SOLICITATION NOTICE
A -- CUSTOM GENONE SEQUENCING
- Notice Date
- 9/13/2009
- Notice Type
- Combined Synopsis/Solicitation
- NAICS
- 541711
— Research and Development in Biotechnology
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Institute of Allergy & Infectious Diseases/AMOB, 10401 Fernwood Drive, Suite 2NE70, MSC 4811, Bethesda, Maryland, 20817
- ZIP Code
- 20817
- Solicitation Number
- NOI-RML-9027
- Archive Date
- 10/7/2009
- Point of Contact
- Julienne Keiser, Phone: 406-363-9370, Lynda Kieres, Phone: 406-363-9210
- E-Mail Address
-
jkeiser@niaid.nih.gov, lkieres@niaid.nih.gov
(jkeiser@niaid.nih.gov, lkieres@niaid.nih.gov)
- Small Business Set-Aside
- Total Small Business
- Description
- This notice is a combined synopsis/solicitation, Notice of Intent. The Government intends to negotiate on a sole source basis with Integrated Genomics, for custom genome sequencing in accordance with the format in Subpart 12.6, in conjunction with FAR 13.5, as applicable, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; quotes are not being requested and a written solicitation will not be issued. Submit offers on NOI-RML #9027. The solicitation documents and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2005-36 dated 9/10/09. 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 541711 and the small business size is 500. SCHEDULE: The National Institute of Allergy and Infectious Disease (NIAID), Rocky Mountain Laboratories (RML), has been charged with performing basic research contributing to the development of diagnostic reagents, therapeutics and vaccines against human bacterial pathogens. Construction of a custom microarray chip containing oligonucleotide sequences representing the open reading frames of 6 (six) bacterial pathogen genomes, condensed into composite, and or single genomes will contribute towards achieving those goals. The contractor shall provide to RML services to construct and provide sequence and annotation files for bacterial genomes that shall conform to specifications defined by our gene chip contractor in the GeneChip® CustomExpress TM Array Design Guide and approved in advance by the Chip Design Team. RML has a need for the contractor to use URLs and RML data, some of which is incorporated into the RML ERGO server to construct final files for each of the genomes discussed below. These final files will be Fasta files of ORFs and annotation files for those ORFs in tab-delimited format with column headers. Two files total, per composite, or single genome effort shall be constructed, one in fasta format and the other in annotation format. Unique identifiers specific to ERGO annotations for all orfs present in the RML ERGO server shall be incorporated into the annotation files. The final Fasta and annotation files shall match the format the chip manufacturer requests. The final Fasta and annotation files shall meet Project Officer specifications. During the production of the files Integrated Genomics shall communicate with the chip manufacturer and the RML Project Officer in order to make sure that compliance with chip design requirements in the form of these files is occurring. A final Conference call will occur with the RML Project Officer and, the chip contractor and Integrated Genomics to make sure that all of the file requirements have been met at the end of the contract. The following genomes, shall be included in this effort: Composite Genome, Genes Only, mycobacterium abscessus (ATCC 19977) (ERGO: MAB), Mycobacterium avium 104 (ERGO: MAI), Mycobacterium bovis BCG str. Pasteur 1173P2 (ERGO: MBO), Mycobacterium smegmatis MC2 (ERGO: MSM), Mycobacterium tuberculosis KZN 1435 (ERGO: MTG), and Mycobaterium ulcerans Agy99 (ERGO: MUL). All genomes shall undergo intra- and inter-comparative analysis in order to identify regions of duplication and uniqueness. For composite genome construction, one genome shall be designated as the backbone genome and shall be represented in the orf and annotation flat files in its near entirety (absent homologous repetitive sequences at a 97% DNA identity or higher). Subsequent genomes that are within the same genus, but that shall make up the composite aspects of the genome shall only be represented at the level of unique sequences not present in the backbone genome (at 96% DNA identity or less). Annotation must reflect this origin of sequence and the connection to the backbone genome. Decisions regarding whether to perform composite construction versus individual genome representation will be based upon the contractor running test analyses, which may or may not involve BLAST searches/comparisons at different levels