RTI International

The Power of GeneBrain; Seeing Complex Data in 3D Advances Population Genetics Project

Client Situation

For the National Institute of Allergy and Infectious Diseases (NIAID), RTI International conducted a study to identify the population genetic factors responsible for immune response to typhoid vaccine. The Population Genetics Project for Typhoid Vaccine (PopGen) recruited 4,000 participants at field sites in India. Blood and saliva samples were collected initially and at defined points in time after vaccination.  Samples were genotyped, used for proteomics, and measured for immune response factors. RTI subcontracted with Digital Infuzion to bring insights in the data analysis phase of the project.

The Digital Infuzion Solution

RTI chose Digital Infuzion’s GeneBrain® for the vaccine study data analysis because of the software’s ability to create advanced mathematical models of data from multiple diverse sources.

Digital Infuzion’s Computational Biology group applied GeneBrain®, the company’s proprietary software, to speed understanding and analysis of population genetics data for PopGen. GeneBrain® is the basis for a service that uses machine-learning algorithms on complex data. This software produces novel interactive 3D visualizations of data sets. It ranks and identifies optimum data feature sets that are predictive or characteristic of sample categories, such as “responsive” or “non-responsive” to vaccine.

Benefits

GeneBrain® was used successfully to:

  • Identify small groups of data features that are characteristic or predictive—even when single markers are not present—traditional statistical analysis could not identify such markers.
  • Create a population genetics model that was highly successful in predicting high or low response based on SNP genotype alone.
  • Identify a small set of mixed type biomarkers that successfully characterized high or low immune response for the subject subset that had multiple data types, therefore suggesting the direction for further statistical analysis.
  • Explain other puzzling demographic findings.
  • Validate the information content of a new technique even at the lowest measurement levels.
  • Lead to the formulation and confirmation by testing of a new hypothesis. This demonstrated the usefulness of the intuitive visual models to scientists who conducted the laboratory research.

 

GeneBrain® 3D visualization of all patients using SNP data reveals some unique distribution of SNP combinations in the PopGen clinical study patients by ethnic background (red or green) and sex (central cluster is female).

This project has been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN266200400067C. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services or RTI International, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. Government or RTI International.

Diverse Data

GeneBrain® analysis on integrated genotype (SNP), DIGE protein and immune factor data used 15 features drawn from four data streams to effectively characterize high (blue) or low (red) patient response to vaccine.

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