Inactive

UPDATE: Please see the attachments for any responses to questions received. The National Institutes of Health BRAIN Initiative is seeking Capability Statements from Small Business Organizations with t... UPDATE: Please see the attachments for any responses to questions received. The National Institutes of Health BRAIN Initiative is seeking Capability Statements from Small Business Organizations with the demonstrated capability of providing large-scale short- and long-read sequencing services using customer-provided RNA and DNA libraries generated from single cells, single nuclei, and bulk samples, from human, non-human primate, and mouse brain tissues, and of ensuring a seamless cloud-based delivery of high quality FASTQ files to the designated data repository. This is a Sources Sought Notice. This is NOT a solicitation for proposals, proposal abstracts, or quotations. The purpose of this sources sought notice is to help the Government obtain information regarding: (1) The availability and capability of qualified sources/availability of competition; and (2) the business size and socioeconomic status (e.g. small or large businesses, HUBZone small businesses; service-disabled, veteran-owned small businesses; 8(a) small businesses; veteran-owned small business; woman-owned small business; woman-owned small businesses; small disadvantage businesses; or large business), relative to the North American Industry Classification System (NAICS) code for the proposed acquisition. Your response to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible. The established NAICS Code is 541714, Research and Development in Biotechnology (except Nanobiotechnology). The U.S. Small Business Administration has established a size standard for 541714 as 1,000 employees or less. An organization that is not considered a small business under the applicable NAICS code should not submit a response to this notice. A determination by the Government to not compete this requirement as a set-aside based upon responses to this Notice is solely within the discretion of the Government. Interested parties are expected to review this Notice and description of services below to familiarize themselves with the requirements of this project; failure to do so will be at your firm's own risk. 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. Currently, the BRAIN Initiative is looking to establish the BRAIN Initiative Cell Atlas Network (BICAN) to broaden and deepen the systematic cell census and atlas efforts with a new emphasis on human brain. The BICAN will be made up of multiple highly interactive components with complementary roles, including: Comprehensive Centers on Human and Non-human Primate Brain Cell Atlases (UM1) (NOT-MH-21-260) Specialized Collaboratories on Human, Non-human Primate, and Mouse Brain Cell Atlases (U01) (NOT-MH-21-261) Coordinating Unit for Biostatistics, Informatics, and Engagement (CUBIE) (U24) (NOT-MH-21-262) BRAIN Initiative Data Archives (R24) (RFA-MH-20-600) Scalable Technologies and Tools Projects (R01) 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 cells/nuclei and bulk samples from human, non-human primate, and mouse brain tissues, using 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). PROJECT REQUIREMENTS: The primary scope of the contract will be to perform RNA and DNA sequencing services as part of the BICAN Sequencing Core program using state-of-the-art quality control (QC), quality assurance (QA) methodologies and tools, and a turnaround time of 7-14 business days (preferred 7 days) following receipt of samples from BICAN-funded laboratories, and to submit high quality demultiplexed FASTQ files to a BRAIN Initiative designated data repository. Contractors will be expected to collaborate and communicate within the BICAN Sequencing Core program and will be required to test libraries utilizing strictly standardized protocols and to deposit the results in structured and well-described formats, to allow for interoperability of the different protocols. Independently, and not as an agent of the Government, the contractor will furnish the necessary services, qualified personnel, materials, equipment not otherwise provided by the Government, to perform short and long-read DNA sequencing services summarized below. Description of Services: The contractor should have the necessary infrastructure to receive pooled and normalized RNA and DNA libraries as listed above from BICAN-funded laboratories and ensure unambiguous chain of custody sample tracking and management protocols and to perform large-scale, high throughput sequencing of single-cell transcriptome and epigenome libraries. The total number of short sequencing reads to be generated per year is estimated to be 5x10^12 (5 trillion) – 5x10^13 (50 trillion). GENERAL TASK 1: Generate a Manual of Operations This task requires the contractor to generate one (1) Manual of Operations specific to all Tasks in which the contractor is proposing services to the Government. They include: A description of the established sequencing pipeline that includes a list of library types sequenced, a diagram of the operation workflow and timeline, communication plan with library submitters and NIH including time schedules, library QC and pooling, sequencing machines/platforms, laboratory information management system (LIMS), informatics pipeline, data QC and storage, data transfer to external sites/cloud-based data archive(s), and process of quality control/assessment/validation of the sequencing pipeline as a whole; General