University of Florida
Bioinformatics

Bioinformatics for SNP-based association studies

We provide bioinformatics support for a number of SNP-based association studies, using the most recent whole-genome technologies. Our contributions include setting up analysis and annotation pipelines, designing and hosting databases, creating and hosting project websites to disseminate data and results.

While at the Children's Hospital Informatics Program, Dr. Riva designed and implemented SNPper, a free online application for the analysis of human SNPs. SNPper, that now counts over 2,000 regular users, was the first application to integrate information about all known human SNPs with the complete sequence of the human genome, in order to analyze SNPs in the context of their genetic location. Over time, it has grown to include genotype and frequency information from the HapMap project, functional information from GeneOntology, data about pathways, phenotypes (from OMIM) and protein structure, and information on high-throughput genotyping microarrays. The main purpose of this tool is to build large sets of SNPs having desired properties, for use in association studies. The Genephony project represents the generalization and evolution of the SNPper architecture.

We are currently involved in a large-scale, NIH-funded project to study the genetic basis of longevity and sickle-cell anemia (collaboration with the Boston University School of Public Health).

Other ongoing collaborations concern the use of SNPs for the investigation of the lupus locus in mouse (with Dr. L. Morel, University of Florida), and for the genotyping of various plant genomes (with Dr. J. Davis and Dr. M. Kirst, University of Florida).

References
  1. A. Riva, I. S. Kohane, A SNP-centric database for the investigation of the human genome, BMC Bioinformatics 2004, 5:33 (Full text)
  2. A. Riva, I. S. Kohane, SNPper: retrieval and analysis of human SNPs, Bioinformatics, 2002 18: 1681-1685. (Abstract)
  3. A. Riva, I. S. Kohane, A Web-Based Tool to Retrieve Human Genome Polymorphisms from Public Databases, Proc. AMIA Symp. 2001:558-562