SOURCES SOUGHT
B -- Targeted Transcriptomic Interrogation for Use with Human, Mouse and Zebrafish Cellular Lysates
- Notice Date
- 6/12/2015
- Notice Type
- Sources Sought
- NAICS
- 541380
— Testing Laboratories
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Institute of Environmental Health Sciences, Office of Acquisitions, Office of Management, 530 Davis Drive, Durham, North Carolina, 27713, United States
- ZIP Code
- 27713
- Solicitation Number
- MG061215-2
- Archive Date
- 7/7/2015
- Point of Contact
- Melissa M Gentry, Phone: 919-541-7894
- E-Mail Address
-
gentry1@niehs.nih.gov
(gentry1@niehs.nih.gov)
- Small Business Set-Aside
- N/A
- Description
- **REQUEST FOR INFORMATION ONLY** "Targeted Transcriptomic Interrogation for Use with Human, Mouse and Zebrafish Cellular Lysates" 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 small business sources; (2) whether they are small businesses; HUBZone small businesses; service-disabled, veteran-owned small businesses; 8(a) small businesses; veteran-owned small businesses; woman-owned small businesses; or small disadvantaged businesses; and (3) their size classification relative to the North American Industry Classification System (NAICS) code for the proposed acquisition. Your responses to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible. I. BACKGROUND: Tox21 is a multiorganization collaboration that uses quantitative high throughput screening (qHTS) technologies to screen thousands of environmental chemicals in in vitro assays. The Division of the National Toxicology Program (NTP) is building on the substantial progress we have made in characterizing biological responses to chemical exposures through our Tox21 Phase I and II qHTS program. We are expanding our interrogation of global biological pathway responses to chemicals in part by incorporating transcriptomic analysis of human cell line responses to exposures in Tox21 Phase III. Excellent progress has been made in identifying a robust set of human genes, the human S1500 gene set, that provide thorough representation of biological pathways and processes that will allow mid to high throughput investigations of human transcriptome responses to large numbers of chemicals over multiple doses and times. Our intention is to focus initially on human cell lines, with particular interest in human hepatocytes with robust xenobiotic metabolic capabilities and, to a limited extent, other human cell types including human iPS-derived neuronal cells. We will also investigate the impact genetic diversity has on developmental processes by utilizing ES and iPS cells from the powerful genetic model system of the diversity outbred mouse lines. These studies will also complement NTP interests in utilizing zebrafish as a model system for investigating chemical effects on developmental processes. Transcriptomics has evolved from microarray platforms to NextGen sequencing of cellular transcripts. However, several factors limit the screening potential of existing transcriptomic platforms including low throughput, low sensitivity, lack of gene specificity, and limited dynamic range of detection. These limiting factors make it impractical for comprehensive assessments of dose- and time-responses to chemical exposures. Tox21 partners envision measurement of a select set of transcripts to assess chemical effects upon in vitro mid- to high throughput screens. The objective of this Sources Sought Notice is to acquire technology for mid- to high-throughput transcriptomic measurement of gene expression changes in human, mouse and zebrafish cellular lysates in vitro after acute chemical exposures. II. REQUIREMENT DESCRIPTION: The NTP requires the capability for multiplexed measurement of a defined set of about 2,500 gene transcripts that have been identified and prioritized as environmentally responsive. This gene set might be used for screening cells or tissues obtained from humans against large numbers of substances using transcriptomic approaches. A Tox21 working group has generated a list of approximately 2500 human genes for in vitro screening of transcriptional changes of cells in 384 well format in response to chemical exposures. Similar gene sets are being developed for use with samples from mice and zebrafish. Additional gene sets for use with other species will be addressed at a later time. The gene set of 2500 has been designed to provide the maximal toxicogenomic information on (1) effects that reflect general cellular responses, independent of cell type or species, and (2) gene expression changes that are specific by organ and/or cell type. For example, recent advances with in vitro liver models such as metabolically competent HepaRG cells and 3D liver organoids or reprogramming of iPS cells to study cellular differentiation offer promising new tools for toxicological research. Similarly, advances are being made in toxicology utilizing additional cell types, e.g. cardiac cells and neuronal cells from humans and mice, as well as developmental models, e.g. zebrafish embryos. By integrating mid to high throughput gene expression profiling with biological functional parameters, these models hold the potential to identify the temporal dynamics of cellular differentiation pathways and the cascades of chemically-induced responses across cellular pathways associated with adverse outcomes and susceptibilities to chemical exposures. Criteria for the selection and evaluation of an appropriate "sentinel" gene set are genes that are (1) representative of the maximal diversity in gene expression changes reported in public gene expression data sets to date, (2) capable of predicting or inferring the gene expression changes for those genes not represented in the gene set in a manner that reflects observed expression changes across the entire transcriptome, and (3) coverage of all major biological pathways. Such a list of environmentally responsive genes may also be useful in biomarker development and basic research efforts. The original list of genes, referred to as the "S1500 gene list," was published for public comment for its likelihood for representing key or "sentinel" genes. The Federal Register (FR) notice [FR Doc. 2013-18058 Filed 7-26-12; 8:45 am] requested input from the scientific community on the "Nomination and Prioritization of Environmentally Responsive Genes for Use in Screening Large Numbers of Substances Using Toxicogenomic Technologies." Following this, an US governmental interagency working group composed of members of the Tox21 community considered the input provided as they developed a consensus strategy to refine and select an appropriate gene set. Requirement Schedule. • ‘S1500 List': NIEHS scientists in the NTP will provide the list of the ‘S1500' human gene set (about 2500 genes) to the vendor for preparation of assay reagents capable of multiplexed measurement of these transcripts in each sample in the wells of a 384 well plate. • Orthologous Mouse and Zebrafish Gene Sets: S1500 gene sets will be prepared for mouse and zebrafish that contain orthologous genes in these species. • Cell Extracts: Cell extracts will be provided to the vendor from 1) in vitro human liver models, 2) mouse cell lines and 3) zebrafish embryos. For example, cell lysates could include human HepaRG, primary human hepatocytes, and/or iPS-derived hepatocytes; lysates from mouse cell lines; and lysates from zebrafish embryos. • Targeted Multiplexed Transcriptomics Assay: Perform a targeted mid- to high-throughput transcriptomics assay for each species (i.e., Tox21 human ‘S1500' gene set) measuring about 2500 genes in each sample well of a 384 well format. There will be two 384 well plates assayed for each species. • Chemical Treatment: Samples will include some cell lysate from those treated with Tox21 compounds at multiple concentrations, focusing on chemicals predicted to have toxic metabolites that would be expected to alter transcriptomic profiles compared to control. • Requests and Response: The contractor shall have in place a process for acknowledging receipt of requests and communications in a timely manner and provide a timeline for any actions based upon those communications. The contractor shall provide draft deliverables prior to finalization and shall revise as required; and shall finalize deliverables within 5 days of notification to do so. Requirement Deliverables. • Clear description will be provided to NTP for methods, equipment, procedures and chemistries needed for transcriptomic analysis. • Information on reagents (e.g. probe sequences) to perform multiplex transcriptomic assay for each species will be provided. • Differential expression of treatments compared to control and statistical analysis of data will be performed for each species. Concentration-response analysis will be performed. • Raw data files for each project will be sent electronically or by delivery of a portable hard drive. • Deliverables shall be delivered in formats usable by the Government such as Microsoft Office Suite and HAWC (including software compatibility and 508 compliance) and will be useable to software titles and versions employed by the Government for its desktop and server environments. This information will be provided by the COR. • For each project on human, mouse and zebrafish, a draft deliverable will be provided to the project leader prior to finalization. After receipt of feedback from the project leader, the contractor shall revise the draft deliverable as needed and post the final version by the agreed upon deadline for each deliverable. Place and Period of Performance. All work is expected to be conducted at the contractor's facility or at a designated and approved subcontractor facility. Government Furnished Information. The government will supply the targeted gene set, the S1500, for humans and will work with the awardee in developing mouse and zebrafish ortholog gene sets to use in the production of the respective custom gene analysis platforms. III. INFORMATION SOUGHT: Interested organizations are required to submit their capability statements and 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 notice described above and should be tailored to the "Project 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) Standard product brochures will not be considered a sufficient response to this Request for Information.   IV. RESPONSE INSTRUCTIONS: The descriptive literature provided in response to this RFI shall 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. 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 to allow the Government to determine the organization's qualifications to perform the work. 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. After a review of the responses received a Request for Proposal (RFP) may be published. However, responses to this notice will not be considered adequate responses to an RFP. 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).
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