SPECIAL NOTICE
99 -- NIEHS National Toxicology Program Next Generation Sequencing Services
- Notice Date
- 9/25/2020 1:28:47 PM
- Notice Type
- Special Notice
- Contracting Office
- NATIONAL INSTITUTE OF HEALTH NIEHS MORRISVILLE NC 27560 USA
- ZIP Code
- 27560
- Solicitation Number
- NIEHS-ENO-092512
- Response Due
- 10/23/2020 1:30:00 PM
- Archive Date
- 11/07/2020
- Point of Contact
- Ejinwaemeonu Ndidi Okeagu, Beth Kuhaneck
- E-Mail Address
-
ejinwaemeonu.okeagu@nih.gov, beth.kuhaneck@nih.gov
(ejinwaemeonu.okeagu@nih.gov, beth.kuhaneck@nih.gov)
- Description
- This exchange is being issued in accordance with Federal Acquisition Regulation (FAR) 15.201(e) as a Request for Information (RFI). The purpose of this RFI is for the National Institute of Environmental Health Sciences (NIEHS) to gain both subject-matter knowledge and industry feedback concerning the subject requirement. This RFI may also be used to identify qualified and interested business concerns. This exchange is not a solicitation for proposals, proposal abstracts, or quotations. The purpose of this exchange is to obtain information regarding: (1) the availability and capability of qualified business sources, (2) socioeconomic status of those qualified business sources, and (3) their size classification relative to the North American Industry Classification System (NAICS) code for the subject effort. Responses to this request will assist NIEHS in determining the appropriate acquisition strategy and method, including whether a socioeconomic based set-aside is optimal. I. BACKGROUND: The National Toxicology Program (NTP) is an interagency program whose mission is to evaluate agents of public health concern by developing and applying tools of modern toxicology and molecular biology. The program maintains an objective, science-based approach in dealing with critical issues in toxicology and is committed to using the best science available to prioritize, design, conduct, and interpret its studies. To that end, NTP is continually evolving to remain at the cutting edge of scientific research and to develop, validate and apply new technologies. The NTP has a service requirement for NextGen sequencing technologies to study the effects of chemically-induced toxicity in support of the high throughput screening and toxicity testing programs. A major premise of this project is that gene alterations underlie organ toxicity and the development of chemically-induced pathology and tumors. Activation of critical genes and other regulatory pathways enhance or repress pathways leading to toxicity or cancer susceptibility. Gene alterations can be interpreted as molecular biomarkers which can precede or inform histopathology and other measures of toxicity. The Contractor selected for this requirement shall provide knowledge and expertise in NextGen genomic, transcriptomic and DNA methylation sequencing by proposed technology platforms from tissues, cell culture systems (2D and 3D) and liquid biopsies. II. REQUIREMENT DESCRIPTION: Scope. The NextGen Sequencing effort will provide for sequencing that includes: sample quality control metrics, sequence library construction; NextGen DNA or RNA sequencing services. The scope of sample analysis is anticipated to be wide-ranging and may involve 2D and/or 3D cell culture systems, tissues, or liquid biopsies (e.g. serum, plasma or urine). Analysis of sample species may include but is not limited to rodents and humans. Technical Requirements.� The technical requirements anticipated for this effort are as follows (Also see the attached draft statement of work for requirement details): NextGen Sequencing � NIEHS anticipates 200 samples per year shall be processed, prepared and indexed for DNA or RNA sequencing on an lllumina sequencing instrument (e.g. NextSeq 500/550 series or NovaSeq 6000). The contractor will deliver a FASTQ sequence file for each sample per flow cell. A flow cell is the unit device samples are sequenced on respective to the Illumina platform selected based on the number of reads required for a project. Samples are loaded onto a flow cell that provides a specific number of reads based on a particular Illumina sequencing platform (see below). The number of samples loaded onto a flow cell and the desired number of sample reads will be determined by NIEHS in consultation with the contractor. NIEHS may order one sequencing flow cell or multiple flow cells for a project. NIEHS anticipates that, during the five (5) year period, up to a maximum of 15 flow cells and 200 samples per year will be needed. NIEHS will provide purified nucleic acids (e.g. DNA, RNA, circulating cell-free DNA) to the contractor. Sample preparation by the contractor for DNA or RNA will include reagents for quality control, library construction, indexing and target enrichment (e.g. exome capture) for NextGen sequence analysis. The following set of general procedures for sequencing will occur with appropriate direction from NIEHS. Preparation of nucleic acid samples for library construction and sequencing: The Contractor shall prepare libraries with nucleic acid samples identified by a unique index. NIEHS shall provide as needed for certain sample types (e.g. circulating cell-free DNA), indexed library samples for sequencing. NIEHS shall specify prior to sequencing (e.g. 1 week), the sequencing read length (e.g. 2 x 100 bp) and shall specify the number of reads needed per sample. Flow Cells. Each sequencing instrument platform contains one or multiple flow cells where sequencing of samples takes place. The number of sequence reads (e.g. # base pairs for each DNA fragment) produced for each sample delivered in a flow cell depends upon the type of Illumina sequencing instrument. The NIEHS requires the need for 15 flow cells per year as apportioned among the various Illumina sequencing platforms, described in the following text: 3 flow cells on the NextSeq 500/550/2000 platform; 5 of the S1 module flow cells on the NovaSeq 6000 platform; 5 of the S2 module flow cells on the NovaSeq 6000 platform; and 2 of the S4 module flow cells on the NovaSeq platform.