2270811 - J.A.pdf

Justification for Other than Full and Open Competition:

Brand Name at or Below the Simplified Acquisition Threshold

Project Title: Reagents for Spatial Transcriptomic of NHP Fiebig in Lymph Node

Identification of the agency and contracting activity

DHHS, NIH, NIAID, VRC

Vaccine Research Center 40 Convent Drive, Bldg. 40, Room 3614, Bethesda, MD 20892

Background and Justification

A. Project Background

Vaccine Research Center (VRC) mission is to discover and develop novel vaccines and biologics targeting infectious diseases of global public health importance. VRC combines a scientific and technological strategy innovation to achieve the design, development, manufacturer and evaluation of vaccines and therapeutics. In 2024, a proof-of-concept Xenium probe-based spatial transcriptomics (ST) was performed on human and non-human primate

(NHP) tissues to establish the technology at the Vaccine Research Center. Currently available Xenium commercial panels are validated for profiling up to 5000 genes from human or mouse species. 10X Xenium In Situ platform

(10X Genomics) enables to visualize, quantify, and analyze up to 5000 genes in human and mouse species at subcellular resolution within intact tissue sections. The use of a multimodal segmentation approach (antibody staining and algorithm) allows more accurate cell clustering to better address the tissue morphology.

B. Project Description

The first custom NHP ST began to explore spatially defined genes during SHIV infection. The small LN dataset allowed comparison of the cell types involved in SHIV acute infection at the peak time of infection to later time points when viral RNAs expression either declined or was sustained.

To characterize NHP Fiebig stages, we propose to design a Xenium custom panel up to 480 genes, including genes that make up lymph node immune cell type (B cells, T cells, NK cells, macrophage populations, endothelial cells) and innate and adaptive immune genes defining immune “niche” of the lymph node. LN biopsies already available in FFPE capturing all Fiebig stages of NHP infected intrarectally or intravenously will be subjected to Xenium technology.

C. Description of the supplies to be purchased:

Product Code Product Quantity

1000691 GEM-X Universal 3' Gene Expression v4, 16 samples 1

1000686 GEM-X Universal 3' Gene Expression v4, 4 samples 1

1000690 Chromium GEM-X Single Cell 3' Chip Kit v4, 4 chips 1

1000215 Dual Index Kit TT Set A, 96 rxn 1

1000242 Dual Index Kit NT Set A, 96 rxn 1

1000702 Chromium GEM-X Single Cell 3 Feature Barcode Kit v4, 16 rxns

1000644 Xenium Standalone Custom 301 to 480 Gene Panel (16 rxns) - Design ID# ZZBE3P

1000665 Xenium Advanced Panel Upgrade (301 to 480 genes) -

Design ID# ZZBE3P

1000662 Xenium Cell Segmentation Add-on Kit (2 rxns) 8

1000487 Xenium Decoding Consumables (1 run, 2 slides) 8

1000461 Xenium Decoding Reagents (1 run, 2 slides) 8

1000460 Xenium Slides & Sample Prep Reagents (2 slides, 2 rxns) 8

Name of manufacturer, producer, or distributor of each brand name product referenced:

10X Genomics 6230 Stoneridge Mall Road Pleasanton, CA 94588-3260

Statutory authority permitting other than full and open competition

☒ 41 USC 253(c)(1) and FAR Part 6.302-1: Brand Name Requirement

Demonstration that the proposed brand name product’s salient characteristics (specific features, qualities and/or the nature of the acquisition) requires use of the authority cited above:

10xGenomics (Manufacturer) offers the required proprietary microfluidic circuits that rapidly partition input samples (e.g. higher molecular weight DNA, single cells), which are then barcoded using the GemCode Technology. This technology is not manufactured by any other vendor than 10X Genomics is not available for any other instrumentation. The requested reagents meet our need to sequence thousands of transcriptomes in a single run from single cells and while obtaining phenotypic data from those same cells. The latter is performed by CITE-seq, which has only been tested on the 10X platform; changing the platform would require about a year of work, be costly and results could not be adequately compared to data from previous studies.

Requirements for the reagent kits:

• Simultaneously measure cell surface protein expression with gene expression

• Simultaneously measure TCR, and 3’ gene expression in the same cells

• Be able to detect protein of low abundance transcripts with increased phenotypic specificity

• Allow cell doublet phenoptyping with hashtag technology that should also allow combining different donor samples

• Allow subcellular gene signature technology probe-based

• The kit must be compatible with the controller

Determination by the Contracting Officer that the anticipated cost/price to the Government will be fair and reasonable

Certification This is to certify that the justification for the proposed acquisition has been reviewed and that to the best of my knowledge and belief the information and/or data provided to support my request (for the requestor) and approval (for the CO) of is accurate and complete.

Official Name & Title Signature Date

Contracting Officer Approval

Addison Miller Contracting Officer

9/10/2025