Presolicitation Notice_Noncompetitive_75N95024Q00448.pdf

PRE-SOLICITATION NOTICE OF INTENT

NON-COMPETITIVE

Notice Number: 75N95024Q00448

INTRODUCTION

PURSUANT TO FAR Subpart 5.2—Synopses of Proposed Contract Actions, THIS IS A

PRE-SOLICITATION NOTICE OF A PROPOSED CONTRACT TO ACTION.

THIS IS A PRE-SOLICITATION NON-COMPETITIVE NOTICE OF INTENT TO AWARD

A CONTRACT OR PURCHASE ORDER WITHOUT PROVIDING FOR FULL OR OPEN

COMPETITION (INCLUDING BRAND-NAME).

The National Institute of Neurological Disorders and Stroke’s (NINDS) intramural research program’s mission is to seek fundamental knowledge about the brain and nervous system and to use that knowledge to reduce the burden of neurological diseases for all people. Multiple NINDS laboratories currently use optimization slides, reagent kits, reagent delivery methods, and specific single-cell kits manufactured by 10X Genomics, Inc., to conduct ongoing research projects.

The National Institute on Drug Abuse (NIDA), Office of Acquisition, on behalf of the NINDS Division of Intramural Research, intends to negotiate and issue a modification to an existing indefinite-delivery, indefinite-quantity (IDIQ) contract between the NINDS and the contractor, 10X Genomics Inc.

This IDIQ contract (Contract No. 75N95023D00018) was awarded as a result of Request for Quotation No. 75N95023Q00139. The proposed modification of the contract would extend the contract ordering period by twelve months, from August 3, 2024 to August 3, 2025. The modification would not result in any other changes to the above-referenced IDIQ contract.

NORTH AMERICAN INDUSTRY CLASSIFICATION SYSTEM (NAICS) CODE

The intended procurement is classified under NAICS 334516 (Analytical Laboratory Instrument Manufacturing) with a small business size standard of 1,000 employees.

REGULATORY AUTHORITY

The resultant modification will include all applicable provisions and clauses of the Federal Acquisition Regulation (FAR) in effect through Federal Acquisition Circular (FAC) 2024-05, dated May 22, 2024.

STATUTORY AUTHORITY

This acquisition is conducted as non-competitive in accordance with the provisions of FAR Subpart 6.302-1, Only one responsible source and no other supplies or services will satisfy agency requirements. derived from the authority provided by 41 U.S.C.

3304(a)(1).

BACKGROUND

NINDS’s intramural research program’s mission is to seek fundamental knowledge about the brain and nervous system and to use that knowledge to reduce the burden of neurological diseases for all people. This acquisition is necessary to continue providing 10X Genomics-manufactured optimization slides, reagent kits, and reagent delivery methods for gene expression analysis and gene profiling, which are currently being used in tandem with NINDS’s Chromium system. These technologies are being used to map gene expression, transcription, and profiling for neurological diseases such as Psychosis, Multiple Sclerosis, Undiagnosed neuroinflammatory diseases, and many other neurological and brain disorders.

DESCRIPTION OF REQUIREMENT

Title: 10x Genomics Inc. Optimization Slides, Reagent Kits, and Reagent Delivery Methods

The purpose of this acquisition is to continue providing 10X Genomics Inc.-manufactured optimization slides, reagent kits, and reagent delivery methods to the laboratories of the National Institute of Neurological Disorders and Stroke (NINDS).

Related previous and continuing research projects being conducted by NINDS laboratories have utilized the 10X Genomics Inc. reagent kits, optimization slides and other consumables in tandem with an existing 10X Genomics Inc. Chromium System.

To maintain the integrity of the research data previously generated, the same reagent kits, optimization slides and consumables must be used for the ongoing and planned, follow-on research projects. These biological technologies are used to map gene expression, transcription, and profiling for neurological diseases such as Psychosis, Multiple Sclerosis, Undiagnosed neuroinflammatory diseases, and many other neurological and brain disorders.

Generic Name of Product:

Items are being procured from the following categories:

• 3' Single Index

• 3' Dual Index

• 3' Cellplex (DI only)

• 5' Single Index

• 5' Dual Index

• Mutliome

• ATAC

• ATAC V2

• Visium FFPE V1

• Visium FF

• 3' HT

• 3' LT

• 5' HT

• Fixed Single Cell

• Nuclei Isolation

• Visium for CytAssist

Other categories may be used based on need at the time it arises and may include other items in addition to the ones listed above.

Purchase Description:

10X Genomics Inc. brand-name only items.

