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

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Mon 12/10/12  – UAB in Birmingham, AL

Time	Topic	Speaker	Video
08:30 – 09:15 AM	Registration	Derry Crawford
09:15 – 09:30 AM	Introductory Remarks	Hemant Tiwari,  PhD
09:30 – 10:45 AM	Overview of Genetics & Genomics (Intro: Sequencing for Variation & Functional Genomics)	Greg Barsh, PhD
10:45 – 11:00 AM	BREAK
11:00 – 12:15 PM	Technical overview of NGS (Platforms; chemistry; library construction)	Shawn Levy, PhD
12:15 – 1:30 PM	Lunch
01:30 – 02:45 PM	Primary Data Analysis (Base calling; alignment; QC; variant calling)	Shawn Levy, PhD
02:45 – 03:00 PM	BREAK
03:00 – 04:15 PM	Copy Number & Structural Variants (biology; experimental methods; analysis)	Devin Absher, PhD
04:15 – 04:30PM	BREAK
04:30- 05:00 PM	Discussion (Q & A)	All Faculty

Tue 12/11/12 – HudsonAlpha Institute for Biotechnology in Huntsville, AL

Time	Topic	Speaker	Video
07:30 – 07:45 AM	Gather in Hotel Lobby for departure
07:45 – 9:15 AM	Bus Transportation to HudsonAlpha in Huntsville
09:15 – 9:30AM	Gather in HudsonAlpha meeting room
09:30 – 10:00 AM	Computing Needs for NGS (Computing & storage needs; data handling)	Braden Boone, MS, MIT
10:00 – 11:00 AM	DNA Sequence Variant Annotation and Analysis	Greg Cooper, PhD
11:00 – 11:15 PM	BREAK
11:15 – 12:15 PM	RNA-seq (mRNA & microRNA; EDGE RNA-seq, a SAGE-like, Counting Method Developed by Greg Barsh’s lab)	Jay Gertz, PhD
12:15 – 01:30 PM	LUNCH
01:30- 02:30 PM	Genome-scale DNA methylation analysis	Devin Absher, PhD
02:30- 03:30 PM	ChIP-seq (protein:DNA Interactions on a Genome-wide Scale)	Rick Myers, PhD
03:30 – 03:45 PM	BREAK
03:45 – 05:00 PM	Discussion (Q & A) & Tour of sequencing facility	All Faculty
05:00 – 06:30 PM	Bus Transportation to Hotel in Birmingham

Wed 12/12/12 – UAB in Birmingham, AL

Time	Topic	Speaker	Video
09:00 – 10:15 AM	Analysis of  Whole Genome Transcriptome Sequencing Data	Xiangqin Cui, PhD
10:15 – 10:30 AM	BREAK
10:30 – 11:45AM	Analysis of NGS data using Galaxy	David Crossman, PhD
11:45 – 01:15 PM	Lunch
01:15 – 02:30 PM	Whole Genome 3D Regulation Analysis Using Sequencing	Shili Lin, PhD
02:30 – 02:45 PM	BREAK
03:00 – 04:15 PM	Cloud Computing and Semantic Web application to High-Dimensional Biomedical Data	Jonas Almeida, PhD
04:15 – 05:00 PM	Discussion (Q & A)	All Faculty

Thu 12/13/12 – UAB in Birmingham, AL

Time	Topic	Speaker	Video
09:00 – 10:15 AM	Rare Variants Association Analysis	Suzanne Leal, PhD
10:15 – 10:30 AM	BREAK
10:30 – 11:45 AM	The 1000 Genomes Project: Behind and Beyond the Creation of Phase 1 Data	Yun Li, PhD
11:45- 01:15 PM	Lunch
01:15 – 02:30 PM	Assembling NGS data	Degui Zhi, PhD
02:30 – 03:00 PM	Discussion (Q & A)	All Faculty