of DNA identity or similarity stringencies. If genomes are syntenous, composite construction can work, if they are nonsyntenous, demonstrating many genomic changes and differences, then independent representation might be the best option. Final decisions on composite versus single or independent representation shall be made following discussion and approval with the Project Officer. Final annotation and flat files shall have unique orf identifiers connected to the ERGO server and compatible with the ERGO server. The Contractor must have access, experience and proprietary rights for interacting with the ERGO server such that interactions will not void or cancel existing service and support contracts for the ERGO SERVER. The chip contractor shall be the sole source for probe pair design, synthesis and manufacturing of the chip. Sequence and annotation files shall be submitted to them by Integrated Genomics following review and approval by the RML project Officer. Step #1: Receipt of all genomic materials: From date of receipt of materials, Total 10 (ten) days. The contractor shall provide to RML confirmation that for each genome category effort, the contractor has all of the necessary materials to proceed effectively. A brief report shall also be provided outlining any areas of potential difficulty. Step 2: Sequence scanning and analysis of all genomes. Duration: 1 (one) month total from end of receipt of materials (Step 1) for all composite, and single genomes to delivery of flat files to the chip contractor. Two flat files for each composite and single genome effort, consisting of a sequence flat file and an annotation file shall be delivered by email, ftp or on CD to the project officer for review and forwarded onto the chip contractor. Flat files delivered to the chip contractor for each genome effort shall be 100% compatible with their design criteria as defined by them. Composite and single genome flat file sets, including, but not limited to fasta orf files and annotation files may be delivered individually per group and invoiced as such, following acceptable review by the project officer. The contractor shall keep all RML-derived data secure and will not release or maintain any of the data beyond this contract effort. If Internet connectivity is needed in order to perform the work, or transfer deliverables, contractor computers will be secure and in compliance with RML IT security procedures and policies. FOB Point shall be Destination, Hamilton, MT. Delivery location is Rocky Mountain Laboratories, 903 S. 4th Street, Hamilton, MT. The following FAR provisions and clauses apply to this acquisition: (B)(1) By submission of an offer, the offeror acknowledges the requirement that a prospective awardee shall be registered in the CCR database prior to award, during performance, and through final payment of any contract, basic agreement, basic ordering agreement, or blanket purchasing agreement resulting from this solicitation; 52.212-1 Instructions to Offerors Commercial Items; FAR52.212-2 Evaluation Commercial Items; FAR 52.212-4 Contract Terms and Conditions Commercial Items; FAR 52-212.5 Contract Terms and Conditions Required to Implement Statues or Executive Orders Commercial Items; FAR52.227-14 Rights In Data General; HHSAR 352.224.70 (b)(f) Confidentiality of Information Clause. By submission of an offer, the offeror acknowledges the requirement that a prospective awardee shall have posted their FAR 52.212-3 Offerors Representations and Certifications Commercial Items at website http://orca.bpn.gov. Award will be based on the capability of the item offered to meet the above stated salient characteristics, delivery, price, past performance, and the best interest of the government. Offers may be mailed to Julienne Keiser at Rocky Mountain Laboratories, 903 S. 4th Street, Hamilton, Mt 59840, faxed to the POC indicated above (Fax - 406-363-9288), or e-mailed at (JKeiser@niaid.nih.gov). Offers must be submitted not later than 4:30 PM (MDST), 9/22/09. Copies of the above-referenced clauses are available from http://www.arnet.gov/far/current/html/52_000_107.html or upon request, either by telephone or fax. All responsible sources may submit an offer that will be considered by this Agency.
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/NIH/AMOB/NOI-RML-9027/listing.html)
- Place of Performance
- Address: ROCKY MOUNTAIN LABS, 903 S. 4TH STREET, HAMILTON, Montana, 59840, United States
- Zip Code: 59840
- Zip Code: 59840
- Record
- SN01952900-W 20090915/090913233040-33f584677ff683ac1199f9400a6970e4 (fbodaily.com)
- Source
-
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