• Genotyping and SNP detection of Streptococcus pneumoniae
• S. pneumoniae comparative analysis tool
• Genotyping and SNP detection of Francisella tularensis
• F. tularensis comparative analysis tool
• Bioinformatic SNP Filter Scripts

The NIAID sponsored Pathogen Functional Genomics Resource Center (PFGRC) at the J. Craig Venter Institute is pleased to announce the release of three new, free open-source software tools: Magnolia, Ginkgo and APEX. Magnolia is a microarray data management and export system for researchers who use PFGRC microarrays. The software greatly simplifies the tasks of organizing experimental data and submitting it to a public data repository. Ginkgo is a Comparative Genomic Hybridization (CGH) and expression microarray data analysis package. Several normalization, data filtering and imputation, and replicate microarray functions are implemented in an intuitive graphical framework. The APEX tool is an implementation of the Absolute Protein Expression quantitation technique. It can compute protein abundance values for LC-MS/MS proteomics datasets, quantifying hundreds or thousands of proteins. Links to additional information on each of these new software tools is available from the PFGRC's bioinformatics page.

The National Institute of Allergy and Infectious Diseases (NIAID) supported Pathogen Functional Genomics Resource Center (PFGRC) designs, constructs, and distributes glass slide DNA microarrays for pathogens and biodefense related organisms (Select A-C agents). Currently, the PFGRC supports DNA microarrays for the 38 organisms listed here. In continuing its efforts to provide the infectious disease and biodefense communities with the microarray resources most relevant to their research efforts, the PFGRC is soliciting input for selection of its next set of reference/species microarrays. The criteria for organism selection may be found here.

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	Streptococcus pneumoniae comparative analysis tool	Catherine McEllistrem, The University of Pittsburg
Whole Genome Resequencing and Single Nucleotide Polymorphism Genotyping of 40 Franciscella tularensis Strains	Franciscella tularensis comparative analysis tool	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)
Scripts for filtering raw SNP calls from Affymetrix GeneChip® resequencing chips	Bioinformatic SNP filter scripts
High Throughput Genotyping using Human DNA Isolated from Stored Serum Specimens	To Be Determined	John W. Belmont, Baylor College of Medicine