title: Bacterial genome reference databases: progress and challenges.
abstract: Accurate and sensitive detection of microbes against a complex background is a problem common to multiple aspects of human health, such as vaccines and other biologicals safety, blood safety, and diagnosing infectious diseases in humans or other hosts. The microbes in question could be bacterial, viral, fungal, or parasitical. To defend against such a broad array of microbes of potential safety concern, we need more than single-target polymerase chain reaction (PCR) assays. Technologies such as highly-multiplexed PCR, broad-spectrum DNA/RNA microarrays, and next-generation sequencing are all potentiallycapable to provide increased protection against microbial contamination. Regulatory processes are currently struggling to keep up with rapid advances in all of these technologies, each of which is firmly based upon nucleic acid sequencing resulting in generation of megabases of data. A major question is the level of quality required for genomic data and metadata for the reference databases that are needed to allow these technologies to be developed, validated, and then used for front-line protection of human health. The background of this general problem is discussed and one example of an ongoing effort to establish quality levels for a bacterial genome reference database is presented.
authors.affiliation: Bioinformatics, Global Security Program, Lawrence Livermore National Lab, Livermore, CA. slezak@llnl.gov.
authors.forename: Tom
authors.initials: T
authors.lastname: Slezak
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics*; D001431:Bacteriological Techniques / Q000592:standards* / Q000639:trends; D004269:DNA, Bacterial / Q000235:genetics*; D000068598:Data Accuracy; D057225:Data Mining; D030541:Databases, Genetic / Q000592:standards* / Q000639:trends; D004059:Diffusion of Innovation; D005544:Forecasting; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000592:standards; D060885:Multiplex Polymerase Chain Reaction / Q000592:standards; D010802:Phylogeny; D011786:Quality Control
chemical_list: D004269:DNA, Bacterial
keywords: Broad-spectrum microarrays; Genome reference databases; Metadata; Multiplex-PCR; Next-generation sequencing