title: Draft versus finished sequence data for DNA and protein diagnostic signature development.
abstract: Sequencing pathogen genomes is costly, demanding careful allocation of limited sequencing resources. We built a computational Sequencing Analysis Pipeline (SAP) to guide decisions regarding the amount of genomic sequencing necessary to develop high-quality diagnostic DNA and protein signatures. SAP uses simulations to estimate the number of target genomes and close phylogenetic relatives (near neighbors or NNs) to sequence. We use SAP to assess whether draft data are sufficient or finished sequencing is required using Marburg and variola virus sequences. Simulations indicate that intermediate to high-quality draft with error rates of 10(-3)-10(-5) (approximately 8x coverage) of target organisms is suitable for DNA signature prediction. Low-quality draft with error rates of approximately 1% (3x to 6x coverage) of target isolates is inadequate for DNA signature prediction, although low-quality draft of NNs is sufficient, as long as the target genomes are of high quality. For protein signature prediction, sequencing errors in target genomes substantially reduce the detection of amino acid sequence conservation, even if the draft is of high quality. In summary, high-quality draft of target and low-quality draft of NNs appears to be a cost-effective investment for DNA signature prediction, but may lead to underestimation of predicted protein signatures.
authors.affiliation: Pathogen Bio-Informatics, Lawrence Livermore National Laboratory, PO Box 808, L-174, Livermore, CA 94551, USA. gardner26@llnl.gov
authors.forename: Shea N
authors.initials: SN
authors.lastname: Gardner
authors.forename: Marisa W
authors.initials: MW
authors.lastname: Lam
authors.forename: Jason R
authors.initials: JR
authors.lastname: Smith
authors.forename: Clinton L
authors.initials: CL
authors.lastname: Torres
authors.forename: Tom R
authors.initials: TR
authors.lastname: Slezak
mesh_terms: D019295:Computational Biology; D016680:Genome, Bacterial; D016679:Genome, Viral; D023281:Genomics / Q000379:methods*; D029024:Marburgvirus / Q000235:genetics / Q000302:isolation & purification; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D012901:Variola virus / Q000235:genetics / Q000302:isolation & purification; D014764:Viral Proteins / Q000737:chemistry
chemical_list: D014764:Viral Proteins