Minimum Salient Characteristics:

Vendor shall provide 10X Genomics brand-name only items as specified below:

• 3' Single Index

• 3' Dual Index

• 3' Cellplex (DI only) o Salient Characteristics - The Chromium Next GEM Single Cell 3’ Reagent Kits enables deep profiling of complex cell populations with high-throughput 3’ digital gene expression and feature analysis of individual cells. Single-cell sequencing provides several advantages, including:

o Single-cell sequencing can detect biologically relevant gene expression signals masked by bulk measurement for a wide dynamic range of individual cells per chip across heterogeneous cell types (up to 8,000 cells per LT chip, up to 80,000 cells per standard throughput chip, up to 320,000 cells per HT chip) o Rare or novel cell types may also be uncovered and characterized based on environmental or experimental conditions.

o Simultaneous assessment of many phenotypes (e.g., gene expression and protein abundance) o Targeted gene expression analysis with pre-designed and custom gene panels

• 5' Single Index & 5' Dual Index o Salient Characteristics - Chromium Next GEM Single Cell 5’ The

Chromium Next GEM Single Cell 5’ Reagent Kits provide a scalable solution for profiling full-length paired V(D)J transcripts on a cell-by-cell basis.

o Delivers paired full-length T-cell and B-cell receptor sequences at the single-cell level using universal and unbiased amplification strategies, thus avoiding amplification and detection bias associated with complex multiplex PCR while revealing deeper biological complexity of antigen specificity on a per-cell basis than single-chain (e.g., TCR) methods.

o The incorporation of a unique molecular identifier (UMI) in the template switch oligo enables transcript quantification and further reduces systematic bias by controlling for non-biological SNVs or other variants introduced by PCR and sequencing error.

o Enables the detection of germline and somatic variation across full-length antigen receptor V(D)J gene sequences.

o Identifies both productive and non-productive recombination events as well as adaptive immune cells with more than one productive T-cell receptor alpha or beta chain.

o Maps transcription start sites, promotor, and alternative promoter elements.

o Targeted gene expression analysis with pre-designed and custom gene panels

• Multiome o Salient Characteristics - Chromium Next GEM Single Cell Multiome ATAC

+ Gene Expression The Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits enable simultaneous profiling of the whole transcriptome and epigenome from the same single cell 10x Genomics Sole Source Document • Rev J • Next GEM 5 o Simultaneously interrogate open chromatin and 3’ gene expression in up to 10,000 individual nuclei per sample (8 samples per run) o Deeply characterize cell types and states with linked transcriptomic and epigenomic analysis.

o Discover new gene regulatory interactions.

o Analyze high-resolution paired transcriptomic and epigenetic data with turnkey software.

• ATAC

o Salient Characteristics - Chromium Next GEM Single Cell ATAC The Chromium Next GEM Single Cell ATAC Reagent Kits enable mapping of the epigenetic landscape at high resolution to define gene regulatory networks and unravel the epigenetic basis of disease and development.

o Profile the open chromatin landscape of up to 10,000 individual nuclei per sample (8 samples per run) in a user-friendly 7 hr. workflow Identify epigenetic mechanisms in rare cell populations from complex samples (as low as 0.5%) Analyze high-resolution epigenetic data by characterizing cellular heterogeneity with turnkey software.

• ATAC V2

o Salient Characteristics - Chromium Next GEM Single Cell Multiome ATAC + Gene Expression The Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits enable simultaneous profiling of the whole transcriptome and epigenome from the same single cell.

Next GEM 5 - Simultaneously interrogate open chromatin and 3’ gene expression in up to 10,000 individual nuclei per sample (8 samples per run)

Deeply characterize cell types and states with linked transcriptomic and epigenomic analysis.

Discover new gene regulatory interactions.

Analyze high-resolution paired transcriptomic and epigenetic data with turnkey software.

• Visium FFPE V1 & Visium FF o Salient Characteristics - Formalin-Fixed Paraffin-Embedded (FFPE) Sample Workflow FFPE tissues are sectioned and placed in the capture areas on the Visium Spatial Gene Expression slide. Utilizing standard H&E or immunofluorescence staining techniques, tissue sections are visualized on the slide to capture the morphological image of each section.

The tissue is de-crosslinked to release mRNA that was sequestered by formalin fixation. Human or mouse whole transcriptome SAM000089, Rev B probe panels, consisting of a pair of specific probes for each targeted gene, are added to the tissue. These probe pairs hybridize to their gene target and are then ligated to one another. The ligation products are released from the tissue upon RNase treatment and permeabilization.

Universal conditions for sample de-crosslinking and tissue permeabilization are used; tissue-specific optimization is not needed for the Visium Spatial Gene Expression Solution for FFPE tissues. For each section mounted on the Visium Spatial Gene Expression slide, ligated probe pairs from the tissue bind with spatially barcoded oligonucleotides present on the capture areas of the slide. The probe pairs are extended to incorporate complements of the spatial barcodes. The spatially barcoded, ligated probe products are released from the slide and PCR amplified. The probe products are further processed to generate an NGS-ready library.

The Visium Spatial Gene Expression library is sequenced using standard short-read sequencers, and data is processed and visualized using 10x Genomics software: Space Ranger analysis pipelines and Loupe Browser visualization software. Unique Platform Characteristics 2, 4, or 16 reaction Visium Spatial Gene Expression kits available All critical and non-standard reagents and slides are included in the kit 2 or 4 (6.5mm x 6.5mm) capture areas per slide 4992 55µm barcoded spots per capture area Each barcoded spot contains millions of captured oligos 100 µm center-to-center distance between spots Highly sensitive to a variety of tissue types

• 3' HT & 3' LT & 5' HT & Fixed Single Cell o Salient Characteristics - Chromium Next GEM Single Cell Fixed RNA The

Chromium Next GEM Single Cell Fixed RNA Reagent Kits enable measurements of single-cell gene expression in fixed human or mouse samples.

