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 |
||
High Throughput Genotyping using Human DNA Isolated from Stored Serum Specimens |
To Be Determined |
John W. Belmont, Baylor College of Medicine |
Comparative genomics of the Bacillus cereus group organisms: Post-genomic advances |
Paul Keim, Northern Arizona University, Flagstaff; Timothy D. Read, Navy Medical Research Center, Rockville, MD. |
|
Investigating Haemophilus influenzae Species Diversity by Comparative Genomic Hybridization (CGH) utilizing the Pangenome Microarray |
M. Kilian, R.D., University of Aarhus, Aarhus, Denmark |
|
Investigation of Bacillus cereus sensu lato diversity by novel gene discovery approach through comparative genomic hybridization |
O.A. Økstad, S. Ravnum and A.B. Kolsto, The Biotechnology Centre of Oslo, University of Oslo and The Institute of Pharmacy, Oslo, Norway |
|
Investigating Genomic Diversity of Yersinia pestis and Yersinia pseudotuberculosis Clade Members through a Microarray-Based Novel Gene Discovery (NGD) Approach |
M. Nikolich and L. Lindler, Division of Bacterial and Rickettsial Diseases, Walter Reed Army Institute of Research; R. Brubaker, Department of Microbiology and Molecular Genetics, Michigan State University |
|
Investigating Microbial Diversity through Multigenome Microarray Applications - High throughput novel gene discovery for identifying the species gene pool |
Mogens Kilian Aarhus University, Denmark; Ole Økstad, Biotechnology Centre of Oslo, Norway; S. Ravnum, University of Oslo, Norway; A. B. Kolsto, institute of Pharmacy, Oslo, Norway |
|
Development of an Insertion Sequence Based Microarray for the Genotypic Characterization of Yersinia pestis |
||
Whole Genome Resequencing and Single Nucleotide Polymorphism Genotyping of 40 Francisella tularensis Strains |
Jeannine Petersen, Martin Schriefer and Charles Ben Beard, Bacterial Diseases Branch, CDC, Fort Collins, CO; Mark Wolcott and David Bedwell, U.S. Army Medical Research Institute of Infectious Disease (USAMRIID), Fort Detrick, MD |