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. We are 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 12/18/17

Time	Topic	Speaker	Video
08:00 – 09:15 AM	Registration	Wanda Skipwith
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 (Local Restaurants)
01:30 – 02:30 PM	Decoding the Regulatory Genome through Functional Genomics and high-throughput assays	Dan Savic, PhD
02:30 – 02:45 PM	Discussion	Dan Savic, PhD
02:45 – 03:00 PM	BREAK
03:00 – 04:00 PM	Introduction to Virtual Machine	Vinodh, MS
04:00 – 06:00 PM	Software Demonstration & Hands-on Computing (R & Bioinformatics File Formats)	Vinodh, MS

Tue 12/19/17

Time	Topic	Speaker	Video
09:00 – 10:00 AM	Variant Calling & Assembly NGS Data	David Crossman, PhD
10:00 – 10:15 AM	Discussion	David Crossman, 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 (Local Restaurants)
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

Wed 12/20/17

Time	Topic	Speaker	Video
09:00 – 10:00 AM	Structural Variant Analysis	Zechen Chong, PhD
10:00 – 10:15 AM	Discussion	Zechen Chong, PhD
10:15 – 10:30 AM	BREAK
10:30 – 11:30 PM	Transcriptome Analysis	Xiangqin Cui, PhD
11:30 – 11:45AM	Discussion	Xiangqin Cui, PhD
11:45 – 01:15 PM	LUNCH BREAK (Local Restaurants)
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 (RNA-Seq, BSmooth, DSS)	Xiangqin Cui, PhD; Karen Conneely, PhD

Thu 12/21/17

Time	Topic	Speaker	Video
09:00 – 10:00 AM	ChiP-Seq Data Analysis	Hao Wu, PhD
10:00 – 10:15 AM	Discussion	Hao Wu, PhD
10:15 – 10:30 AM	BREAK
10:30- 11:30 PM	Single Cell RNA-Seq Analysis	Hao Wu, PhD
11:30 – 11:45 PM	Discussion	Hao Wu, PhD
11:45- 01:15 PM	LUNCH BREAK (Local Restaurants)
01:15- 03:00 PM	Software Demonstration & Hands-on Computing (ChipSeq)	Hao Wu, PhD
03:00 PM	Adjourn