Task 2: Large Scale Single Cell Transcriptome Sequencing General Task 3: Large Scale Single Cell Epigenome Sequencing General Task 4: Bulk Tissue Transcriptome and Epigenome Sequencing General Task 5: Whole Genome Sequencing General Task 6: Novel Omics Sequencing The Manual of Operations will be reviewed annually and, should there be a change in technique, a Task Order will be issued for the revision of the Manual of Operations. The performance period for Task 1 is anticipated to be 6 months. GENERAL TASK 2: Large Scale Single-Cell Transcriptome Sequencing Phase I task requires coordinating and collaborating with other BICAN researchers, Sequencing Core contractors, and NIH BRAIN Initiative staff to conduct a pilot study and establish common QC/QA metrics and uniformity of the BICAN sequencing pipelines across the different sites. Contractors must describe how they will coordinate and participate in BICAN in-person meetings and conference calls as well as the pilot study to develop standard operating procedures within the network of Sequencing Core contractors, BICAN investigators, and NIH staff. The Sequencing Core contractor will interact with the BICAN laboratories and other contractors to generate a report that establishes: (1) a submission and tracking process of the sequencing libraries, (2) QC/QA metrics of the sequencing libraries for the large-scale sequencing, including the QC workflow at labs of both library submitters and Sequencing Core, (3) QC/QA metrics of sequencing data, including methods for data cleaning and harmonization, (4) process and timeline of data transfer to the NIH designated partners/data archive(s), (5) quality performance uniformity of the sequencing pipelines, including results of the pilot study and comparative analysis of the pilot data across all participating labs Phase I will be required for the initial task order request; the performance period for Phase I is anticipated to be 6 months. Phase I may be required for subsequent task orders, at the request of the Government. Phase II task requires obtaining large-scale, high-throughput sequencing of RNA-seq libraries constructed from single cells, single nuclei, and other minute quantity preparations by BICAN selected studies: 10X Genomics Single Cell Multiome Gene Expression or Single Cell 3’ Dual Index Gene Expression Takara Bio SMART-seq v4 Single-cell or single-nucleus transcriptome sequencing must include sufficient read depth and coverage, as defined in Phase I task report. The numbers of reads and sequencing cycles are to be finalized during Phase I to allow for successful cell type detection. Single-cell or single-nucleus transcriptome sequencing data, following cleaning, QC/QA, and library demultiplexing must be securely transmitted to NIH BRAIN Initiative designated partners/data archive(s). The contractor should submit monthly summary reports. The performance period for Task 2 is anticipated to be 12 months. The contractor shall prepare a technology evaluation proposal and conduct Phase I task study when promising technologies and library types are identified and requested by the Government, which include but are not limited to new 10X Genomics protocols (e.g., Chromium X), sci-RNA-seq, scifi-RNA-seq, smart-seq3, and Slide-seq. Phase II task may be adjusted to adopt the new single-cell transcriptomics technologies following the validation of new technologies. GENERAL TASK 3: Large Scale Single-Cell Epigenome Sequencing Phase I task requires coordinating and collaborating with other BICAN researchers, contractors, and NIH BRAIN Initiative staff to conduct a pilot study and establish common QC/QA metrics and uniformity of the BICAN sequencing pipelines across different sites. Contractors must describe how they will coordinate and participate in BICAN in-person meetings and conference calls as well as the pilot study to develop standard operating procedures within the network of contractors, investigators, and NIH staff. The Sequencing Core contractor will interact with the BICAN labs and other contractors to generate a report that establishes (1) a submission and tracking process of the sequencing libraries, (2) QC/QA metrics of the sequencing libraries for the large-scale sequencing, including the QC workflow at labs of both library submitters and Sequencing Core, (3) QC/QA metrics of sequencing data, including methods for data cleaning and harmonization, (4) process and timeline of data transfer to the NIH designated partners/data archive(s), (5) quality performance uniformity of the sequencing pipelines, including results of the pilot study and comparative analysis of the pilot data across all participating labs Phase I will be required for the initial task order request; the performance period for Phase 1 is anticipated to be 6 months. Phase I may be required for subsequent task orders, at the request of the Government. Phase II task requires obtaining large-scale, high-throughput sequencing of epigenome libraries from single nuclei and other minute quantity preparations by BICAN selected studies: 10X Genomics Single Cell Multiome ATAC Single-nuclei methylC-Seq (snmC-seq) Single-cell epigenome sequencing must include adequate read depth and coverage to allow for successful cell type detection. The numbers of reads and sequencing cycles are to be finalized during Phase I to allow for cell type detection. Single-cell epigenome sequencing data, following cleaning, QC/QA, and library demultiplexing must be securely transmitted to NIH BRAIN Initiative designated partners/data