2012 AGAR workshop

Dates: Monday, January 9th - Tuesday, January 10th, 2012
Location: The Texas Biomedical Research Institute, San Antonio, Texas
Organizers: The American Association of Anthropological Genetics (AAAG) Education Committee in collaboration with the Texas Biomedical Research Institute  (details below)

The Application of Genomics to Anthropological Research (AGAR) Workshop was held from January 9-10, 2012 at the Texas Biomedical Research Institute in San Antonio.  The workshop, which was co-sponsored by AAAG and Texas Biomed, provided students and scholars interested in evolutionary anthropology with a thorough introduction into the theory and application of state-of-the-art genomic research.  The goal of this event was to provide anthropologists previously unfamiliar with the field of genomics sufficient knowledge to apply (and at a minimum to understand the application of) genomic tools to their future research. 

Schedule of Events

Day 1 – Monday: Methodological issues regarding genomic applications
8:30 - 9:00 a.m.	Registration -- Denny Building
9:00 - 10:00 a.m.	Introduction to next generation sequencing - Joanne Curran (Texas Biomedical Research Institute) General introduction to different sequencing platforms and basic metho dological concepts, such as read-depth, read-pairs, library construction (and tagging), read-length, etc.
10:00 - 11 a.m.	Calling variants: SNPs, indels and structural variation a regarding next-generation sequencing - Juan Peralta (Universidad de Costa Rica) A comparison of Sanger sequencing, microarray data (SNP, copy number variants, etc.) and other next-generation sequencing techniques.  This session will also feature information on controls, quality checks, false-positive rates.
11:00 - 11:30 a.m.	Tour of Genomics and Computing Facilities
11:30 a.m. - 12:30 p.m.	Structural variation – August Blackburn (University of Texas Health Science Center) Introduction to different types of genomic structural variations, including copy number variants (CNVs) with an emphasis of methods of “discovering” and “genotyping” such variations using next generation tools.
12:30 - 1:30 p.m.	Lunch
1:30 - 2:30 p.m.	Large scale analyses of the sequencing data - John Blangero (Texas Biomedical Research Institute) Analyses of genomic sequence data within the context of association studies and population genetics.
2:30 - 3:30 p.m.	Gene Discovery – Stefan Czerwinski (Wright State University) The Fels Longitudinal study is the longest running study of its kind and has collected data on many traits of anthropological and biomedical interest. The genomic era brings new opportunities and new challenges for identifying genes underlying these phenotypes.
3:30 - 4:00 p.m.	Coffee Break
4:00 - 5:00 p.m.	Transcriptomics – Harald Gӧring (Texas Biomedical Research Institute) The era of -omics is not limited to sequence variation. This session will focus on the investigation of genome-wide transcript data.
5:00 - 6:00 p.m.	Exome sequencing and human adaptation – Abigail Bigham (University of Michigan) This session will discuss analyses of exome sequencing data to identify adaptive variation in the genome.
6:00 - 8:00 p.m.	Dinner featuring plenary talk by Lynn Jorde, University of Utah
8:00 - 10:00 p.m.	Mixer
Day 2– Tuesday: Applications of genomic tools to anthropological questions
9:00 - 10:00 a.m.	Ancient genomics and library preparation – Nadin Rohland (Harvard Medical School) This session will focus on technical issues regarding extracting ancient DNA, preparation of large-scale genome libraries, array capture and sequencing.
10:00 - 11:00 a.m.	In depth analyses of population history – Krishna Veeramah (University of Arizona) In this session we will discuss how whole-genome sequencing data can be used to capitalize on recently developed methods that exploit population genetic theory to infer historical parameters such as divergence times, population sizes and migration rates as well as perform model testing.
11:00 a.m. - 1 p.m.	Lunch
1:00 - 2:00 p.m.	Pathogens and genome evolution – Anne Stone (Arizona State University) Pathogens have played a critical role in human evolution, thus revealing their evolutionary dynamics may provide novel insights into the history of modern human populations.  This session will focus on how unique features of human pathogen data may be utilized to study important events and behaviors in human evolution.
2:00 - 3:00 p.m.	Comparative genomics and primate genomics – Omer Gokcumen (Harvard) Methods, challenges and future directions in large-scale comparison of primate genomes within and across species using next-generation sequencing.
3:00 - 3:30 p.m.	Coffee Break
3:30 - 5:00 p.m.	Chalk-talk discussions of potential anthropological genomic projects Here, the group will discuss 3 possible research questions and projects suggested by the participants, and provide advice on how to design and optimize such projects.
5:00 - 5:30 p.m.	Concluding remarks