Fresh human or mouse samples are fixed with paraformaldehyde to preserve biological states at collection and enable short- or long-term storage and transport.

Batch process and multiplex samples to improve operational efficiency and reduce experimental variability

Scale single-cell studies by multiplexing up to 16 samples and 128,000 cells per channel, for up to 128 samples and >1,000,000 cells per run

Deeply interrogate cell types and states with simultaneous gene and cell surface protein expression.

• Nuclei Isolation o Salient Character tics - Chromium Nuclei Isolation The Chromium Nuclei

Isolation Kit is an all-in-one solution for the standardized isolation of nuclei from frozen tissue for use in 10x Genomics Single Cell assays.

Easily isolate nuclei from 3-5mg of frozen tissues (up to 8 in parallel) in an hour with little to no sample preparation optimization A unified workflow for a wide range of tissues that simplifies sample processing Characterize the heterogeneity of tissues more completely by preserving cells often lost during fresh tissue dissociation Use reliable, standardized reagents designed for 10x Genomics single-cell sequencing assays

• The equipment shall be compatible with the following existing 10X Genomics Inc.

Equipment:

o CC = Chromium Controller o iX = Chromium iX o X = Chromium X o Visium CytAssist

This acquisition is restricted to:

10X Genomics Inc.

6230 Stoneridge Mall Road Pleasanton, CA 94588-3260

PERIOD OF PERFORMANCE

The ordering period end date of the above-referenced IDIQ contract will be extended from August 4, 2024 to August 3, 2025.

CONTRACT TYPE

Delivery orders awarded under the IDIQ contract will continue to be Firm-Fixed-Price orders, incorporating the terms and conditions of the above-referenced IDIQ contract.

REASON FOR NON-COMPETITIVE ACTION

The above-referenced IDIQ contract was awarded after comprehensive market research was conducted, including the issuance of a pre-solicitation notice of intent to award a contract or purchase order without providing for full or open competition (including brand-name) via sam.gov. One response was received however the responding vendor was not able to provide all the necessary items via its GSA or BPA contract.

The continued use of the optimization slides, reagent kits, and reagent delivery methods specifically compatible with the Chromium system is critical to maintaining the integrity of the data already generated and analyzed. The use of other reagent kits and delivery methods may jeopardize the integrity, quality, and results of the research projects as the kits, optimization slides and/or delivery methods would not be compatible with the 10X Genomics Inc. Chromium system.

It is anticipated that the research findings will have a direct impact on how patients can be stratified for future clinical trials, on assessing target engagement, and on predicting neurological disease outcomes.

Modifying the above-referenced IDIQ contract solely to extend the ordering period for 12 months is the only efficient and effective way of ensuring the integrity and quality of the results from ongoing research projects that use the 10X Genomics-manufactured Chromium system with 10x Genomics’ optimization slides, reagent kits, and delivery methods. Additionally, for the timeframe that the required items will be used, modification to extend the ordering period is the only way to avoid a lapse in the ordering period resulting in a lapse in NINDS’s ability to timely obtain the required 10X Genomics Inc. optimization slides, reagent kits, and delivery methods.

Delivery of items in stock will be shipped overnight. If an item is back ordered, the contractor shall notify NINDS within 2 business days of delivery order issuance. All deliveries required under this contract shall be packaged, marked, and shipped per the Government’s specifications. At a minimum, all deliverables shall be marked with the contract number, Contractor name, and NINDS customer delivery address. The Contractor shall guarantee that all required materials shall be delivered in immediate usable and acceptable condition.

CLOSING STATEMENT

This notice of intent is NOT a request for competitive proposals; however, interested parties may identify their interest and capability to respond to this notice.

Responses to this notice must contain sufficient information to establish the interested parties’ bona-fide capability of fulfilling all requirements described herein. The statement must also include the contractor’s Unique Entity Identifier (UEI) number, Taxpayer Identification Number (TIN), and its certification of business size. All responders must have an active registration to receive contract awards in the System for Award Management (SAM), which can be accessed at www.sam.gov.

A determination by the Government to not compete the proposed contract action based upon responses to this notice is solely within the discretion of the Government. The information received will normally be considered solely for the purpose of determining whether to proceed on a non-competitive basis or to conduct a competitive procurement for the requirement. The determination of whether to proceed with the proposed IDIQ contract modification is solely within the discretion of the Government.

All responses must be received by 4:00 PM Eastern Time on July 31, 2024 and reference Notice No. 75N95024Q00448 in the Subject line. All responses must be emailed to Marlene Milgram, Contract Specialist, at marlene.milgram@nih.gov.

All responsible sources may submit a capability statement, proposal, or quotation, which shall be considered by the agency.

mailto:marlene.milgram@nih.gov