archive(s). The contractor should submit monthly summary reports. The performance period for Task 3 is anticipated to be 12 months. The contractor shall prepare a technology evaluation proposal and conduct Phase I task study when promising technologies are identified and requested by the Government, which include but are not limited to sci-ATAC-seq, Hi-C, and ChIP-seq. Phase II task may be adjusted to adopt the new single-cell epigenomics technologies following the validation of new technologies. GENERAL TASK 4: Bulk Tissue Transcriptome and Epigenome Sequencing Phase I task requires coordinating and collaborating with other BICAN researchers, contractors, and NIH BRAIN Initiative staff to conduct a pilot study and establish common QC/QA metrics and uniformity of the BICAN sequencing pipelines across different sites. Contractors must describe how they will coordinate and participate in BICAN in-person meetings and conference calls as well as the pilot study to develop standard operating procedures within the network of contractors, investigators, and NIH staff. The Sequencing Core contractor will interact with the BICAN labs and other contractors to generate a report that establishes (1) a submission and tracking process of the sequencing libraries, (2) QC/QA metrics of the sequencing libraries for the large-scale sequencing, including the QC workflow at labs of both library submitters and Sequencing Core, (3) QC/QA metrics of sequencing data, including methods for data cleaning and harmonization, (4) process and timeline of data transfer to the NIH designated partners/data archive(s), (5) quality performance uniformity of the sequencing pipelines, including results of the pilot study and comparative analysis of the pilot data across all participating labs Phase I will be required for the initial task order request; the performance period for Phase 1 is anticipated to be 6 months. Phase I may be required for subsequent task orders, at the request of the Government. Phase II of the task requires obtaining state of the art transcriptome and epigenome sequence profiles from bulk tissue obtained from BICAN selected studies. Sequencing approaches must include sufficient sequencing depth and read lengths for complete transcriptome and epigenome assembly, as determined in Phase I. For transcriptome sequence profiles, libraries are prepared from multiple brain regions to enable both small and long RNA species detection for transcriptome sequencing. For epigenome sequencing profiles, libraries are prepared from multiple brain regions to enable ensemble analysis of chromatin accessibility, DNA 3D conformation, and DNA methylation and hydroxymethylation. RNA and DNA sequence profile data (raw, processed, and segmented/interpreted), following cleaning, QC/QA, and assembly, must be securely transmitted to NIH BRAIN Initiative designated partners/data archive(s). The contractor should submit monthly summary reports. The performance period for Task 4 is anticipated to be 12 months. The contractor shall prepare a technology evaluation proposal when promising technologies are identified and requested by the Government. This task may be adjusted to adopt the new transcriptomics and epigenomics technologies following the validation of new technologies. GENERAL TASK 5: Whole Genome Sequencing for 50 samples up to maximum capacity (to be proposed in increments of 10) Phase I task requires coordinating and collaborating with other BICAN researchers, contractors, and NIH BRAIN Initiative staff to conduct a pilot study and establish common QC metrics and uniformity of the BICAN sequencing pipelines across different sites. Contractors must describe how they will coordinate and participate in BICAN in-person meetings and conference calls as well as the pilot study to develop standard operating procedures within the network of contractors, investigators, and NIH staff. The Sequencing Core contractor will interact with the BICAN labs and other contractors to generate a report that establishes (1) a submission and tracking process of the sequencing libraries, (2) QC metrics of the sequencing libraries for the large-scale sequencing, including the QC workflow at labs of both library submitters and Sequencing Core, (3) QC metrics of sequencing data, including methods for data cleaning and harmonization, (4) process and timeline of data transfer to the NIH designated partners/data archive(s), (5) quality performance uniformity of the sequencing pipelines, including results of the pilot study and comparative analysis of the pilot data across all participating labs Phase I will be required for the initial task order request; the performance period for Phase 1 is anticipated to be 6 months. Phase I may be required for subsequent task orders, at the request of the government. Phase II task requires obtaining Whole Genome Sequencing (WGS) from BICAN selected studies. WGS must include sufficient read lengths and coverage to allow for successful rare variant detection, as determined in Phase I. WGS data, following cleaning, QC/QA, and assembly must be securely transmitted to NIH BRAIN Initiative designated partners/data archive(s). The contractor should submit monthly summary reports. The performance period for Task 5 is anticipated to be 12 months. The contractor shall prepare a technology evaluation proposal when promising technologies are identified and requested by the Government. This task may be adjusted to adopt the new technologies following the validation of new technologies. GENERAL TASK 6: Novel Omics