SOLICITATION NOTICE
68 -- DNA Sequencing & Genone Analysis
- Notice Date
- 2/26/2003
- Notice Type
- Solicitation Notice
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Institute of Allergy & Infectious Diseases/AMOB, 10401 Fernwood Drive MSC 4811 Room 2NE70-A, Bethesda, MD, 20817
- ZIP Code
- 20817
- Solicitation Number
- RML-RFQ-3017
- Archive Date
- 3/25/2003
- Point of Contact
- Julienne Keiser, Purchasing Agent, Phone 406-363-9370, Fax 406-363-9376, - Rebecca Guenthner, Chief Contracting Officer, Phone 301-402-2284, Fax 301-480-3695,
- E-Mail Address
-
Jkeiser@niaid.nih.gov, rguenthner@niaid.nih.gov
- Small Business Set-Aside
- Total Small Business
- Description
- This notice is a combined synopsis/solicitation for commercial items prepared in accordance with format in Subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; quotes being requested & a written solicitation will not be issued. This procurement is being issued as a request for quotation. Submit offers on RML-RFQ-3017. Solicitation documents and incorporated provisions & clauses are those in effect through Federal Acquisition Circular 2001-12 dated 1/27/03. This acquisition will be processed under Simplified Acquisition Procedures (SAP) and is a Small Business Set-Aside. The North American Industry Classification System (NAICS) code for this procurement is 325414 & the small business size is 500. SCHEDULE: Laboratory of Human Bacterial Pathogenesis performs work on bacterial pathogen genomes. Chemical sequence is critical for the rapid development of diagnostics, vaccines & chemotherapeutics. LHBP has an existing contract to sequence seven streptococcal genomes to a completion state of 10-20 contigs. The 7 genomes are in various states of completion & LHBP needs to implement a contract that will focus on finishing all seven genomes to total completion. Independently, the Contractor shall provide to LHBP services to produce complete & accurate finished genome sequences for 7 bacterial genomes currently under contract. Work stated shall not start for a given genome until that genome has reached the end point specified in the first contract. Contractor shall provide the following 8 steps: 1)Rapid Gap Closure and polishing. 2)Manual analysis of base calling. 3)Final Genome PCR verification. 4)Targeted PCR analysis of critical regions. 5)SNP Analysis. 6)Genome updates. 7)Focused analysis. 8)Final 7-genome update. Labor categories for the anticipated could include Project Manager, Bioinformatics Scientist(s), Technical Personnel, Chemists & other such categories as may be suggested by the contractor & approved in advance by the Project Officer. This is a 8-12 month effort, where the final product will be the production of 7 genomes, at Q40 or higher quality per base, 1 contig per genome, annotated, & comparatively analyzed for conserved & unique open reading frames (ORFs). Files must be compatible, transferred into and readable by the RML server & RML computing systems infrastructure, which involves a Finch & ERGO server. RML systems are PC, MAC & Unix/Linux-based. Each genome is estimated to be approximately 1.8-2.0MB in size. Weekly progress reports shall be provided to Project Officer describing the current status of all genomes & efforts underway for each in the following steps. Step(1) Rapid Gap Closure & Polishing: Fast-paced primer design & synthesis for primer-walking using plasmid clones, or PCR fragments shall be performed. Gaps shall be closed & quality of sequence raised to Q40 or higher per base. Manual editing of assembly, shall be used for problematic areas. Manual editing of individual sequencing runs & nucleotides should also be performed. Contractor shall deliver each genome in a state where genomic sequence has 1 contig per genetic element. Duration shall not exceed 2 months per genome. Step(2) Manual analysis of base calling: technical & bioinformatics specialists shall perform manual analysis of each base pair in the finished, single contig consensus sequence. This process shall be performed following completion of Steps 1 and 3. Additional sequencing must be performed if errors are identified & need corrected. Duration shall not exceed 2 weeks per genome. Step(3) Final, total Genome PCR verification: Complete set of PCR primer pairs for each genome shall be designed using proficient PCR primer design software. PCR primer pairs shall be ~4-kb & shall span the entire genome of interest. PCR fragments shall overlap by ~500 base pairs (BPs). Primers shall be purchasable in a 96 well microtiter plate format. Primers shall be high quality & free of contamination. Written protocols for reagents & conditions shall be provided to LHBP. Duration shall not exceed 2.5 weeks for first genome & 2 weeks for each additional genome. Step(4)Targeted PCR analysis of critical regions. Target-specific primers shall be designed & synthesized to verify assembly of Project Officer-selected specific genome regions of interest. Regions will not exceed 100kb. Primers shall be purchasable in a 96 well microtiter plate format. Primers shall be high quality & free of contamination. A written protocol describing reagents & conditions shall be provided. The duration shall not exceed 2.5 weeks per request. Step(5)SNP Analysis. Contractor shall provide a detailed analysis on single nucleotide polymorphisms(SNP) for a targeted genome. SNPs shall be identified as synonymous or non- synonymous in all regions, but not limited to ORF or intergenic regions. For incomplete target genomes, contractor shall provide probability values for all SNPs. Non-synonymous SNPs shall be cataloged according to virulent, metabolic & regulatory subsystems. Reports shall be in Excel or Microsoft Word format. Delivery & installation of SNP data shall be on CD-ROM & incorporatable into the RML ERGO server(Step #6) Duration shall not exceed 1 week per request. Step(6)Genome updates into RML ERGO server. Genomes shall be loaded into the RML ERGO server when requested. Data files for ORF calling, Protein & RNA encoding regions shall be made by contractor for un-annotated genomes. Genome SNP data shall be importable in this context. Automated functional assignments of protein encoding regions shall be performed. All Streptococcus genome ORFs shall have SPY aliases. All genome updates shall be performed via secure tunnel. CD-Rom disks of the genome update data shall also be provided. The duration shall not exceed 1 week per request. Step(7)Focused effort and analysis of targeted regions. A Ph.D.