SISG INTEGRATIVE GENOMICS MODULE IG1

This new module starts the integrative genomics stream by providing participants with an overview of the statistical genetic methods used to analyze both the microbiome and the metabolome. We treat them together because of the important interactions between the domains, with microbial metabolism thought to be a driver of inflammatory disease, and conversely metabolic variation impacting microbial diversity. While human biology will form the background for much of the treatment, the concepts covered apply to analyses where host species interact with microbes.

The course addresses such questions as how to study genetic mechanisms controlling microbial diversity; the impact of host genetic variation on microbiomes; studying gene expression variation in microbes; quantifying metabolite concentrations in serum and other bodily fluids; metabolite quantitative trait locus mapping/association; and meta-analysis of omic datasets.

Learning Objectives: After attending this module, participants will be able to: 

1. Use QIIME-2 to perform basic bioinformatic analysis of microbial diversity, and know which metrics to use.

2. Know how to perform comparative microbial species abundance from 16S data. 

3. Be familiar with the statistical hypothesis testing framweworks for differential microbial gene expression. 

4. Perform basic association mapping between host genotypes and microbiome. 

5. Know the different platforms used to measure metabolite abundance and be aware of their advantages and pitfalls.

6. Perform genetic analysis of metabolite abundance and know how to visualize differential metabolism.
7. Estimate pathway enrichment scores from metabolite data.

Ran Blekhman is an Associate Professor in the Section of Genetic Medicine at the University of Chicago. He studies how host genomic factors control and interact with the microbiome, employing computational, statistical, network-theory, data mining, and population genetic analytical approaches. Ran’s work is equally motivated by biomedical concerns, and understanding the evolution of host-microbe interactions. Access his publications here.

Youssef Idaghdour is also an Associate Professor of Biology, at the Abu Dhabi campus of New York University. He is interested in how genotype-environment interactions shape health and disease, particularly with respect to malaria susceptibility in sub-Saharan Africa. A native of Morocco, Youssef also studies genetics across North Africa, often using metabolomic methods. He has hosted two editions of the Winter Institute in Statistical Genetics in Abu Dhabi. Learn more about Youssef’s work here.