Sequencing This task requires obtaining omics sequencing profiles that are novel to the BICAN program. Measures can include characterization of any transcriptome and epigenome changes in cell type and state whether transitory, permanent, or mutable. Sequencing approaches and library types may include but are not limited to: a) RNA isoform long-read sequencing, b) subcellular compartment RNA sequencing, c) ribosome sequencing, and d) DNA hydroxymethylation sequencing. Novel Omics profile data following cleaning, QC/QA, and assembly must be securely transmitted to NIH BRAIN Initiative designated partners/data archive(s). The contractor should submit monthly summary reports. The performance period for Task 6 is anticipated to be 12 months. When promising technologies and sequencing libraries are identified and requested by the Government, the contractor shall prepare a technology evaluation proposal and conduct a feasibility study. The performance period for the feasibility study is anticipated to be 6 months. This task requires coordinating and collaborating with other BICAN researchers, contractors, and NIH staff to establish common QC metrics and uniformity of the BICAN sequencing pipelines across different sites. Task order contractors must participate in BICAN in-person meetings and conference calls relevant to this task dealing with quality control, data transfer, and other issues as appropriately outlined by the NIH BICAN network and requested by the Government. The Phase I task order requires a report outlining the standard operating procedures for sequencing of samples from the BICAN network. If requested, Phase II requires sequencing from BICAN studies, using guidelines established during Phase I. PURPOSE AND OBJECTIVES: The Contractor shall execute a broad range of RNA and DNA libraries sequencing services and shall provide a seamless cloud-based delivery of demultiplexed FASTQ files to a BRAIN Initiative designated data repository. The Contractor shall coordinate and track the submission of libraries from the different BICAN-funded investigators, perform requested sequencing on these samples and shall provide results to the Government via cloud-based data delivery to the BRAIN Initiative designated data repository. The end-goal of this BICAN program is to create reference cell atlases of brain and make the data available to the research community. ANTICIPATED CONTRACT TYPE: A Multiple Award Indefinite Delivery, Indefinite Quantity (IDIQ) contract type is anticipated. The Government anticipates more than one award; however, the final number will be based on the results of the competition and is undetermined at this time. The anticipated program ceiling for the acquisition is $150,000,000.00 for 5 years across all contracts issued. ANTICIPATED PERIOD OF PERFORMANCE: The contract will consist of a 5-year ordering period of performance estimated to be begin on or about 9/1/2022 and continue through 8/31/2026. It is anticipated that more than one award will be made in each of the task categories. Task orders will be placed as needed by the BRAIN Initiative and will specify actual performance dates and task areas to be covered. PERFORMANCE LOCATION: Each task order will specify the method and location. NORTH AMERICAN INDUSTRY CLASSIFICATION SYSTEM (NAICS) CODE: The intended procurement will be classified under the NAICS code 541714, "Research and Development in Biotechnology (except Nanobiotechnology)" with a size standard of 1,000 employees. CAPABILITY STATEMENT/INFORMATION SOUGHT: Interested organizations are required to submit their capability statements via email to Valerie.Whipple@nih.gov and Christine.Frate@nih.gov, and should not exceed five (5) pages in length; not including a standard product brochure that clearly details the ability to perform the aspects of the notice described in the Statement of Work and should be tailored to the "Project Requirements" as concise as possible. Capability statements should also include the following information: 1. DUNS Number 2. CAGE Code: 3. Organization Name: 4. Company Address: 5. Point of Contact (including name, title, addresses, telephone number, fax number and Email address) 6. Business size (e.g. small or large): 7. Socio-economic Status (e.g., 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): 8. GSA Contract Number: 9. Clear and convincing documentation of your capability and ability to provide the services specified in this notice. 10. Examples of prior completed contracts and other related information. Note that standard product brochures will not be considered a sufficient response to this Sources Sought Notice. 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). 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. Potential Quoters 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 pre-solicitation synopsis and solicitation may be published in Federal Business Opportunities. However, responses to this notice will not be considered adequate responses to a solicitation. Interested parties may identify their interest and capability to respond to the requirement. The Government shall consider all responses received by July 26, 2021 at 9:00 AM EST. Written responses to this synopsis shall contain sufficient documentation to establish their capability to fulfill this requirement. The BRAIN Initiative will not be responsible for any costs incurred by interested parties in responding to this notice. Please email, with the sources sought notice number in the subject line to the Contracting Officer listed below.