- Streptococcus pneumoniae
- Genotyping and SNP detection of Streptococcus pneumoniae
- S. pneumoniae Sequence Download Tool
- Francisella tularensis
- Genotyping and SNP detection of Francisella tularensis
- F. tularensis Comparative Analysis Tool
- Haemophilus influenzae
- Genome Sequencing and Species Microarray for H. influenzae
- High Throughput Genotyping using Human DNA Isolated from Stored Serum Specimens
- Bioinformatic SNP Filter Scripts
- Poster Presentations
Hot Topics
Comparative Genomics
Reagents and resources developed by the PFGRC are used to conduct research studies in microbial comparative genomics. These studies generally compare the sequence and/or genome content of large collections of closely related species and strains associated with infectious disease and/or biodefense. Several platforms are utilized in these studies, including DNA microarrays for gene discovery and comparative genomic hybridizations and Affymetrix GeneChip resequencing technology for the identification of single nucleotide polymorphisms (SNPs).
The PFGRC's comparative genomics research has led to three studies with on-line, interactive SNP analysis tools which may be of interest to investigators. The tools allow the user to compare the SNP profiles of numerous strains of a particular species. This was first applied to a study of Bacillus anthracis Ames and a set of diverse B. anthracis strains (in collaboration with Jacques Ravel, the J. Craig Venter Institute and Paul Keim, Northern Arizona University). The B. anthracis interactive SNP tool is not currently available, however extensive data resulting from this collaboration are available on the JCVI's Pathema web site. The Affymetrix GeneChip resequencing platform was initially evaluated in a pilot project to identify SNPs and determine genetic variation in 85 Streptococcus pneumoniae strains (in collaboration with Catherine McEllistrem, The University of Pittsburg). This pilot project led to a more extensive application of the Affymetrix GeneChip resequencing technology in the identification of SNPs across 40 strains of the biodefense agent Francisella tularensis (in collaboration with Jeannine Peterson, Martin Schriefer, and Charles Ben Beard, Bacterial Disease Branch, CDC, Fort Collins, CO, Mark Walcott and David Bedwell, US Army Medical Research Institute of Infectious Disease (USAMRIID), and Luther Lindler, Department of Homeland Security (DHS) and Walter Reed Army Institute of Research (WRAIR)). The PFGRC will now apply its resources to clinical genomics, studying the genetic variation in human populations as correlated with responses to infection, vaccine, and therapy. One pilot study is now underway, in collaboration with John W. Belmont, Baylor College of Medicine, to analyze a small set of human subject DNA samples utilizing the Affymetrix Genome-Wide Human SNP Array 6.0.
The table below provides links to current comparative genomics resources provided by the PFGRC
Project Description / Publications |
Reagents and Resources |
Collaborators |
Genotyping and SNP detection of Streptococcus pneumoniae isolates by resequencing arrays |
Catherine McEllistrem, The University of Pittsburg |
|
Whole Genome Resequencing and Single Nucleotide Polymorphism Genotyping of 40 Franciscella tularensis Strains |
Jeannine Peterson, Martin Schriefer, |
|
Scripts for filtering raw SNP calls from Affymetrix GeneChip® resequencing chips |
||
Genome Sequencing and Species Microarray for H. influenzae |
||
High Throughput Genotyping using Human DNA Isolated from Stored Serum Specimens |
John W. Belmont, Baylor College of Medicine |
|
Poster Presentations |