� Key Personnel. Certain skilled experienced technical personnel are essential for accomplishing the work to be performed. At a minimum, the following personnel have been defined as key for this contract: Principal Investigator (Pl) - The Pl shall oversee the conduct of NextGen sequencing using lllumina sequencing instrumentation including production of NextGen data, data analysis, packaging and transmission, and coordination of personnel that staff the genomics facility. The Pl shall have an MS., Ph.D., M.D., or equivalent in the biological sciences, chemistry, and/or medical sciences. Genomic Facility Leader - The Genomics Leader shall manage and conduct the day�to-day operations of a NextGen sequencing facility. This person shall have experience constructing RNA and DNA sequencing libraries, QA/QC procedures in production of NextGen data, data packaging and transmission, and coordination of genomics facility staff. The leader shall coordinate with bioinformatic staff preparation of NextGen data for export to NIEHS. The Genomics leader shall be capable of molecular skills for sequence validation and cloning of transcripts derived from NextGen data. The Genomics Facility Leader shall have demonstrated skills in molecular biology, biochemistry, and accompanying instrumentation. The Genomics leader shall have a Ph.D., M.D., or equivalent in the biological sciences, chemistry, and/or medical sciences. Project Manager - The Project Manager shall coordinate communications (e.g. virtual conferences, sample delivery, data exchange) between NIEHS and the Contractor. The program manager should have a basic knowledge of NextGen sequencing and have at least a B.S. or equivalent in biology or chemistry. Place and Period of Performance. The opportunities for sample degradation and compromising the quality of data are greater with the continued movement of samples to various sites for analysis, therefore; analysis shall take place in a single facility or facilities within close proximity (i.e. university campus) located within the contiguous United States. III. INFORMATION SOUGHT: Interested organizations are requested to submit their capability statements, which should not exceed ten (10) pages in length; not including a standard product brochure that clearly details the ability to perform the aspects of the work described above and should be tailored to the work requirements as concise as possible.� Each response should also include the following business information: a.������ DUNS number b.�� ���� Organization Name c.������� Company Address d.�� ���� Point of Contact (including name, title, addresses, telephone number, fax number and Email address) e.������ Business size f.������� Socio-economic status g.�� ���� Teaming Agreements (if necessary) NIEHS requests that the following information be addressed with submissions: Capabilities, approaches, and experience in providing sequencing germane to the scope of this effort. Unique value proposition (if any) as it pertains to new and/or innovative technologies and methods, germane to the scope of this effort. Ability to support projects and service customers that are located in Raleigh-Durham Metropolitan area. Recommendations and/or commentary on the following: The current draft statement of work. Current market environmental factors and/or conditions relevant to this effort. A description of at least two projects (w/ reference information) similar in nature to this requirement. IV. RESPONSE INSTRUCTIONS: The descriptive literature provided in response to this RFI should not exceed 10 pages.��� Disclaimer and Important Notes. This notice does not obligate the government to award a contract or otherwise pay for the information provided in response to this request. The government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed. Respondents are advised that the government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. Confidentiality. No proprietary, classified, confidential, or sensitive information should be included in your response. The government reserves the right to use any non-proprietary technical information in any resultant solicitation(s).
- Web Link
-
SAM.gov Permalink
(https://beta.sam.gov/opp/c548303ade844df6bd7880ae01327b82/view)
- Place of Performance
- Address: Durham, NC 27709, USA
- Zip Code: 27709
- Country: USA
- Zip Code: 27709
- Record
- SN05811394-F 20200927/200925230151 (samdaily.us)
- Source
-
SAM.gov Link to This Notice
(may not be valid after Archive Date)
| FSG Index | This Issue's Index | Today's SAM Daily Index Page |