Omics-Based Predictive Modeling of Age-Dependent Outcome to Influenza Infection
- Elodie Ghedin, NYU
- Bin Zhang and Eric Schadt, Icahn School of Medicine at Mt. Sinai
The focus of this project is to develop computational models that integrate large-scale Omics data collected over the course of influenza A virus infections to predict severe disease outcome. Our ultimate goal is to leverage the power of large-scale data and mathematical modeling to identify risk-stratifying prognostic biomarkers that could be used in the development of point of care testing.
- Ted Ross, University of Georgia
- David Kelvin, Alyson Kelvin, UHN Toronto
- Clayton Wiley, Stephanie Bissel, University of Pittsburgh
- Brian Bot, Larsson Omberg, SAGE Bionetworks
Dynamics of Influenza Evolution and Transmission in the Obese Host
- Stacey Schultz-Cherry, St. Jude Children’s Research Hospital
- Paul Thomas, St. Jude Children’s Research Hospital
The objectives of this project are to characterize the intra-host and inter-host evolutionary dynamics of influenza virus in the obese ferret model (diet-induced obesity – DIO) developed by the Schultz-Cherry lab.
The Schultz-Cherry Lab is developing a number of ferret reagents, including a Fluidigm chip. You can access the list of genes that are represented on this chip here. The ferret (Mustela putorius furo) genome (produced by the Broad Institute) was used to determine sequences to design qPCR primers to the genes listed in collaboration with Fluidigm. Validation of the primers involved use of universal ferret cDNAs made from ferret tissues (uninfected and infected) and involved a 15 step 2-fold serial dilution series of cDNA in triplicate with non-template controls.
Validation of immune response primer-probes on the ferret FLUIDIGM chip. Universal cDNA was prepared from DNAse-treated RNA from ferret blood +/- influenza-infected ferret tissue and pre-amplified with a pool of 48 primers in a specific target amplification. Exonuclease-treated product was serially diluted and run in a PCR reaction using each primer pair individually. The Dynamic Array Integrated Fluidics Circuit (IFC) chip was primed in the IFC controller MX according to manufacturer’s instructions (Fluidigm). Upon completion of priming, the chip was loaded with the samples and run on the Biomark HD PCR system.