NIH BRAIN Initiative: BRAIN Initiative Cell Atlas Network (BICAN)

UPDATE: Please see the attachments for any responses to questions received. 

This is a Request for Information (RFI). This is NOT a solicitation for proposals, proposal abstracts, or quotations. The purpose of this RFI is to obtain knowledge and information for project planning purposes.

A.  Introduction

The NIH BRAIN Initiativeis soliciting information regarding potential sources’ capabilities and pricing structure across academic, commercial, and government sectors for performing large-scale DNA sequencing of libraries constructed from single brain cells/nuclei and bulk brain tissues, with proper quality assurance (QA), quality control (QC), and rapid turnaround time.

The purpose of this Request for Information (RFI) is to identify potential DNA sequencing service providers and to collect information from interested organizations regarding their sequencing library sample requirements as well as capability and capacity to provide DNA sequencing services.

An additional purpose of this RFI is to seek feedback and consumer considerations from potential end-users (library producing groups) of centralized DNA sequencing service providers.

All interested organizations are invited to submit information in response to this RFI as per the specifications detailed in Section D: Information Requested.  Issuance of this RFI does not in any way obligate NIH BRAIN Initiativeto award a contract nor does it commit NIH BRAIN Initiativeto pay for costs incurred in the preparation and submission of any response.

By issuing this RFI, the NIH BRAIN Initiativedoes not express an intent, commitment, or promise to purchase any supplies or services.  Responses to this RFI will not be considered by NIH BRAIN Initiativeas offers to enter into a contract; this RFI is for information collection purposes only.

B.  Background

Guided by the recommendations of the Advisory Committees to the NIH Director in their BRAIN 2025 and the BRAIN 2.0 reports, the NIH BRAIN Initiative has launched a 3-year BRAIN Initiative Cell Census Consortium (BICCC, 2014-2017), followed by a 5-year BRAIN Initiative Cell Census Network (BICCN, 2017-2022) to generate a systematic brain cell census in multiple mammalian species. At this time, the BRAIN Initiative is looking to establish the BRAIN Initiative Cell Atlas Network (BICAN, NOT-MH-21-260, NOT-MH-21-261, NOT-MH-21-262) to broaden and deepen the systematic cell census and atlas efforts with a new emphasis on human brain. The overarching goal of BICAN is to build reference brain cell atlases that will be widely used throughout the research community, providing a molecular and anatomical foundational framework for the study of brain function and disorders. The BICAN is a large-scale effort to study single-cell and bulk transcriptome profiles (e.g., coding and non-coding RNAs, and RNA isoforms), as well as single-cell and bulk epigenome profiles (e.g., chromatin accessibility, chromatin conformation, DNA methylation) in relation to the brain cell type diversity and genetic variations.  The expected RNA and DNA sequencing libraries will be generated from single cell/nucleus and bulk samples from human, non-human primate, and mouse brain tissues, using the methods including but not limited to:

10X Genomics single-cell protocols (Chromium Single Cell Gene Expression, Single Cell ATAC, Single Cell Multiome), TaKaRa SMART-seq, snmC-seq2, snATAC-seq, sci-RNA-seq, sci-ATAC-seq, Slide-seq, Hi-C, etc. (cf. BICCN).

Information is requested for both short-read and long-read sequencing services. 

C. Information Sought/Capability Statement: The information requested in this RFI is intended for planning purposes only.Interested organizations should include relevant and specific information on each of the following questions below.

1. The following information should be included at the beginning of the RFI response:

• Organization’s Name Organization’s Address;
• Organization’s Website (if available);
• Organization’s DUNS Number1(if available);
• Size of Organization (# of staff and sequencing facility sq. footage);
• Organization’s Point of Contact (POC);
• POC’s Title;
• POC’s Email Address;
• POC’s Phone Number;

2.   Please briefly summarize in 1-page your organization’s resources and equipment of the DNA sequencing facility.

3.   Please provide summary information about your organization’s leadership, technical expertise and experience, and participation in prior NIH-funded scalable sequencing projects.

4.  Please provide the following information about your organization’s capabilities and capacity:

• an overview of the high throughput sequencing pipeline and workflow, including library sample requirements, QC and chain of custody tracking, sequencing data management protocols, data QA/QC, data security, data format and delivery options including data storage and delivery of both raw data and analyzed data;

• the library types sequenced, including single cell/nucleus and bulk tissue libraries (e.g., RNA-seq, ATAC-seq, mC-seq, Hi-C/3C-seq);

• experience with short-read and long-read sequencing;

• the total number of library samples and base pairs sequenced, and the total size of sequencing data generated each year since the establishment of the sequencing operation;

• the shortest, longest, and median turnaround time (# days) from the receipt of the library samples to the delivery of the sequencing data, describing the difference if the turnaround time is dependent on the library types and QA/QC;

• the quality assurance surveillance procedures implemented for obtaining and evaluating feedback from the customers to enhance customer satisfaction;

• sequencing service costs that should be included and identified:
  • pricing structure and cost items for the sequencing service provided;
  • all-inclusive unit costs (e.g., costs per megabase and per million reads) and bulk discount (i.e., price per sequencing order volume); describe the difference if the all-inclusive unit cost is dependent on the library types.

5.   Please provide feedback on any potential problems involving the use of centralized DNA sequencing service providers, for example, potential problems involving the transfer of DNA libraries, sample requirements and QA/QC. Please include any recommendations and/or considerations to circumvent identified problems.

D.  Instructions for Response Submission

1. Please note that organizations are not required to submit responses to all questions; however, interested parties are encouraged to submit as much information as possible. Information and all correspondence and documents relating to the RFI shall be in English.
2. The response is limited to ten (10) pages.  A cover page and an executive summary may be included, but is not required. The 10-page limit does not include the cover page, executive summary, or references, if requested or included.
3. All responses to this notice must be submitted electronically to the Contracting Officer.  Facsimile responses are NOT accepted.
4. All responses to this RFI shall be submitted via email in one (1) pdf document to:  Valerie Whipple (valerie.whipple@nih.gov) and Christine Frate (christine.frate@nih.gov) no later than 2:00 pm EST on July 2, 2021.

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. Information provided will be used to assess tradeoffs and alternatives available for the potential requirement and may lead to the development of a solicitation. 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. Any solicitation resulting from the analysis of information obtained will be announced to the public in Federal Business Opportunities in accordance with the FAR Part 5. However, responses to this notice will not be considered adequate responses to a solicitation.

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).