-level bioinformatisist scientist shall oversee production of the 7 genomes. Scientist shall be in direct contact with all project managers, supervisors & technical staff, & shall be responsible for analysis of & reports on the 7 genomes. Scientist shall construct reports that shall include, but not limited to, single/multiple graphics DNA sequence(s), charts, figures, tables, or text as requested. Duration shall not exceed 2 weeks from time of request to submitted report. Step(8)Final 7 genome update. The final set of gene annotation for all 7 sequenced & analyzed genomes, shall be installed onto the ERGO RML server at RML site. The data & format shall be comprehensive & compatible with all genome data, formats & scripts presently on RML ERGO server. Installation of data set shall also include 8 hours of tutorial on ERGO & RML server. Duration shall not exceed 3 weeks from time of completion of the 7th genome. Quality Assurance: Scientist shall hold a PhD in Bacteriology or Microbiology from an accredited University in the U.S. Contractor shall provide sufficient personnel to complete this entire work effort. NIH, RML-derived data will be maintained secure & will not be released, made public or maintained in any form beyond this contract. If Internet connectivity is needed to perform the work, contractor computers will be secure & in compliance with RML-IT security procedures & policies. Contractor-supplied software shall be kept current & up-to-date with security patches & upgrades. Internet connectivity and/or remote access shall be coordinated with NIAID IT staff to ensure security & compliance with NIAID IT procedures & policies. REPORTING REQUIREMENTS & DELIVERABLES: Trace data for all primer-walking/finishing reactions shall be in SCF format, & be posted on contractor?s secure server available for FTP download. Sequence data shall be convertible to FASTA format & posted on secure server for FTP download, if requested by RML. Assembled sequence & final gene annotation shall be converted to flat file format & shall be delivered to RML on the CD described above. Final list of all-unique & conserved ORFs & intergenic sequences for each genome as compared to all Streptococcus genomes sequenced within this contract & those that are publicly available or sequenced at LHBP shall be provided in flat file format. Final manual verified sequence, described as such, shall be converted to flat file format & delivered to RML on a CD. A set of ordered primers, covering the entire genome, in 96-well format per each genome (7 sets total). Each set will be accompanied by a full description, including, but not limited to primer sequences. A set of ordered amplified DNA fragments in microtiter plates (7 sets total). A Report on PCR results & procedures including gel images of PCR fragments (7 reports total) shall be provided. Confirmed sequence for each genome will be converted to flat file format & will be delivered to RML on a CD. A set of ordered PCR primers to specified target region in 96-well format. Each set will be accompanied by a full description, including, but not limited to primer sequences. Report on the results of the PCR analysis (including gel images). The contractor shall provide a detailed analysis & report containing information on single nucleotide polymorphisms (SNPs) for a target genome compared against S. pyogenes M1 & all other S. pyogenes genomes in the ERGO database. Information on gene against complete genes SNPs from other genomes shall be provided. Information on analysis shall be provided for coding & non-coding regions, for synonymous & non-synonymous nucleotide changes, with non-synonymous SNPs cataloged according to metabolic & regulatory subsystems. Report shall be packaged as ASCII text files that shall be sent to RML on CD-ROM. As an option, the data can be installed on the RML ERGO server by the contractor via a genome update process. The RML-ERGO server shall be updated with genome information via tunnel into the NIH-RML ERGO server from the contractor. Upon formal request by the Project Officer the contractor shall provide an in depth, focused effort & analysis report in graphical/text format (no flat files). The final set of gene annotation for all 7 sequenced & analyzed genomes, including any new finishing data, shall be installed on the ERGO server at the RML site. Installation shall include an additional 8 hours of on-site tutorial instruction by the contractor. All data (trace data, contigs, annotated sequence) generated within the scope of this project will be completely deleted from the contractor?s equipment upon completion of this step, unless otherwise specified by RML. FOB Point shall be Destination, Hamilton, MT. Delivery as annotated above. Following FAR provisions & clauses apply to this acquisition: FAR52.212-1 Instructions to Offerors-Commercial; FAR52.212-2 Evaluation-Commercial Items; FAR52.212-4 Contract Terms&Conditions-Commercial Items; FAR52.212-5 Contract terms & Conditions Required to Implement Statues or Executive Orders-Commercial Items; FAR52.246-2 Inspection of Supplies-Fixed Price, FAR52.227-14 Rights In Data-General. Offerors must include along with their offer a completed copy of provisions at FAR52.212-3 Offerors Representations & Certifications-Commercial Items. Award will be based on capability to meet above stated salient characteristics, delivery, price & past performance. Offers may be mailed or faxed to POC indicated above(Fax-406-363-9376). Offers must be submitted not later than 4:30 PM(MDST) 3/06/03. Copies of above-referenced clauses are available upon request, either by telephone or fax. All responsible sources may submit an offer that will be considered by this Agency.
- Place of Performance
- Address: Rocky Mountain Laboratories, 903 S. 4th Street, Hamilton, MT
- Zip Code: 59840
- Country: USA
- Zip Code: 59840
- Record
- SN00265568-W 20030228/030226213151 (fbodaily.com)
- Source
-
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