAB in Birmingham, AL

Time	Topic	Speaker	Video
09:00 – 10:00 AM	Microbiome/ Metagenome	Nengjun Yi, PhD
10:00 – 10:15 AM	Discussion	Nengjun Yi, PhD
10:15 – 10:30 AM	BREAK
10:30 – 11:30 PM	ChiP-Seq Data Analysis	Hao Wu, PhD
11:30 – 11:45AM	Discussion	Hao Wu, PhD
11:45 – 01:15 PM	LUNCH BREAK
01:15 – 02:15 PM	Methylation using Bisulfite Sequencing	Karen Conneely, PhD
02:15 – 02:30PM	Discussion	Karen Conneely, PhD
02:30 – 02:45 PM	BREAK
02:45- 06:00 PM	Software Demonstration & Hands-on Computing (ChipSeq) & Methylation Data	Hao Wu, PhD; Karen Conneely, PhD

Thu 12/15/16 – UAB in Birmingham, AL

Time	Topic	Speaker	Video
09:00 – 10:00 AM	RNA-Seq Analysis Methods	Xiangqin Cui, PhD
10:00 – 10:15 AM	Discussion	Xiangqin Cui, PhD
10:15 – 10:30 AM	BREAK
10:30- 11:30 PM	Single Cell Sequencing	Hao Wu, PhD
11:30 – 11:45 PM	Discussion	Hao Wu, PhD
11:45- 01:15 PM	Lunch Break
01:15- 02:15 PM	Software Demonstration of Analysis of Microbiome data	Ranjit Kumar, PhD
02:15 – 02:30 PM	BREAK
02:30 – 05:00 PM	Software Demonstration RNA-Seq Software Demonstration single cell RNA-Seq	Xiangqin Cui, PhD Hao Wu, PhD
05:00 PM	Adjourn