Broad Spectrum Human Papillomavirus Genotyping using Single Moledcule Whole Genome Sequencing

Broad Spectrum Human Papillomavirus Genotyping using Single Molecule Whole Genome Sequencing 2015-86203 The Centers for Disease Control and Prevention (CDC) Procurement and Grants Office (PGO) intends to award a sole source purchase order to Georgia Tech Research Corporation, 505 10th Street, Atlanta, GA 30318 for the development and application of bioinformatics algorithms (instructions) and bioinformatic diagnostic applications of genomic testing, or pipelines, which includes custom scripts and algorithms, reference sequences, and databases. The work results in the automation of whole genome annotation and Single Molecule Sequencing HPV genotype tests. The bioinformatics algorithms obtained from the vendor will integrate the information from these tests to automate determination of HPV types, variants and physical status of HPV genotypes. The scope of work includes designing a framework for the development of customized software that implements automation of these determinations given a sample from a single sequencing reaction. Georgia Tech Research Corporation has unique expertise in genome analysis and genome annotation. It has also developed the proprietary software tools used in pioneering genome projects. Georgia Tech Center for Bioinformatics & Computational Genomics has been able to solve a number of long standing programs, particularly the one of automatic gene prediction in eukaryotic genomes by come-up with "unique in the filed" automatic software tools. It also has unique "know-how" or expertise in developing custom built pipelines for genome annotation where their original algorithms play a central role. The bioinformatics component of the HPV project includes a number of bioinformatics tasks that require development of novel algorithms to automate determination of varied characteristics of HPV. The Georgia Tech Center for Bioinformatics & Computational Genomics has the capacity to apply it proprietary GeneMark software to new genome data sets and to customize the software as the additional data (both genome sequences and RNA-Seq data) is produced. Georgia Tech Research Corporation has the required experience expertise in genome analysis and genome annotation in a portable format and access to the proprietary GeneMark software for its application to eukaryotic genome sequence data. The delivery time is a 12-month base period from the award date. The anticipated award date is 28 September 2015. The estimated amount for the purchase order is estimated at $50,000. This is not a small business set-aside acquisition. The North American Industry Classification Code is 541330. This advertisement ends in 10 days in accordance with FAR 5.203(A)(1). Any interested parties are welcome to submit their qualification and ability to provide the specified services via e-mail, CTTucker@cdc.gov and Klemaster@cdc.gov. Please include reference number 2015-86203. Please respond by 8 September 2015. This is not a Request for Quote (RFQ). A determination not to compete based on responses received, and to proceed with a noncompetitive award is solely at the discretion of the Government. Information received will be considered solely for the purpose of determining whether or not to conduct a competitive procurement.